Proteomics is evolving as a multi-faceted tool for addressing various biochemical and biomedical queries in the field of scientific research. This involves various stages, ranging from sample preparation to data analysis and biological interpretation. Sample preparation involves isolating proteins from the sample source, purifying and digesting them to initiate shotgun proteomics. Shotgun proteomics identifies proteins by bottom-up proteomic approaches where proteins are identified from the fragmentation spectra of their own peptides. Paper I: deals with the simplification of functional characterization for nanoparticles intended for use in biomedicine. Proteomics was constructive in differentiating and semi-quantifying the surface of protein corona. This could be beneficial in predicting the interactions between nanoparticles and a biological entity like the cell or a receptor protein and provide initial valuable information related to targeting, uptake and safety. Paper II: deals with understanding effects of TiO2 nanoparticles on endothelial cells. A combinatorial approach, involving transcriptomics and proteomics was used to identify aberrations in the permeability and integrity of endothelial cells and tissues. Our study also investigated the correlation of size and how they motivated a differential cellular response. In case of intravenous entry for nanoparticles in targeted drug delivery systems, endothelial cells are the first barrier encountered by these drug carriers. This evaluation involving endothelial cell response could be very instrumental during the designing of NP based drug delivery systems. Paper III: Pharmaceuticals and its metabolites could be very hazardous, especially if its disposal is not managed properly. Since water bodies are the ultimate sink, these chemicals could end up there, culminating in toxicity and other ‘mixture effects’ in combination with other factors. To evaluate the effects of the pharmaceutical, propranolol and climatic factors like low salinity conditions, a microcosm exposure was designed and shotgun proteomics helped understand its impact on mussel gills. In this study too, a combination of transcriptomics and proteomics unveiled molecular mechanisms altered in response to stressors, both individually and in combination. Paper IV: An interplay of various factors like EBF1 and PAX5 determines B-cell lineage and commitment. This might have been materialized by direct and transient proteinprotein interactions. A unique method called BioID helped screen relevant interactions in living cells by the application of a promiscuous biotin ligase enzyme capable of tagging proteins through biotinylation based on a proximity radius. Biotinylation of endogenous proteins enabled their selective isolation by exploiting the high affinity of biotin and streptavidin on streptavidin coated agarose beads, leading to their identification by mass spectrometry. The biotinylated proteins were potential candidate interactors of EBF1 and PAX5, which were later confirmed by sequencing techniques like ChIP-Seq, ATAC seq, and visualization techniques like proximity ligation assay (PLA).

This book concisely describes the role of omics in precision medicine for cancer therapies. It outlines our current understanding of cancer genomics, shares insights into the process of oncogenesis, and discusses emerging technologies and clinical applications of cancer genomics in prognosis and precision-medicine treatment strategies. It then elaborates on recent advances concerning transcriptomics and translational genomics in cancer diagnosis, clinical applications, and personalized medicine in oncology. Importantly, it also explains the importance of high-performance analytics, predictive modeling, and system biology in cancer research. Lastly, the book discusses current and potential future applications of pharmacogenomics in clinical cancer therapy and cancer drug development.

Technologies collectively called omics enable simultaneous measurement of an enormous number of biomolecules; for example, genomics investigates thousands of DNA sequences, and proteomics examines large numbers of proteins. Scientists are using these technologies to develop innovative tests to detect disease and to predict a patient's likelihood of responding to specific drugs. Following a recent case involving premature use of omics-based tests in cancer clinical trials at Duke University, the NCI requested that the IOM establish a committee to recommend ways to strengthen omics-based test development and evaluation. This report identifies best practices to enhance development, evaluation, and translation of omics-based tests while simultaneously reinforcing steps to ensure that these tests are appropriately assessed for scientific validity before they are used to guide patient treatment in clinical trials.

Salivary Diagnostics surveys one of the most exciting areas of research in oral biology. Regarded as the mirror of the body, saliva has immense potential to yield real clinical improvements in our ability to diagnose, and hence treat, oral and systemic conditions. The composition of saliva and other oral fluids reflects the tissue fluid levels of therapeutic, hormonal, and immunological molecules, as well as the presence of markers for systemic and oral disease.

The definitive guide to peptidomics- a hands-on lab reference The first truly comprehensive book about peptidomics for protein and peptide analysis, this reference provides a detailed description of the hows and whys of peptidomics and how the techniques have evolved. With chapters contributed by leading experts, it covers naturally occurring peptides, peptidomics methods and new developments, and the peptidomics approach to biomarker discovery. Explaining both the principles and the applications, Peptidomics: Methods and Applications: * Features examples of applications in diverse fields, including pharmaceutical science, toxicity biomarkers, and neuroscience * Details the successful peptidomic analyses of biological material ranging from plants to mammals * Describes a cross section of analytical techniques, including traditional methodologies, emerging trends, and new techniques for high throughput approaches An enlightening reference for experienced professionals, this book is sufficiently detailed to serve as a step-by-step guide for beginning researchers and an excellent resource for students taking biotechnology and proteomics courses. It is an invaluable reference for protein chemists and biochemists, professionals and researchers in drug and biopharmaceutical development, analytical and bioanalytical chemists, toxicologists, and others.

Precision Medicine and Artificial Intelligence: The Perfect Fit for Autoimmunity covers background on artificial intelligence (AI), its link to precision medicine (PM), and examples of AI in healthcare, especially autoimmunity. The book highlights future perspectives and potential directions as AI has gained significant attention during the past decade. Autoimmune diseases are complex and heterogeneous conditions, but exciting new developments and implementation tactics surrounding automated systems have enabled the generation of large datasets, making autoimmunity an ideal target for AI and precision medicine. More and more diagnostic products utilize AI, which is also starting to be supported by regulatory agencies such as the Food and Drug Administration (FDA). Knowledge generation by leveraging large datasets including demographic, environmental, clinical and biomarker data has the potential to not only impact the diagnosis of patients, but also disease prediction, prognosis and treatment options. - Allows the readers to gain an overview on precision medicine for autoimmune diseases leveraging AI solutions - Provides background, milestone and examples of precision medicine - Outlines the paradigm shift towards precision medicine driven by value-based systems - Discusses future applications of precision medicine research using AI - Other aspects covered in the book include regulatory insights, data analytics and visualization, types of biomarkers as well as the role of the patient in precision medicine

With the completion of sequencing projects and the advancement of a- lytical tools for protein identification, proteomics—the study of the expressed part of the genome—has become a major region of the burgeoning field of functional genomics. High-resolution 2-D gels can reveal virtually all p- teins present in a cell or tissue at any given time, including posttranslationally modified proteins. Changes in the expression and structure of most cellular proteins caused by differentiation or external stimuli can be displayed and eventually identified using 2-D protein gels. 2-D Proteome Analysis Protocols covers all aspects of the use of 2-D protein electrophoresis for the analysis of biological problems. The contri- tors include many of the leaders in the fields of biochemistry and analytical chemistry who were instrumental in the development of high-resolution 2-D gels, immobilized pH gradients, computer analysis, and mass spectromet- based protein identification methodologies. This book is intended as a benchtop manual and guide both for novices to 2-D gels and for those aficionados who wish to try the newer techniques. Any group using protein biochemistry—especially in the fields of molecular biology, biochemistry, microbiology, and cell biology—should find this book eminently useful. 2-D Proteome Analysis Protocols takes the researcher through the c- plete process of working with 2-D protein gels from making the protein - tract to finally identifying the proteins of interest. It includes protocols for generating 2-D protein extracts from most of the standard model organisms, including bacteria, yeast, nematode, Drosophila, plants, mouse, and human.

Between 1973 and 2016, the ways to manipulate DNA to endow new characteristics in an organism (that is, biotechnology) have advanced, enabling the development of products that were not previously possible. What will the likely future products of biotechnology be over the next 5â€"10 years? What scientific capabilities, tools, and/or expertise may be needed by the regulatory agencies to ensure they make efficient and sound evaluations of the likely future products of biotechnology? Preparing for Future Products of Biotechnology analyzes the future landscape of biotechnology products and seeks to inform forthcoming policy making. This report identifies potential new risks and frameworks for risk assessment and areas in which the risks or lack of risks relating to the products of biotechnology are well understood.

With the advent of new technologies and acquired knowledge, the number of fields in omics and their applications in diverse areas are rapidly increasing in the postgenomics era. Such emerging fields—including pharmacogenomics, toxicogenomics, regulomics, spliceomics, metagenomics, and environomics—present budding solutions to combat global challenges in biomedicine, agriculture, and the environment. OMICS: Applications in Biomedical, Agricultural, and Environmental Sciences provides valuable insights into the applications of modern omics technologies to real-world problems in the life sciences. Filling a gap in the literature, it offers a broad, multidisciplinary view of current and emerging applications of omics in a single volume. Written by highly experienced active researchers, each chapter describes a particular area of omics and the associated technologies and applications. Topics covered include: Proteomics, epigenomics, and pharmacogenomics Toxicogenomics and the assessment of environmental pollutants Applications of plant metabolomics Nutrigenomics and its therapeutic applications Microalgal omics and omics approaches in biofuel production Next-generation sequencing and omics technology for transgenic plant analysis Omics approaches in crop improvement Engineering dark-operative chlorophyll synthesis Computational regulomics Omics techniques for the analysis of RNA splicing New fields, including metagenomics, glycomics, and miRNA Breast cancer biomarkers for early detection Environomics strategies for environmental sustainability This timely book explores a wide range of omics application areas in the biomedical, agricultural, and environmental sciences. Throughout, it highlights working solutions as well as open problems and future challenges. Demonstrating the diversity of omics, it introduces readers to state-of-the-art developments and trends in omics-driven research.