Microbiology (non-medical) Books

Book SynopsisMost previous publications on the classification of tapeworms (cestodes) have been based on compilations from the literature and are now dated. Thus there is a real need for up-to-date keys based on the re-examination of specimens and on a re-evaluation of the characters employed in cestode taxonomy. This book fulfils this need and provides keys to enable specialists and non-specialists to identify cestodes to generic level. The keys are dichotomous and are based largely on morphological characters. The authors have re-examined many specimens, including type specimens where possible. As a result, the keys reflect new ideas and have lead to reappraisals of cestode taxonomy, particularly at family and generic level, with many reallocations and synonymies. The authors include 19 international authorities from the UK, USA, Australia, Brazil, France, Norway, Italy, Switzerland, Poland, Bulgaria and the Ukraine. The book includes approximately 1700 illustrations and is a standard work on tapTable of Contents1: Key to the orders of the cestoda, A Jones, R A Bray, and L F Khalil 2: Order Amphilinidea, D I Gibson 3: Order Gyrocotylidea, D I Gibson 4: Order Spathebothriidea, D I Gibson 5: Order Caryophyllidea, J S Mackiewicz 6: Order Diphyllidea, L F Khalil 7: Order Trypanorhyncha, R A Campbell and I Beveridge 8: Order Tetraphyllidea, L Euzet 9: Order Lecanicephalidea, L Euzet 10: Order Pseudophyllidea, R A Bray, A Jones and K I Anderson 11: Order Haplobothriidea, A Jones 12: Order Nippotaeniidea, R A Bray 13: Order Proteocephalidea, A A Rego 14: Order Tetrabothriidea, E P Hoberg 15: Order Cyclophyllidea. Key to families, A Jones, R A Bray and L F Khalil 16: Family Mesocestoididae, R L Rausch 17: Family Anoplocephalidae, I Beveridge 18: Family Catenotaeniidae, J C Quentin 19: Family Nematotaeniidae, M K Jones 20: Family Progynotaeniidae, L F Khalil 21: Family Acoleidae, L F Khalil 22: Family Dioecocestidae, A Jones 23: Family Amabiliidae, A Jones 24: Family Davaineidae, A Jones and R A Bray 25: Family Dilepididae, F V Bona 26: Family Dipylidiidae, A Jones 27: Family Paruterinidae, B B Georgiev and V V Kornyushin 28: Family Metadilepididae, V V Kornyushin and B B Georgiev 29: Family Hymenolepididae, B Czaplinski and C Vaucher 30: Family Taeniidae, R L Rausch 31: Lists of genera, A Jones, R A Bray and L F Khalil

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Book SynopsisThe first comprehensive monograph on periphyton, this book contains contributions by scientists from around the globe. Multi-disciplinary in nature, it covers both basic and applied aspects of periphyton, and is applicable worldwide in natural, extensive and intensive managed systems. Periphyton, as described in this book, refers to the entire complex of attached aquatic biota on submerged substrates, including associated non-attached organisms and detritus. Thus the periphyton community comprises bacteria, fungi, protozoa, algae, zooplankton and other invertebrates. Periphyton is important for various reasons: as a major contributor to carbon fixation and nutrient cycling in aquatic ecosystems; as an important source of food in aquatic systems; as an indicator of environmental change. It can also be managed to improve water quality in lakes and reservoirs; it can greatly increase aquaculture production; it can be used in waste water treatment. The book provides an international reviewTable of Contents1: Periphyton and Aquatic Production: An Introduction, M E Azim, SaitamaUniversity, Japan, M C M Beveridge, A A van Dam, The Netherlandsand M C J Verdegem, 2: Periphyton Structure, Diversity and Colonization, M E Azim and T Asaeda,Saitama University, Japan 3: Periphyton Dynamics and Influencing Factors, J E Vermaat, VrijeUniversiteit Amsterdam, The Netherlands 4: Periphyton in the Aquatic Ecosystem and Food Webs, R G Wetzel,University of North Carolina, USA 4: Periphyton in Freshwater Lakes and Wetlands, L G Goldsborough,University of Manitoba, Canada, R L McDougal, Ducks Unlimited Canada,Canada and A K North, Red River Basin Commission, CanadaEXPLOITATION 5: Utilization of Periphyton for Fish Production in Ponds: a Systems EcologyPerspective, A A van Dam and M C J Verdegem 6: Adaptations to Feeding in Herbivorous Fish (Cyprinidae and Cichlidae),F A Sibbing, Wageningen University, The Netherlands and F Witte, LeidenUniversity, The Netherlands 7: Traditional Brush Park Fisheries in Natural Waters, R L Welcomme,Imperial College of Science, Technology and Engineering, London, UK 8: Periphyton (Biofilms) as Biological Indicators in Managed AquaticEcosystems, S Sabater, University of Girona, Spain and W Admiraal,University of Amsterdam, The NetherlandsMANAGEMENT 9: Effect of Periphyton on Water Quality, A Milstein, Agriculture ResearchOrganization (ARO), Israel 10: Similarities between Microbial and Periphytic Biofilms in AquacultureSystems, M C J Verdegem, E H Eding, V Sereti, R N Munubi, R A Santacruz-Reyes, Wageningen University, The Netherlands, and A A van Dam 11: Periphyton-based Pond Polyculture, M E Azim and M A Wahab, BangladeshAgricultural University, Bangladesh 12: Research on Periphyton-based Aquaculture in India, P Keshavanath andB Gangadhar, University of Agricultural Sciences, Bangalore, India 13: Periphyton-based Cage Aquaculture, S M H Huchette, University of Melbourne, Australia and M C M Beveridge 14: Utility of Added Substrates in Shrimp Culture, J H Tidwell,Kentucky State University, USA and D Bratvold, University of Georgia, USA 15: Importance of Periphyton in Abalone Culture, T Kawamura,University of Tokyo, Japan, R D Roberts, Cawthron Institute,New Zealand and H Takami, Tohoku National Fisheries Research Institute,Japan 14: Periphyton-based Aquaculture in Asia: Livelihoods and Sustainability,S W Bunting, M Karim, University of Stirling, Scotland, UK andM A Wahab 15: Periphyton Ecology, Exploitation and Management: Knowledge Gapsand Directions for Future Research, M C J Verdegem, A A van Dam,M E Azim and M C M Beveridge"

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Book SynopsisThe increasing use of integrated crop management, often requiring a reduction in the reliance upon chemical control, means that the need to rapidly identify pest nematodes has never been greater. This second edition of this standard reference work familiar to all plant nematologists is therefore even more useful than its predecessor published in 1986.The in-depth description of the life histories of the genera of the Tylenchida have been retained and brought up-to-date through the inclusion of all the research carried out between the publication of the last edition and this new edition. This expanded edition includes detailed diagnoses of well over 200 genera and familial and ordinal groups, and is well-illustrated with drawings of type or representative species. These, together with comprehensive lists of species and genera and their synonymies provide the foundation for the status and validation of each taxon within the Tylenchida. A considerable amount of information is provided regTable of Contents1: Introduction, historical review and techniques 2: Morphological characters and taxonomic methods 3: Order Tylenchida 4: Suborder Tylenchina 5: Infraorder Anguinata 6: Suborder Hoplolaimina 7: Superfamily Dolichodoroidea 8: Suborder Criconematina 9: Family Criconematidae 10: Suborder Hexatylina

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Book SynopsisFire blight is a major disease of apples, pears and certain woody ornamental plants. It is caused by the bacterium Erwinia amylovora. This organism was one of the first plant pathogenic bacteria to be extensively investigated, and has become a model for study by bacteriologists in the development of their subject. Written by leading research workers from the USA, Europe and New Zealand, this book is the first comprehensive volume for twenty years to address this subject.Table of Contents1: What is Fire Blight? Who is Erwinia amylovora? How to Control It? Joël L Vanneste, HortResearch, New Zealand Part I: The Disease 2: Epidemiology of Fire Blight, 3: Distribution and Economic Importance of Fire Blight, 4: Genetic Diversity and Host Range of Erwinia amylovora, 5: Migration of Erwinia amylovora in Host Plant Tissues, Part II: The Pathogen 6: Erwinia amylovora: General Characteristics, Biochemistry and Serology, 7: Exopolysaccharides of Erwinia amylovora: Structure, Biosynthesis, Regulation, Role in Pathogenicity of Amylovoran and Levan, 8: hrp Genes and Harpins of Erwinia amylovora: a Decade of Discovery, 9: Disease-specific Genes of Erwinia amylovora: Keys to Understanding Pathogenesis and Potential Targets for Disease Control, 10: Iron and Fire Blight: Role in Pathogenicity of Desferrioxamine E, the Main Siderophore of Erwinia amylovora, Part III: Control of Fire Blight 11: Chemical Control of Fire Blight, 12: The Development of Streptomycin-resistant Strains of Erwinia amylovora, 13: Breeding for Resistance to Fire Blight, 14: Transgenic Varieties and Rootstocks Resistant to Fire Blight, 15: Fire Blight Risk Assessment Systems and Models, 16: Biological Control of Fire Blight, 17: Integrated Orchard and Nursery Management for the Control of Fire Blight,

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Book SynopsisThis well illustrated book provides an historical and unified overview of a century and a half of research on the development, life cycles, transmission and evolution of the nematodes found in vertebrates throughout the world. This second, expanded edition includes relevant data from some 450 new references that have appeared from 1989 to 1999. The volume includes nematode parasites of humans, domestic animals and wildlife including fish. After an introductory chapter outlining general principles, the author systematically describes the biological characteristics of the 27 superfamilies of nematodes, followed by families, subfamilies, genera and species.Table of Contents1: Introduction PART I: CLASS SECERNENTEA 1: Order Rhabditida 2: Order Strongylida (The Bursate Nematodes) 3: Order Oxyurida 4: Order Ascaridida 5: Order Spirurida - Suborder Camallanina 6: Order Spirurida - Suborder SpirurinaPART II - CLASS ADENOPHOREA 7: Order Enoplida - Suborder Dioctophymatina 8: Order Enoplida - Suborder Trichinellina

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Book SynopsisThis volume provides background theory and practical protocols for bioassays of bacteria, viruses, fungi, microsporidia and nematodes that can be used as biological control agents against insect pests of agricultural and medical importance. In addition, experimental design and statistics, computational modelling for bioassay analysis, and relevant legislation are described. With contributions from internationally recognised scientists from their respective fields, this book will be of particular value to researchers both experienced and inexperienced in this area.Table of Contents1: Bioassays of Bacillus thuringiensis 2: Bioassays of Bacillus thuringiensis products used against agricultural pests, A Navon, The Volcani Center, Israel 3: Bioassays of genetically engineered Bacillus thuringiensis plant products, SR Sims, Whitmire Micro-Gen, USA 4: Bioassays of Bacillus thuringiensis subsp. israelensis, O Skovmand, Laboratoire de Lutte Contre Les Insects Nuisible, France and N Becker, German Mosquito Control Association, Germany 5: Production of Bacillus thuringiensis insecticides for experimental uses, S Braun, The Hebrew University of Jerusalem, Israel 6: Bioassays of replicating bacteria against soil-dwelling insect pests, TA Jackson and DJ Saville, Agresearch, New Zealand 7: Bioassays of entomopathogenic viruses, KA Jones, University of Greenwich, UK 8: Bioassays of entomogenous fungi, TM Butt, University of Wales, UK and MS Goettel, Lethbridge Research Centre, Canada 9: Bioassays of microsporidia, JV Maddox, WM Brooks, North Carolina State University, USA and LF Solter, Illinois Natural History Survey & Illinois Agricultural Experiment Station, USA 10: Bioassays of entomopathogenic nematodes, I Glazer, The Volcani Center, Israel and EE Lewis, Virginia Polytechnic Institute and State University, USA 11: Statistical and computational analysis of bioassay data, R Marcus, The Volcani Center, Israel and DM Eaves, Simon Frazer University, Canada 12: Legislation affecting the collection, use and safe handling of entomopathogenic microbes and nematodes, D Smith, CABI Bioscience UK Centre (Egham), UK

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Book SynopsisThis major reference work contains essential information on arthropod-borne infections affecting humans and domesticated animals. The encyclopedia is a key reference source for anyone working in medical and veterinary science, and related fields. Features of The Encyclopedia of Arthropod-transmitted Infections are:150 entries, describing arboviral, viral, bacterial and rickettsial, spirochaetal, protozoal and filarial infections, and the vectors that transmit themInformation on disease distribution, clinical symptoms, diagnosis, transmission cycles, vector life-cycles, and treatment and control measures. Figures, tables and photographs illustrate the text. Following each entry is a selected bibliography, to aid further reading on the topicOver 80 different international authors, with expertise in medicine, veterinary science, parasitology, entomology, epidemiology, microbiology, and zoology have contributed to the encyclopedia.Table of Contents1: African horse sickness 2: Blackflies 3: Cat scratch disease 4: Epidemic haemorrhagic fever 5: Getah virus disease 6: Hepatozoonosis - canine 7: Louse-borne typhus 8: Malaria - avian 9: Malaria - human 10: Nairobi sheep disease 11: Omsk haemorrhagic fever 12: Powassan encephalitis 13: Q fever 14: Rickettsial pox 15: Stratford virus 16: Tataguine virus 17: Triatomine bugs 18: West Nile virus 19: Zika virus

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Book SynopsisThis second edition of the popular advanced student textbook (previously published as Worms and Disease: A Manual of Medical Helminthology) has been thoroughly updated and revised since it was first published in 1975. It includes contributions and a chapter by Prof. Derek Wakelin, University of Nottingham, UK. An authoritative handbook covering all human helminth infections with particular emphasis on diagnosis, treatment, clinical manifestations, pathogenesis, epidemiology and control. Practical guidelines are given for estimating the clinical and public significance of helminthiases, vital in areas where the majority of inhabitants are infected with many helminths but only a few are sick.Table of Contents1: The Trematodes 2: The Cestodes 3: The Acanthocephalans 4: The Nematodes 5: Oher Groups 6: Immunology of Helminths 7: Epidemiological Aspects of Helminth Infections 8: Helminthological Techniques

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Book SynopsisThis book, in three volumes, presents a detailed revision of the systematics and taxonomy of the platyhelminth class Trematoda, subclasses Aspidogastrea and Digenea, with keys for the identification of these parasites at the superfamily, family, subfamily and generic levels.The trematodes are parasitic worms infecting all vertebrate groups and include families of significance to human and animal health, with considerable economic impact. Volume 1 covers the subclass Aspidogastrea and order Strigeida, while the second and third volumes will cover the orders Echinostomida and Plagiorchiida.Table of Contents1: Class Trematoda Rudolphi, 1808 2: Subclass Aspidogastrea Faust & Tang, 1936 3: Subclass Digenea Carus, 1863 4: Superfamily Azygioidea Liihe, 1909 5: Superfamily Bivesiculoidea Yamaguti, 1934 6: Superfamily BrachylaimoideaJoyeux & Foley, 1930 7: Family Brachylaimidae Joyeux & Foley, 1930 8: Family Hasstilesiidae Hall, 1916 9: Family Leucochloridiidae Poche, 1907 10: Family Leucochloridiomorphidae Yamaguti, 1958 11: Family Moreauiidae Johnston, 1915 12: Family Ovariopteridae Leonov, Spasskii & Kulikov, 1963 13: Family Panopistidae Yamaguti, 1958 14: Family Thapariellidae Srivastava 15: Superfamily Bucephaloidea Poche, 1907 16: Superfamily Clinostomoidea Lühe, 1901 17: Family Clinostomidae Lühe, 1901 18: Family Liolopidae Odhner, 1912 19: Superfamily Cyclocoeloidea Stossich, 1902 20: Family Cyclocoelidae Stossich, 1902 21: Family Eucotylidae Cohn, 1904 22: Family Typhlocoelidae Harrah, 1922 23: Superfamily Diplostomoidea Poirier, 1886 24: Family Diplostomidae Poirier, 1886 25: Family Bolbocephalodidae Strand, 1935 26: Family Brauninidae Wolf, 1903 27: Family Cyathocotylidae Mühling, 1898 28: Family Proterodiplostomidae Dubois, 1936 29: Family Strigeidae Railliet, 1919 30: Superfamily Gymnophalloidea Odhner, 1905 31: Family Gymnophallidae Odhner, 1905 32: Family Botulisaccidae Yamaguti, 1971 33: Family Callodistomidae Odhner, 1910 34: Family Fellodistomidae Nicoll, 1909 35: Family Tandanicolidae Johnston, 1927 36: Superfamily Hemiuroidea Looss, 1899 37: Family Hemiuridae Looss, 1899 38: Family Accacoeliidae Odhner, 1911 39: Family Bathycotylidae Dollfus, 1932 40: Family Derogenidae Nicoll, 1910 41: Family Dictysarcidae Skrjabin & Guschanskaja, 1955 42: Family Hirudinellidae Dollfus, 1932 43: Family Isoparorchiidae Travassos, 1922 44: Family Lecithasteridae Odhner, 1905 45: Family Ptychogonimidae Dollfus, 1937 46: Family Sclerodistomidae Odhner, 1927 47: Family Sclerodistomoididae Gibson & Bray, 1979 48: Family Syncoeliidae Looss, 1899 49: Superfamily Schistosomatoidea Stiles & Hassall, 1898 50: Family Schistosomatidae Stiles & Hassall, 1898 51: Family Sanguinicolidae von Graff, 1907 52: Family Spirorchiidae Stunkard, 1921 53: Superfamily Transversotrematoidea Witenberg, 1944

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Book SynopsisThis is the third of three volumes of Keys to the Trematoda, a series on the systematics and identification of the Class Trematoda. It covers five superfamilies with the Order Plagiorchiida and the family Didymozoidae, with the keys for their identification at the family, subfamily and generic levels. It also includes a key to all dignean superfamilies, including those treated in detail in volumes oneand two.Trade Review"Keys to the Trematoda will become the standard reference on the group for many years. Given the infrequency of appearance of such large works, this is likely to remain the definitive work for the first half of this century and to find a place on book-shelves all over the planet." David Blair, School of Tropical Biology, Australia "...we consider the Keys to represent a valuable contribution to taxonomic research on trematodes...Keys to the Trematoda will undoubtedly represent an indispensable source of basic information about the systematics of these helminths." Scholz & Horak, Folia Parasitologica, 2003 "The editors and the authors have succeeded in preparing a book which is valuable to experts, practising Parasitologists and beginners, and they should be congratulated on their great success" Zdzislaw Swiderski & Boyko B. Georgiev Acta Parasitologica, 2005, 50(4)"Table of Contents1: Introduction and Key to Superfamilies 2: Superfamily Opisthorchioidea Looss, 1899 3: Family Opisthorchiidae Looss, 1899 4: Family Cryptogonimidae Ward, 1917 5: Family Heterophyidae Leiper, 1909 6: Superfamily Monorchioidea Odhner, 1911 7: Family Monorchiidae Odhner, 1911 8: Family Lissorchiidae Magath, 1917 9: Superfamily Gorgoderoidea Looss, 1899 10: Family Gorgoderidae Looss, 1899 11: Family Anchitrematidae Mehra, 1935 12: Family Brachycoeliidae Looss, 1899 13: Family Braunotrematidae Yamaguti, 1958 14: Family Collyriclidae Ward, 1917 15: Family Cortrematidae Yamaguti, 1958 16: Family Dicrocoeliidae Looss, 1899 17: Family Mesocoeliidae Dollfus, 1929 18: Family Orchipedidae Skrjabin, 1913 19: Family Paragonimidae Dollfus, 1939 20: Family Prouterinidae Foreyt, Schell & Beyer, 1996 21: Family Troglotrematidae Odhner, 1914 22: Superfamily Plagiorchioidea Lühe, 1901 23: Family Plagiorchiidae Luhe, 1901 24: Family Auridistomidae Stunkard, 1924 25: Family Cephalogonimidae Looss, 1899 26: Family Choanocotylidae Jue Sue & Platt, 1998 27: Family Dolichoperoididae Johnston & Angel, 1940 28: Family Echinoporidae Krasnolobova & Timofeeva, 1965 29: Family Encyclometridae Mehra, 1931 30: Family Gekkonotrematidae Yamaguti, 1971 31: Family Glypthelminthidae Cheng, 1959 32: Family Haematoloechidae Freitas & Lent, 1939 33: Family Leptophallidae Dayal, 1938 34: Family Macroderoididae McMullen, 1937 35: Family Meristocotylidae Fischthal & Kuntz, 1964 36: Family Mesotretidae Poche, 1926 37: Family Ocadiatrematidae Fischthal & Kuntz, 1981 38: Family Omphalometridae Looss, 1899 39: Family Opisthogonimidae Travassos, 1928 40: Family Orientocreadiidae Yamaguti, 1958 41: Family Reniferidae Pratt, 1902 42: Family Styphlotrematidae Baer, 1924 43: Family Telorchiidae Looss, 1899 44: Family Thrinascotrematidae Jue Sue & Platt, 1999 45: Family Urotrematidae Poche, 1926 46: Superfamily Microphalloidea Ward, 1901 47: Family Microphallidae Ward, 1901 48: Family Anenterotrematidae Yamaguti, 1958 49: Family Diplangidae Yamaguti, 1971 50: Family Eumegacetidae Travassos, 1922 51: Family Exotidendriidae Mehra, 1935 52: Family Faustulidae Poche, 1926 53: Family Gyrabascidae Macy, 1935 54: Family Lecithodendriidae Luhe, 1901 55: Family Leyogonimidae Dollfus, 1951 56: Family Pachypsolidae Yamaguti, 1958 57: Family Phaneropsolidae Mehra, 1935 58: Family Pleurogenidae Looss, 1899 59: Family Prosthogonimidae Luhe, 1909 60: Family Renicolidae Dollfus, 1939 61: Family Renschetrematidae Yamaguti, 1971 62: Family Stomylotrematidae Poche, 1926 63: Family Taiwantrematidae Fischthal & Kuntz, 1981 64: Family Zoogonidae Odhner, 1902 65: Family Didymozoidae Monticelli, 1888 66: Genera incertae sedis, genera inquirenda, nomina nuda, larval or collective names and recently erected genera

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Book SynopsisParasites have evolved numerous complex and fascinating ways of interacting with their hosts. The subject attracts the interest of numerous biologists from the perspective of ecology and behavioural biology, as well as from those concerned with more applied aspects of parasitology. However, until now there has been no recent book to synthesize this field.This book, written by leading authorities from the USA, Europe, Australia and New Zealand, provides the most comprehensive coverage of this important topic on the market.Table of ContentsPart I: Foraging for Hosts 1: Trematode transmission strategies, C Combes, Université Perpignan, France, P Bartoli, Campus Universitaire de Luminy, France and A Théron, Université Perpignan, France 2: Entomopathogenic nematode host-search strategies, J F Campbell and E E Lewis 3: Flexibility in host-search and patch-use strategies of insect parasitoids, L E M Vet, L Hemerik, Wageningen University, The Netherlands, M E Visser, Netherlands Institute of Ecology, The Netherlands and F L Wäckers, Wageningen University, The Netherlands Part II: Host Acceptance and Infection 4: Host discrimination by seed parasites, F J Messina, Utah State University, USA 5: Soil and plant interactions’ impact on plant-parasitic nematode host finding and recognition, A F Robinson, USDA-ARS, USA 6: Environmental control of nematode life cycles, M E Viney, University of Bristol, UK Part III: Interactions among parasites within host 7: The interactions between larval parasitoids and their hosts, M R Strand, University of Georgia, USA 8: Inter-specific interactions in trematode communities, K Lafferty, University of California, USA 9: Niche restriction and mate finding in vertebrate hosts, K Rohde, University of New England, Australia 10: Parasite sex determination, R E L Paul, Institut Pasteur, France Part IV: Parasite-Host Interactions 11: Interactions between intestinal nematodes and vertebrate hosts, M V K Sukhdeo, S C Sukhdeo and A D Bansemir, Rutgers University, USA 12: Parasite manipulation of host behaviour, R Poulin, University of Otago, New Zealand 13: Parasite manipulation of vector behaviour, J G C Hamilton and H Hurd, Keele University, UK 14: Parasite virulence, J Schall, University of Vermont, USA 15: The behavioural ecology of social parasitism in ants, R J Stuart, University of Florida, USA Part V: Synthesis 16: Parasite behavioural ecology in a field of diverse perspectives, E E Lewis, J F Campbell and M V K Sukhdeo

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Book SynopsisLyme borreliosis commonly known as lyme disease is now acknowledged as the most highly prevalent arthropod-borne human disease in northern temperate regions of the world. This book describes the basic characteristics of the disease, the biology of the pathogens in their vectors and vertebrate hosts, their ecology in different regions of the world and the global epidemiology of the disease. The final chapters address the prevention and control measures that have resulted from this knowledge.Table of ContentsI: History and Characteristics of Lyme Borreliosis 2: Ecological Research on Borrelia burgdorferi sensu lato: Terminology and Some Methodical Pitfalls 3: Molecular and Cellular Biology of Borrelia burgdorferi sensu lato 4: Vectors of Borrelia burgdorferi sensu lato 5: Borrelia burgdorferi sensu lato in the Vertebrate Host 6: Ecology of Borrelia burgdorferi sensu lato in Europe 7: Ecology of Borrelia burgdorferi sensu lato in Russia 8: Ecology of Borrelia burgdorferi sensu lato in Japan and East Asia 9: Ecology of Borrelia burgdorferi sensu lato in North America 10: Epidemiology of Lyme Borreliosis 11: Vaccination against Lyme Borreliosis 12: Environmental Management for Lyme Borreliosis Control

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Book SynopsisThis volume details techniques on the study of Isolation, characterization, and exploration of actinobacteria in industrial, food, agricultural, and environmental microbiology. Chapters cover a wide range of basic and advanced techniques associated with research on isolation, characterization and identification of actinobacteria in soil, sediment, estuarine, water, Saltpan, Mangroves, plants, lichens, sea weeds, sea grass, animals-crab, snail, shrimp.  Authoritative and cutting-edge, Methods in Actinobacteriology aims to be a useful practical guide to researches to help further their study in this field. Table of Contents1. Isolation of Actinobacteria from Soil and Marine Sediment Samples Savitha, T., Ashraf Khalifa, and Sankaranarayanan A 2. Isolation of Actinobacteria from Water Sources Tamalika Chakraborty, Sumana Roy, Dipanjan Mandal, Jeenatara Begum, and Abhijit Sengupta 3. Isolation of Actinobacteria from Deep Sea AparanaKumari,K. V. and Bhaskara Rao 4. Isolation of Actinobacteria from Estuary Ashraf Khalifa and Sankaranarayanan A 5.Isolation of Actinobacteria from Sponges Neethu Kamarudheen and K.V. Bhaskara Rao 6. Isolation of Actinobacteria from Shrimp Shijila Rani A.S., Babu S., Anbukumaran A., Prakash P., Veeramani S., and Ambikapathy V. 7. Isolation of Actinobacteria from Coral Reef Babu S., Shijila Rani A.S., Anbukumaran A, Praksah, P., and Ambikapathy V. 8. Isolation of Actinobacteria from Earthworm Cast Anbukumaran, A.,Shijila Rani, A.S., Ambikapathy, V., Veeramani, S. Shanmgapriya, R. and Babu, S. 9. Isolation of Actinobacteria from Compost Samples Savitha T, Ashraf Khalifa, and Sankaranarayanan A 10. Isolation of Gut Actinobacteria from Fecal and Tissue Samples Priyanka Sarkar 11. Isolation of Gut Actinobacteria from Termites Malavika S., Sahana Kranthi, Shishira Rao H. S., Shreyanka S. Moily, and Martin Paul A 12. Isolation of Gut Actinobacteria from Fishes S. Thejaswini, Sruthy Jojy, Aditi Vijayan, and Martin Paul A 13. Isolation of Actinobacteria from Mangrove Plants Babu S., Anbukumaran A., Ambikapathy V., Veeramani S., Shijila Rani A.S., and Prakash, P 14. Isolation of Actinobacteria from Seaweeds Apsara S. Babu and K. V. Bhaskara Rao 15. Isolation of Actinobacteria from Hills Veerapagu M, Jeya KR, and Sankaranarayanan A 16. Isolation of Endophytic Actinobacteria from Flowers, Fruits, and Seeds of Higher Plants Jayanthi.D, Martin Paul.A, and Leena Sebastian 17. Isolation of Actinobacteria from Desert Soils Ashraf Khalifa and Sankaranarayanan, A. 18. Isolation of Epiphytic Actinobacteria from Rhizosphere of Spermatophytes Shravya.S, Meghana.S.J ,and Jayanthi.D 19. Isolation of Epiphytic Actinobacteria from Lichens Shabeena Banu M.S., Nargis Begum T., G. Vinothini, D.Dhanasekaran, and Thajuddin N. 20. Isolation of Endophytic Actinobacteria from Lichens Shabeena Banu M.S., Nargis Begum T., D. Dhanasekaran, and Thajuddin N. 21. Isolation of Psychrophilic and Psychrotolerant Actinobacteria Manigundan.K, B. Abirami, V. Gopikrishnan, M. Radhakrishnan, and P.V. Bhaskar 22. Isolation of Halophilic Actinobacteria from different habitats Martin Paul, A. and Jayanthi, D. 23. Isolation of Thermophilic Actinobacteria from Different Habitats Pranjali Chole, Lokesh Ravi, and Kannabiran Krishnan 24. Isolation of Stone Dwelling Actinobacteria Shabari Girish, Lokesh Ravi, and Kannabiran Krishnan 25. Cultivation Techniques of Rare Actinobacteria Ramasamy Vijayakumar, Durairaj Thirumurugan, Alagappan Cholarajan, and Suresh Selvapuram Sudalaimuthu Raja 26. Chemo-taxonomical Characterization of Actinobacteria Ramasamy Vijayakumar and Suresh S.S. Raja 27. Application of Bioinformatic Tools for Phylogenetic Analysis Manigundan.K.,Jerrine Joseph, M. Radhakrishnan, Mary Shamya, and Wilson Aruni 28. Methods for Whole-genome Analysis of Actinobacteria through Bioinformatics Approaches Indrani Sarkar, Gargi Sen, and Arnab Sen 29. Nanopore Based Long Read Sequencing Technology to Obtain Highly Contiguous Whole Genome Sequence of Actinobacterial Genomes like Streptomyces sp.. Sankaranarayanan Gomathinayagam, Loganathan Karthik, and KodiveriMuthukaliannan Gothandam 30. Mining genomes of Actinobacteria Sushant Parab, Davide Corà, and Federico Bussolino 31. Comparative genomics of Actinobacteria Sushant Parab,Davide Corà, and Federico Bussolino 32. Biosynthetic Gene Cluster Analysis in Micromonospora Species Using Antismash: Secondary Metabolite Genome Mining Pipeline Manickasamy Mukesh Kumar, Narayanan Rajagopal, and Dhanasekaran Dharumadurai 33. Biosynthetic Gene Cluster Analysis in Actinobacterial Genera Streptomyces spp. Markéta Macho, Daniela Ewe, Vishal Ahuja, Jihen Thabet, Avik Banerjee, Kumar Saurav, and Subhasish Saha 34. PCR based Determination of Secondary Metabolite Genes in Actinobacterial Cultures K. Manigundan, B. Abirami, V. Gopikrishnan, Jerrine Joseph, and M. Radhakrishnan 35. Molecular Mass Determination of Bacteriocin by SDS-PAGE analysis Santhosh Arul M,.Jayashankar, and HaripriyaDayalan 36. MALDI-TOF Analysis of Actinobacterial Peptides with Respect to MASCOT Database Shanmugaraj Gowrishankar, Arumugam Kamaladevi, and Shunmugiah Karutha Pandian 37. Protocols for Preclinical Evaluation and Molecular Docking of Antimicrobial Compounds from Streptomyces sp.- Drug Likeliness Evaluation, ADME-Toxicity Investigation, Docking modes between the Ligand and the target Enzyme and Active Site Prediction Anirudh Sreenivas B.K, Akshaya B, Lokesh Ravi, and Kannabiran Krishnan 38. Energy-based Pharmacophore Hypothesis Combined with Molecular Simulation Protocol for The Screening Of Bioactive Compounds From the Class of Actinobacteria Thirunavukkarasu Muthu Kumar and KaruppasamyRamanathan 39. Receptor cavity-based approach combined with Autodock protocol for the screening of antiviral compounds from Streptomyces sp. K. Rohini, and V. Shanthi 40. Pharmacophore Based Hypothesis Combined with Molecular Docking Protocol for the Screening Of Anti-Cancer Compounds from Streptomyces sp. S. Saranyadevi, R. Priyanka and V. Shanthi 41. Methods of Identification and Validation of Drug Target Jerrine Joseph, M. Radhakrishnan, K. Manigundan,V. Gopikrishnan, Mary Shamya, and Wilson Aruni 42. Transcriptome profiles of Streptomyces sp. Sushant Parab, Davide Corà, and Federico Bussolino 43. Culture of Actinobacteria, Isolation, and Characterization of their Bioactive Compounds Charles SanthanarajuVairappan 44. Miniaturized Production of Bioactive Extracts from Actinobacteria B. Abirami, M. Radhakrishnan, K. Manigundan, Jerrine Joseph, V. Gopikrishnan, and R. Balagurunathan 45. Screening, Characterization, and Identification of Antibacterial Compounds From Actinobacteria Savitha, T., Ashraf Khalifa, and Sankaranarayanan A 46. Isolation, Identification, and Screening of Polyene Antifungal Compound Producing Streptomyces sampsonii MDCE7 from agroforestry soil Radhakrishnan Srinivasan and Varadharajan Mohan 47. Screening of Actinobacterial Cultures for Antimycobacterial Activity using Mycobacterium smegmatis Ramachandran Chelliah and Deog-Hwan Oh 48. Screening of Actinobacterial Extracts/Compounds for Antimycobacterial Activity by Luciferase Reporter Phage (LRP) Assay Shuai Wei,Shucheng Liu, Ramachandran Chelliah, and Deog-Hwan Oh 49. Screening of Actinobacteria for Anti-TB Activity by MicroplateAlamarBlue Assay (MABA) Shuai Wei, Shucheng Liu, Ramachandran Chelliaha, nd Deog-Hwan Oh 50. Screening of Actinobacteria for anti-TB Activity by Agar Dilution Assay Ramachandran Chelliah and Deog-Hwan Oh 51. Antiplasmodial activity of Halophilic Actinobacteria Dharumadurai Dhanasekaran and Saravanan Karthikeyan 52. An invitroAntiamoebic Activity of Actinobacteria KarthiyayiniBalakrishnan, Dhanasekaran Dharumadurai, Thirumurugan Ramasamy, and Muthuselvam Manickam 53. Screening for Antiviral Activity: MTT Assay Ramachandran Chelliah, Fazle Elahi, and Deog-Hwan Oh 54. Screening for Anticancer Activity: 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium (MTT) Assay Ramachandran Chelliah and Deog-Hwan Oh 55. Screening for Anticancer Activity: Dual Staining Method Ramachandran Chelliah and Deog-Hwan Oh 56. Screening for Anticancer Activity: Neutral Red Uptake Assay Ramachandran Chelliah and Deog-Hwan Oh 57. Screening for Anticancer Activity: Lactic Acid Dehydrogenase Assay Ramachandran Chelliah and Deog-Hwan Oh 58. Screening for Anticancer Activity: DNA Fragmentation Assay InamulHasan Madar, Ghazala Sultan, Ramachandran Chelliah, and Deog-Hwan Oh 59. Screening for Anticancer Activity: Trypan Blue Exclusion Assay InamulHasan Madar, Ghazala Sultan, Ramachandran Chelliah, and Deog-Hwan Oh 60. In vitro Evaluation of Antimitotic Properties Of Actinobacterial Extracts Using Onion Root Tip Assay Gopikrishnan. V., M. Radhakrishnan, K. Manigundan, T. Shanmugasundaram, and Jerrine Joseph 61. Screening for Antioxidant Activity: Diphenylpicrylhydrazine (DPPH) Assay Momna Rubab, Ramachandran Chelliah and Deog-Hwan Oh 62. Screening for Antioxidant Activity: Nitric Oxide Scavenging Assay Ramachandran Chelliah, Eric Banan-MwineDaliri, and Deog-Hwan Oh 63. Screening for Antioxidant Activity: Metal Chelating Assay Ramachandran Chelliah and Deog-Hwan Oh 64. Screening for Antioxidant Activity: Total Antioxidant Assay Ramachandran Chelliah, Eric Banan-MwineDaliri, and Deog-Hwan Oh 65. Screening for Antioxidant Activity: Hydrogen Peroxide Scavenging Assay Ramachandran Chelliah, Eric Banan-MwineDaliri, and Deog-Hwan Oh 66. In vitro Evaluation Of Actinobacterial Extracts For Anti Inflammatory Properties B. Abirami, K. Manigundan, Mary Shamya, Jerrine Joseph, S. Shanmugasundaram, and M. Radhakrishnan 67. Screening and production of anti freeze Proteins from Actinobacteria B. Abirami, M. Radhakrishnan, K. Manigundan, V. Gopikrishnan1, S.T. Somasundaram2, and P.V. Bhaskar 68. In vitro Evaluation of Actinobacterial Extracts for Immunomodulatory Properties B. Abirami, K. Manigundan, M. Radhakrishnan, V. Gopikrishnan, Jerrine Joseph, T. Shanmugasundaram, and T. Somasundaram 69. Screening of Actinobacteria for Enzyme Inhibitor Activity Ramachandran Chelliah, Eric Banan-MwineDaliri, and Deog-Hwan Oh 70. Screening of Actinobacteria for Quorum Sensing Inhibition Ramachandran Chelliah, Eric Banan-MwineDaliri, and Deog-Hwan Oh 71. Screening of Actinobacterial Extracts for Anti-biofilm Activity Ramachandran Chelliah, Eric Banan-MwineDaliri, and Deog-Hwan Oh 72. Screening of Actinobacteria for Microbial Induced Calcium Precipitation (MICP) K. Manigundan, B. Abirami, V. Gopikrishnan, and M. Radhakrishnan 73. Immobilization of Actinobacterial Cells – Sodium Alginate and Calcium Chloride Method Gopikrishnan, V., K. Manigundan, B. Abirami, and M. Radhakrishnan 74. Production of Actinobacteria Amylase by Fermentation in Solid State Using Residues Of Licuri Palm (Syagruscoronata) Milena Santos Aguiar, Rafael Resende Maldonado, Andrea Limoeiro Carvalho, and Elizama Aguiar-Oliveira 75. Production Of Lipase By Actinobacteria IsabelyFernanda Pizarro, HandrayFernandes de Souza, Janaínados Santos Ferreira, Rafael Resende Maldonad, and Eliana Setsuko Kamimura 76. Isolation And Cultivation Of Actinobacteria By Submerged Fermentation For The Production Of Keratinase Rafael Resende Maldonado, TaísRosângelaCorreia Souza, Simone Kubeneck, Elizama Aguiar-Oliveira, and Helen Treichel 77. Screening of Cellulase from Actinobacteria Varsha N Swamy, M A Haneen, and M.Jayashankar 78. Screening of Pectinase from Actinobacteria M A Haneen, M.Jayashankar, And Varsha N Swamy 79. Screening of Protease from Actinobacteria AshwithaGopal ,Varsha N Swamy,Santhosh Arul, and M.Jayashankar 80. Screening and analysis of Actinobacterial Bioherbicides For Weed Management Prem Anand K and Suthindhiran K 81. In vitro Assessment of Actinobacteria for Survivability Under Simulated Gastro-Intestinal Transit G.Vinothini, M.S. ShabeenaBanu, S. Seema, and D.Dhanasekaran q82. In vitro Assessment of Actinobacteria for Survivability Under Simulated Gastro-Intestinal Transit G.Vinothini, M.S. ShabeenaBanu, S. Seema, and D.Dhanasekaran 83. Screening of Actinobacterial Probiotics by Anti-Pathogenic Activity Test Peng Chen, Zhongkun Zhou, Yunhao Ma,Rentao Zhang, Mengze Sun 84. Screening and Analysis of Probiotic Actinobacteria in Poultry Farming Mônica Roberta Mazalli and Rafael Resende Maldonado 85. Vitamin B12 Producing Actinobacteria as Probiotics for Poultry Production Firdosh Shah and Mitesh Dwivedi 86. Qualitative and Quantitative Estimation of Phosphate Solubilizing Actinobacteria Shreya Desaiand NatarajanAmaresan 87. Estimation of Nitrogen Production by Actinobacteria Shreya Desaiand NatarajanAmaresan 88. Screening of Actinobacteria for Siderophore Production Caroline Mercy Andrew Swamidoss, Ramachandran Chelliah, and Deog-Hwan Oh 89. Isolation and Screening of Symbiotic Actinobacteria From Root Nodules of Actinorhizal plant Casuarina sp Dharumadurai Dhanasekaran and Saravanan Karthikeyan 90. Biocontrol Activity of Actinobacteria Against Plant Pathogens Shreya Desaiand NatarajanAmaresan 91. An In vitro nematicidalactivity ofactinobacteria- Juvenile mortality and Egg hatching inhibition Vijayakumar Vishnu Raja and DharumaduraiDhanasekaran 92. Estimation of Auxin Production by Actinobacteria Shreya Desaiand NatarajanAmaresan 93. Screening of Actinobacteria for Mosquitocidal Activity Caroline Mercy Andrew Swamidoss, Ramachandran Chelliah, and Deog-Hwan Oh 94. Extraction, Characterization, and Identification of Odorous Metabolites from Streptomyces Dharumadurai Dhanasekaran, Saravanan Karthikeyan, Saravanan Chandraleka, Govindhan Sivaranjani, and Selvanathan Latha 95. Screening of Actinobacteria for Biosurfactant Production Ramachandran Chelliah, Eric Banan-MwineDaliri, and Deog-Hwan Oh 96. Optimization and Characterization of Biosurfactant from Streptomyces Vishal Ahuja, Markéta Macho, Jihen Thabet, Avik Banerjee, Daniela Ewe, Subhasish Saha, and Kumar Saurav 97. Production of Vitamin B12from Streptomyces species Camil Rex M,Akshaya B, Lokesh Ravi, and Kannabiran Krishnan 98. Screening of Microbes for the Production of Pigment (Melanin) Ramachandran Chelliah and Deog-Hwan Oh 99. Exploration and Characterization ofMelanin Pigment Produced by Actinomycetes Puja Gupta, Madangchanok imchen, and Ranjith Kumavath 100. Isolation and Production of Prodigiosin Pigments from Streptomyces spp. Leena Sebastian, Martin Paul, A., and Jayanthi, D. 101. Aerobic and Anaerobic Decolourization of Textile Dyes Using Actinobacteria Ramasamy Vijayakumar and Suresh S.S. Raja 102. Bioleaching of heavy metals from e-waste using actinobacteria Gopikrishnan, V., K. Manigundan, PR. Meganathan, and M. Radhakrishnan 103. Biosynthesis and Characterization of Silver Nanoparticles From Actinobacteria Vimala. R.T.Va,Rajivgandhi. Gb,d,S. Sridharana,Jayapriya. Mc,Ramachandran. Gd, Chenthis Kanisha. Cd, Manoharan. Nd,Wen-Jun Lib 104. Biosynthesis and Characterization of Gold Nanoparticles from Actinobacteria Vimala. R.T.V, Rajivgandhi. G, S. Sridharan, Jayapriya. M, Ramachandran. G, Chenthis Kanisha. C, Manoharan. N, Wen-Jun Li 105. Antimicrobial Activity of Extracellular Green-Synthesized Nanoparticles By Actinobacteria Vimala. R.T.V, Rajivgandhi. G, S. Sridharan, Jayapriya. M, Ramachandran. G, Chenthis Kanisha. C, Manoharan. N, and Wen-Jun Li 106. Antibiofilm Activity of Extracellular Green-Synthesized Nanoparticles By Actinobacteria Vimala. R.T.V, Rajivgandhi. G, S. Sridharan, Jayapriya. M, Ramachandran. G, Chenthis Kanisha. C, Manoharan. N, Wen-Jun Li 107. Cytotoxic Activity of Extracellular Green Synthesized Nanoparticles by Actinobacteria Vimala. R.T.V, Rajivgandhi. G, S. Sridharan, Jayapriya. M, Ramachandran. G, Chenthis Kanisha. C, Manoharan. N, and Wen-Jun Li 108. Sporicidal Activity of Extracellular Green-Synthesized Nanoparticles by Actinobacteria Vimala. R.T.V, Rajivgandhi. G, S. Sridharan, Jayapriya. M, Ramachandran. G, Chenthis Kanisha. C, Manoharan. N, and Wen-Jun Li

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Book SynopsisIsolation of Bacteriophages for Clinically Relevant Bacteria.- Observation of Bacteriophage Ultrastructure by Cryo-electron Microscopy.- Bacteriophage Taxonomy: A Continually Evolving Discipline.- Guidelines to Compose an Ideal Bacteriophage Cocktail.- Rapid Bench to Bedside Therapeutic Bacteriophage Production.- Bacteriophage Production in Compliance with Regulatory Requirements.- Nano/micro formulations for bacteriophage delivery.- Phage-Host Interaction Analysis using Flow Cytometry.- Bacteriophage control of infectious biofilms.- Studying bacteriophage efficacy using a zebrafish model.- Use of Galleria mellonella as an animal model for studying the antimicrobial activity of bacteriophages with potential use in phage therapy.- Interaction of Bacteriophages with the Immune System: Induction of Bacteriophage-specific Antibodies.- Bacteriophage Treatment of Infected Diabetic Foot Ulcers.- A Review of Phage Therapy for BonTable of Contents

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Book SynopsisManaging risk when working with Orbiviruses with a special emphasis on Epizootic haemorrhagic disease virus.- Recognition of Field Signs, Necropsy Procedures and Evaluation of Macroscopic Lesions of Cervids Infected with Epizootic Hemorrhagic Disease Virus.- Virus Isolation of Epizootic Haemorrhagic Disease Virus in Cell Culture.- Purification of epizootic haemorrhagic disease virus (and other Orbiviruses) particles from infected mammalian or insect cells.- Confocal microscopy of fluorescently labelled EHDV infected cell cultures.- Epizootic Haemorrhagic Disease Virus Titration.- Virus neutralisation test for detecting and quantifying serum neutralising antibodies to epizootic haemorrhagic disease virus (serotypes 1, 2, and 4-8).- Epizootic Hemorrhagic Disease Agar Gel Immunodiffusion Assay.- Detection of EHDV antibodies using enzyme-linked immunosorbent assay (ELISA).- Real-time RT-PCR for the diagnosis of epizootic haemorrhagic disease virus.- Real-time RT-PCR assays for typing of

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Book SynopsisPoxvirus Epidemiology.- Mpox Specimen Collection, Storage, Preparation, and Laboratory Diagnostics by PCR.- A Quantitative Real-Time PCR Assay for Measuring Poxvirus Replication and Cell Binding.- Orthopoxvirus Genome Sequencing, Assembly, and Analysis.- Bioinformatics for the Structural Genomics of Poxviruses.- Construction and Isolation of Recombinant Vaccinia Virus by Homologous Recombination Using Fluorescent Protein Markers.- Rapid Generation of Recombinant Poxviruses Using CRISPR/Cas9 Gene Editing.- Cas9-Mediated Poxvirus Recombinant Recovery (CASPRR) for Fast Recovery of Recombinant Vaccinia Viruses.- Use of a Poxvirus K3 Ortholog as a Positive Selection Marker for Construction of Recombinant Vaccinia Virus with Modified Host Range.- Orthopoxvirus Purification for High Containment Laboratories.- Evaluation of Vaccinia Virus Infection in Mice Using Two-Reporter Recombinant Virus.- Bioluminescence Imaging to Study Recombinant Orthopoxvirus Infection in Animal Models.- Methods t

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Book SynopsisMismatch of Supply and Demand: Marburg Virus Disease Outbreaks Need Countermeasures but Will Not Provide Opportunity for Clinical Trials.- Marburg Virus Medical Countermeasures.- Isolation and Propagation of Marburg viruses.- Validation of Marburg Virus Inactivation by AVL Buffer.- Generation, Recovery, and Propagation of a Recombinant Vesicular Stomatitis Virus Expressing the Marburg Virus Glycoprotein.- Visualizing the Internalization of Marburg Virus-Like Particles into Living Cells.- Proximity Proteomics to Profile Ebola Virus Protein Interactome in its Functional Context.- Monoclonal Antibody Production Against Filoviruses from Immunized Mice.- Marburg Virus Minigenome Assays.- Transcription- and Replication-Competent Virus-Like Particle Systems for Marburg Virus.- Generation of Biologically Contained Marburg Virus.- Recovery of Recombinant Marburg Virus by Reverse Genetics.- In Vivo Investigation of Filovirus Glycoprotein-Mediated Infection in a BSL2 Setting.- Evaluating

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Book SynopsisExplores the utility and potential of extremophiles in sustainability and biotechnology Many extremophilic bio-products are already used as life-saving drugs. Until recently, however, the difficulty of working with these microbes has discouraged efforts to develop extremophilic microbes as potential drug reservoirs of the future. Recent technological advances have opened the door to exploring these organisms anew as sources of products that might prove useful in clinical and environmental biotechnology and drug development. Extremophiles features outstanding articles by expert scientists who shed light on broad-ranging areas of progress in the development of smart therapeutics for multiple disease types and products for industrial use. It bridges technological gaps, focusing on critical aspects of extremolytes and the mechanisms regulating their biosynthesis that are relevant to human health and bioenergy, including value-added products of commercial signTable of ContentsContributors xv Introduction xix 1 MOLECULAR EVOLUTION OF EXTREMOPHILES 1 Debamitra Chakravorty, Ashwinee Kumar Shreshtha, V. R. Sarath Babu, and Sanjukta Patra 1.1 Introduction 1 1.2 Molecular Evolution of Thermophiles 2 1.3 Molecular Evolution of Psychrophiles 4 1.4 Molecular Evolution of Halophiles 6 1.5 Molecular Evolution of Alkaliphiles 7 1.6 Molecular Evolution of Acidophiles 8 1.7 Molecular Evolution of Barophiles 10 1.8 Engineering Extremophiles 12 1.9 Case Studies 17 1.10 Implications of Engineered Extremophiles on Ecology, Environment, and Health 20 1.11 Conclusions and Recommendations 20 2 ATTAINING EXTREMOPHILES AND EXTREMOLYTES: METHODOLOGIES AND LIMITATIONS 29 Debamitra Chakravorty and Sanjukta Patra 2.1 Introduction 29 2.2 Extremophiles: Types and Diversity 30 2.3 Extremolytes 54 2.4 Conclusions 64 3 STRATEGIES FOR THE ISOLATION AND CULTIVATION OF HALOPHILIC MICROORGANISMS 75 Aharon Oren 3.1 Introduction 75 3.2 Thalassohaline and Athalassohaline Hypersaline Environments 76 3.3 Case Studies 79 3.4 The Upper Salinity Limits of Different Types of Energy Generation 85 3.5 Final Comments 88 4 HALOPHILIC PROPERTIES AND THEIR MANIPULATION AND APPLICATION 95 Tsutomu Arakawa, Hiroko Tokunaga, Matsujiro Ishibashi, and Masao Tokunaga 4.1 Introduction 95 4.2 Industrial Applications of Halophilic Organisms and Their Proteins 96 4.3 Extreme and Moderate Halophiles and Their Proteins 98 4.4 Generation of Low-Salt Stable Extreme-Halophilic Proteins 99 4.5 Interconversion of Halophilic and Nonhalophilic Proteins 105 4.6 Soluble Expression of Recombinant Proteins 110 4.7 Natively Unfolded Proteins 113 4.8 Organic Solvent Tolerance 113 5 FEATURES AND APPLICATIONS OF HALOPHILIC ARCHAEA 123 Ximena C. Abrevaya 5.1 Introduction 123 5.2 General Features 124 5.3 Applications of Halophilic Archaea 130 5.4 Concluding Remarks 143 6 BIOTECHNOLOGICAL APPLICATIONS OF COLD-ADAPTED BACTERIA 159 Laura Garcia-Descalzo, Alberto Alcazar, Fernando Baquero, and Cristina Cid 6.1 Introduction 159 6.2 Molecular Mechanisms of Adaptation to Cold Environments 162 6.3 Exopolysaccharides 163 6.4 Lipids 164 6.5 Proteins 164 6.6 Biotechnological Applications of Cold-Adapted Enzymes 168 6.7 Biodegradation and Bioremediation in Cold Environments 169 6.8 Conclusions 172 7 ECOLOGY AND BIOTECHNOLOGY OF EXTREMOPHILIC MICROORGANISMS, PARTICULARLY ANAEROBIC HERMOPHILES 175 Francesco Canganella 7.1 Introduction 175 7.2 Thermophiles 176 7.3 Acidophiles 187 7.4 Alkaliphiles 191 7.5 Halophiles 193 7.6 Piezophiles 194 8 THE ROLE OF EXTREMOPHILIC MICROORGANISMS AND THEIR BIOPRODUCTS IN FOOD PROCESSING AND PRODUCTION 205 Jane A. Irwin 8.1 Introduction 205 8.2 Enzymes from Extremophiles in Food Processing 206 8.3 Alkaliphiles, Acidophiles, and Piezophiles 217 8.4 Extremophiles in Food Spoilage and Contamination 218 8.5 Extremophiles as Pathogens of Food Species 221 8.6 Conclusions 222 9 EXTREMOPHILES AND THEIR APPLICATION TO BIOFUEL RESEARCH 233 M.P. Taylor, R. Bauer, S. Mackay, M. Tuffin, and D.A. Cowan 9.1 Introduction 233 9.2 Extremophiles and Fuels 235 9.3 Exploiting Extremophilic Enzymes in Biomass Conversion to Biofuel 241 9.4 Conclusions and Future Prospects 249 10 SUSTAINABLE ROLE OF THERMOPHILES IN THE SECOND GENERATION OF ETHANOL PRODUCTION 267 Anuj K. Chandel, Ellen C. Giese, Om V. Singh, and Silvio Silverio da Silva 10.1 Introduction 267 10.2 Thermophilic Cellulases for Deconstruction of the Plant Cell Wall 269 10.3 Ethanol Production at Elevated Temperatures 274 10.4 Future Perspectives and Challenges 281 10.5 Conclusions 283 11 ECOFRIENDLY ASPECTS OF THE USE OF EXTREMOPHILIC ENZYMES IN TEXTILE SUBSTRATES 291 Bipin J. Agrawal and Sandhya Mishra 11.1 Introduction 291 11.2 Biopolymeric Fibers 292 11.3 Extremophilic Enzymes and Their Use in the Textile Industry 293 11.4 Utilization of Extremophilic Enzymes in Textile Wet Processing 297 11.5 Finishing with Extremophilic Enzymes 306 11.6 Role of Enzymes in Textile After-Care 311 11.7 Role of Enzymes in Effluent Treatment of Textiles 314 11.8 Conclusions 315 12 THE USE OF EXTREMOPHILIC MICROORGANISMS IN THE INDUSTRIAL RECOVERY OF METALS 319 Carlos A. Jerez 12.1 Introduction 319 12.2 Biomining Extremophiles and Their Industrial Applications 320 12.3 Molecular Studies in Acidophilic Biomining Microorganisms 322 12.4 Microbial Resistance to Acid and Metals 324 13 BACTERIAL POLYMERS PRODUCED BY EXTREMOPHILES: BIOSYNTHESIS, CHARACTERIZATION, AND APPLICATIONS OF EXOPOLYSACCHARIDES 335 Nicolaus Barbara, Anzelmo Gianluca, and Poli Annarita 13.1 Introduction 335 13.2 EPS Produced by Extremophilic Bacteria 336 13.3 Examples of Proposed EPS Biosynthesis from Extremophiles 345 13.4 Physicochemical Investigations for Potential Applications 349 14 BIOMEDICAL APPLICATIONS OF EXOPOLYSACCHARIDES PRODUCED BY MICROORGANISMS ISOLATED FROM EXTREME ENVIRONMENTS 357 Ignacio J. Molina, Carmen Ruiz-Ruiz, Emilia Quesada, and Victoria B´ejar 14.1 Introduction 357 14.2 Chemical Composition and Structure of EPSs 358 14.3 Physical Properties of EPSs 358 14.4 Biological Functions of EPSs 359 14.5 Exopolysaccharides Deriving from Extremophilic Organisms 359 14.6 Clinical Applications of EPSs 359 14.7 Exopolysaccharides of Halophilic Microorganisms 361 14.8 Concluding Remarks 362 15 BIOSYNTHESIS OF EXTREMOLYTES: RADIATION RESISTANCE AND BIOTECHNOLOGICAL IMPLICATIONS 367 Erin Copeland, Nicholas Choy, Prashant Gabani, and Om V. Singh 15.1 Introduction 367 15.2 Biotechnological Implications of Extremolytes 369 15.3 Fermentative Production of Extremolytes 371 15.4 Commercialization of Extremolytes and Extremozymes 380 15.5 Product Recovery 382 15.6 Conclusions 383 16 SMART THERAPEUTICS FROM EXTREMOPHILES: UNEXPLORED APPLICATIONS AND TECHNOLOGICAL CHALLENGES 389 Raj Kumar and Ajeet Singh 16.1 Introduction 389 16.2 Extremolytes as Protein Protectants 391 16.3 Extremolytes as Cell Protectants 391 16.4 Novel Therapeutics in the Developmental Stage 393 16.5 Homeland Security and Military Medicine 394 16.6 Technological Gaps in Therapeutic Product Development Using Extremophiles 396 16.7 Conclusions 397 Acknowledgment 398 References 398 Index 403

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Book SynopsisA quick, concise reference to pathogenic microorganisms and the diseases they cause, this book is divided into specific groups of pathogenic microorganisms including bacteria, protozoa, fungi, viruses, and prions.Table of ContentsPreface xi About the Authors xiii 1 Introduction 1 Koch’s Postulate 2 Terminology 3 Major Categories of Pathogenic Microorganisms 4 Transmission of Infectious Disease (Mode of Dissemination) 5 Universal Precautions 6 2 Host-Microbe Interactions 9 Resident Microbiota 9 Host Defenses 11 3 Antibiotics and Other Chemotherapeutic Agents 17 Classification of Antibiotics 17 Summary of the Mechanisms of Action 24 4 Antiseptics and Disinfectants 25 Physical Control of Microorganisms 25 Chemical Control of Microorganisms 27 5 Gram-Positive Cocci 31 Bacterial Taxonomy (An Overview) 31 Clinically Important Gram-Positive Cocci 32 Gram-Positive Cocci Related to Streptococcus Species 38 6 Gram-Positive Bacilli 41 Clostridium Species 41 Lactobacillus Species 46 Bacillus Species 46 Listeria Species 49 7 Gram-Positive Bacteria with Rudimentary Filaments 53 Corynebacterium diphtheriae 53 Mycobacterium Species 54 8 Gram-Negative Cocci 61 Neisseria Species 61 Moraxella catarrhalis 64 Haemophilus influenzae 65 An Overview of Gram-Negative Bacteria 67 9 Gram-Negative Bacilli 69 Specimen Collection 69 Media and Laboratory Diagnosis 69 Enterobacteriaceae 71 Glucose Nonfermenters 78 Uncommon Nonfermentative Taxa 81 10 Miscellaneous Gram-Negative Bacteria 83 Brucella melitensis 83 Bordetella pertussis 85 Francisella tularensis 86 Pasteurella Species 87 Vibrio cholerae 88 Aeromonas Species 90 Campylobacter Species 90 Legionella Species 92 Gardnerella vaginalis 93 Chlamydia Species 94 Rickettsia rickettsii 95 Bacteroides Species 96 Calymmatobacterium granulomatis 96 Cardiobacterium hominis 96 Streptobacillus moniliformis 96 Spirillum minus 97 11 Spirochetes and Bacteria without a Cell Wall 99 Spirochetes 99 Bacteria without a Cell Wall 103 12 Actinomycetes 107 Anaerobic Actinomycetes 108 Aerobic Actinomycetes 108 Thermophilic Actinomycetes 112 13 Introduction to Pathogenic Fungi and Superficial Mycoses 113 Yeast-Like Fungi 113 Molds or Filamentous Fungi 114 Dimorphic Fungi 114 Superficial Mycoses 115 Mucocutaneous Mycoses 121 14 Subcutaneous and Systemic Mycoses 125 Subcutaneous Mycoses 125 Systemic Mycoses 127 Diseases Caused by Dimorphic Fungi 127 Diseases Caused by Yeast-Like Fungi 135 Diseases Caused by Filamentous Fungi 138 Diseases Caused by Miscellaneous Filamentous Fungi 143 15 Unicellular Parasites 145 Laboratory Methods in Parasitology 145 Diseases Caused by Lumen-Dwelling Protozoa 146 Blood- and Tissue-Dwelling Protozoa 149 16 Multicellular Parasites 155 Lumen-Dwelling Helminths 155 Blood- and Tissue-Dwelling Helminths 161 17 Viruses and Prions 165 Laboratory Diagnosis 166 Double-Stranded DNA Viruses 166 Single-Stranded DNA Viruses 171 Double-Stranded RNA Viruses 171 Single-Stranded RNA Viruses 171 Prions 179 Bibliography and Suggested Reading 181 Index 185

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Book SynopsisLactic acid bacteria (LAB) have historically been used as starter cultures for the production of fermented foods, especially dairy products. Over recent years, new areas have had a strong impact on LAB studies: the application of ?omics? tools; the study of complex microbial ecosystems, the discovery of new LAB species, and the use of LAB as powerhouses in the food and medical industries. This second edition of Biotechnology of Lactic Acid Bacteria: Novel Applications addresses the major advances in the fields over the last five years. Thoroughly revised and updated, the book includes new chapters. Among them: The current status of LAB systematics; The role of LAB in the human intestinal microbiome and the intestinal tract of animals and its impact on the health and disease state of the host; The involvement of LAB in fruit and vegetable fermentations; The production of nutraceuticals and aroma compounds by LAB; and Table of ContentsList of Contributors xiii Preface xviii1. Updates on Metabolism in Lactic Acid Bacteria in Light of “Omic” Technologies 1Magdalena Kowalczyk, Baltasar Mayo, María Fernández, and Tamara Aleksandrzak-Piekarczyk1.1. Sugar Metabolism 11.1.1. Practical Aspects of Sugar Catabolism 31.2. Citrate Metabolism and Formation of Aroma Compounds 41.2.1. Citrate Transport 41.2.2. Conversion of Citrate into Pyruvate and Production of Aroma Compounds 61.2.3. Conversion of Citrate into Succinate 61.2.4. Bioenergetics of Citrate Metabolism 61.3. The Proteolytic System of Lactic Acid Bacteria 61.3.1. Protein Degradation 71.3.2. Peptidases 81.3.3. Technological Applications of the Proteolytic System 101.3.4. Amino Acid Catabolism 101.4. LAB Metabolism in Light of Genomics Comparative Genomics and Metagenomics 121.5. Novel Aspects of Metabolism Regulation in the Post]genomic Age 121.6. Functional Genomics and Metabolism 161.6.1. Transcriptomics Proteomics and Metabolomics 161.6.2. Global Phenotypic Characterization of Microbial Cells 171.7. Systems Biology of LAB 17Acknowledgments 18References 182. Systematics of Lactic Acid Bacteria: Current Status 25Giovanna E. Felis, Elisa Salvetti, and Sandra Torriani2.1. Families and Genera of Lactic Acid Bacteria 252.2. A Focus on the Family Lactobacillaceae 272.3. Taxonomic Tools in the Genomic Era 29References 303. Genomic Evolution of Lactic Acid Bacteria: From Single Gene Function to the Pan]genome 32Grace L. Douglas, M. Andrea Azcarate-Peri,l and Todd R. Klaenhammer3.1. The Genomics Revolution 323.2. Genomic Adaptations of LAB to the Environment 333.2.1. LAB Evolution in the Dairy Environment 333.2.2. LAB Evolution in Vegetable and Meat Fermentations 343.2.3. Fast]evolving LAB 353.2.4. LAB in the GI Tract 353.3. “Probiotic Islands”? 363.4. Stress Resistance and Quorum Sensing Mechanisms 393.5. The Impact of Genome Sequencing on Characterization Taxonomy and Pan]genome Development of Lactic Acid Bacteria 403.6. Functional Genomic Studies to Unveil Novel LAB Utilities 453.7. Conclusions 47References 474. Lactic Acid Bacteria: Comparative Genomic Analyses of Transport Systems 55Graciela L. Lorca, Taylor A. Twiddy, and Milton H. Saier Jr.4.1. Introduction 554.2. Channel]forming Proteins 564.3. The Major Facilitator Superfamily 594.4. Other Large Superfamilies of Secondary Carriers 604.5. ABC Transporters 644.6. Heavy Metal Transporters 654.7. P-type ATPases in Prokaryotes 684.8. The Prokaryote-specific Phosphotransferase System (PTS) 684.9. Multidrug Resistance Pumps 714.10. Nutrient Transport in LAB 714.11. Conclusions and Perspectives 72Note 73Acknowledgments 73References 735. Novel Developments in Bacteriocins from Lactic Acid Bacteria 80Ingolf F. Nes, Christina Gabrielsen, Dag A. Brede, and Dzung B. Diep5.1. Introduction 805.2. Characteristics and Classification of Bacteriocins 805.2.1. Class Ia: Lantibiotics 815.2.2. Class II: The Non-lantibiotics 815.3. Mode of Action 845.4. Bacteriocin Resistance 865.5. Applications 885.5.1. Opportunities and Hurdles in Application of Bacteriocins 885.5.2. Application of Bacteriocins in Medical-related and Personal Hygiene Products 885.5.3. Bacteriocin]producing Probiotics 905.6. Future Perspectives 92References 936. Bacteriophages of Lactic Acid Bacteria and Biotechnological Tools 100Beatriz Martínez, Pilar García, Ana Rodríguez, Mariana Piuri, and Raúl R. Raya6.1. Introduction 1006.2. Bacteriophages of Lactic Acid Bacteria 1016.2.1. Classification of Lactococcal Phages 1036.3. Antiphage Strategies 1036.3.1. Natural Mechanisms of Phage Resistance 1036.3.2. Genetically Engineered Antiphage Systems 1056.4. Phage-Based Molecular Tools 1066.4.1. Phage Integrases and Integration Vectors 1066.4.2. CRISPR Applications 1086.4.3. Recombineering 1106.5. LAB Phages as Biocontrol Tools 1136.6. Conclusions 113References 1137. Lactic Acid Bacteria and the Human Intestinal Microbiome 120François P. Douillard and Willem M. de Vos7.1. Introduction 1207.2. Ecology of the Human Intestinal Tract 1217.2.1. The Human Microbiome in the Upper and Lower Intestinal Tract 1217.2.2. Lactic Acid Bacteria Associated with the Human Intestine 1227.2.3. Metagenomic Studies of the Intestine in Relation to LAB 1237.3. A Case Study: The Lactobacillus rhamnosus Species 1247.3.1. Genomic Diversity of Lact. rhamnosus and Intestinal Adaptation 1247.3.2. Lact. rhamnosus Metabolism and Adaptation to the Intestine 1267.3.3. Host Interaction Factors in Lact. rhamnosus 1277.3.4. The Lact. rhamnosus Species: Autochthonous or Allochthonous in the Human Intestine? 1277.4. Concluding Perspectives and Future Directions 129Acknowledgments 130References 1308. Probiotics and Functional Foods in Immunosupressed Hosts 134Ivanna Novotny Nuñez, Martin Manuel, Palomar Alejandra de Moreno de LeBlanc, Carolina Maldonado Galdeano, and Gabriela Perdigón8.1. Introduction 1348.2. Probiotic Fermented Milk in a Malnutrition Model 1358.3. Probiotic Administration in Stress Process 1388.4. Conclusions 140Acknowledgments 141References 1419. Lactic Acid Bacteria in Animal Production and Health 144Damien Bouchard, Sergine Even, and Yves Le Loir9.1. Introduction 1449.2. Lactic Acid Bacteria and Probiotics 1459.3. Classifications and Regulatory Criteria of Probiotics in Animal Health 1469.4. Probiotic LAB and Animal Production Sectors 1479.4.1. Probiotics in Ruminants 1479.4.2. Probiotics in Pigs 1509.4.3. Probiotics in Poultry 1529.5. Conclusions 154References 15410. Proteomics for Studying Probiotic Traits 159Rosa Anna Siciliano and Maria Fiorella Mazzeo10.1. Introduction 15910.2. Mass Spectrometric Methodologies in Proteomics 16010.2.1. The Classical Approach: 2-DE Separation and Protein Identification by Mass Spectrometry 16010.2.2. Gel-Free Proteomic Approaches 16010.3. Proteomics for Studying Molecular Mechanisms of Probiotic Action 16110.3.1. Adaptation Mechanisms to the GIT Environment 16110.3.2. Adhesion Mechanisms to the Host Mucosa 16210.3.3. Molecular Mechanisms of Probiotic Immunomodulatory Effects 16410.3.4. Probiotics and Prebiotics 16410.4. Concluding Remarks and Future Directions 165References 16611. Engineering Lactic Acid Bacteria and Bifidobacteria for Mucosal Delivery of Health Molecules 170Thibault Allain, Camille Aubry, Jane M. Natividad, Jean-Marc Chatel, Philippe Langella, and Luis G. Bermúdez-Humarán11.1. Introduction 17011.2. Lactococcus lactis: A Pioneer Bacterium 17111.3. Lactobacillus spp. as a Delivery Vector 17111.4. Bifidobacteria as a New Live Delivery Vehicle 17111.5. Engineering Genetic Tools for Protein and DNA Delivery 17211.5.1. Cloning Vectors 17211.5.2. Expression Systems 17311.6. Therapeutic Applications 17611.6.1. Inflammatory Bowel Disease (IBD) 17611.6.2. Anti-protease Enzyme-producing LAB: The Tole of Elafin 17611.6.3. Antioxidant Enzyme-producing Lactococci and Lactobacilli 17711.7. Allergy 17811.7.1. Use of LAB in Food Allergy 17811.7.2. Allergic Airways Diseases 17911.8. Autoimmune Diseases 18011.8.1. Type 1 Diabetes Mellitus 18011.8.2. Celiac Disease 18011.9. Infectious Diseases 18111.9.1. Mucosal Delivery of Bacterial Antigens 18111.9.2. Mucosal Delivery of Viral Antigens 18111.9.3. Parasitic Diseases 183References 18412. Lactic Acid Bacteria for Dairy Fermentations: Specialized Starter Cultures to Improve Dairy Products 191Domenico Carminati, Giorgio Giraffa, Miriam Zago, Mariángeles Briggiler Marcó, Daniela Guglielmotti, Ana Binetti, and Jorge Reinheimer12.1. Introduction 19112.2. Adjunct Cultures 19112.2.1. Ripening Cultures 19212.2.2. Protective Cultures 19312.2.3. Probiotic Cultures 19512.2.4. Exopolysaccharide-producing Starters 19612.3. Phage-Resistant Starters 19912.4. New Sources of Starter Strains 20112.5. Conclusions 202References 20313. Lactobacillus sakei in Meat Fermentation 209Marie-Christine Champomier-Vergès and Monique Zagorec13.1. Introduction 20913.2. Genomics and Diversity of the Species Lactobacillus sakei 21013.3. Post-genomic Vision of Meat Fitness Traits of Lactobacillus sakei 21213.3.1. Energy Sources 21213.3.2. Stress Response 21313.4. Conclusions 214References 21414. Vegetable and Fruit Fermentation by Lactic Acid Bacteria 216Raffaella Di Cagno, Pasquale Filannino, and Marco Gobbetti14.1. Introduction 21614.2. Lactic Acid Bacteria Microbiota of Raw Vegetables and Fruits 21614.3. Fermentation of Vegetable Products 21814.3.1. Spontaneous Fermentation 21814.3.2. The Autochthonous Starters 21814.4. Main Fermented Vegetable Products 22114.4.1. Sauerkrauts 22114.4.2. Kimchi 22214.4.3. Pickled Cucumbers 22314.5. Physiology and Biochemistry of LAB during Vegetable and Fruit Fermentation 22314.5.1. Metabolic Adaptation by LAB during Plant Fermentation 22414.6. Food Phenolic Compounds: Antimicrobial Activity and Microbial Responses 22414.6.1. Effect of Phenolics on the Growth and Viability of LAB 22414.6.2. Metabolism of Phenolics by LAB 22614.7. Health-promoting Properties of Fermented Vegetables and Fruits 22614.8. Alternative Sources of Novel Probiotics Candidates 22614.9. Vehicles for Delivering Probiotics 22814.10. Conclusions 229References 22915. Lactic Acid Bacteria and Malolactic Fermentation in Wine 231Aline Lonvaud-Funel15.1. Introduction 23115.2. The Lactic Acid Bacteria of Wine 23115.2.1. Origin 23115.2.2. Species 23215.2.3. Identification 23215.2.4. Typing at Strain Level 23315.2.5. Detection of Specific Strains 23315.3. The Oenococcus Oeni Species 23315.4. Evolution of Lactic Acid Bacteria during Winemaking 23415.4.1. Interactions between Wine Microorganisms 23515.4.2. Environmental Factors 23615.5. Lactic Acid Bacteria Metabolism and its Impact on Wine Quality 23715.5.1. Sugars 23715.5.2. Carboxylic Acids 23715.5.3. Amino Acids 24015.5.4. Other Metabolisms with Sensorial Impact 24115.6. Controlling the Malolactic Fermentation 24215.7. Conclusions 243References 24416. The Functional Role of Lactic Acid Bacteria in Cocoa Bean Fermentation 248Luc De Vuyst and Stefan Weckx16.1. Introduction 24816.2. Cocoa Crop Cultivation and Harvest 24916.3. The Cocoa Pulp or Fermentation Substrate 25016.4. Fresh Unfermented Cocoa Beans 25116.5. Cocoa Bean Fermentation 25216.5.1. Rationale 25216.5.2. Farming Practices 25316.6. Succession of Microorganisms during Cocoa Bean Fermentation 25616.6.1. The Spontaneous Three-phase Cocoa Bean Fermentation Process 25616.6.2. Yeast Fermentation 25716.6.3. LAB Fermentation 26016.6.4. AAB Fermentation 26416.7. Biochemical Changes in the Cocoa Beans during Fermentation and Drying 26616.8. Optimal Fermentation Course and End of Fermentation 26816.9. Further Processing of Fermented Cocoa Beans 26916.9.1. Drying of Fermented Cocoa Beans 26916.9.2. Roasting of Fermented Dry Cocoa Beans 27016.10. Use of Starter Cultures for Cocoa Bean Fermentation 27116.10.1. Rationale 27116.10.2. Experimental Use of Cocoa Bean Starter Cultures 27116.11. Concluding Remarks 273References 27317. B-Group Vitamins Production by Probiotic Lactic Acid Bacteria 279Jean Guy LeBlanc, Jonathan Emiliano Laiño, Marianela Juárez del Valle, Graciela Savoy de Giori, Fernando Sesma, and María Pía Taranto17.1. Introduction 27917.2. B-Group Vitamins 28017.2.1. Riboflavin (Vitamin B2 ) 28117.2.2. Folates (Vitamin B9) 28417.3. Probiotics In Situ 28617.3.1. Vitamin B12 (Cobalamin) 28817.3.2. Cobalamin Biosynthesis by Lactobacillus reuteri 28917.4. Conclusions 291Acknowledgments 292References 29218. Nutraceutics and High Value Metabolites Produced by Lactic Acid Bacteria 297Elvira M. Hebert, Graciela Savoy de Giori, and Fernanda Mozzi18.1. Introduction 29718.2. Nutraceutics 29818.2.1. Low-calorie Sugars 29818.2.2. Short-Chain Fatty Acids 30018.2.3. Conjugated Linoleic Acid (CLA) 30118.2.4. Bioactive Peptides 30118.2.5. Gamma-aminobutyric Acid (GABA) 30318.2.6. Vitamins 30518.3. Exopolysaccharides 30618.4. Commodity Chemicals 30718.5. Conclusions 308References 30819. Production of Flavor Compounds by Lactic Acid Bacteria in Fermented Foods 314Anne Thierry, Tomislav Pogačic, Magalie Weber, and Sylvie Lortal19.1. Introduction 31419.2. Flavor and Aroma Compounds 31519.2.1. Volatile Compounds: Diversity Analytical Methods 31519.2.2. Contribution of Volatile Aroma Compounds to Flavor 31619.2.3. Origin of Aroma Compounds 31619.3. LAB of Fermented Foods and their Role in Flavor Formation 31619.3.1. Biochemical Processes of Flavor Compound Formation in Food and Potential of LAB 32419.3.2. Flavor Compounds Produced from Carbohydrate Fermentation by LAB 32419.3.3. Flavor Compounds from Amino Acid Conversion by LAB 32619.3.4. Flavor Compounds from Lipids in LAB 32719.3.5. Synthesis of Esters 32819.3.6. Interspecies and Intraspecies Variations of Aroma Compound Production 32819.4. Biotic and Abiotic Factors Modulating the Contribution of LAB to Flavor Formation 33119.4.1. General Scheme of Flavor Formation in Fermented Foods In Situ 33119.4.2. Factors Modulating the Expression of the Flavor-related Activities of LAB 33219.4.3. Factors Determining the Real Contribution of LAB to Food Flavor 33319.5. Conclusions and Research Perspectives 333References 33420. Lactic Acid Bacteria Biofilms: From their Formation to their Health and Biotechnological Potential 341Jean-Christophe Piard and Romain Briandet20.1. Lactic Acid Bacteria Biofilms are Ubiquitous in a Wide Variety of Environments from Nature to Domesticated Settings 34120.2. Biofilm Life Cycle and Bacterial Factors Involved in LAB Biofilm Lifestyle 34620.3. Health and Biotechnological Potential of LAB Biofilms and Underlying Mechanisms 35220.4. Conclusions 354Acknowledgments 355References 355Index 362

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Book SynopsisThe first and only comprehensive reference/solutions manual for managing food safety in low-moisture foods The first book devoted to an increasingly critical public health issue, Control of Salmonella and Other Bacterial Pathogens in Low-Moisture Foods reviews the current state of the science on the prevalence and persistence of bacterial pathogens in low-moisture foods and describes proven techniques for preventing food contamination for manufacturers who produce those foods. Many pathogens, such as Salmonella, due to their enhanced thermal resistance in dry environments, can survive the drying process and may persist for prolonged periods in low-moisture foods, especially when stored in refrigerated environments. Bacterial contamination of low-moisture foods, such as peanut butter, present a vexing challenge to food safety, and especially now, in the wake of widely publicized food safety related events, food processors urgently need up-to-Table of ContentsList of Contributors xi 1 Introduction and Overview 1Richard Podolak and Darryl G. Black 1.1 Introduction 1 1.2 Definition of Low-Moisture Foods (LMF) and Water Activity Controlled Foods 2 1.3 Salmonella as a Continuing Challenge and Ongoing Problem in Low-Moisture Foods 4 1.4 Foodborne Outbreaks of Salmonella spp. and Other Implicated Microbial Pathogens in Low-Moisture Foods 6 1.5 Major Safety Concerns in Low-Moisture Foods 16 1.6 Content and Brief Book Chapter Review 17 1.7 Goal of the Book 21 1.8 How to Use the Book 21 References 22 2 Regulatory Requirements for Low-Moisture Foods – The New Preventive Controls Landscape (FSMA) 29Jeffrey T. Barach and George E. Dunaif 2.1 Introduction 29 2.2 FSMA Sanitation and cGMPs 32 2.3 FSMA Preventive Controls 34 2.4 Process Controls 35 2.5 Sanitation Controls 36 2.6 Supplier Controls 37 2.7 Summary of Requirements for Low-Moisture FSMA Regulated Products 38 References 39 3 Potential Sources and Risk Factors 41Elizabeth M. Grasso]Kelley, Ai Kataoka and Lisa Lucore 3.1 Introduction 41 3.2 Raw Ingredients Control and Handling 43 3.3 Pest Control 49 3.4 Salmonella Harborage in the Facility 55 3.5 Conclusions 62 References 62 4 Persistence of Salmonella and Other Bacterial Pathogens in Low-Moisture Foods 67Elena Enache, Richard Podolak, Ai Kataoka and Linda J. Harris 4.1 Introduction 67 4.2 Factors Affecting Survival of Salmonella and Other Pathogens in Low-Moisture Foods 67 4.3 Recovery of Salmonella Cells Stressed by Low-Moisture Foods 75 4.4 Mechanism of Salmonella Survival in Food Product and Processing Environment 75 4.5 Other Vegetative Pathogens 79 4.6 Summary 79 References 80 5 Best Industry Practices to Control Salmonella in Low-Moisture Foods 87Lisa Lucore, David Anderson, Elizabeth M. Grasso]Kelley and Ai Kataoka 5.1 Introduction 87 5.2 Sanitation Practices 89 5.3 Current Good Manufacturing Practice 112 References 114 6 Heat Resistance of Salmonella and Other Bacterial Pathogens in Low-Moisture Foods 121Richard Podolak, Lisa Lucore and Linda J. Harris 6.1 Introduction 121 6.2 Factors Affecting Heat Resistance of Foodborne Pathogens 122 6.3 Use of Published Heat Resistance Data to Establish Lethal Process Lethality in Low-Moisture Foods 133 6.4 Summary 143 References 143 7 Validation Requirements in Heat-Processed Low-Moisture Foods 149David Anderson, Nathan Anderson, Linda J. Harris and Wilfredo Ocasio 7.1 Introduction 149 7.2 Definitions 150 7.3 Tasks of Validation 150 7.4 Task 1: Assemble a Validation Team 151 7.5 Task 2: Identify the Hazard to be Controlled Through Hazard Analysis 151 7.6 Task 3: Identify a Validation Approach for the Control Measure 152 7.7 Task 4: Conduct the In-Production Validation 163 7.8 Task 5: Write the Results of the Validation in a Validation Report 165 7.10 Task 6: Implement the Control Measure, Monitors and Record Review 167 7.11 Task 7: Verify that the Control Measure is Operating as Intended 168 7.12 Task 8: Re-evaluate the Control Measure Periodically 169 7.13 Conclusion 170 References 171 8 Test Methods for Salmonella in Low-Moisture Foods 175Elena Enache, Shaunti Luce and Lisa Lucore 8.1 Introduction 175 8.2 Sampling Plans 175 8.3 Types of Methods 184 8.4 Matrices Testing Challenges 192 8.5 Conclusion 194 References 194 9 Techniques to Determine Thermal Inactivation Kinetics for Pathogenic Bacteria and their Surrogate Organisms in Low-Moisture Foods 197Shirin J. Abd, Carrie M.H. Ferstl and Wilfredo Ocasio 9.1 Introduction 197 9.2 Kinetics of Microbial Destruction 198 9.3 Experimental Design and Execution 200 References 215 10 Modeling and Statistical Issues Related to Salmonella in Low Water Activity Foods 219Sofia M. Santillana Farakos, Michelle Danyluk, Donald Schaffner, Régis Pouillot, Linda J. Harris and Bradley P. Marks 10.1 An Introduction to Modeling Salmonella in Low Water Activity Foods 219 10.2 Developing a Predictive Model for Salmonella in Low Water Activity Foods 220 10.3 Model Validation 226 10.4 Models in Risk Assessment 228 10.5 Summary 234 References 234 11 Spoilage Microorganisms in Low-Moisture Foods 241Melinda Hayman and Richard Podolak 11.1 Introduction 241 11.2 Microorganisms Associated with the Spoilage of Low-Moisture Foods 241 11.3 Factors Influencing Heat Resistance of Fungi in Low-Moisture Foods 244 11.4 Heat Resistance of Fungi in Low-Moisture Foods 247 11.5 Heat Resistance of Yeasts in Low-Moisture Foods 247 11.6 Preventing and Reducing Spoilage in Low-Moisture Foods 250 11.7 Conclusions 251 References 251 Index 255

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Book SynopsisThe aim of this new book series (Diatoms: Biology and Applications) is to provide a comprehensive and reliable source of information on diatom biology and applications. The first book of the series, Diatoms Fundamentals & Applications, is wide ranging, starting with the contributions of amateurs and the beauty of diatoms, to details of how their shells are made, how they bend light to their advantage and ours, and major aspects of their biochemistry (photosynthesis and iron metabolism). The book then delves into the ecology of diatoms living in a wide range of habitats, and look at those few that can kill or harm us. The book concludes with a wide range of applications of diatoms, in forensics, manufacturing, medicine, biofuel and agriculture. The contributors are leading international experts on diatoms. This book is for a wide audience researchers, academics, students, and teachers of biology and related disciplines, written to both act as an introduction to diatoms and to Table of ContentsForeword xvii Preface xxiii 1 A Memorial to Frithjof Sterrenburg: The Importance of the Amateur Diatomist 1 Janice L. Pappas 1.1 Introduction 1 1.2 Background and Interests 3 1.3 The Personality of an Amateur Diatomist 7 1.4 The Amateur Diatomist and the Importance of Collections 11 1.5 The Amateur Diatomist as Expert in the Tools of the Trade 12 1.6 The Amateur Diatomist as Peer-Reviewed Scientific Contributor 15 1.7 Concluding Remarks 20 Acknowledgments 21 References 21 2 Alex Altenbach – In Memoriam of a Friend 29 Wladyslaw Altermann References 31 3 The Beauty of Diatoms 33 Mary Ann Tiffany and Stephen S. Nagy 3.1 Early History of Observations of Diatoms 33 3.2 Live Diatoms 35 3.3 Shapes and Structures 35 3.4 Diatom Beauty at Various Scales 36 3.5 Valves During Morphogenesis 37 3.6 Jamin-Lebedeff Interference Contrast Microscopy 39 3.7 Conclusion 40 Acknowledgments 40 References 41 4 Current Diatom Research in China 43 Yu Xin Zhang 4.1 Diatoms for Energy Conversion and Storage 43 4.1.1 Introduction 43 4.1.2 Diatom Silica: Structure, Properties and Their Optimization 46 4.1.3 Diatoms for Lithium Ion Battery Materials 48 4.1.4 Diatoms for Energy Storage: Supercapacitors 51 4.1.5 Diatoms for Solar Cells 56 4.1.6 Diatoms for Hydrogen Storage 58 4.1.7 Diatoms for Thermal Energy Storage 59 4.2 Diatoms for Water Treatment 61 4.2.1 Support for Preparation of Diatomite-Based Adsorption Composites 61 4.2.2 Catalyst and Template for Preparation of Porous Carbon Materials 63 4.2.3 Modification of Surface and Porous Structure 66 4.2.4 Support for Preparation of Diatomite-Based Metal Oxide Composites 75 4.3 Study of Tribological Performances of Compound Dimples Based on Diatoms Shell Structures 86 References 88 5 Cellular Mechanisms of Diatom Valve Morphogenesis 99 Yekaterina D. Bedoshvili and Yelena V. Likhoshway 5.1 Introduction 99 5.2 Valve Symmetry 100 5.3 Valve Silification Order 102 5.4 Silica Within SDV 103 5.5 Macromorphogenesis Control 104 5.6 Cytoskeletal Control of Morphogenesis 106 5.7 The Role of Vesicles in Morphogenesis 107 5.8 Valve Exocytosis and the SDV Origin 108 5.9 Conclusion 110 References 110 6 Application of Focused Ion Beam Technique in Taxonomy-Oriented Research on Ultrastructure of Diatoms 115 Andrzej Witkowski, Tomasz Płociński, Justyna Grzonka, Izabela Zgłobicka, Małgorzata Bąk, Przemysław Dąbek, Ana I. Gomes and Krzysztof J. Kurzydłowski 6.1 Introduction 116 6.2 Material and Methods 117 6.3 Results 117 6.3.1 Complex Stria Ultrastructure 117 6.3.1.1 Biremis lucens (Hustedt) Sabbe, Witkowski & Vyverman 1995 117 6.3.1.2 Olifantiella mascarenica Riaux-Gobin & Compere 2009 120 6.4 Discussion 123 6.4.1 Cultured Versus Wild Specimens 124 6.5 Conclusions 124 Acknowledgements 126 References 126 7 On Light and Diatoms: A Photonics and Photobiology Review 129Mohamed M. Ghobara, Nirmal Mazumder, Vandana Vinayak, Louisa Reissig, Ille C. Gebeshuber, Mary Ann Tiffany and Richard Gordon 7.1 Introduction 130 7.2 The Unique Multiscale Structure of the Diatom Frustules 130 7.3 Optical Properties of Diatom Frustules 139 7.3.1 The Frustule as a Box with Photonic Crystal Walls 143 7.3.2 Light Focusing Phenomenon 146 7.3.3 Photoluminescence Properties 151 7.3.4 Probable Roles of the Frustule in Diatom Photobiology 152 7.4 Diatom Photobiology 153 7.4.1 Underwater Light Field 153 7.4.2 Cell Cycle Light Regulation 154 7.4.3 The Phototactic Phenomenon in Pennates 154 7.4.4 Chloroplast Migration (Karyostrophy) 156 7.4.5 Blue Light and Its Effects on Microtubules of Cells 157 7.4.6 Strategies for Photoregulation Under High Light Intensity 159 7.4.7 Strategies for Photoregulation Under Ultraviolet Radiation (UV) Exposure 159 7.4.8 Diatoms and Low Light 160 7.4.9 Diatoms and No Light 161 7.4.10 Light Piping and Cellular Vision 161 7.5 Diatom and Light Applications 162 7.5.1 In Photocatalysis 162 7.5.2 Bio-Based UV Filters 164 7.5.3 In Solar Cells 165 7.5.4 Applications Based on Luminescence Properties 167 7.5.5 Cloaking Diatoms 167 7.6 Conclusion 169 Acknowledgement 169 Glossary 169 References 171 8 Photosynthesis in Diatoms 191 Matteo Scarsini, Justine Marchand, Kalina M. Manoylov and Benoît Schoefs 8.1 Introduction 191 8.2 The Chloroplast Structure Reflects the Two Steps Endosymbiosis 194 8.3 Photosynthetic Pigments 196 8.3.1 Chlorophylls 196 8.3.2 Carotenoids 197 8.4 The Organization of the Photosynthetic Apparatus 197 8.5 Non-Photochemical Quenching (NPQ) 200 8.6 Carbon Uptake and Fixation 202 8.7 Conclusions and Perspectives 204 Acknowledgment 205 References 205 9 Iron in Diatoms 213 John A. Raven 9.1 Introduction 213 9.2 Fe Acquisition by Diatoms 214 9.3 Fe-Containing Proteins in Diatoms and Economy of Fe Use 214 9.4 Iron Storage 219 9.5 Conclusions and Prospects 220 Acknowledgements 220 References 220 10 Diatom Symbioses with Other Photoauthotroph 225 Rosalina Stancheva and Rex Lowe 10.1 Introduction 225 10.2 Diatoms with a N2-Fixing Coccoid Cyanobacterial Endosymbiont 226 10.3 Diatoms with N2-Fixing Filamentous Heterocytous Cyanobacterial Endosymbionts 233 10.4 Epiphytic, Endogloeic and Endophytic Diatoms 235 10.5 Diatom Endosymbionts in Dinoflagellates 238 Acknowledgements 239 References 239 11 Diatom Sexual Reproduction and Life Cycles 245 Aloisie Poulíčková and David G. Mann 11.1 Introduction 245 11.2 Centric Diatoms 247 11.2.1 Life Cycle and Reproduction 247 11.2.2 Gametogenesis and Gamete Structure 250 11.2.3 Spawning 251 11.3 Pennate Diatom Life Cycles and Reproduction 252 11.4 Auxospore Development and Structure 257 11.4.1 Incunabula 259 11.4.2 Perizonium 260 11.5 Induction of Sexual Reproduction 261 Acknowledgments 262 References 263 12 Ecophysiology, Cell Biology and Ultrastructure of a Benthic Diatom Isolated in the Arctic 273 Ulf Karsten, Rhena Schumann and Andreas Holzinger 12.1 Introduction 274 12.2 Environmental Settings in the Arctic 274 12.3 Growth as Function of Temperature 275 12.4 Growth After Long-Term Dark Incubation 277 12.5 Cell Biological Traits After Long-Term Dark Incubation 279 12.6 Ultrastructural Traits 282 12.7 Conclusions 283 Acknowledgements 284 References 284 13 Ecology of Freshwater Diatoms – Current Trends and Applications 289 Aloisie Poulíčková and Kalina Manoylov 13.1 Introduction 289 13.2 Diatom Distribution 292 13.3 Diatom Dispersal Ability 292 13.4 Functional Classification in Diatom Ecology 294 13.5 Spatial Ecology and Metacommunities 296 13.6 Aquatic Ecosystems Biomonitoring 299 13.7 Conclusions 301 References 301 14 Diatoms from Hot Springs of the Kamchatka Peninsula (Russia) 311 Tatiana V. Nikulina, E. G. Kalitina, N. A. Kharitonova, G. A. Chelnokov, Elena A. Vakh and O. V. Grishchenko 14.1 Introduction 311 14.2 Materials and Methods 313 14.3 Description of Sampling Sites 313 14.3.1 Malkinsky Geothermal Field 314 14.3.2 Nachikinsky Geothermal Field 317 14.3.3 Verkhnaya-Paratunka Geothermal Field 317 14.3.3.1 Goryachaya Sopka Hot Spring 318 14.3.3.2 Karimshinsky Hot Spring 318 14.3.4 Mutnovsky Geothermal Field 318 14.3.4.1 Dachny Hot Springs 319 14.3.4.2 Verkhne-Vilyuchinsky Hot Spring 319 14.4 Results 320 14.4.1 Malkinsky Geothermal Field 320 14.4.2 Nachikinsky Geothermal Field 320 14.4.3 Verkhnaya-Paratunka Geothermal Field 326 14.4.3.1 Goryachaya Sopka Hot Spring 326 14.4.3.2 Karimshinsky Hot Spring 326 14.4.4 Mutnovsky Geothermal Field 326 14.4.4.1 Dachny Hot Springs 326 14.4.4.2 Verkhne-Vilyuchinsky Hot Spring 327 14.5 Summary 330 References 331 15 Biodiversity of High Mountain Lakes in Europe with Special Regards to Rila Mountains (Bulgaria) and Tatra Mountains (Poland) 335 Nadja Ognjanova-Rumenova, Agata Z. Wojtal, Elwira Sienkiewicz, Ivan Botev and Teodora Trichkova 15.1 Introduction 335 15.1.1 Factors Which Control the Diatom Distribution 336 15.1.2 Biodiversity Assessment 337 15.2 Recent Datom Biodiversity in High Mountain Lakes in bulgaria and Poland 338 15.2.1 The Rila Lakes, Bulgaria 338 15.2.2 The Tatra Lakes, Poland 339 15.3 Diatom Community Changes in High-Mountain Lakes in Bulgaria and Poland from Pre-Industrial Times to Present Day 340 15.3.1 The Rila Mts. 340 15.3.2 Tatra Mts. 342 15.4 Monitoring Data ‘2015’ and Correlations Between the Data Sets of the Rila Mts. and the Tatra Mts. 344 15.4.1 The Rila Lakes 344 15.4.2 The Tatra Lakes 346 15.5 Red-List Data: Cirque “Sedemte Ezera”, Rila Mts. and Tatra Mts. 349 15.5.1 Cirque “Sedemte Ezera”, Rila Mts. 349 15.5.2 Tatra Mts. 349 15.6 Summary 349 Acknowledgements 351 References 351 16 Diatoms of the Southern Part of the Russian Far East 355 Tatiana V. Nikulina and Lubov A. Medvedeva 16.1 History of the Study of Freshwater Algae of the Southern Part of the Russian Far East 355 16.1.1 The Primorye Territory 357 16.1.1.1 Lakes and Reservoirs 357 16.1.1.2 Rivers and Streams 358 16.1.2 The Amur Region 360 16.1.2.1 The Upper Amur 360 16.1.2.2 The Middle Amur 360 16.1.3 The Jewish Autonomous Region 361 16.1.4 The Khabarovsk Territory 361 16.1.4.1 The Middle Amur 361 16.1.4.2 The Lower Amur 361 16.1.5 The Sakhalin Region 362 16.1.5.1 Sakhalin Island 362 16.1.5.2 Moneron Island 363 16.1.5.3 The Kuril Islands 363 16.2 Diatom Flora of the Southern Part of the Russian Far East 363 References 377 17 Toxic and Harmful Marine Diatoms 389 Stephen S. Bates, Nina Lundholm, Katherine A. Hubbard, Marina Montresor and Chui Pin Leaw 17.1 Introduction 390 17.2 Harmful Diatoms 391 17.2.1 How Diatoms May Cause Harm 391 17.2.2 Diatom Oxylipins 391 17.2.2.1 Polyunsaturated Aldehydes (PUAs) 391 17.2.2.2 Oxylipin Production by Pseudo-nitzschia 396 17.3 Toxic Diatoms 397 17.3.1 Diatoms That Produce Β-N-Methylamino-L-Alanine (BMAA) 397 17.3.2 Nitzschia navis-varingica 400 17.3.3 Nitzschia bizertensis 400 17.3.4 Pseudo-nitzschia spp 401 17.3.4.1 New Species 401 17.3.4.2 Distribution 401 17.3.4.3 Sexual Reproduction 401 17.3.4.4 Genomic Insights Into Pseudo-nitzschia and Its Population Genetic Structure 410 17.3.4.5 New Knowledge of Pseudo-nitzschia 411 17.3.5 Identification of Toxic Diatoms 414 17.3.5.1 Classical Methods 414 17.3.5.2 Molecular Approaches 415 17.4 Gaps in Knowledge and Thoughts for Future Directions 417 References 418 18 Diatoms in Forensics: A Molecular Approach to Diatom Testing in Forensic Science 435 Vandana Vinayak and S. Gautam 18.1 Introduction 435 18.2 Postmortem Forensic Counter Measures 438 18.3 Differences in Drowned Victims vs Those that Die of Other Causes 439 18.4 Techniques to Identify Diatoms in Biological Sample 440 18.4.1 Morphological Analysis of Water Samples 441 18.4.2 Role of Site Specific Diatoms 442 18.5 Case Studies 443 18.5.1 Case 1 443 18.5.2 Case 2 443 18.5.3 Case 3 444 18.6 Identification of Diatom Using Molecular Tools in Tissue and Water Samples 446 18.7 Differentiation of Diatom DNA in the Tissue of a Drowned Victim 447 18.8 Polymerase Chain Reaction (PCR) 448 18.9 Diatom DNA Extraction from Biological Samples of a Drowned Victim 448 18.9.1 Biological Samples 448 18.9.2 Plankton/Diatom Isolation from Tissues Using Colloidal Silica Gradient and Phenol Chloroform Method for DNA Extraction 454 18.10 Best Barcode Markers for Diatoms to Diagnose Drowning 454 18.10.1 Cytochrome C Oxidase Subunit 1 (COI) 455 18.10.2 Nuclear rDNA ITS Region 456 18.10.3 Nuclear Small Subunit rRNA Gene 457 18.11 DNA Sequencing 457 18.12 Advancement in Sequencing Leads to Advancement of Data Interpretation 458 18.13 Conclusion and Future Perspectives 459 Acknowledgements 459 List of Abbreviations Used 460 References 460 19 Diatomite in Use: Nature, Modifications, Commercial Applications and Prospective Trends 471 Mohamed M. Ghobara and Asmaa Mohamed 19.1 The Nature of Diatomite 471 19.1.1 Diatomite Formation 472 19.1.2 Diatom Frustule’s Resistance Against Dissolution (The Reason for Their Preservation Over Millions of Years) 473 19.2 The History of Discovery and Ancient Applications 475 19.3 Diatomite Occurrence and Distribution 476 19.4 Diatomite Mining and Processing 477 19.5 Diatomite Characterization 479 19.6 Diatom Frustules Modifications 480 19.7 Diatomite in Use 481 19.7.1 Diatomite-Based Filtration 482 19.7.1.1 Water Filtration 483 19.7.1.2 Beer Filtration 484 19.7.1.3 Recent Trends in Diatomite-Based Separation Techniques 485 19.7.1.4 Reuse of Spent DE Filter Media 485 19.7.2 Diatomite for Thermal Insulation 485 19.7.3 Diatomite-Based Building Materials 487 19.7.4 Diatomaceous Earth as an Insecticide 488 19.7.5 Diatomaceous Earth as a soil amendment 488 19.7.6 Diatomaceous Earth as a Filler 489 19.7.7 Diatomaceous Earth as Abrasive Material 490 19.7.8 Diatomaceous Earth as Animals’ and Human’s Food Additives 490 19.7.9 Diatomaceous Earth and Nanotechnology 491 19.7.9.1 Diatomaceous Earth in Solar Energy Harvesting Systems 491 19.7.9.2 Diatomaceous Earth-Based Superhydrophobic Surfaces 491 19.7.9.3 Diatomaceous Earth Composites as Catalysts 492 19.7.9.4 Diatomaceous Earth-Based Supercapacitors 492 19.7.9.5 Diatomaceous Earth-Based Pharmaceutical and Biomedical Applications 492 19.7.9.6 Diatomaceous Earth-Based Lab-on-a-Chip 494 19.7.10 Non-Industrial Applications 494 19.8 Diatomite Fabrication and Future Aspects 495 19.9 Conclusion 495 Acknowledgements 496 References 496 20 Diatom Silica for Biomedical Applications 511 Shaheer Maher, Moom Sin Aw and Dusan Losic 20.1 Introduction 511 20.2 Diatoms: Natural Silica Microcapsules for Therapeutics Delivery 513 20.2.1 Structure 513 20.2.2 Surface Modification of Diatoms 514 20.2.3 Diatoms Applications as Drug Carriers 516 20.2.4 Diatoms as a Source of Biodegradable Carriers for Drug Delivery Applications 522 20.2.4.1 Diatoms as a Source of Biodegradable Silicon Micro and Nano Carriers for Drug Delivery 525 20.2.5 Diatom Silica for Other Biomedical Applications 527 20.2.5.1 Tissue Engineering 527 20.2.5.2 Haemorrhage Control 528 20.3 Conclusions 530 Acknowledgements 531 References 531 21 Diafuel™(Diatom Biofuel) vs Electric Vehicles, a Basic Comparison: A High Potential Renewable Energy Source to Make India Energy Independent 537 Vandana Vinayak, Khashti Ballabh Joshi and Priyangshu Manab Sarma 21.1 Introduction 538 21.2 Debate on Relation of Green House Gas Emissions (GHG) with CO2 and Temperature 539 21.3 Outcomes of Paris Agreement 2015 541 21.4 Energy Demands for India 542 21.5 Critics Talking About Entry of EV in Market 545 21.6 Comparison Between Electric Vehicles vs Vehicles with Diafuel™ at Large 546 21.6.1 Electric Vehicles 546 21.6.1.1 Status of EV in India 548 21.6.1.2 Predicted Impact of EV on Global and Indian Network Versus Their Energy Sources 549 21.6.2 Diafuel™ 550 21.6.2.1 Diafuel™ Industrial Production 552 21.6.2.2 Designing an Energy Self-Sufficient Indian House Producing Diafuel™ 554 21.6.2.3 Working Prototype of Diatom Panels for the Indian House 555 21.6.2.4 Advantages of Diafuel™ 556 21.7 Source for Generation of Electricity to Drive EVs 557 21.7.1 Resources with Zero Carbon Emission 558 21.7.1.1 Nuclear Power 559 21.7.1.2 Solar Energy for Faster Adoption and Manufacturing of Electric & Hybrid Vehicles in India 559 21.7.1.3 Wind Power 560 21.7.1.4 Barriers for Wind and Solar Energy 561 21.8 CO2 Emissions by Electric Vehicle vs Gasoline Driven Vehicles 562 21.9 Depletion of Earth Metals to Run EV’s vs Abundant Resources for Diafuel™ 564 21.9.1 Can Diafuel™ be the Answer 566 21.9.2 Harvesting Diafuel™ from Diatoms 566 21.10 Current Status 567 21.10.1 Data Analysis and Comparison Between EV and Diafuel™ 569 21.11 Conclusions 569 Acknowledgement 574 List of Abbreviations Used 574 References 574 22 Bubble Farming: Scalable Microcosms for Diatom Biofuel and the Next Green Revolution 583 Richard Gordon, Clifford R Merz, Shawn Gurke and Benoît Schoefs 22.1 Introduction 584 22.1.1 The Bubble Farming Concept 588 22.1.2 Bubble Injection, Sampling, Harvesting and Sealing, Maybe by Drones 592 22.1.3 Approach 594 22.2 Mechanical Properties 594 22.2.1 Optimal Bubble Size 596 22.3 Optical Properties 597 22.4 Surface Properties 599 22.4.1 Gas Exchange Properties 599 22.5 Toxicity Restrictions 609 22.5.1 Algal Oil Droplet Properties 611 22.6 Biofilms 611 22.7 Bacterial Symbionts 612 22.7.1 Soil as a Source of CO2 613 22.8 Demand 614 22.8.1 The Choice of Diatoms vs Other Algae 614 22.9 Exponential Growth vs Stationary Phase 617 22.10 Carbon Recycling 619 22.11 Packaging 619 22.11.1 Crop Choice by Farmers 620 22.11.2 Bubble Farming vs Photobioreactors and Raceways 620 22.12 Summary 620 Acknowledgements 626 References 626 Index 655

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Book SynopsisWritten and edited by some of the most well-respected authors in the area of the adaptation of plants and animals to climate change, this groundbreaking new work is an extremely important scientific contribution to the study of global warming. Global climate change is one of the most serious and pressing issues facing our planet. Rather than a silver bullet or a single study that solves it, the study of global climate change is like a beach, with each contribution a grain of sand, gathered together as a whole to create a big picture, moving the science forward. This new groundbreaking study focuses on the adaptation and tolerance of plants and animal life to the harsh conditions brought on by climate change or global warming. Using the papers collected here, scientists can better understand global climate change, its causes, results, and, ultimately, the future of life on our planet. The first section lays out a methodology and conceptual direction of the work aTable of ContentsPreface xvii Abstract xix Contributing Authors xxi Modeling and Approaches 1 1 Critical Impacts on Complex Biological and Ecological Systems: Basic Principles of Modeling 3Rem G. Khlebopros, Vladislav G. Soukhovolsky 1.1 Complex Ecological Systems: The Principle of Decomposition, Taking into Account the Characteristic Times of Components 5 1.2 Analysis of Critical Impacts on Complex Systems and Extreme Principles of Modeling 12 1.2.1 Meta-Models of Phase Transitions for Describing Critical Events in Complex Systems 13 1.2.2 A Model of Outbreak as Second-Order Phase Transition 14 1.2.3 The Effect of Modifying Factors on the Development of an Outbreak 21 1.2.4 The Impact of Chemical Compounds on Biological Objects 23 References 26 2 Criticality Concept and Some Principles for Sustainability in Closed Biological Systems and Biospheres 29Nicholas P. Yensen, Karl Y. Biel 2.1 Introduction 31 2.2 History of Manmade Closed Ecosystems 32 2.3 Classification of Closed Biological Systems 33 2.3.1 Terminology 33 2.3.2 Micro Systems 35 2.3.3 Macro Systems 37 2.3.4 The Term Biosphere 39 2.3.5 Noosphere 40 2.4 The Concept of Criticality 40 2.4.1 The Volume-Criticality Principle 42 2.5 Microbiospheres: Descriptions and Discussion 44 2.5.1 The Ecosphere, a Synthetic Microbiosphere 44 2.6 Bioboxes 45 2.7 Experimental vs. Mathematical Models 45 2.7.1 Retrograde Phylogenetic Extinction 46 2.8 Humanospheres: Examples and Discussion 46 2.8.1 Biotubes 47 2.8.2 Shepelev, BIOS 1, 2, and 3 49 2.8.3 Biosphere 2 Laboratory 51 2.8.4 Closed System Missions 52 2.8.5 Open System Missions 53 2.8.6 The End of Biosphere 2 Laboratory or a New Era for Biosphere 2 Laboratory? 54 2.9 The Earth (Biosphere 1) Description and Discussion 55 2.9.1 Earth, a Sample Size of One 55 2.9.2 Biosphere 1 Properties 55 2.10 Oxygen Flux in Closed Systems 59 2.11 The Future of Closed System Work: Concepts and Strategies 61 2.11.1 Education, Research and Consortium Concepts 61 2.11.2 Ecosystems for Space 62 2.11.3 Closed System Challenges 63 2.12 General Conclusions 63 Abbreviations 64 Literature Cited and Used 64 Appendix I. A Description of Biosphere 2 Laboratory 70 3 Accelerated Method for Measuring and Predicting Plants’ Stress Tolerance 73Karl Y. Biel, John N. Nishio 3.1 Introduction 75 3.2 Background 75 3.2.1 Interaction between Anabolism and Catabolism 76 3.2.2 Cooperation between Photosynthesis and Respiration under Stress 78 3.3 How is Stress Tolerance Measured? 79 3.3.1 Testing Possible Artifacts of the Stress Test 81 3.3.2 Effect of Temperature and Chemical Additions on the Oxygen Evolution Stress Assay 84 3.4 Practical Applications 88 3.4.1 Whole Leaf Physiological Responses 90 3.4.2 Effect of Dark and Sodium Nitrate on the Photosynthetic Stress Resistance Index and Photosynthesis in Leaf Slices under Anoxic Conditions 97 3.4.3 Post-Illumination Respiration 98 3.5 Discussion 98 3.6 Perspectives for Application of Method 107 Acknowledgments 109 Abbreviations 110 References 110 Appendix I. Additional Materials and Methods 117 Appendix II. Preliminary Analysis of the Utility of a Novel Stress Resistance Assay on Three Garst Lines of Zea mays, a C4 Plant 118 Results 119 General Conclusion 122 Suggestions 122 Hypotheses 123 4 The Hypotheses of Halosynthesis, Photoprotection, Soil Remediation via Salt-Conduction, and Potential Medical Benefits 125Karl Y. Biel, Nicholas P. Yensen 4.1 Introduction 127 4.2 The Haloconductor Theory 128 4.2.1 The Remediation of Saline Soils 128 4.2.2 New Approach for Soil Remediation via Salt Conducting Plants 130 4.2.3 Advantages of Conductor Plants for Soil Remediation 133 4.2.4 Productivity Considerations 134 4.2.5 Intriguing Productivity Curves in a Clonal Conductor Plant 136 4.3 The Halosynthesis Hypothesis 138 4.3.1 Concept Description and Terminology 139 4.3.2 Hydraulic Considerations and Salt Gradient from Soil to Shoot Surface 140 4.3.3 Salt Glands and Evapotranspirational Halosynthesis 143 4.3.4 The Photoelectric Effect 144 4.3.5 Epidermal Electro-Halosynthesis 144 4.3.6 Salt-Gland Electro-Halosynthesis 144 4.4 Physico- and Bio-Chemical Protection Synergisms 148 4.4.1 Biochemical Protection against Oxygen Radicals 151 4.5 A Case Study, Distichlis 153 4.5.1 Ecophysiology 153 4.5.2 Taxonomy and Geographic Distribution 153 4.5.3 Root-Soil Restructuring Capacity 154 4.5.4 Salt Tolerance 155 4.5.5 Photosynthesis 155 4.5.6 Ammonia Nutrition as a Protector against Salinity 157 4.5.7 Soil Salt Removal and Benefits to Changes in Soil Properties 158 4.6 Potential Medical Benefit of Photo-Halosynthesis 159 4.7 Predictions and Potential Tests of Hypotheses 163 4.7.1 Salt Conduction 163 4.7.2 Halodispersion 165 4.7.3 Metabolism 166 4.7.4 Protection 166 4.7.5 Halosynthesis 166 4.8 General Conclusions 167 Acknowledgments 167 References 167 5 Protective Role of Silicon in Living Organisms 175Vladimir V. Matichenkov, Irina R. Fomina, Karl Y. Biel 5.1 Introduction 176 5.1.1 Agriculture 176 5.1.2 Medicine 177 5.1.3 Microorganisms and Plants 177 5.2 Forms of Silicon 179 5.3 Silicon Cycle in Soil–Plant System 182 5.4 Silicon and Flora 183 5.4.1 Localization of Silicon in Plants 184 5.4.2 Forms of Silicon in Plants 187 5.4.3 Silicon and Water Storage in Plants 188 5.5 Silicon and Plants’ Resistance to Extreme Environments 189 5.6 Silicon as Matrix for Organic Compounds Synthesis 191 5.6.1 Hypothesis on Silicon Participation in Protection of Living Organisms under Stress Conditions 192 5.6.1.1 Premises of Hypothesis 192 5.6.1.2 Hypothesis 195 5.7 New Technologies 197 5.8 General Conclusion 198 Acknowledgments 199 References 199 6 Methanol as Example of Volatile Mediators Providing Plants’ Stress Tolerance 209Karl Y. Biel, Irina R. Fomina 6.1 Introduction 211 6.2 Methanol Application for the Regulation of Productivity 212 6.3 Emission of Methanol from Plants 213 6.3.1 Factors Affecting the Methanol Emission 214 6.3.2 Methanol Sources in Plants 216 6.3.3 Pectin Methylesterases 216 6.3.4 Utilization of Methanol by Plants 218 6.3.5 Ethanol-Water-Soluble Fraction in Different Parts of Plants 219 6.3.6 Ethanol-Water-Insoluble Fractions in Plants 222 6.3.7 DNA Methylation in Plants 223 6.4 Hypothesis of Methanol Influence on Different Levels of Cell Metabolism in C3 Plants 226 6.5 Conclusion 231 Acknowledgments 231 Abbreviations 232 References 232 Experiments 249 7 Patterns of Carbon Metabolism within Leaves 251Karl Y. Biel, Irina R. Fomina, Galina N. Nazarova, Vladislav G. Soukhovolsky, Rem G. Khlebopros, John N. Nishio 7.1 Introduction 253 7.2 Interactions among Light, Leaf Anatomy, the Metabolic Activity, and Environmental Stress Tolerance across Leaves 253 7.2.1 Anatomy and Pattern of Enzymes within the Leaf of Spinacia oleracea 255 7.2.1.1 Leaf Anatomy 255 7.2.1.2 What are the Roles of the Different Cells? 259 7.2.2 Enzyme Activity 263 7.2.2.1 How Does Inverting the Leaves Alter the Distribution of Enzyme Activity within Spinacia oleracea Leaf? 263 7.2.2.2 Summary of Enzyme Activity across Leaves 267 7.2.2.3 Functional Significance to Profiles of Enzyme Activity across Spinacia oleracea Leaves 268 7.2.3 CO2/O2 Gas Exchange 271 7.2.3.1 CO2 Gas Exchange 271 7.2.3.2 HCO3 –-Dependent Oxygen Evolution 274 7.2.4 Enzyme Activity, Carbon Metabolism, and Stress Tolerance across Spinacia oleracea Leaves 276 7.2.5 Light Regulation of Photosynthetic Enzyme Activity across Leaves 281 7.3 Model of Optimal Photosynthesis within a Mesophytic Leaf 282 7.4 General Conclusion 287 Acknowledgments 288 References 288 8 4-Hydroxyphenethyl Alcohol and Dihydroquercetin Increase Adaptive Potential of Barley Plants under Soil Flooding Conditions 301Tamara I. Balakhnina 8.1 Introduction 302 8.1.1 Effect of Soil Flooding on Plants 302 8.2 Effect of 4-Hydroxyphenethyl Alcohol on Growth and Adaptive Potential of Barley Plants at Optimal Soil Watering and Flooding 304 8.2.1 Plant Reactions 304 8.2.1.1 Seed Germination 304 8.2.1.2 Plant Growth 305 8.2.1.3 Lipid Peroxidation Intensity 308 8.2.1.4 Guaiacol Peroxidase Activity 309 8.2.1.5 Discussion 311 8.3 Dihydroquercetin Protects Barley Seeds against Mold and Increases Seedling Adaptive Potential Under Soil Flooding 313 8.3.1 Plant Reactions 313 8.3.1.1 Seed Germination 313 8.3.1.2 Growth Parameters 313 8.3.1.3 Intensity of Lipid Peroxidation 316 8.3.1.4 Activity of Ascorbate Peroxidase 318 8.3.1.5 Discussion 320 Acknowledgments 322 Abbreviations 322 References 323 9 Cooperation of Photosynthetic and Nitrogen Metabolisms 329Anatoly A. Ivanov, Anatoly A. Kosobryukhov 9.1 Introduction 331 9.2 Carbon Uptake and Rubisco 332 9.2.1 Dependence of Carbon Assimilation on Nitrogen Supply 334 9.3 Alternative Electron Acceptors in Photosynthesis 336 9.4 Nitrogen Metabolism 337 9.4.1 Primary Assimilation of Inorganic Nitrogen 337 9.4.1.1 Nitrate Reductase 339 9.4.1.2 Ferredoxin-Dependent Nitrite Reductase 342 9.4.1.3 Glutamine Synthetase/Glutamate Synthase (GS/GOGAT) Cycle 343 9.4.1.4 Glutamate Dehydrogenase 346 9.4.2 Relationship of Photorespiration and Nitrogen Metabolism 346 9.5 Relationship of Carbon and Nitrogen Metabolism in Stress Conditions 349 9.5.1 High CO2 Concentration in the Atmosphere 349 9.5.1.1 Plants’ Growth 349 9.5.1.2 Rubisco Content 350 9.5.1.3 Photosynthetic Acclimation 351 9.5.1.4 Photosynthesis and Nitrogen Content 353 9.5.1.5 Metabolic Changes 355 9.5.2 Low CO2 Concentration in the Atmosphere 360 9.5.3 Water Stress 368 9.5.3.1 Osmotic Homeostasis 368 9.5.3.2 Variability of Plant Response to Drought 369 9.5.3.3 Reactive Oxygen Species 370 9.5.3.4 Metabolic Changes 371 9.5.3.5 Stomata Conductivity and Rubisco Activity 371 9.5.3.6 Enzymes of Nitrogen Metabolism 373 9.5.3.7 Sucrose-Phosphate Synthase 375 9.5.3.8 Increased Plant Resistance to Drought by Nitrogen Supply 376 9.5.4 Salt Stress 377 9.5.4.1 Assimilation of Nitrogen in Salinity Conditions 378 9.5.4.2 Isocitrate Dehydrogenase and Fd-GOGAT 379 9.5.4.3 Proline Accumulation 380 9.5.4.4 Photosynthesis, Photorespiration and Reactive Oxygen Species 380 9.6 Conclusion 381 Abbreviations 382 References 382 10 Physiological Parameters of Fucus vesiculosus and Fucus serratus in the Barents Sea during a Tidal Cycle 439Inna V. Ryzhik, Anatoly A. Kosobryukhov, Evgeniya F. Markovskaya, Mikhail V. Makarov 10.1 Introduction 441 10.2 Materials and Methods 442 10.3 Results 444 10.3.1 Water Content in Algal Thalli 444 10.3.2 The Rate of Photosynthesis 445 10.3.3 Photosynthetic Pigments: Content and Proportion 445 10.3.4 Dependence of the Photosynthetic Rate on the Water Content in the Thallus 446 10.3.5 Potential Rate of Photosynthesis of Fucus vesiculosus 446 10.3.6 Lipid Peroxidation and Catalase Activities in Fucus vesiculosus 448 10.4 Discussion 449 Abbreviations 455 References 455 History and Biography – Tribute 461 11 Benson’s Protocol 463Arthur M. Nonomura, Karl Y. Biel, Irina R. Fomina, Wai-Ki “Frankie” Lam, Daniel P. Brummel, Allison Lauria, Michael S. McBride 11.1 Introduction 465 11.2 Benson–Bassham–Calvin and Lectin Cycles 468 11.3 Types of Photosynthetic Carbon Metabolism in Prokaryotes and Eukaryotes 471 11.4 Regulation of Photosynthates 471 11.5 The Origin and Development of the Carbon Reactions of Photosynthesis 472 11.6 The Next Steps 473 11.6.1 Materials and Methods 474 11.6.2 Results 480 11.6.3 Conclusion 498 11.7 Felicitation 499 References 502 12 Recollection of Yuri S. Karpilov’s Scientific and Social Life 509Karl Y. Biel, Irina R. Fomina 12.1 Introduction 510 12.2 Some Contradictory Discoveries 510 12.3 Official Statement of a Young Scientist in the USSR and His Deed 511 12.4 From the Memories, by Karl Biel 515 12.5 Australian Scientist Professor Barry Osmond Visited Karpilov’s Laboratory in 1971 525 12.6 Moving from Tiraspol to Pushchino, Moscow Region, to the Institute of Photosynthesis of the USSR Academy of Sciences 527 12.7 International Botanical Congress… 530 12.8 And after That, Soon… Unexpected Tragedy 530 12.9 Short Biography of Yuri S. Karpilov 533 Acknowledgments 534 Abbreviations 534 References 534 13 Dr. Nicholas Yensen’s Curriculum Vitae 543Karl Y. Biel, Irina R. Fomina 13.1 Introduction 544 13.2 Biographical Note about Dr. Nicholas Patrick Yensen 545 13.2.1 Education 545 13.2.2 Teaching Experience 545 13.2.3 Founder and Leader of Scientific Organizations 546 13.2.4 Member of Board of Directors, Consultant, and Chairman 546 13.2.5 Languages 547 13.2.6 Oratorical Talent 547 13.2.7 Dr. Yensen’s International Teamwork, Expeditions and Visitations 547 13.2.8 Distinctions 549 13.2.9 Articles, Videos and Documentaries about Dr. Yensen’s Work 549 13.2.10 Skill and Avocation 550 13.3 Conclusion 550 13.4 Addendum 552 Acknowledgements 552 Publications (selected) 553 14 Rem Khlebopros: Life in Science 557Vladislav G. Soukhovolsky, Irina R. Fomina 14.1 Introduction 558 14.2 Life in Science 559 14.3 Selected Scientific Publications and Speeches by Rem G. Khlebopros 566 14.3.1 Video-Interviews about Ecology in Krasnoyarsk 566 14.3.2 Books 566 14.3.3 Articles 567 Acknowledgments 571 Index 573

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Book SynopsisEnvironmental and Agricultural Microbiology Uniquely reveals the state-of-the-art microbial research/advances in the environment and agriculture fields Environmental and Agricultural Microbiology: Applications for Sustainability is divided into two parts which embody chapters on sustenance and life cycles of microorganisms in various environmental conditions, their dispersal, interactions with other inhabited communities, metabolite production, and reclamation. Though books pertaining to soil & agricultural microbiology/environmental biotechnology are available, there is a dearth of comprehensive literature on the behavior of microorganisms in the environmental and agricultural realm. Part 1 includes bioremediation of agrochemicals by microalgae, detoxification of chromium and other heavy metals by microbial biofilm, microbial biopolymer technology including polyhydroxyalkanoates (PHAs) and polyhydroxybutyrates (PHB), their production, degradability behaviorsTable of ContentsPreface xvii Part 1: Microbial Bioremediation and Biopolymer Technology 1 1 A Recent Perspective on Bioremediation of Agrochemicals by Microalgae: Aspects and Strategies 3Prithu Baruah and Neha Chaurasia 1.1 Introduction 4 1.2 Pollution Due to Pesticides 6 1.2.1 Acute Effects 8 1.2.2 Chronic Effects 9 1.3 Microalgal Species Involved in Bioremediation of Pesticides 9 1.4 Strategies for Phycoremediation of Pesticides 13 1.4.1 Involvement of Enzymes in Phycoremediation of Pesticides 13 1.4.2 Use of Genetically Engineered Microalgae 13 1.5 Molecular Aspects of Pesticide Biodegradation by Microalgae 14 1.6 Factor Affecting Phycoremediation of Pesticides 16 1.6.1 Biological Factor 16 1.6.2 Chemical Factor 16 1.6.3 Environment Factor 17 1.7 Benefit and Shortcomings of Phycoremediation 17 1.7.1 Benefits 17 1.7.2 Shortcomings 17 1.8 Conclusion and Future Prospects 18 References 18 2 Microalgal Bioremediation of Toxic Hexavalent Chromium: A Review 25Pritikrishna Majhi, Satyabrata Nayak and Saubhagya Manjari Samantaray 2.1 Introduction 25 2.1.1 Chromium Cycle 27 2.2 Effects of Hexavalent Chromium Toxicity 27 2.2.1 Toxicity to Microorganisms 27 2.2.2 Toxicity to Plant Body 28 2.2.3 Toxicity to Animals 29 2.3 Chromium Bioremediation by Microalgae 30 2.3.1 Cyanobacteria 30 2.3.2 Green Algae 31 2.3.3 Diatoms 31 2.4 Mechanism Involved in Hexavalent Chromium Reduction in Microalgae 32 2.5 Conclusion 33 References 34 3 Biodetoxification of Heavy Metals Using Biofilm Bacteria 39Adyasa Barik, Debasish Biswal, A. Arun and Vellaisamy Balasubramanian 3.1 Introduction 40 3.2 Source and Toxicity of Heavy Metal Pollution 41 3.2.1 Non-Essential Heavy Metals 42 3.2.1.1 Arsenic 42 3.2.1.2 Cadmium 43 3.2.1.3 Chromium 43 3.2.1.4 Lead 44 3.2.1.5 Mercury 45 3.2.2 Essential Heavy Metals 45 3.2.2.1 Copper 45 3.2.2.2 Zinc 46 3.2.2.3 Nickel 46 3.3 Biofilm Bacteria 47 3.4 Interaction of Metal and Biofilm Bacteria 47 3.5 Biodetoxification Mechanisms 48 3.5.1 Biosorption 48 3.5.2 Bioleaching 50 3.5.3 Biovolatilization 52 3.5.4 Bioimmobilization 54 3.6 Conclusion 55 References 55 4 Microbial-Derived Polymers and Their Degradability Behavior for Future Prospects 63Mohammad Asif Ali, Aniruddha Nag and Maninder Singh 4.1 Introduction 63 4.2 Polyamides 65 4.2.1 Bioavailability and Production 66 4.2.2 Biodegradability of Polyamides 66 4.2.3 Degradation of Nylon 4 Under the Soil 67 4.2.4 Fungal Degradation of Nylon 6 and Nylon 66 (Synthetic Polyamide) 67 4.2.5 Itaconic Acid-Based Heterocyclic Polyamide 68 4.2.6 Summary and Future Development 69 4.3 Polylactic Acid 69 4.3.1 Availability and Production 70 4.3.2 Polymerization Method 71 4.3.3 Biodegradability of Polylactic Acid 73 4.3.4 Copolymerization Method 73 4.3.5 Blending Method 73 4.3.6 Nanocomposite Formation 74 4.3.7 Summary 74 4.4 Polyhydroxyalkanoates 74 4.4.1 Biosynthesis of Polyhydroxyalkanoates 75 4.4.2 Application of PHAs 75 4.4.3 Biodegradability of PHAs 76 4.4.4 Degradability Methods 76 4.4.5 Summary 77 4.5 Conclusion and Future Development 77 References 78 5 A Review on PHAs: The Future Biopolymer 83S. Mohapatra, K. Vishwakarma, N. C. Joshi, S. Maity, R. Kumar, M. Ramchander, S. Pattnaik and D. P. Samantaray 5.1 Introduction 84 5.2 Green Plastic: Biodegradable Polymer Used as Plastic 85 5.3 Difference Between Biopolymer and Bioplastic 88 5.4 Polyhydroxyalkanoates 88 5.5 Polyhydroxyalkanoates and Its Applications 89 5.6 Microorganisms Producing PHAs 90 5.7 Advantages 96 5.8 Conclusion and Future Prospective 96 References 96 6 Polyhydroxybutyrate as an Eco-Friendly Alternative of Synthetic Plastics 101Shikha Sharma, Priyanka Sharma, Vishal Sharma and Bijender Kumar Bajaj 6.1 Introduction 102 6.2 Bioplastics 104 6.3 Bioplastics vs. Petroleum-Based Plastics 106 6.4 Classification of Biodegradable Polymers 107 6.5 PHB-Producing Bacteria 109 6.6 Methods for Detecting PHB Granules 113 6.7 Biochemical Pathway for Synthesis of PHB 114 6.8 Production of PHB 116 6.8.1 Process Optimization for PHB Production 117 6.8.2 Optimization of PHB Production by One Variable at a Time Approach 118 6.8.3 Statistical Approaches for PHB Optimization 120 6.9 Production of PHB Using Genetically Modified Organisms 123 6.10 Characterization of PHB 125 6.11 Various Biochemical Techniques Used for PHB Characterization 126 6.11.1 Fourier Transform Infrared Spectroscopy 127 6.11.2 Differential Scanning Calorimetry 127 6.11.3 Thermogravimetric Analysis 128 6.11.4 X-Ray Powder Diffraction (XRD) 128 6.11.5 Nuclear Magnetic Resonance Spectroscopy 128 6.11.6 Microscopic Techniques 129 6.11.7 Elemental Analysis 130 6.11.8 Polarimetry 130 6.11.9 Molecular Size Analysis 130 6.12 Biodegradation of PHB 131 6.13 Application Spectrum of PHB 132 6.14 Conclusion 135 6.15 Future Perspectives 135 Acknowledgements 136 References 136 7 Microbial Synthesis of Polyhydroxyalkanoates (PHAs) and Their Applications 151N.N.N. Anitha and Rajesh K. Srivastava 7.1 Introduction 153 7.2 Conventional Plastics and Its Issues in Utility 156 7.2.1 Synthetic Plastic and Its Accumulation or Degradation Impacts 158 7.3 Bioplastics 159 7.3.1 Polyhydroxyalkanoates 160 7.3.1.1 Microorganisms in the Production of PHAs 164 7.4 Fermentation for PHAs Production 171 7.5 Downstream Process for PHAs 173 7.6 Conclusions 175 References 176 8 Polyhydroxyalkanoates for Sustainable Smart Packaging of Fruits 183S. Pati, S. Mohapatra, S. Maity, A. Dash and D. P. Samantaray 8.1 Introduction 183 8.2 Physiological Changes of Fresh Fruits During Ripening and Minimal Processing 185 8.3 Smart Packaging 186 8.4 Biodegradable Polymers for Fruit Packaging 188 8.5 Legal Aspects of Smart Packaging 189 8.6 Pros and Cons of Smart Packaging Using PHAs 189 8.7 Conclusion 190 References 191 9 Biosurfactants Production and Their Commercial Importance 197Saishree Rath and Rajesh K. Srivastava 9.1 Introduction 198 9.2 Chemical Surfactant Compounds 200 9.2.1 Biosurfactant Compounds 202 9.3 Properties of Biosurfactant Compound 205 9.3.1 Activities of Surface and Interface Location 205 9.3.2 Temperature and pH Tolerance 205 9.3.3 Biodegradability 206 9.3.4 Low Toxicity 206 9.3.5 Emulsion Forming and Breaking 206 9.4 Production of Biosurfactant by Microbial Fermentation 206 9.4.1 Factors Influencing the Production of Biosurfactants 209 9.4.1.1 Environmental Conditions 209 9.4.1.2 Carbon Substrates 210 9.4.1.3 Estimation of Biosurfactants Activity 211 9.5 Advantages, Microorganisms Involved, and Applications of Biosurfactants 211 9.5.1 Advantages of Using Biosurfactants 211 9.5.1.1 Easy Raw Materials for Biosurfactant Biosynthesis 211 9.5.1.2 Low Toxic Levels for Environment 211 9.5.1.3 Best Operation With Surface and Interface Activity 212 9.5.1.4 Good Biodegradability 212 9.5.1.5 Physical Variables 212 9.5.2 Microbial Sources 212 9.5.3 Production of Biosurfactants 213 9.5.3.1 Production of Rhamnolipids 213 9.5.3.2 Regulation of Rhamnolipids Synthesis 214 9.5.3.3 Commercial Use of Biosurfactants 214 9.6 Conclusions 215 References 216 Part 2: Microbes in Sustainable Agriculture and Biotechnological Applications 219 10 Functional Soil Microbes: An Approach Toward Sustainable Horticulture 221C. Sarathambal, R. Dinesh and V. Srinivasan 10.1 Introduction 221 10.2 Rhizosphere Microbial Diversity 222 10.3 Plant Growth–Promoting Rhizobacteria 223 10.3.1 Nitrogen Fixation 224 10.3.2 Production of Phytohormones 225 10.3.3 Production of Enzymes That can Transform Crop Growth 225 10.3.4 Microbial Antagonism 226 10.3.5 Solubilization of Minerals 226 10.3.6 Siderophore and Hydrogen Cyanide (HCN) Production 228 10.3.7 Cyanide (HCN) Production 229 10.3.8 Plant Growth–Promoting Rhizobacteria on Growth of Horticultural Crops 229 10.4 Conclusion and Future Perspectives 235 References 235 11 Rhizosphere Microbiome: The Next-Generation Crop Improvement Strategy 243M. Anandaraj, S. Manivannan and P. Umadevi 11.1 Introduction 244 11.2 Rhizosphere Engineering 245 11.3 Omics Tools to Study Rhizosphere Metagenome 246 11.3.1 Metagenomics 246 11.3.2 Metaproteomics 248 11.3.3 Metatranscriptomics 249 11.3.4 Ionomics 250 11.4 As Next-Generation Crop Improvement Strategy 251 11.5 Conclusion 252 References 252 12 Methane Emission and Strategies for Mitigation in Livestock 257Nibedita Sahoo, Swati Pattnaik, Matrujyoti Pattnaik and Swati Mohapatra 12.1 Introduction 258 12.2 Contribution of Methane from Livestock 259 12.3 Methanogens 259 12.3.1 Rumen Microbial Community 260 12.3.2 Methanogens Found in Rumen 260 12.3.3 Enrichment of Methanogens from Rumen Liquor 261 12.3.4 Screening for Methane Production 261 12.3.5 Isolation of Methanogens 261 12.3.6 Molecular Characterization 261 12.4 Methanogenesis: Methane Production 262 12.4.1 Pathways of Methanogenesis 262 12.4.2 Pathway of CO2 Reduction 262 12.4.3 CO2 Reduction to Formyl-Methanofuran 263 12.4.4 Conversion of the Formyl Group from Formyl-Methanofuran to Formyl-Tetrahydromethanopterin 263 12.4.5 Formation of Methenyl-Tetrahydromethanopterin 263 12.4.6 Reduction of Methenyl-Tetrahydromethanopterin to Methyl-Tetrahydromethanopterin 263 12.4.7 Reduction of Methyl-Tetrahydromethanopterin to Methyl-S-Coenzyme M 264 12.4.8 Reduction of Methyl-S-Coenzyme M to CH4 264 12.5 Strategies for Mitigation of Methane Emission 264 12.5.1 Dietary Manipulation 264 12.5.1.1 Increasing Dry Matter Intake 264 12.5.1.2 Increasing Ration Concentrate Fraction 265 12.5.1.3 Supplementation of Lipid 265 12.5.1.4 Protozoa Removal 266 12.5.2 Feed Additives 266 12.5.2.1 Ionophore Compounds 266 12.5.2.2 Halogenated Methane Compound 267 12.5.2.3 Organic Acid 267 12.5.3 Microbial Feed Additives 268 12.5.3.1 Vaccination 268 12.5.3.2 Bacteriophages and Bacteriocins 269 12.5.4 Animal Breeding and Selection 270 12.6 Conclusion 270 References 271 13 Liquid Biofertilizers and Their Applications: An Overview 275Avro Dey 13.1 Introduction 275 13.1.1 Chemical Fertilizer and its Harmful Effect 277 13.2 Biofertilizers “Boon for Mankind” 278 13.3 Carrier-Based Biofertilizers 279 13.3.1 Solid Carrier-Based Biofertilizers 279 13.3.2 Liquid Biofertilizer 279 13.4 Sterilization of the Carrier 282 13.5 Merits of Using Liquid Biofertilizer Over Solid Carrier-Based Biofertilizer 282 13.6 Types of Liquid Biofertilizer 283 13.7 Production of Liquid Biofertilizers 285 13.7.1 Isolation of the Microorganism 285 13.7.2 Preparation of Medium and Growth Condition 285 13.7.3 Culture and Preservation 286 13.7.4 Preparation of Liquid Culture 286 13.7.5 Fermentation and Mass Production 287 13.7.6 Formulation of the Liquid Biofertilizers 287 13.8 Applications of Biofertilizers 288 13.9 Conclusion 290 References 291 14 Extremozymes: Biocatalysts From Extremophilic Microorganisms and Their Relevance in Current Biotechnology 293Khushbu Kumari Singh and Lopamudra Ray 14.1 Introduction 294 14.2 Extremophiles: The Source of Novel Enzymes 295 14.2.1 Thermophilic Extremozymes 296 14.2.2 Psychrophilic Extremozymes 299 14.2.3 Halophilic Extremozymes 300 14.2.4 Alkaliphilic/Acidiophilic Extremozymes 300 14.2.5 Piezophilic Extremozymes 301 14.3 The Potential Application of Extremozymes in Biotechnology 301 14.4 Conclusion and Future Perspectives 303 References 304 15 Microbial Chitinases and Their Applications: An Overview 313Suraja Kumar Nayak, Swapnarani Nayak, Swaraj Mohanty, Jitendra Kumar Sundaray and Bibhuti Bhusan Mishra 15.1 Introduction 314 15.2 Chitinases and Its Types 315 15.3 Sources of Microbial Chitinase 317 15.3.1 Bacterial Chitinases 317 15.3.2 Fungal Chitinases 319 15.3.3 Actinobacteria 321 15.3.4 Viruses/Others 322 15.4 Genetics of Microbial Chitinase 322 15.5 Biotechnological Advances in Microbial Chitinase Production 323 15.5.1 Media Components 324 15.5.2 Physical Parameters 325 15.5.3 Modes and Methods of Fermentation 325 15.5.4 Advances Biotechnological Methods 326 15.6 Applications of Microbial Chitinases 327 15.6.1 Agricultural 328 15.6.1.1 Biopesticides 328 15.6.1.2 Biocontrol 328 15.6.2 Biomedical 329 15.6.3 Pharmaceutical 329 15.6.4 Industrial 330 15.6.5 Environmental 330 15.6.5.1 Waste Management 331 15.6.6 Others 331 15.7 Conclusion 332 References 332 16 Lithobiontic Ecology: Stone Encrusting Microbes and their Environment 341Abhik Mojumdar, Himadri Tanaya Behera and Lopamudra Ray 16.1 Introduction 341 16.2 Diversity of Lithobionts and Its Ecological Niche 342 16.2.1 Epiliths 342 16.2.2 Endoliths 343 16.2.3 Hypoliths 344 16.3 Colonization Strategies of Lithobionts 345 16.3.1 Temperature 346 16.3.2 Water Availability 346 16.3.3 Light Availability 347 16.4 Geography of Lithobbiontic Coatings 348 16.4.1 Bacteria 348 16.4.2 Cyanobacteria 349 16.4.3 Fungi 349 16.4.4 Algae 349 16.4.5 Lichens 350 16.5 Impacts of Lithobiontic Coatings 351 16.5.1 On Organic Remains 351 16.5.2 On Rock Weathering 351 16.5.3 On Rock Coatings 352 16.6 Role of Lithobionts in Harsh Environments 352 16.7 Conclusion 353 Acknowledgement 353 References 353 17 Microbial Intervention in Sustainable Production of Biofuels and Other Bioenergy Products 361Himadri Tanaya Behera, Abhik Mojumdar, Smruti Ranjan Das, Chiranjib Mohapatra and Lopamudra Ray 17.1 Introduction 362 17.2 Biomass 363 17.3 Biofuel 364 17.3.1 Biodiesel 365 17.3.1.1 Microalgae in Biodiesel Production 365 17.3.1.2 Oleaginous Yeasts in Biodiesel Production 366 17.3.1.3 Oleaginous Fungi in Biodiesel Production 366 17.3.1.4 Bacteria in Biodiesel Production 367 17.3.2 Bioalcohol 367 17.3.2.1 Bioethanol 367 17.3.2.2 Biobutanol 368 17.3.3 Biogas 369 17.3.4 Biohydrogen 369 17.4 Other Bioenergy Products 370 17.4.1 Microbial Fuel Cells 370 17.4.1.1 Microbes Used in MFCs 372 17.4.1.2 Future Aspects of Microbial Fuel Cells 372 17.4.2 Microbial Nanowires in Bioenergy Application 374 17.4.2.1 Pili 375 17.4.2.2 Outer Membranes and Extended Periplasmic Space 375 17.4.2.3 Unknown Type—MNWs Whose Identity to be Confirmed 375 17.4.3 Microbial Nanowires in Bioenergy Production 376 17.5 Conclusion 376 References 376 18 Role of Microbes and Microbial Consortium in Solid Waste Management 383Rachana Jain, Lopa Pattanaik, Susant Kumar Padhi and Satya Narayan Naik 18.1 Introduction 384 18.2 Types of Solid Waste 384 18.2.1 Domestic Wastes 385 18.2.2 Institutional and Commercial Wastes 385 18.2.3 Wastes From Street Cleansing 385 18.2.4 Industrial Wastes 385 18.2.5 Nuclear Wastes 385 18.2.6 Agricultural Wastes 385 18.3 Waste Management in India 386 18.4 Solid Waste Management 390 18.4.1 Municipal Solid Waste Management 390 18.5 Solid Waste Management Techniques 390 18.5.1 Incineration 392 18.5.2 Pyrolysis and Gasification 392 18.5.3 Landfilling 393 18.5.4 Aerobic Composting 394 18.5.5 Vermicomposting 397 18.5.6 Anaerobic Digestion 401 18.5.6.1 Enzymatic Hydrolysis 402 18.5.6.2 Fermentation 402 18.5.6.3 Acetogenesis 403 18.5.6.4 Methanogenesis 403 18.5.7 Bioethanol From Various Solid Wastes 404 18.6 Conclusion 413 References 413 Index 423

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Book SynopsisDIATOM GLIDING MOTILITY Moving photosynthetic organisms are still a great mystery for biologists and this book summarizes what is known and reports the current understanding and modeling of those complex processes. The book covers a broad range of work describing our current state of understanding on the topic, including: historic knowledge and misconceptions of motility; evolution of diatom motility; diatom ecology & physiology; cell biology and biochemistry of diatom motility, anatomy of motile diatoms; observations of diatom motile behavior; diatom competitive ability, unique forms of diatom motility as found in the genus Eunotia; and models of motility. This is the first book attempting to gather such information surrounding diatom motility into one volume focusing on this single topic. Readers will be able to gather both the current state of understanding on the potential mechanisms and ecological regulators of motility, as well as possible models anTable of ContentsPreface xxvii 1 Some Observations of Movements of Pennate Diatoms in Cultures and Their Possible Interpretation 1Thomas Harbich 1.1 Introduction 2 1.2 Kinematics and Analysis of Trajectories in Pennate Diatoms with Almost Straight Raphe along the Apical Axis 3 1.3 Curvature of the Trajectory at the Reversal Points 9 1.4 Movement of Diatoms in and on Biofilms 13 1.5 Movement on the Water Surface 16 1.6 Formation of Flat Colonies in Cymbella lanceolata 23 1.7 Conclusion 29 References 29 2 The Kinematics of Explosively Jerky Diatom Motility: A Natural Example of Active Nanofluidics 33Ahmet C. Sabuncu, Richard Gordon, Edmond Richer, Kalina M. Manoylov and Ali Beskok 2.1 Introduction 34 2.2 Material and Methods 35 2.2.1 Diatom Preparation 35 2.2.2 Imaging System 35 2.2.3 Sample Preparation 36 2.2.4 Image Processing 36 2.3 Results and Discussion 41 2.3.1 Comparison of Particle Tracking Algorithms 41 2.3.2 Stationary Particles 42 2.3.3 Diatom Centroid Measurements 43 2.3.4 Diatom Orientation Angle Measurements 46 2.3.5 Is Diatom Motion Characterized by a Sequence of Small Explosive Movements? 49 2.3.6 Future Work 50 2.4 Conclusions 51 Appendix 52 References 59 3 Cellular Mechanisms of Raphid Diatom Gliding 65Yekaterina D. Bedoshvili and Yelena V. Likhoshway 3.1 Introduction 65 3.2 Gliding and Secretion of Mucilage 67 3.3 Cell Mechanisms of Mucilage Secretion 68 3.4 Mechanisms of Gliding Regulation 71 3.5 Conclusions 72 Acknowledgments 72 References 73 4 Motility of Biofilm-Forming Benthic Diatoms 77Karen Grace Bondoc-Naumovitz and Stanley A. Cohn 4.1 Introduction 77 4.2 General Motility Models and Concepts 86 4.2.1 Adhesion 87 4.2.2 Gliding Motility 89 4.2.3 Motility and Environmental Responsiveness 91 4.3 Light-Directed Vertical Migration 93 4.4 Stimuli-Directed Movement 94 4.4.1 Nutrient Foraging 94 4.4.2 Pheromone-Based Mate-Finding Motility 97 4.4.3 Prioritization Between Co-Occurring Stimuli 99 4.5 Conclusion 99 References 100 5 Photophobic Responses of Diatoms – Motility and Inter-Species Modulation 111Stanley A. Cohn, Lee Warnick and Blake Timmerman 5.1 Introduction 112 5.2 Types of Observed Photoresponses 112 5.2.1 Light Spot Accumulation 112 5.2.2 High-Intensity Light Responses 114 5.3 Inter-Species Effects of Light Responses 118 5.3.1 Inter-Species Effects on High Irradiance Direction Change Response 119 5.3.2 Inter-Species Effects on Cell Accumulation into Light Spots 123 5.4 Summary 123 References 131 6 Diatom Biofilms: Ecosystem Engineering and Niche Construction 135David M. Paterson and Julie A. Hope 6.1 Introduction 135 6.1.1 Diatoms: A Brief Portfolio 135 6.1.2 Benthic Diatoms as a Research Challenge 136 6.2 The Microphytobenthos and Epipelic Diatoms 136 6.3 The Ecological Importance of Locomotion 137 6.4 Ecosystem Engineering and Functions 139 6.4.1 Ecosystem Engineering 139 6.4.2 Ecosystem Functioning 140 6.5 Microphytobenthos as Ecosystem Engineers 141 6.5.1 Sediment Stabilization 141 6.5.2 Beyond the Benthos 143 6.5.3 Diatom Architects 144 6.5.4 Working with Others: Combined Effects 144 6.5.5 The Dynamic of EPS 145 6.5.6 Nutrient Turnover and Biogeochemistry 145 6.6 Niche Construction and Epipelic Diatoms 146 6.7 Conclusion 149 Acknowledgments 150 References 150 7 Diatom Motility: Mechanisms, Control and Adaptive Value 159João Serôdio 7.1 Introduction 159 7.2 Forms and Mechanisms of Motility in Diatoms 160 7.2.1 Motility in Centric Diatoms 160 7.2.2 Motility in Pennate Raphid Diatoms 161 7.2.3 Motility in Other Substrate-Associated Diatoms 162 7.2.4 Vertical Migration in Diatom-Dominated Microphytobenthos 163 7.3 Controlling Factors of Diatom Motility 164 7.3.1 Motility Responses to Vectorial Stimuli 164 7.3.1.1 Light Intensity 164 7.3.1.2 Light Spectrum 165 7.3.1.3 UV Radiation 166 7.3.1.4 Gravity 166 7.3.1.5 Chemical Gradients 167 7.3.2 Motility Responses to Non-Vectorial Stimuli 167 7.3.2.1 Temperature 167 7.3.2.2 Salinity 168 7.3.2.3 pH 168 7.3.2.4 Calcium 168 7.3.2.5 Other Factors 169 7.3.2.6 Inhibitors of Diatom Motility 169 7.3.3 Species-Specific Responses and Interspecies Interactions 169 7.3.4 Endogenous Control of Motility 170 7.3.5 A Model of Diatom Vertical Migration Behavior in Sediments 170 7.4 Adaptive Value and Consequences of Motility 172 7.4.1 Planktonic Centrics 172 7.4.2 Benthic Pennates 173 7.4.3 Ecological Consequences of Vertical Migration 175 7.4.3.1 Motility-Enhanced Productivity 175 7.4.3.2 Carbon Cycling and Sediment Biostabilization 176 Acknowledgments 176 References 176 8 Motility in the Diatom Genus Eunotia Ehrenb. 185Paula C. Furey 8.1 Introduction 185 8.2 Accounts of Movement in Eunotia 188 8.3 Motility in the Context of Valve Structure 194 8.3.1 Motility and Morphological Characteristics in Girdle View 194 8.3.2 Motility and Morphological Characteristics in Valve View 196 8.3.3 Motility and the Rimoportula 198 8.4 Motility and Ecology of Eunotia 198 8.4.1 Substratum-Associated Environments 199 8.4.2 Planktonic Environments 201 8.5 Motility and Diatom Evolution 202 8.6 Conclusion and Future Directions 203 Acknowledgements 204 References 205 9 A Free Ride: Diatoms Attached on Motile Diatoms 211Vincent Roubeix and Martin Laviale 9.1 Introduction 211 9.2 Adhesion and Distribution of Epidiatomic Diatoms on Their Host 213 9.3 The Specificity of Host-Epiphyte Interactions 215 9.4 Cost-Benefit Analysis of Host-Epiphyte Interactions 217 9.5 Conclusion 219 References 219 10 Towards a Digital Diatom: Image Processing and Deep Learning Analysis of Bacillaria paradoxa Dynamic Morphology 223Bradly Alicea, Richard Gordon, Thomas Harbich, Ujjwal Singh, Asmit Singh and Vinay Varma 10.1 Introduction 224 10.1.1 Organism Description 224 10.1.2 Research Motivation 227 10.2 Methods 228 10.2.1 Video Extraction 228 10.2.2 Deep Learning 230 10.2.3 DeepLabv3 Analysis 234 10.2.4 Primary Dataset Analysis 234 10.2.5 Data Availability 235 10.3 Results 235 10.3.1 Watershed Segmentation and Canny Edge Detection 235 10.3.2 Deep Learning 236 10.4 Conclusion 243 Acknowledgments 245 References 245 11 Diatom Triboacoustics 249Ille C. Gebeshuber, Florian Zischka, Helmut Kratochvil, Anton Noll, Richard Gordon and Thomas Harbich Glossary 249 11.1 State-of-the-Art 251 11.1.1 Diatoms and Their Movement 251 11.1.2 The Navier-Stokes Equation 252 11.1.3 Low Reynolds Number 253 11.1.4 Reynolds Number for Diatoms 254 11.1.5 Further Thoughts About Movement of Diatoms 254 11.1.6 Possible Reasons for Diatom Movement 255 11.1.7 Underwater Acoustics, Hydrophones 256 11.1.7.1 Underwater Acoustics 256 11.1.7.2 Hydrophones 257 11.2 Methods 257 11.2.1 Estimate of the Momentum of a Moving Diatom 257 11.2.2 On the Speed of Expansion of the Mucopolysaccharide Filaments 258 11.2.2.1 Estimation of Radial Expansion 258 11.2.2.2 Sound Generation 261 11.2.3 Gathering Diatoms 266 11.2.3.1 Purchasing Diatom Cultures 267 11.2.3.2 Diatoms from the Wild 267 11.2.4 Using a Hydrophone to Detect Possible Acoustic Signals from Diatoms 269 11.2.4.1 First Setup 269 11.2.4.2 Second Setup 271 11.3 Results and Discussion 272 11.3.1 Spectrograms 272 11.3.2 Discussion 277 11.4 Conclusions and Outlook 277 Acknowledgements 279 References 279 12 Movements of Diatoms VIII: Synthesis and Hypothesis 283Jean Bertrand 12.1 Introduction 283 12.2 Review of the Conditions Necessary for Movements 284 12.3 Hypothesis 285 12.4 Analysis – Comparison with Observations 288 12.4.1 Translational Apical Movement 288 12.4.2 The Transapical Toppling Movement 290 12.4.3 Diverse Pivoting 290 12.5 Conclusion 291 Acknowledgments 292 References 292 13 Locomotion of Benthic Pennate Diatoms: Models and Thoughts 295Jiadao Wang, Ding Weng, Lei Chen and Shan Cao 13.1 Diatom Structure 295 13.1.1 Ultrastructure of Frustules 295 13.1.2 Bending Ability of Diatoms 297 13.2 Models for Diatom Locomotion 300 13.2.1 Edgar Model for Diatom Locomotion 300 13.2.2 Van der Waals Force Model (VW Model) for Diatom Locomotion 302 13.2.2.1 Locomotion Behavior of Diatoms 302 13.2.2.2 Moving Organelles and Pseudopods 304 13.2.2.3 Chemical Properties of Mucilage Trails 307 13.2.2.4 Mechanical Properties of Mucilage Trails 310 13.2.2.5 VW Model for Diatom Locomotion 314 13.3 Locomotion and Aggregation of Diatoms 319 13.3.1 Locomotion Trajectory and Parameters of Diatoms 319 13.4 Simulation on Locomotion, Aggregation and Mutual Perception of Diatoms 323 13.4.1 Simulation Area and Parameters 323 13.4.2 Diatom Life Cycle and Modeling Parameters 323 13.4.3 Simulation Results of Diatom Locomotion Trajectory with Mutual Perception 326 13.4.4 Simulation Results of Diatom Adhesion with Mutual Perception 327 13.4.5 Adhesion and Aggregation Mechanism of Diatoms 331 References 332 14 The Whimsical History of Proposed Motors for Diatom Motility 335Richard Gordon 14.1 Introduction 336 14.2 Historical Survey of Models for the Diatom Motor 338 14.2.1 Diatoms Somersault via Protruding Muscles (1753) 338 14.2.2 Vibrating Feet or Protrusions Move Diatoms (1824) 338 14.2.3 Diatoms Crawl Like Snails (1838) 342 14.2.4 The Diatom Motor is a Jet Engine (1849) 344 14.2.5 Rowing Diatoms (1855) 346 14.2.6 Diatoms Have Protoplasmic Tank Treads (1865) 350 14.2.7 Diatoms as the Flame of Life: Capillarity (1883) 354 14.2.8 Bellowing Diatoms (1887) 355 14.2.9 Jelly Powered Jet Skiing Diatoms (1896) 355 14.2.10 Bubble Powered Diatoms (1905) 358 14.2.11 Diatoms Win: “I Have No New Theory to Offer and See No Reason to Use Those Already Abandoned” (1940) 360 14.2.12 Is Diatom Motility a Special Case of Cytoplasmic Streaming? (1943) 360 14.2.13 Diatom Adhesion as a Sliding Toilet Plunger (1966) 365 14.2.14 Diatom as a Monorail that Lays Its Own Track (1967) 366 14.2.15 The Diatom as a “Compressed Air” Coanda Effect Gliding Vehicle (1967) 368 14.2.16 The Electrokinetic Diatom (1974) 371 14.2.17 The Diatom Clothes Line or Railroad Track (1980) 372 14.2.18 Diatom Ion Cyclotron Resonance (1987) 374 14.2.19 Diatoms Do Internal Treadmilling (1998) 375 14.2.20 Surface Treadmilling, Swimming and Snorkeling Diatoms (2007) 376 14.2.21 Acoustic Streaming: The Diatom as Vibrator or Jack Hammer (2010) 378 14.2.22 Propulsion of Diatoms Via Many Small Explosions (2020) 379 14.2.23 Diatoms Walk Like Geckos (2019) 380 14.3 Pulling What We Know and Don’t Know Together, about the Diatom Motor 381 14.4 Membrane Surfing: A New Working Hypothesis for the Diatom Motor (2020) 393 Acknowledgments 397 References 397 Appendix 420 Index 421

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Book SynopsisLearn the various microbiological aspects one deals with in environment management and the remediation of toxic contaminants in the environment In recent years, the accumulation of hazardous contaminants has caused a broad-based deterioration in global environmental quality. These have had wide-ranging negative social impacts, affecting climate, soil and water ecosystems, and more. As traditional methods of contaminant mitigation have proven inadequate to the task, microbial-based remediation offers the clearest, most environmentally friendly path forward for this crucial aspect of global environmental stewardship. Microbes Based Approaches for the Management of Hazardous Contaminants offers comprehensive coverage of novel and indigenous microbes and their applications in contaminant mitigation. Surveying all the major microbial products and methods for degrading and remediating hazardous pollutants, it offers a key tool in the fight against global environmental degradation. The result

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Book SynopsisTable of ContentsPreface xvii About the Authors xix Part I Introduction to Viruses 1 1 Overview of Molecular Biology 3 Contributing Author: Sarah Forster 1.1 Cell Basics 4 1.1.1 Cytoplasm 5 1.1.2 Ribosomes 5 1.1.3 Nucleus 6 1.2 Cell Replication 6 1.2.1 Nucleic Acids 6 1.2.2 DNA Replication 7 1.2.3 RNA Structure and Role 9 1.2.4 Protein Synthesis 9 1.3 Cellular Transport 11 1.3.1 Plasma Membrane 11 1.3.2 Cell Signaling 11 1.4 Immune Defense 12 1.4.1 Innate Immunity 12 1.4.2 Adaptive Immunity 13 1.4.2.1 Humoral Immunity 13 1.4.2.2 Cellular Immunity 14 1.5 Applications 14 1.6 Chapter Summary 16 1.7 Problems 16 References 16 2 Basics of Virology 19 2.1 Viral Basics and Terminology 19 2.2 Viral Life Cycle 21 2.2.1 Attachment (Connection) 21 2.2.2 Penetration (Entry) 22 2.2.3 Uncoating 22 2.2.4 Replication 23 2.2.5 Assembly 23 2.2.6 Maturation and Release 23 2.3 Virus Structure and Classification 24 2.3.1 DNA Viruses 25 2.3.2 RNA Viruses 25 2.3.3 Reverse Transcription Viruses (Retroviruses) 27 2.4 Viruses in Context of the Tree of Life 27 2.5 Viral Genetics 28 2.5.1 Antigenic Shift 28 2.5.2 Antigenic Drift 29 2.5.3 Phenotypic Mixing 29 2.5.4 Complementation 29 2.6 Applications 29 2.7 Chapter Summary 31 2.8 Problems 31 References 32 3 Pandemics, Epidemics, and Outbreaks 33 3.1 Human Viral Diseases 34 3.2 Ebola and Marburg Viruses 35 3.2.1 Symptoms 36 3.2.2 Diagnosis 37 3.2.3 Prevention and Treatment 37 3.3 Human Immunodeficiency Disease (HIV) 38 3.3.1 HIV Symptoms 39 3.3.1.1 Stage 1: Acute Infection 39 3.3.1.2 Stage 2: Chronic HIV Infection (Latent Phase) 39 3.3.1.3 Stage 3: Acquired Immunodeficiency Syndrome (AIDS) 39 3.3.2 Diagnosis 40 3.3.3 HIV Prevention and Treatment 40 3.4 Influenza 41 3.4.1 Influenza Symptoms 41 3.4.2 Influenza Diagnosis 42 3.4.3 Influenza Prevention and Treatment 42 3.4.4 Influenza Pandemics 43 3.5 Coronaviruses 44 3.5.1 Symptoms 45 3.5.1.1 Typical Acute Symptoms 45 3.5.1.2 Post-COVID Conditions 46 3.5.1.3 COVID-19 Multiorgan System Effects (MIS) 46 3.5.2 COVID-19 Diagnosis 47 3.5.3 COVID-19 Prevention and treatment 48 3.6 Current and Emerging Viral Threats 48 3.7 Applications 51 3.8 Chapter Summary 52 3.9 Problems 53 References 53 4 Virus Prevention, Diagnosis, and Treatment 57 4.1 Vaccination Successes and Challenges 58 4.2 Current Vaccine Technology 59 4.2.1 Live-attenuated vaccines 60 4.2.2 Inactivated vaccines 61 4.2.3 Recombinant Subunit Vaccines 61 4.2.4 Viral Vector Vaccines 62 4.2.5 Messenger RNA (mRNA) Vaccines 62 4.3 U.S.-Approved Vaccines and Requirements 63 4.3.1 Commercially Available Viral Vaccines 63 4.3.2 Vaccination Requirements 63 4.4 Viral Testing and Diagnosis 64 4.4.1 Viral Testing 65 4.4.2 Antibody Testing 66 4.5 Antiviral Treatment Options 66 4.5.1 HIV 67 4.5.1.1 Nucleoside Reverse Transcriptase Inhibitors (NRTIs) 67 4.5.1.2 Non-nucleoside Reverse Transcriptase Inhibitors (NNRTIs) 67 4.5.1.3 Protease Inhibitors (PIs) 67 4.5.1.4 Fusion Inhibitors (FIs) 67 4.5.1.5 Integrase Strand Transfer Inhibitors (INSTIs) 67 4.5.1.6 CCR5 Antagonists 67 4.5.1.7 Attachment Inhibitors 68 4.5.1.8 Post-Attachment Inhibitors 68 4.5.1.9 Pharmacokinetic Enhancers 68 4.5.2 Influenza 68 4.5.3 Hepatitis C virus (HCV) 68 4.5.4 Other Treatment Options 69 4.6 Applications 70 4.7 Chapter Summary 71 4.8 Problems 72 References 72 5 Safety Protocols and Personal Protection Equipment 75 Contributing Author: Emma Parente 5.1 Regulations and Oversight of Safety Protocols 76 5.2 Protective and Safety Systems 76 5.2.1 Personal Protective Devices and Practices 76 5.2.2 Antimicrobial Suppression And Eradication 77 5.3 Disinfection Categories and Procedures 78 5.4 Occupational Health and Safety Administration Hazmat Regulations 79 5.4.1 HAZMAT Level A Protection 80 5.4.2 HAZMAT Level B Protection 81 5.4.3 Level C Protection 82 5.4.4 Level D Protection 83 5.5 Bio Level Safety and Security 83 5.6 COVID-Related Safety Precautions 84 5.6.1 Personal Protective Equipment 84 5.6.2 Transmission Control 85 5.7 Applications 85 5.8 Summary 87 5.9 Problems 87 References 88 6 Epidemiology and Virus Transmission 91 6.1 Overview of Epidemiology 92 6.2 Government Agencies’ Contributions to Public Health 94 6.2.1 The Role of the Centers for Disease Control and Prevention (CDC) 94 6.2.2 The World Health Organization (WHO): Successes and Challenges 95 6.3 Epidemiologic Study Design 96 6.3.1 Outbreak Case Example 98 6.3.2 Clinical Trials 99 6.4 Virus Transmission 100 6.4.1 Modes of Transmission 101 6.5 Applications 102 6.6 Chapter Summary 104 6.7 Problems 105 References 105 Part II Practical and Technical Considerations 109 7 Engineering Principles and Fundamentals 111 Contributing Author: Vishal Bhatty 7.1 History of Engineering 112 7.2 Problem Solving: The Engineering Approach 113 7.2.1 Problem-Solving Methodology 114 7.2.2 Engineering and Scientific Sources 115 7.3 Units and Conversion Constants 115 7.3.1 The Metric System 115 7.3.2 The SI System 117 7.4 Dimensional Analysis 117 7.5 Process Variables 119 7.6 The Conservation Laws 121 7.7 Thermodynamics and Kinetics 125 7.8 Applications 126 7.9 Chapter Summary 130 7.10 Problems 130 References 131 8 Legal and Regulatory Considerations 133 8.1 The Regulatory System 134 8.1.1 Laws, Regulations, Plans and policy: The Differences 135 8.1.2 Policies and Plans 137 8.2 The Role of Individual States 138 8.3 Key Government Agencies 140 8.3.1 Environmental Protection Agency (EPA) 140 8.3.2 Centers for Disease Control and Prevention (CDC) 141 8.3.3 Food and Drug Administration (FDA) 141 8.3.4 Occupational Health and Safety Administration (OSHA) 141 8.3.5 Legal Considerations during a Public Health Crisis 142 8.4 Public Health Emergency Declarations 143 8.5 Key Environmental Acts 145 8.6 The Clean Air Act 145 8.7 Regulation of Toxic Substances 147 8.7.1 Toxic Water Pollutants: Control and Classification 150 8.7.2 Drinking Water 150 8.7.3 Surface Water Treatment Rules (SWTR) 151 8.8 Regulations Governing Infectious Diseases 153 8.8.1 Vaccination Laws 155 8.8.2 State Healthcare Worker and Patient Vaccination Laws 155 8.8.3 State-Mandated Childhood Vaccinations 155 8.9 Applications 155 8.10 Chapter Summary 159 8.11 Problems 159 References 160 9 Emergency Planning and Response 163 9.1 The Importance of Emergency Planning and Response 164 9.2 Planning for Emergencies 166 9.2.1 Preparedness Training 166 9.3 Plan Implementation 167 9.3.1 Notification of Public and Regulatory Officials 168 9.4 EP&R for Epidemics and Pandemics 169 9.4.1 Federal Public Health and Medical Emergency Preparedness 170 9.4.2 Emergency Operations Center 170 9.4.3 Disease Containment 172 9.4.4 Public Notification of Pandemic Quarantines and Lockdowns 173 9.4.5 The National Strategy for Pandemic Influenza (NSPI) 173 9.5 EP&R for Industrial Accidents 174 9.5.1 Emergency Planning and Community Right-to-Know Act (epcra) 175 9.5.2 The Planning Committee 177 9.6 EP&R for Natural Disasters 179 9.7 Current and Future Trends 181 9.8 Applications 181 9.9 Chapter Summary 184 9.10 Problems 184 References 185 10 Ethical Considerations within Virology 189 Contributing Author: Paul DiGaetano, Jr. 10.1 Core Ethics Principles 190 10.2 Important Tenets of Ethical Research 191 10.2.1 Conducting Research During a Health Crisis 192 10.2.2 Scientific Cooperation During a Health Crisis 192 10.2.3 Fair and Ethical Study Design and Implementation 193 10.3 Ethical Dilemmas in Public Health 193 10.3.1 Public Health Surveillance 193 10.3.2 Ethical Evaluation of Nonpharmaceutical Interventions 195 10.3.3 Ethical Consideration Involving Restrictions of Movement 197 10.4 Ethical Considerations Regarding Medical Interventions 199 10.4.1 Emergency Use Of Medical Interventions 200 10.5 Applications 201 10.6 Chapter Summary 202 10.7 Problems 203 References 203 11 Health and Hazard Risk Assessment 205 11.1 Introduction to Risk Assessment 207 11.2 The Health Risk Assessment Process 209 11.3 Dose–Response Assessment 211 11.4 The Hazard Risk Assessment Process 213 11.5 Hazard Risk Versus Health Risk 214 11.5.1 Health Risk Assessment (HRA) Example 215 11.5.2 Hazard Risk Assessment (HRZA) Example 215 11.6 COVID-19 Pandemic Hazard Risk 216 11.7 The Uncertainty Factor 217 11.8 Applications 218 11.9 Chapter Summary 220 11.10 Problems 220 References 221 Part III Engineering Considerations 223 12 Introduction to Mathematical Methods 225 Contributing Author: Julian Theodore 12.1 Differentiation 226 12.2 Integration 228 12.2.1 The Trapezoidal Rule 228 12.2.2 Simpson’s Rule 229 12.3 Simultaneous Linear Algebraic Equations 230 12.3.1 Gauss–Jordan Reduction 231 12.3.2 Gauss Elimination 232 12.3.3 Gauss–Seidel Approach 232 12.4 Nonlinear Algebraic Equations 233 12.5 Ordinary Differential Equations 234 12.6 Partial Differential Equations 237 12.7 Applications 237 12.8 Chapter Summary 240 12.9 Problems 240 References 241 13 Probability and Statistical Principles 243 13.1 Probability Definitions and Interpretations 244 13.2 Introduction to Probability Distributions 246 13.3 Discrete Probability Distributions 247 13.3.1 The Binomial Distribution 248 13.3.2 Multinomial Distribution 248 13.3.3 Hypergeometric Distribution 249 13.3.4 Poisson Distribution 250 13.4 Continuous Probability Distributions 250 13.4.1 Measures of Central Tendency and Scatter 251 13.4.2 The Normal Distribution 252 13.4.3 The Lognormal Distribution 256 13.4.4 The Exponential Distribution 257 13.4.5 The Weibull Distribution 258 13.5 Contemporary Statistics 259 13.5.1 Confidence Intervals for Means 260 13.5.2 Confidence Intervals for Proportions 260 13.5.3 Hypothesis Testing 261 13.5.4 Hypothesis Test for Means and Proportions 261 13.5.5 The F Distribution 262 13.5.6 Analysis of Variance (ANOVA) 262 13.5.7 Nonparametric Tests 264 13.6 Applications 264 13.7 Chapter Summary 268 13.8 Problems 268 References 269 14 Linear Regression 271 14.1 Rectangular Coordinates 272 14.2 Logarithmic Coordinates 273 14.3 Methods of Plotting Data 275 14.4 Scatter Diagrams 275 14.5 Curve Fitting 278 14.6 Method of Least Squares 280 14.7 Applications 284 14.8 Chapter Summary 287 14.9 Problems 288 References 288 15 Ventilation 289 15.1 Introduction to Industrial Ventilation Systems 290 15.2 Components of Ventilation Systems 291 15.3 Fans, Valves and Fittings, and Ductwork 293 15.3.1 Fans 293 15.3.2 Valves and Fittings 295 15.4 Selecting Ventilation Systems 296 15.5 Key Process Equations 298 15.5.1 Regarding Friction Losses 299 15.6 Ventilation Models 300 15.7 Model Limitations 302 15.8 Infection Control Implications 303 15.9 Applications 305 15.10 Chapter Summary 309 15.11 Problems 310 References 310 16 Pandemic Health Data Modeling 313 16.1 COVID-19: A Rude Awakening 315 16.2 Earlier Work 316 16.3 Planning for Pandemics 318 16.4 Generating Mathematical Models 319 16.5 Pandemic Health Data Models 324 16.6 In Review 329 16.7 Applications 331 16.8 Chapter Summary 338 16.9 Problems 338 References 339 17 Optimization Procedures 341 17.1 The History of Optimization 342 17.2 The Scope of Optimization 344 17.3 Conventional Optimization Procedures 346 17.4 Analytical Fomulation of the Optimum 347 17.5 Contemporary Optimization: Concepts in Linear Programming 350 17.6 Applied Concepts in Linear Programming 351 17.7 Applications 355 17.8 Chapter Summary 357 17.9 Problems 358 References 359 Index 361

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Book SynopsisProvides an introduction to this world of microbes. As well as looking at a selection of infectious diseases, including how they are prevented and treated, this book explores the importance of microbes in the environment, in the production and preservation of food, and their applications in biotechnology.Trade Review“The book encourages a better understanding of the microbial word with many practical implications in biotechnological phenomena that will be the foundation of the next years. Also, the book gives interesting information about the lessons from nature and presents excellent and suggestive illustrations.” (Environmental Engineering and Management Journal, 1 February 2014) “The author does not sacrifice accuracy when clearly and concisely presenting the latest developments in molecular biology, food microbiology, microbial evolution, biotechnology, etc. Summing Up: Highly recommended. Lower- and upper-division undergraduates and general readers.” (Choice, 1 August 2013)Table of ContentsPreface ix 1 The Background 1 1.1 Meet the cast 1 1.2 Food for microbes 13 1.3 Basic molecular biology 15 2 Microbes and Health 19 2.1 Microbes in the body 19 2.2 Defences against infection 26 3 Microbial Infections 33 3.1 Diseases of the past 33 3.2 Diseases of the present 45 3.3 Opportunist infections 50 3.4 ‘New’ diseases 52 3.5 Animal diseases 58 4 Prevention and Cure 63 4.1 Epidemics 63 4.2 Antibiotics 72 5 Microbes and Food – Friend and Foe 83 5.1 Food spoilage 83 5.2 Food preservation 86 5.3 Fermented foods 88 5.4 Food poisoning and food-borne diseases 91 6 Microbes and the Environment 97 6.1 Water 100 6.2 Soil 107 6.3 Plants 108 6.4 Biodegradation 112 6.5 Extreme environments 116 7 Microbial Evolution – Genes and Genomes 119 7.1 Evolution and inheritance 119 7.2 Horizontal gene transfer 122 7.3 Variation in gene expression 128 7.4 Gene cloning and sequencing 131 8 Microbial Development and Communication 141 8.1 Cell division 141 8.2 Motility 145 8.3 Biofilms 146 8.4 Quorum sensing 150 8.5 Bacterial sporulation 152 8.6 Multicellular behaviour 153 8.7 Biological clocks 156 9 Microbial Biotechnology – Practical Uses of Microbes 159 9.1 Amino acids 160 9.2 Biofuels 161 9.3 Microbes and metals 163 9.4 Oil spills 166 9.5 Sewage and water treatment 168 9.6 Antibiotics and other medical products 170 9.7 Vaccines 172 9.8 Proteins 177 10 Controversies and Speculations 181 10.1 Evolution and the origins of life 181 10.2 Is there life elsewhere in the universe? 186 10.3 Creating new life 187 10.4 Is it safe? Assessment of risk, risk versus benefit 187 10.5 Superbugs and killer viruses 192 10.6 Microbes and climate change 193 10.7 Microbes and non-infectious diseases 195 10.8 Epilogue 200 Appendix 1: Explanations 201 A1.1 Monomers and polymers 201 A1.1.1 Sugars and polysaccharides 201 A1.1.2 Amino acids and proteins 202 A1.1.3 Nucleic acids 204 A1.1.4 Fats and lipids 205 A1.2 Enzymes and catalysis 206 A1.2.1 Oxidation and reduction, respiration and photosynthesis 206 A1.2.2 Hydrolysis 208 A1.2.3 Polymerization 208 Appendix 2: Abbreviations and Terminology 211 A2.1 Abbreviations and jargon 211 A2.2 Numbers 213 A2.3 Units 214 Appendix 3: Further Reading 215 Subject Index 217 Index of Names 229

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Book SynopsisWe can't see them, but microbes are the dominant form of life on Earth. They make up half of the world's biomass. They were here billions of years before we were, and they will be here after we are gone. Without their activity, life as we know it would be impossible. Even within our own bodies, there are ten times as many bacterial cells as human cells. Understanding Microbes provides a clear, accessible introduction to this world of microbes. As well as looking at a selection of infectious diseases, including how they are prevented and treated, the book explores the importance of microbes in the environment, in the production and preservation of food, and their applications in biotechnology. This lively and engaging book provides the basics of microbiology, in a contemporary context. It will be equally useful for students across the biological, environmental and health sciences, and for the curious reader wanting to learn more about this fascinating subject.Trade Review“The book encourages a better understanding of the microbial word with many practical implications in biotechnological phenomena that will be the foundation of the next years. Also, the book gives interesting information about the lessons from nature and presents excellent and suggestive illustrations.” (Environmental Engineering and Management Journal, 1 February 2014) CHOICE 2014 Outstanding Academic Title “The author does not sacrifice accuracy when clearly and concisely presenting the latest developments in molecular biology, food microbiology, microbial evolution, biotechnology, etc. Summing Up: Highly recommended. Lower- and upper-division undergraduates and general readers.” (Choice, 1 August 2013) Table of ContentsPreface ix 1 The Background 1 1.1 Meet the cast 1 1.2 Food for microbes 13 1.3 Basic molecular biology 15 2 Microbes and Health 19 2.1 Microbes in the body 19 2.2 Defences against infection 26 3 Microbial Infections 33 3.1 Diseases of the past 33 3.2 Diseases of the present 45 3.3 Opportunist infections 50 3.4 ‘New’ diseases 52 3.5 Animal diseases 58 4 Prevention and Cure 63 4.1 Epidemics 63 4.2 Antibiotics 72 5 Microbes and Food – Friend and Foe 83 5.1 Food spoilage 83 5.2 Food preservation 86 5.3 Fermented foods 88 5.4 Food poisoning and food-borne diseases 91 6 Microbes and the Environment 97 6.1 Water 100 6.2 Soil 107 6.3 Plants 108 6.4 Biodegradation 112 6.5 Extreme environments 116 7 Microbial Evolution – Genes and Genomes 119 7.1 Evolution and inheritance 119 7.2 Horizontal gene transfer 122 7.3 Variation in gene expression 128 7.4 Gene cloning and sequencing 131 8 Microbial Development and Communication 141 8.1 Cell division 141 8.2 Motility 145 8.3 Biofilms 146 8.4 Quorum sensing 150 8.5 Bacterial sporulation 152 8.6 Multicellular behaviour 153 8.7 Biological clocks 156 9 Microbial Biotechnology – Practical Uses of Microbes 159 9.1 Amino acids 160 9.2 Biofuels 161 9.3 Microbes and metals 163 9.4 Oil spills 166 9.5 Sewage and water treatment 168 9.6 Antibiotics and other medical products 170 9.7 Vaccines 172 9.8 Proteins 177 10 Controversies and Speculations 181 10.1 Evolution and the origins of life 181 10.2 Is there life elsewhere in the universe? 186 10.3 Creating new life 187 10.4 Is it safe? Assessment of risk, risk versus benefit 187 10.5 Superbugs and killer viruses 192 10.6 Microbes and climate change 193 10.7 Microbes and non-infectious diseases 195 10.8 Epilogue 200 Appendix 1: Explanations 201 A1.1 Monomers and polymers 201 A1.1.1 Sugars and polysaccharides 201 A1.1.2 Amino acids and proteins 202 A1.1.3 Nucleic acids 204 A1.1.4 Fats and lipids 205 A1.2 Enzymes and catalysis 206 A1.2.1 Oxidation and reduction, respiration and photosynthesis 206 A1.2.2 Hydrolysis 208 A1.2.3 Polymerization 208 Appendix 2: Abbreviations and Terminology 211 A2.1 Abbreviations and jargon 211 A2.2 Numbers 213 A2.3 Units 214 Appendix 3: Further Reading 215 Subject Index 217 Index of Names 229

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Book SynopsisThe second edition of Virology is an accessible introduction designed to enable students to understand the principles of virus structure, replication and genetics. The aim of this book is to help the reader appreciate the relevance of virology in the modern world, including the fields of vaccines, anti-viral drugs and cancer.Table of ContentsPreface to Second Edition xix Preface to First Edition xxi Abbreviations Used in This Book xxiii Greek Letters Used in This Book xxvii Color Coding for Molecules xxix Chapter 1 Viruses and Their Importance 1 Chapter 2 Methods Used in Virology 9 Chapter 3 Virus Structure 27 Chapter 4 Virus Transmission 45 Chapter 5 Attachment and Entry of Viruses into Cells 55 Chapter 6 Transcription, Translation, and Transport 65 Chapter 7 Virus Genome Replication 83 Chapter 8 Assembly and Exit of Virions from Cells 93 Chapter 9 Outcomes of Infection for the Host 101 Chapter 10 Classification and Nomenclature of Viruses 115 Chapter 11 Herpesviruses (and Other dsDNA Viruses) 121 Chapter 12 Parvoviruses (and Other ssDNA Viruses) 135 Chapter 13 Reoviruses (and Other dsRNA Viruses) 145 Chapter 14 Picornaviruses (and Other Plus-Strand RNA Viruses) 155 Chapter 15 Rhabdoviruses (and Other Minus-Strand RNA Viruses) 169 Chapter 16 Influenza Virus 183 Chapter 17 Retroviruses 195 Chapter 18 Human Immunodeficiency Viruses 207 Chapter 19 Hepadnaviruses (and Other Reverse-Transcribing DNA Viruses) 223 Chapter 20 Bacterial Viruses 237 Chapter 21 Origins and Evolution of Viruses 263 Chapter 22 Emerging Viruses 277 Chapter 23 Viruses and Cancer 289 Chapter 24 Survival of Infectivity 301 Chapter 25 Virus Vaccines 307 Chapter 26 Anti-viral Drugs 315 Chapter 27 Prions 327 Virologists’ Vocabulary 335 Index 347

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Book Synopsis1st Prize, 'New Authored Books' category, Royal Society of Medicine and Society of Authors Medical Book Awards 2008 Overall, I am impressed by the up-to date information content and structure provided in Bacteriology of Humans. It is truly an ecological perspective helpful for undergraduate/graduate majors in microbiology and immunology.Trade Review“Overall, I am impressed by the up-to date information content and structure provided in Bacteriology of Humans. It is truly an ecological perspective helpful for undergraduate/graduate majors in microbiology and immunology.” (American Society for Microbiology, June 2009) “Wilson provides the reader with an up-to-date, comprehensive census of the indigenous microorganisms that inhabit the human body and in so doing contributes significantly to this rapidly advancing area of study. The narrative is clearly written; the index is excellent; there are numerous bibliographic citations. Each chapter is rich with tables, diagrams, color micrographs, and charts … .Each section serves as a valuable resource for understanding the influence of microbes on human health and disease. Highly recommended.” (Choice Reviews, December 2008) “This comprehensive, yet accessible text provides an up-to-date guide to the development, composition and distribution of these microbial communities. This is an excellent and informative reference book … it should be on the shelf of every major science and medical library. The content, organization, and presentation make this book a unique resource. The author introduces a valuable framework for understanding the important role that the indigenous human microflora plays.” (Doody's Book Reviews, October 2008)Table of ContentsPreface. Abbreviations of genera. 1. The human–microbe symbiosis. 1.1. Overview of the nature and distribution of the microbial communities inhabiting humans. 1.2. Environmental determinants that affect the distribution and composition of microbial communities. 1.3. Host characteristics that affect the indigenous microbiota. 1.4. Techniques used to characterize the microbial communities inhabiting humans. 1.5. The epithelium – site of host–microbe interactions. 1.6. Further reading. 2. The indigenous microbiota of the skin. 2.1. Anatomy and physiology of human skin. 2.2. Cutaneous antimicrobial defense systems. 2.3. Environmental determinants operating at different skin regions. 2.4. The indigenous microbiota of the skin. 2.5. Overview of the cutaneous microbiota. 2.6. Sources of data used to compile figures. 2.7. Further reading. 3. The indigenous microbiota of the eye. 3.1. Anatomy and physiology of the eye. 3.2. Antimicrobial defense systems of the eye. 3.3. Environmental determinants on the conjunctival surface. 3.4. The indigenous microbiota of the eye. 3.5. Overview of the ocular microbiota. 3.6. Sources of data used to compile figures. 3.7. Further reading. 4. The indigenous microbiota of the respiratory tract. 4.1. Anatomy and physiology of the respiratory tract. 4.2. Antimicrobial defense systems of the respiratory tract. 4.3. Environmental determinants within the respiratory tract. 4.4. Indigenous microbiota of the respiratory tract. 4.5. Overview of the respiratory microbiota 4.6. Sources of data used to compile figures 4.7. Further reading. 5. The indigenous microbiota of the urinary system of females. 5.1. Anatomy and physiology of the urinary system of females. 5.2. Antimicrobial defenses of the female urinary system. 5.3. Environmental determinants within the female urethra. 5.4. The indigenous microbiota of the female urethra. 5.5. Overview of the microbiota of the urinary tract of females. 5.6. Sources of data used to compile figures. 5.7. Further reading. 6. The indigenous microbiota of the reproductive system of females. 6.1. Anatomy and physiology of the female reproductive system. 6.2. Antimicrobial defense systems of the female reproductive system. 6.3. Environmental determinants at different regions of the reproductive system. 6.4. The indigenous microbiota of the female reproductive system. 6.5. Overview of the microbiota of the female reproductive system. 6.6. Sources of data used to compile figures. 6.7. Further reading. 7. The indigenous microbiota of the urinary and reproductive systems of males. 7.1. Anatomy and physiology. 7.2. Antimicrobial defenses of the male urinary and reproductive systems. 7.3. Environmental determinants within the male urinary and reproductive systems. 7.4. The indigenous microbiota of the male urinary and reproductive systems. 7.5. Overview of the microbiota of the male urinary and reproductive systems. 7.6. Sources of data used to compile figures. 7.7. Further reading. 8. The indigenous microbiota of the oral cavity. 8.1. Anatomy and physiology of the oral cavity. 8.2. Antimicrobial defense systems of the oral cavity. 8.3. Environmental determinants at the various sites within the oral cavity. 8.4. The indigenous microbiota of the oral cavity. 8.5. Overview of the oral microbiota. 8.6. Sources of data used to compile figures. 8.7. Further reading. 9. The indigenous microbiota of the gastrointestinal tract. 9.1. Anatomy and physiology of the gastrointestinal tract. 9.2. Antimicrobial defense systems of the gastrointestinal tract. 9.3. Environmental determinants within different regions of the gastrointestinal tract. 9.4. The indigenous microbiota of the gastrointestinal tract. 9.5. Overview of the indigenous microbiota of the gastrointestinal tract. 9.6. Sources of data used to compile figures. 9.7. Further reading. 10. The future. 10.1. Further reading. Index

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Book SynopsisI. Concepts & Methods.- 1.Concepts in Viral Disease Epidemiology & Control.- 2.Virologic Detection & Characterization.- 3.Immunologic Detection & Characterization.- 4.Surveillance & Epidemiologic Investigation.- 5.Viral Dynamics & Mathematical Models.- II. Viruses Causing Acute Syndromes.- 6.Adenoviruses.- 7.Alphaviruses:Equine Encephalitis & Others.- 8.Arenaviruses:Lassa Fever, Lymphocytic Choriomeningitis & Others.- 9.Bunyaviruses:Hantavirus & Others.- 10.Coronaviruses: Severe Acute Respiratory Syndrome & Others.- 11.Enteroviruses &Parechoviruses: Echoviruses, Coxsackieviruses, & Others.- 12.Enteroviruses:Enterovirus 71.- 13.Enteroviruses:Polio.- 14.Filoviruses: Marburg & Ebola.- 15.Flaviviruses: Dengue.- 16.Flaviviruses: Yellow Fever, Japanese B, West Nile & Others.- 17.Hepatitis A Virus.- 18.Hepatitis E Virus.- 19.Influenza Viruses.- 20.Noroviruses, Sapoviruses, & Astroviruses.- 21.Orthopoxviruses: Variola, Vaccinia, Cowpox & Monkeypox.- 22.Paramyxoviruses: Henipaviruses.- 23.Paramyxoviruses: Measles.- 24.Paramyxoviruses: Mumps.- 25.Paramyxoviruses Parainfluenza Virus.- 26.Paramyxoviruses: Respiratory Syncytial Virus & Metapneumovirus.- 27. Parvoviruses.- 28.Rhabdovirus: Rabies.- 29. Rhinoviruses: Colds.- 30. Rotaviruses.- 31. Rubella Virus.-III. Viruses Causing Acute & Chronic Syndromes &/or Malignancy.- 32. Hepatitis viruses: Hepatitis B & Hepatitis D.- 33.Hepatitis viruses: Hepatitis C.- 34. Hepatitis viruses: Hepatocellular Carcinoma.- 35. Human Herpesviruses: Cytomegalovirus.- 36.Human Herpesviruses: Herpes Simplex Types 1 & 2.- 37.Human Herpesvirus: Human Herpesvirus 6.- 38.Human Herpesviruses: Infectious Mononucleosis & Other Non-Malignant Diseases.- 39.Human Herpesviruses: Kaposi Sarcoma & Other Malignancies.- 40.Human Herpesviruses: Malignant Lymphoma.- 41.Human Herpesviruses: Nasopharyngeal Carcinoma & Other EpithelialTumors.- 42.Human Herpesviruses: Varicella & Zoster.- 43.Human Immunodeficiency Viruses Types 1 & 2.- 44.Human Papillomaviruses: Cervical Cancer & Warts.- 45.Human T Cell Leukemia Viruses Types 1 & 2.- 46.Polyomaviruses: Progressive Multifocal Leukoencephalopathy & Other Diseases.- IV Other Transmissible Agents.- 47.Prions & Transmissible Spongiform Encephalopathy.Table of ContentsI. Concepts & Methods.- 1.Concepts in Viral Disease Epidemiology & Control.- 2.Virologic Detection & Characterization.- 3.Immunologic Detection & Characterization.- 4.Surveillance & Epidemiologic Investigation.- 5.Viral Dynamics & Mathematical Models.- II. Viruses Causing Acute Syndromes.- 6.Adenoviruses.- 7.Alphaviruses:Equine Encephalitis & Others.- 8.Arenaviruses:Lassa Fever, Lymphocytic Choriomeningitis & Others.- 9.Bunyaviruses: Hantavirus & Others.- 10.Coronaviruses: Severe Acute Respiratory Syndrome & Others.- 11.Enteroviruses & Parechoviruses: Echoviruses, Coxsackieviruses, & Others.- 12.Enteroviruses:Enterovirus 71.- 13.Enteroviruses:Polio.- 14.Filoviruses: Marburg & Ebola.- 15.Flaviviruses: Dengue.- 16.Flaviviruses: Yellow Fever, Japanese B, West Nile & Others.- 17.Hepatitis A Virus.- 18.Hepatitis E Virus.- 19.Influenza Viruses.- 20.Noroviruses, Sapoviruses, & Astroviruses.- 21.Orthopoxviruses: Variola, Vaccinia, Cowpox & Monkeypox.- 22.Paramyxoviruses: Henipaviruses.- 23.Paramyxoviruses: Measles.- 24.Paramyxoviruses: Mumps.- 25.Paramyxoviruses Parainfluenza Virus.- 26.Paramyxoviruses: Respiratory Syncytial Virus & Metapneumovirus.- 27. Parvoviruses.- 28.Rhabdovirus: Rabies.- 29. Rhinoviruses: Colds.- 30. Rotaviruses.- 31. Rubella Virus.- III. Viruses Causing Acute & Chronic Syndromes &/or Malignancy.- 32. Hepatitis viruses: Hepatitis B & Hepatitis D.- 33.Hepatitis viruses: Hepatitis C.- 34. Hepatitis viruses: Hepatocellular Carcinoma.- 35. Human Herpesviruses: Cytomegalovirus.- 36.Human Herpesviruses: Herpes Simplex Types 1 & 2.- 37.Human Herpesvirus: Human Herpesvirus 6.- 38.Human Herpesviruses: Infectious Mononucleosis & Other Non-Malignant Diseases.- 39.Human Herpesviruses: Kaposi Sarcoma & Other Malignancies.- 40.Human Herpesviruses: Malignant Lymphoma.- 41.Human Herpesviruses: Nasopharyngeal Carcinoma & Other Epithelial Tumors.- 42.Human Herpesviruses: Varicella & Zoster.- 43.Human Immunodeficiency Viruses Types 1 & 2.- 44.Human Papillomaviruses: Cervical Cancer & Warts.- 45.Human T Cell Leukemia Viruses Types 1 & 2.- 46.Polyomaviruses: Progressive Multifocal Leukoencephalopathy & Other Diseases.- IV Other Transmissible Agents.- 47.Prions & Transmissible Spongiform Encephalopathy.

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Book SynopsisFor three centuries, concepts of the state have been animated by one of the most powerful metaphors in politics: the body politic, a claustrophobic and bounded image of sovereignty. Climate change, neoliberalism, mass migration, and other aspects of the late Anthropocene have increasingly revealed the limitations of this metaphor. Just as the human body is not whole and separate from other bodies—comprising microbes, bacteria, water, and radioactive isotopes—Stefanie R. Fishel argues that the body politic of the state exists in dense entanglement with other communities and forms of life. Drawing on insights from continental philosophy, science and technology studies, and international relations theory, this path-breaking book critiques the concept of the body politic on the grounds of its very materiality. Fishel both redefines and extends the metaphor of the body politic and its role in understanding an increasingly posthuman, globalized world politics. By conceiving of bodies and states as lively vessels, living harmoniously with multiplicity and the biosphere, she argues that a radical shift in metaphors can challenge a politics based on fear to open new forms of global political practice and community. Reframing the concept of the body politic to accommodate greater levels of complexity, Fishel suggests, will result in new configurations for the political and social organization necessary to build a world in which the planet’s inhabitants do not merely live but actively thrive.Trade Review"How do bodies matter in international relations? In The Microbial State, Stefanie R. Fishel offers up a lively, timely, scientifically-engaged, philosophically-rich, and persuasive answer to that question. This wonderfully readable and teachable book presents ‘politics’ as a swarm of activities immanent to a biosphere, and ‘human agency’ as a power profoundly entangled with the goings-on of our microbial messmates."—Jane Bennett, author of Vibrant Matter: A Political Ecology of Things"An important intervention that will contribute in powerful and novel ways to the ongoing debates on corporeality, materialism, and international relations. Stefanie R. Fishel's work is certain to become influential."—Mark B. Salter, editor of Making Things International 1 and Making Things International 2"Fishel’s style of is not only academic; it shares new perspectives on crossing disciplinary boundaries through IR and biology while it remains enjoyable to read. This amusing book is full of possibilities and raises even more questions when it ends."—Politics, Religion & Ideology "Fishel’s biopolitical project seeks to extend this kind of thinking about the immune system, as something much more than just a line of defence, from the body to the State as a way of challenging the exclusionary state’s presentation of outsiders as potential contaminants and threats." —Radical PhilosophyTable of ContentsContentsPreface and AcknowledgmentsIntroduction: Involutionary Politics1. Corporeal Politics2. Lively Subjects, Bodies Politic3. States in Nature, Nature in States4. Posthuman PoliticsCoda: New Metaphors for Global LivingNotesIndex

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Book SynopsisA fascinating ethnography of microbes that opens up new spaces for anthropological inquiry The trillions of microbes in and on our bodies are determined by not only biology but also our social connections. Gut Anthro tells the fascinating story of how a sociocultural anthropologist developed a collaborative “anthropology of microbes” with a human microbial ecologist to address global health crises across disciplines. It asks: what would it mean for anthropology to act with science? Based partly at a preeminent U.S. lab studying the human microbiome, the Center for Genome Sciences at Washington University, and partly at a field site in Bangladesh studying infant malnutrition, it examines how microbes travel between human guts in the “field” and in microbiome laboratories, influencing definitions of health and disease, and how the microbiome can change our views on evolution, agency, and life.As lab scientists studied the interrelationships between gut microbes and malnutrition in resource-poor countries, Amber Benezra explored ways to reconcile the scale and speed differences between the lab, the intimate biosocial practices of Bangladeshi mothers and their children, and the looming structural violence of poverty. In vital ways, Gut Anthro is about what it means to collaborate—with mothers, local field researchers in Bangladesh, massive philanthropic global health organizations, with the microbiome scientists, and, of course, with microbes. It follows microbes through various enactments in scientific research—microbes as kin, as data, and as race. Revealing how racial categories are used in microbiome research, Benezra argues that microbial differences need transdisciplinary collaboration to address racial health disparities without reifying race as a straightforward biological or social designation.Gut Anthro is a tour de force of science studies and medical anthropology as well as an intensely personal and deeply theoretical accounting of what it means to do anthropology today. Cover alt text:Black background overlaid with a pink organic path suggestive of a human digestive system. Title appears within the guts as if being processed.Trade Review"From start to finish, Gut Anthro demonstrates how relations are integral to science. With bold, page-turning prose, Amber Benezra traces microbiokinships from kitchen tables to scientific laboratories, offering a refreshingly honest analysis of how knowledge and process are one and the same. Miscarriage. Diarrhea. Career ambitions. Humanitarian hubris. Anthropological complicity. We learn from microbes—and the messy, fragile, tenacious humans that study them—how much the minute details of mundane life matter. Alternately hopeful and unsettling, this is a book that expertly does what microbes have always done: change how we see, how we collaborate, and who we are."—Emily Yates-Doerr, author of The Weight of Obesity: Hunger and Global Health in Postwar Guatemala"This is an utterly arresting ethnographic examination of a networked bioscience project that stretches from sample collection in Bangladesh to data analysis at a U.S. university. Amber Benezra offers an account—rigorous, revelatory, wrenching—of the vexed promises of acting as both participant and observer in the contact zones of today’s international biomedical research."—Stefan Helmreich, Massachusetts Institute of Technology

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Book SynopsisAssesses a promising new approach to restoring the health of our bodies and our planet Most of us are familiar with probiotics added to milk or yogurt to improve gastrointestinal health. In fact, the term refers to any intervention in which life is used to manage life—from the microscopic, like consuming fermented food to improve gut health, to macro approaches such as biological pest control and natural flood management. In this ambitious and original work, Jamie Lorimer offers a sweeping overview of diverse probiotic approaches and an insightful critique of their promise and limitations. During our current epoch—the Anthropocene—human activity has been the dominant influence on climate and the environment, leading to the loss of ecological abundance, diversity, and functionality. Lorimer describes cases in which scientists and managers are working with biological processes to improve human, environmental, and even planetary health, pursuing strategies that stand in contrast to the “antibiotic approach”: Big Pharma, extreme hygiene, and industrial agriculture. The Probiotic Planet focuses on two forms of “rewilding” occurring on vastly different scales. The first is the use of keystone species like wolves and beavers as part of landscape restoration. The second is the introduction of hookworms into human hosts to treat autoimmune disorders. In both cases, the goal is to improve environmental health, whether the environment being managed is planetary or human. Lorimer argues that, all too often, such interventions are viewed in isolation, and he calls for a rethinking of artificial barriers between science and policy. He also describes the stark and unequal geographies of the use of probiotic approaches and examines why these patterns exist. The author’s preface provides a thoughtful discussion of the COVID-19 pandemic as it relates to the probiotic approach. Informed by deep engagement with microbiology, immunology, ecology, and conservation biology as well as food, agriculture, and waste management, The Probiotic Planet offers nothing less than a new paradigm for collaboration between the policy realm and the natural sciences. Trade Review"This brilliant book delivers an incisive reading of probiotic cultural practices today—taking in everything from home fermentation to permaculture to rewilding. Jamie Lorimer expertly shows us that social and scientific projects that aim at re-calibrating microbial, bodily, and ecological worlds are experiments in the politics of symbiosis. In our days of viral peril, The Probiotic Planet is a vital reminder of the multiple futures biology may yet prepare."—Stefan Helmreich, author of Sounding the Limits of Life: Essays in the Anthropology of Biology and Beyond"Moving between human intestines and forests patches, The Probiotic Planet maps a diverse and emerging terrain of ecological experimentation, both formal and vernacular. A transdisciplinary analysis that brings detailed attention to scientific practices into dialogue with critical social theory, this book is also a bold and important experiment in its own right."—Heather Anne Swanson, director, Aarhus University Centre for Environmental Humanities "Lorimer unravels the multiplicities of present-day scientific designs for the future."—Los Angeles Review of Books "This book bridges the gap between two widely separated topics: healing the planet by rewilding, and internal sanitation of the body by natural allies."—Anthropos "The book is well referenced... and the text is supported by appropriate and readable tables and charts."—CHOICE Table of ContentsContentsIntroduction: Life in the Anthropocene1. The Probiotic Turn: Rewilding and Biome Restoration2. Thinking like Gaia: The Science of the Probiotic Turn3. Symbiopolitics: Governing through Keystone Species4. Wild Experiments: The Controlled Decontrolling of Ecological Controls5. Geographies of Dysbiosis: The Patchiness of the Probiotic Turn6. Future-Pasts: The Temporalities of the Probiotic Turn7. Probiotic Value: Putting Keystone Species to WorkConclusions: A Spectrum of ProbioticsAcknowledgmentsGlossary NotesBibliographyIndex

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Book SynopsisOral-based diagnostics have the potential to detect systemic disease and evidence of exposure to various harmful substances, as well as provide biomarkers of health and disease status. Integration of novel approaches to oral-based diagnostics is expanding to include genomics, proteomics, bioinformatics, and nanotechnology. Improved technologies for diagnostics are resulting in more "user-friendly" methods. Efforts to translate bench assays to commercial products in the area of oral diagnostics have increased recently, as witnessed by the appearance of several new oral-based diagnostic products in the marketplace. Collaborative academic, government, and industry relationships in this arena are also forming, all of which will undoubtedly serve to rapidly advance the field. This volume brings together contributions from leaders in the areas of toxicology, pathology, oral biology, dental research, and clinical medicine. NOTE: Annals volumes are available for sale as individual books or as a journal. For information on institutional journal subscriptions, please visit www.blackwellpublishing.com/nyas. ACADEMY MEMBERS: Please contact the New York Academy of Sciences directly to place your order (www.nyas.org). Members of the New York Academy of Science receive full-text access to the Annals online and discounts on print volumes. Please visit http://www.nyas.org/MemberCenter/Join.aspx for more information about becoming a memberTable of ContentsDedication to Irwin Mandel: Daniel Malamud. Introduction: Daniel Malamud and R. Sam Niedbala. Part I: Biochemistry/Physiology of Saliva: Implications for Diagnostics:. 1. Implications for Diagnostics in the Biochemistry and Physiology of Saliva: Arie V. Nieuw Amerongen, Antoon J. M. Ligtenberg, and Enno C. I. Veerman. 2. Point-of-Care Diagnostics Enter the Mouth: Lawrence A. Tabak. 3. Autoimmune Diseases and Sjögren’s Syndrome: An Autoimmune Exocrinopathy: Philip C. Fox. 4. Salivary Proteome and Its Genetic Polymorphisms: Frank G. Oppenheim, Erdjan Salih, Walter L. Siqueira, Weimin Zhang, and Eva J. Helmerhorst. Part II: Drug and Small Molecule Detection in Saliva:. 5. Interpretation of Oral Fluid Tests for Drugs of Abuse: Edward J. Cone and Marilyn A. Huestis. 6. Methamphetamine Disposition in Oral Fluid, Plasma, and Urine: Marilyn A. Huestis and Edward J. Cone. 7. Salivary α-Amylase in Biobehavioral Research: Recent Developments and Applications: Douglas A. Granger, Katie T. Kivlighan, Mona El-Sheikh, Elena Gordis, and Laura R. Stroud. 8. The Use of Oral Fluid for Therapeutic Drug Management: Clinical and Forensic Toxicology: Loralie J. Langman. Part III: Meeting Unmet Needs in Diagnostics:. 9. Visualization and Other Emerging Technologies as Change Makers for Oral Cancer Prevention: Miriam P. Rosin, Catherine F. Poh, Martial Guillard, P. Michele Williams, Lewei Zhang, and Calum Macaulay. 10. Genomic Targets in Saliva: Bernhard G. Zimmermann, Noh Jin Park, and David T. Wong. 11. Saliva and the Clinical Pathology Laboratory: Michael A. Pesce and Steven L. Spitalnik. Part IV: Oral Samples/Oral Diseases:. 12. Oral Diseases: From Detection to Diagnostics: Antoon J. M. Ligtenberg, Johannes J. De Soet, Enno C. I. Veerman, and Arie V. Nieuw Amerongen. 13. A Novel Caries Risk Test: Paul C. Denny, Patricia A. Denny, Jona Takashima, Joyce Galligan, and Mahvash Navazesh. 14. Analysis of Gingival Crevicular Fluid as Applied to the Diagnosis of Oral and Systemic Diseases: Ira B. Lamster and Joseph K. Ahlo. 15. Oral Fluid–Based Biomarkers of Alveolar Bone Loss in Periodontitis: Janet S. Kinney, Christoph A. Ramseier, and William V. Giannobile. 16. Human Breath Odors and Their Use in Diagnosis: Chris L. Whittle, Steven Fakharzadeh, Jason Eades, and George Preti. Part V: Molecular and Protein Markers of Disease:. 17. Molecular and Protein Markers of Disease: Michael Glick. 18. Subclinical Cardiovascular Disease Markers Applicable to Studies of Oral Health: Multiethnic Study of Atherosclerosis: David R. Jacobs, Jr., and Richard S. Crow. 19. Do Salivary Antibodies Reliably Reflect Both Mucosal and Systemic Immunity?: Per Brandtzaeg. 20. Oxytocin: Behavioral Associations and Potential as a Salivary Biomarker: C. Sue Carter, Hossein Pournajafi-Nazarloo, Kristin M. Kramer, Toni E. Ziegler, Rosemary White-Traut, Deborah Bello, and Dorie Schwertz. 21. Human Saliva Proteome Analysis: Shen Hu, Joseph A. Loo, and David T. Wong. Part VI: Horizons in Oral Diagnostics:. 22. Genomics and Proteomics: The Potential Role of Oral Diagnostics: Hans J. Tanke. 23. SPR Imaging-Based Salivary Diagnostics System for the Detection of Small Molecule Analytes: Elain Fu, Timothy Chinowsky, Kjell Nelson, Kyle Johnston, Thayne Edwards, Kristen Helton, Michael Grow, John W. Miller, and Paul Yager. 24. Saliva-Based Diagnostics Using 16S rRNA Microarrays and Microfluidics: E. Michelle Starke, James C. Smoot, Jer-Horng Wu, Wen-Tso Liu, Darrell Chandler, and David A. Stahl. 25. Integrated Microfluidic Platform for Oral Diagnostics: Amy E. Herr, Anson V. Hatch, William V. Giannobile, Daniel J. Throckmorton, Huu M. Tran, James S. Brennan, and Anup K. Singh. 26. Development of a Microfluidic Device for Detection of Pathogens in Oral Samples Using Upconverting Phosphor Technology (UPT): William R. Abrams, Cheryl A. Barber, Kurt McCann, Gary Tong, Zongyuan Y. Chen, Michael G. Mauk, Jing Wang, Alex Volkov, Pete Bourdelle, Paul L. A. M. Corstjens, Michel Zuiderwijk, Keith Kardos, Shang Li, Hans J. Tanke, R. Sam Niedbala, Daniel Malamud, and Haim Bau. 27. Microsensor Arrays for Saliva Diagnostics: David R. Walt, Timothy M. Blicharz, Ryan B. Hayman, David M. Rissin, Michaela Bowden, Walter L. Siqueira, Eva J. Helmerhorst, Nerline Grand-Pierre, Frank G. Oppenheim, Jasvinder S. Bhatia, Frederic F. Little, and Jerome S. Brody. 28. Oral Fluid Nanosensor Test (OFNASET) with Advanced Electrochemical-Based Molecular Analysis Platform: Vincent Gau and David Wong. 29. Lab-on-a-Chip Methods for Point-of-Care Measurements of Salivary Biomarkers of Periodontitis: Nicolaos Christodoulides, Pierre N. Floriano, Craig S. Miller, Jeffrey L. Ebersole, Sanghamitra Mohanty, Priya Dharshan, Michael Griffin, Alexis Lennart, Karri L. Michael Ballard, Charles P. King, Jr., M. Chris Langub, Richard J. Kryscio, Mark V. Thomas, and John T. McDevitt. Part VII: Short Papers:. 30. A Microfluidic System for Saliva-Based Detection of Infectious Diseases: Zongyuan Chen, Michael G. Mauk, Jing Wang, William R. Abrams, Paul L. A. M. Corstjens, R. Samuel Niedbala, Daniel Malamud, and Haim H. Bau. 31. Rapid Assay Format for Multiplex Detection of Humoral Immune Responses to Infectious Disease Pathogens (HIV, HCV, and TB): Paul L. A. M. Corstjens, Zongyuang Chen, Michel Zuiderwijk, Haim H. Bau, William R. Abrams, Daniel Malamud, R. Sam Niedbala, and Hans J. Tanke. 32. Patterns of Salivary Estradiol and Progesterone across the Menstrual Cycle: Beatrice K. Gandara, Linda Leresche, and Lloyd Mancl. 33. Layered Peptide Arrays: A Diverse Technique for Antibody Screening of Clinical Samples: Gallya Gannot, Michael A. Tangrea, Rodrigo F. Chuaqui, John W. Gillespie, and Michael R. Emmert-Buck. 34. Whole Saliva Proteolysis: Wealth of Information for Diagnostic Exploitation: Eva J. Helmerhorst. 35. Saliva-Based HIV Testing among Secondary School Students in Tanzania using the OraQuick® Rapid HIV1/2 Antibody Assay: Carol Holm-Hansen, Balthazar Nyombi, and Mramba Nyindo. 36. Lab-on-a-Chip Technologies for Oral-Based Cancer Screening and Diagnostics: Capabilities, Issues, and Prospects: Michael G. Mauk, Barry L. Ziober, Zongyuan Chen, Jason A. Thompson, and Haim H. Bau. 37. Evaluation of UPlink–RSV: Prototype Rapid Antigen Test for Detection of Respiratory Syncytial Virus Infection: Vijaya K. Mokkapati, R. Sam Niedbala, Keith Kardos, Ronelito J. Perez, Ming Guo, Hans J. Tanke, and Paul L. A. M. Corstjens. 38. Immunoassay-Based Diagnostic Point-of-Care Technology for Oral Specimen: Sarvan Munjal, Peter Miethe, Lutz Netuschil, Friedhelm Struck, Kurt Maier, and Claus Bauermeister. 39. Evaluation of Immunoassay-Based MMP-8 Detection in Gingival Crevicular Fluid on a Point-of-Care Platform: S. K. Munjal, N. Prescher, F. Struck, T. Sorsa, K. Maier, and L. Netuschil. 40. Rapid Quantitative Chairside Test for Active MMP-8 in Gingival Crevicular Fluid: First Clinical Data: N. Prescher, K. Maier, S. K. Munjal, T. Sorsa, C.-D. Bauermeister, F. Struck, and L. Netuschil. 41. Salivary Biomarkers Associated with Alveolar Bone Loss: F. A. Scannapieco, Pby Ng, K. Hovey, E. Hausmann, A. Hutson, and J. Wactawski-Wende. 42. Salivary Protein/Peptide Profiling with SELDI-TOF-MS: Raymond Schipper, Arnoud Loof, Jolan De Groot, Lucien Harthoorn, Waander Van Heerde, and Eric Dransfield. 43. Acquired Enamel Pellicle and Its Potential Role in Oral Diagnostics: W. L. Siqueira, E. J. Helmerhorst, W. Zhang, E. Salih, and F. G. Oppenheim. 44. Gender-Specific Differences in Salivary Biomarker Responses to Acute Psychological Stress: Noriyasu Takai, Masaki Yamaguchi, Toshiaki Aragaki, Kenji Eto, Kenji Uchihashi, and Yasuo Nishikawa. Index of Contributors

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Book SynopsisAspergillosis, the leading fungal cause of mortality in immunocompromised patients, presents a serious worldwide challenge—particularly in the face of increasing antifungal resistance. Bringing together the world’s leaders in the Aspergillus and aspergillosis fields to promote cross-disciplinary collaboration among clinicians, industry, and scientific experts, the “Advances Against Aspergillosis” conference was held January 26–28, 2012 in Istanbul, Turkey. This first of two Annals volumes contains short reviews encapsulating recent clinical findings on aspergillosis. Among the topics included are the application of diagnostic markers to invasive aspergillosis in children, risk stratification for invasive aspergillosis in immunocompromised patients, use of biological agents for the treatment of fungal asthma and allergic bronchopulmonary aspergillosis, immune regulation in idiopathic bronchiectasis, and management of chronic pulmonary aspergillosis. NOTE: Annals volumes are available for sale as individual books or as a journal. For information on institutional journal subscriptions, please visit: http://ordering.onlinelibrary.wiley.com/subs.asp?ref=1749-6632&doi=10.111/(ISSN)1749-6632. ACADEMY MEMBERS: Please contact the New York Academy of Sciences directly to place your order (www.nyas.org). Members of the New York Academy of Science receive full-text access to Annals online and discounts on print volumes. Please visit http://www.nyas.org/MemberCenter/Join.aspx for more information on becoming a member.Table of ContentsPreface for Advances Against Aspergillosis Karl V. demons David S. Perlin Malcolm Richardson vii Aspergillosis in the Clinic Application of diagnostic markers to invasive aspergillosis in children Emmanuel Roilides Zoi-Dorothea Pana 1 Azole resistance in Aspergillus: global status in Europe and Asia Sevtap Arikan-Akdagli 9 The impact of azole resistance on aspergillosis guidelines Sarah P. Georgiadou Dimitrios P. Kontoyiannis 15 Risk stratification for invasive aspergillosis in immunocompromised patients Raoul Herbrecht Pierre Bories Jean-Charles Moulin Marie-Pierre Ledoux Valérie Letscher-Bru 23 Invasive aspergillosis in the intensive care unit George Dimopoulos Frantezeska Frantzeskaki Garyfallia Poulakou Apostolos Armaganidis 31 Management of chronic pulmonary aspergillosis Koichi Izumikawa Masato Tashiro Shigeru Kohno 40 The use of biological agents for the treatment of fungal asthma and allergic bronchopulmonary aspergillosis Richard B. Moss 49 Multifocal pulmonary aspergillomas: case series and review Matthew Pendleton David W. Denning 58 Immune regulation in idiopathic bronchiectasis Rosemary J. Boyton Daniel M. Altmann 68 Aspergillus bronchitis without significant immunocompromise Ales Chrdle Sahlawati Mustakim Rowland J. Bright-Thomas Caroline G. Baxter Timothy Felton David W. Denning 73

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Book SynopsisFrank Bowden, a specialist in the field of infectious disease and sexual health, looks at one bug at a time, weaving around them the stories of his patients and their families, the doctors and the difficulties they face and the horrors and successes of hospitals and health care programs. Through Bowden's own work in the field, we encounter Swine Flu, Golden Staph, SARS, Hepatitis, and HIV, and learn crucial lessons about public health and the human experience of disease.

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Book SynopsisThis book aims to give detailed information on various instruments, techniques and experiment protocols of microbiology and soil biology. The beauty of this book as it comprises chapters for the beginner’s viz. basic microbiological techniques and media preparation for biologists as well as the incorporation of advanced techniques for post graduate and research scholars. This laboratory manual gives a comprehensive idea about the various instruments, their working, troubleshooting and their applications based on student’s feedback, teacher’s input and authors own experiences of 14 years of teaching and research.

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Book SynopsisThousands of different microbial species colonize the human body, and are essential for our survival. This book presents a review of the current understanding of human microbiomes, the functions that they bring to the host, how we can model them, their role in health and disease and the methods used to explore them. Current research into areas such as the long-term effect of antibiotics makes this a subject of considerable interest. This title is essential reading for researchers and students of microbiology.Table of Contents1: The Stomach and Small and Large Intestinal Microbiomes 2: The Oral Microbiome 3: The Human Urogenital Microbiome 4: The Lung Microbiome 5: The Human Skin Microbiome 6: Function of the Human Gut Microbiota 7: Models of the Human Microbiota and Microbiome In Vitro 8: In Vivo and Animal Models of the Human Gut Microbiome 9: The Gut Microbiota in Health and Disease 10: Next-generation Sequencing Methods to Investigate the Human Microbiome 11: Metabonomics for Understanding Gut Microbiome and Host Metabolic Interplay

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Book SynopsisMycobacteria are bacterial pathogens which cause diseases in humans and non-human animals. This monograph primarily covers the most important and widely researched groups of mycobacteria: members of the Mycobacterium tuberculosis complex (MTC) and Mycobacterium leprae, across a wide range of host species. M. tuberculosis and M. bovis are particularly relevant with the increasing drug resistance and co-infection with HIV associated with M. tuberculosis and the possible cross-infection of badgers and cattle associated with M. bovis. This book provides a reference for researchers working in different fields, creating a work which draws together information on different pathogens, and by considering the diseases in a zoonotic context, provides a One Health approach to these important groups of diseases.Table of ContentsIntroduction: The Many Hosts of Mycobacteria: An Interdisciplinary Approach to Understanding Mycobacterial Diseases Part I: Tuberculosis in Humans 1: Introduction and Epidemiology of Mycobacterium tuberculosis Complex in Humans 2: Comparative Mycobacteriology of the Mycobacterium tuberculosis Complex 3: Immunopathogenesis of Tuberculosis in Humans 4: Current Methods for Diagnosis of Human Tuberculosis and Considerations for Global Surveillance 5: Development of Next-generation TB Vaccines: Comparative Approaches in Humans and Animals 6: The Continuing Co-evolution of Mycobacterium tuberculosis and Homo sapiens Part II: Tuberculosis in Domesticated and Companion Animal Species 7: The Global Distribution of Mycobacterium bovis 8: Immunopathogenesis of Mycobacterium bovis Infection of Cattle 9: Diagnosis of Mycobacterium bovis Infection in Cattle 10: Vaccination of Cattle Against Tuberculosis 11: Mycobacterium bovis/M. caprae Infection in Goats and Sheep: Introduction, Epidemiology and Control Measures 12: Mycobacterial Infections in Camelids 13: Tuberculosis in Companion Animal Species Part III: Mycobacterial Infections in Zoo Species 14: Mycobacterial Infections in Elephants 15: Mycobacterial Infections in Other Zoo Animals Part IV: Tuberculosis in Wildlife 16: Tuberculosis in Badgers (Meles meles) 17: Tuberculosis in Pigs and Wild Boar 18: Australian Brushtail Possum: A Highly Susceptible Host for Mycobacterium bovis 19: Tuberculosis in Wild and Captive Deer 20: Tuberculosis in South African Wildlife: Lions, African Buffalo and Other Species 21: Novel Mycobacterium tuberculosis Complex spp. in Group-living African Mammals Part V: In Vivo Laboratory Models of Tuberculosis 22: Rabbit Model of Mycobacterial Diseases 23: Laboratory Models of Tuberculosis: Guinea Pigs 24: Of Mice and Mycobacteria: Lessons from a Manipulatable Model 25: Non-human Primate Laboratory Models of Tuberculosis Part VI: Other Mycobacterial Diseases 26: Mycobacterium leprae in Humans 27: Animal Models for Leprosy Research 28: Mycobacterium avium subsp. paratuberculosis Infection, Immunology and Pathology of Livestock 29: Nontuberculous Mycobacterial Infections

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