Biology, life sciences Books

Book SynopsisIt is easy to understand how cells are produced from preexisting cells. And it is possible to imagine how space dust condensed to form inanimate planets. But what stumps most people is how inanimate matter suddenly formed the first living cell. This problem has vexed scientists and philosophers over the millennia, but recent research has cracked open this black box that is the origin of life. After formally defining evolution, this book presents the modern classic experiments that show how abiotic molecules can be formed from inorganic starting materials. Once biologically important molecules such as lipids and RNA were formed, they could self-assemble into complex shapes that exhibit life-like traits such as growth, reproduction, competition and energy storage. Biologists have produced all these behaviors in non-living vesicles to the point it becomes difficult to distinguish when to know if an object is living or not. In addition, this book addresses the important question of how religion and science can coexist without one threatening the other.

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Book SynopsisOne of the overarching themes in nature is that form meets function, meaning that the shape of an object determines how well the object can perform its function. This book begins with some basics about specificity of shapes and the four increasing levels of protein structure. Most of this book examines how epinephrine (adrenaline) can cause the liver to release glucose when a person experiences a fight or flight response. Whenever someone gets scared, all of their cells are bathed in epinephrine. A subset of those cells will respond directly to this hormone, and the liver cells prepare other cells for the extra energy they might need to survive. This book presents some of the data that revealed how the information of fear is carried inside liver cells. This book will also consider how and why some cell membranes are wavy. In short, this book looks at the structure/function relationship at the molecular level.

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Book SynopsisPerhaps the most important chemical reactions on the planet take place inside a plant's chloroplasts. In this tiny green organelle, plants have the capacity to capture the energy in light and use that energy to convert CO2 gas into building blocks used to produce all four categories of biological molecules—lipids, carbohydrates, proteins and nucleic acids. Animals could not survive if plants did not exist. Not only do they provide us with oxygen to breathe, they also generate the starting materials for everything we eat. Rather than focusing on names and trivial details, this book shows how plants harvest energy in a way that self-regulates. Plants shift how they process light energy to maximize their productivity and minimize their exposure to dehydration. All of this regulation is carried out inside every plant on earth. In addition to plants, there are microbial primary producers that can harvest energy from a range of environmental sources so that no place on earth is devoid of life.

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Book SynopsisThis book examines three ways plants respond to their changing environment. The first example can be found in all plants. Despite the extreme changes in weather, plants have to stay where they are and respond to whatever nature produces. Plants have the capacity to respond quickly and yet they can evolve in a single generation. The second example addresses how an individual leaf has to respond rapidly and repeatedly to maintain the proper balance of carbon dioxide (CO2) and water so that it can photosynthesize but not dry out. This delicate balance is governed by a pair of cells that regulate the size of openings on leaves. The final chapter examines a unique example of a leaf that can move fast enough to trap insects and digest them. This book presents data that led to our understanding of how plants function on different time scales.

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Book SynopsisWhy do some children look more like one parent than another? How can two parents with dark hair have a child with red hair? How can two dark-skinned parents have a baby that has light skin? Everyone has wondered these questions, but in order to understand such unexpected outcomes, an understanding of what Gregor Mendel discovered—the rules of genetics—is necessary. This book reproduces Mendel's original data that Mendel used to discover how traits are passed from one generation to the next. In addition to the rules governing DNA inheritance, this book also examines how cells reproduce—all cells. Do bacterial cells reproduce the same way animal cells do? And when a person has a cut that needs to heal, do those cells reproduce the same way that sperm and egg cells are produced? How do all these cells keep track of how much DNA is needed in order to function properly? Data will be examined that explains how reproduction works for every cell on the planet.

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Book SynopsisEveryone who has taken any biology class knows that DNA is the heritable material. However, very few people know the evidence that led to this conclusion. Science is a discipline based on evidence not acceptance based on faith in a teacher or other authority. This book presents the historical and scientific context to understand how we know DNA is the heritable material. Furthermore, how the structure of DNA reveals its function will be discussed. The famous double helix shape foretold how it would be replicated. Two biochemists conducted the research to confirm that each of the two strands serve as template for new DNA synthesis. Despite its central role in cell function, the order of bases in DNA is not the full story. This book also introduces the topic of epigenetics by presenting the first animal experiments that showed epigenetic changes can lead to a change in phenotype even though the DNA is not mutated.

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Book SynopsisMany people were taught that DNA is the ""blueprint of the cell,"" but what does that really mean? If taken literally, it would reveal a static image of what the cell looks like, but that would be incorrect. DNA codes the necessary information to produce a living being but the DNA itself is insufficient to bring a cell to life. DNA must be transcribed into segments of RNA and the RNA must generate proteins from unassembled amino acids. The conversion of DNA information into functional proteins is often referred to as central dogma, which reflects its critical role in life. However, every cell in a body contains the same genes but only a subset of genes is needed to be activated in any given cell for a cell to function properly. This book will explore many of the classic experiments that led to our current understanding central dogma. Furthermore, real data are used to discover that central dogma information is not linear and that cells must cut and paste together segments of RNA in order to build the functional proteins of cells.

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Book SynopsisThis textbook introduces readers in an accessible and engaging way to the nuts and bolts of protein expression and engineering. Various case studies illustrate each step from the early sequence searches in online databases over plasmid design and molecular cloning techniques to protein purification and characterization. Furthermore, readers are provided with practical tips to successfully pursue a career as a protein engineer. With protein engineering being a fundamental technique in almost all molecular biology labs, the book targets advanced undergraduates and graduate students working in molecular biology, biotechnology and related scientific fields. Table of ContentsPart I: Chapter 1: A brief history of protein engineeringChapter 2: From DNA to functional protein – A refresherChapter 3: Basic laboratory and computational techniquesPart II:Chapter 4: Protein engineering strategiesChapter 5: Computational tools for protein engineeringChapter 6: Gene isolationChapter 7: Rational design Chapter 8: Directed evolutionChapter 9: Protein modificationPart III:Chapter 10: Career prospect of a protein engineerChapter 11: Conversations with protein engineers

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Book SynopsisThis comprehensive guide to gene cloning provides beginning and advanced readers with the background, standard techniques, practical applications, and ethical and safety considerations in the field. A one-stop reference for students, researchers in academia and industry, and anyone interested in a thorough but accessible overview.Table of Contents1. The recombinant DNA technology era 1.1 Important timelines 1.2 Scientist and their contribution to recombinant DNA technology 1.3 Recent advances2. Vectors: Guide to gene delivery vehicles 2.1 Plasmid, Cosmid, Phasmid, Bacteriophage 2.2 YAC and BAC 2.3 Shuttle vector 2.4 Expression vector3. Gene isolation methods: Beginners guide 3.1 Isolation of genomic and PCR amplification 3.2 Gene synthesis 3.3 cDNA library 3.4 Genomic library4. Gene cloning strategies: overview 4.1 Restriction and ligation-based cloning 4.2 Ligation-independent cloning 4.3 PCR-based cloning4.4 Recombination-based cloning 4.5 Mating-Assisted Genetically Integrated Cloning5. DNA cutters and connecters in recombinant DNA technology 5.1 RM system 5.2 Restriction enzymes 5.3 Sequence specific, G+C content, Methylation 5.4 Elimination of RM in host6 Fundamental techniques of recombinant DNA transfer 6.1 Chemical transformation in Bacteria, Fungi and animal cell 6.2 Physical transformation in Bacteria, Fungi and animal cell 7. Screening of recombinants 7.1 Colony hybridisation 7.2 Antibiotic based screening 7.3 Colony PCR 7.4 Plasmid Miniprep 7.5 Southern blotting 7.6 DNA Sequencing 7.7 Protein expression SDS PAGE, western blotting8. Recent Trends and Advances 8.1 Basics of gene editing 8.2 Zinc finger nucleases 8.3 Transcription activators like effectors 8.4 RNA interference 8.4 CRISPR Cas system 8.5 Cre-lox mechanism9. Application of Recombinant DNA Technology 9.1 Health, Medical and Diagnostics, Pharmaceuticals, Agriculture, , Industry 9.2 Health: Gene therapy, Diagnostics, 9.3 Pharmaceuticals: Vaccines, Insulin, Antibiotics, antibodies 9.4 Environment: Bioremediation, Bio indicators 9.5 Industry: Enzyme 9.6 Agriculture: Yield improvement, tolerant plants, transgenic for secondary metabolites 10. Ethical and safety concerns of recombinant DNA technology 10.1 Questionable knowledge dissemination 10.2 Uncertainties about misuse of technology 10.3 Potential risk of engineered organisms

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Book SynopsisPart I: Whetting Your Appetite.- Chapter 1: Introduction.- Chapter 2: Content of this Book.- Part II: Learning and Setting Up Our Playground.- Chapter 3: The World of Linux.- Part III: Working with Linux.- Chapter 4: The First Touch.- Chapter 5:  Working with Files.- Chapter 6: Remote Connections.- Chapter 7: Playing with Text and Data Files.- Chapter 8: Get More Out of the Shell.- Chapter 9: Installing BLAST+ and ClustalW.- Part IV: Processing and Programming.- Chapter 10: Shell Programming.- Chapter 11: Regular Expressions.- Chapter 12: Sed.- Chapter 13: AWK.- Chapter 14: Other Programming Languages.- Part V: Advanced Data Analysis.- Chapter 15: GitHub Repositories and Jupyter Notebooks.- Chapter 16: Relational Databases with MariaDB.- Chapter 17: The Statistics Suite R.- Part VI: Worked Examples.- Chapter 18: BLASTing Forensic PCR Primers.- Chapter 19: In Search of Differences in Proteomes.- Chapter 20: Virtual Sequencing of mtDNA.- Chapter 21: DNA Sequence Analysis of MinION Nanopore Reads.- Chapter 22: Querying for Potential Redox-Regulated Enzymes.- Chapter 23: Exploring of Early SARS-CoV2 Mutations. Chapter 24: Genome-Wide Association Studies (GWAS).

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Book SynopsisChapter 1 - History of the Thymus.- Chapter 2 -Thymus Ontogeny and Development.- Chapter 3 -The ins and outs of thymic epithelial.- Chapter 4 - From T-Lineage Specification to Intrathymic Maturation.- Chapter 5 - Intrathymic cell migration.- Chapter 6 -Thymic crosstalk.- Chapter 7 - The Autoimmune Regulator (AIRE) Gene.- Chapter 8 - Aire mutations and Autoimmune Diseases.- Chapter 9 -The thymus as a mirror.- Chapter 10 -The CRISPR-Cas9 system.- Chapter 11 -Age-related thymic involution.- Chapter 12 - T-cell Recovery After Autologous.

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Book Synopsis Advanced computational methods in protein simulations.- Enhanced sampling and free energy calculations in protein simulations.- Design of protein structure and function.- Artificial intelligence in protein structure prediction.- Optimized methods for site identification in proteins.- Machine Learning tools for Peptide Protein Interaction Prediction.- Simulating Protein Ligand Binding with Neural Network Potentials.- Prediction of protein complex structures using protein protein interaction data.- Advances in X ray crystallography and cryo EM structural studies ofprotein structure and function.- Fluorescence microscopy methods for studying dynamics of fluorescent proteins in vivo.- Nanoscale fluorescence imaging of proteins.- Multiplexed protein imaging methods.- Determining protein structure by combining protein chemistry with mass spectrometry.- NMR spectroscopy techniques as a tool for characterizing the interactions in protein-protein complexes.- Electrophysiology tools in the study of ion channel proteins.

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Book SynopsisPersonalized 3D Myocardial Infarct Geometry Reconstruction from Cine MRI with Explicit Cardiac Motion Modeling.- Microvascular Retinal Digital Twins from Non-Invasive Clinical Images.- Validating Digital Twins with Tactile-Visual Liver Phantoms for Robot-Assisted Surgical Workflows.- A Real-Time Digital Twin for Type 1 Diabetes using Simulation-Based Inference.- Retrospective Evaluation of a Patient-Specific Liver Digital Twin to Predict Thermal Ablation Outcomes in HCC.- Acoustic Simulation with Deep Learning for Low-intensity Transcranial Focused Ultrasound Digital Twins.- Towards Digital Twin of RF Ablation: Real-Time Prediction of Time-Dependent Thermal Effects Using Transformer.- Finite-Element Electrophysiological Modeling of Human Uterine Smooth Muscle Using a Reduced Tong Model.- TF-TransUNet1D: Time-Frequency Guided Transformer U-Net for Robust ECG De-noising in Digital Twin.- DeformMLP: Effective Deformation Prediction for Breast Cancer Using Graph To-pology-Assisted MLPs.- Rule-based Key-Point Extraction for MR-Guided Biomechanical Digital Twins of the Spine.- Towards Robust Algorithms for Surgical Phase Recognition via Digital Twin Repre-sentation.- Personalized 4D Whole Heart Geometry Reconstruction from Cine MRI for Cardiac Digital Twins.- Secure Medical Digital Twins: A Use-Case Driven Approach.- Explainable Prediction of Recurrence After Prostate Cancer Radiotherapy Using in Silico Digital Twin Model and Machine Learning.

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Book SynopsisWhat are active materials? This book aims to introduce and redefine conceptions of matter by considering materials as entities that ‘sense’ and respond to their environment. By examining the modeling of, the experiments on, and the construction of these materials, and by developing a theory of their structure, their collective activity, and their functionality, this volume identifies and develops a novel scientific approach to active materials. Moreover, essays on the history and philosophy of metallurgy, chemistry, biology, and materials science provide these various approaches to active materials with a historical and cultural context. The interviews with experts from the natural sciences included in this volume develop new understandings of ‘active matter’ and active materials in relation to a range of research objects and from the perspective of different scientific disciplines, including biology, physics, chemistry, and materials science. These insights are complemented by contributions on the activity of matter and materials from the humanities and the design field. Discusses the mechanisms of active materials and their various conceptualizations in materials science. Redefines conceptions of active materials through interviews with experts from the natural sciences. Contextualizes, historizes, and reflects on different notions of matter/materials and activity through contributions from the humanities. A highly interdisciplinary approach to a cutting-edge research topic, with contributions from both the sciences and the humanities.

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