Download or read book Discovery and Quantification of Crustacean Neuropeptides Using Mass Spectrometry and Informatics Approaches written by Nhu Vu and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of endogenous peptides is important for discovering critical elements involved in many physiological processes and disorders. Neuropeptides are endogenous peptide hormones that regulate these processes by binding to receptors to initiate cellular signaling pathways. Discovery of neuropeptide function is an increasingly popular avenue for disease therapeutics research, resulting in increased need for improved neuropeptide characterization methods. Although mass spectrometry (MS) is well-suited for neuropeptide analysis due to its high sensitivity and capacity for untargeted, global neuropeptide measurements, there are still technical challenges that must be overcome. For example, neuropeptide sequences within a peptide family are highly homologous and therefore must be analyzed in their intact form to obtain high sequence coverage for confident identification and often require high resolution instrumentation. This becomes more challenging as sequence length and post-translational modification complexity increases. In this thesis, I will discuss my efforts in improving MS-based neuropeptidomic workflows, specifically in relation to "top-down" protein and peptide characterization, while highlighting improvements in identification and quantification of peptides through optimized fragmentation and cysteine reactive labeling. I will also discuss my contributions to our group's novel software, HyPep, enabling utility for confident neuropeptide identification. Altogether, these methods have contributed to increased neuropeptide coverage and can be translated to the analysis of other peptide classes.This thesis begins with two reviews of recent developments in MS-based analysis of neuropeptides. Each review outlines examples of how advancements in MS sample preparation, MS acquisition, data analysis, and technology has increased our understanding of neuropeptides, and provides insight on promising directions for further development within each section. My research contributions in Professor Lingjun Li's research group started by applying peptidomics workflows to quantify changes in neuropeptide expression due to hypoxia stress in a crustacean animal model, C. sapidus. Using the same animal model, we also increased the number of detectable neuropeptides using matrix-assisted laser desorption/ionization (MALDI)-MS imaging by incorporating novel tissue wash steps during sample preparation. Over 100 putative peptidomic biomarkers for different levels of hypoxia severity and duration were discovered within multiple tissue types. Four neuropeptide biomarkers were examined for functional activity and two neuropeptides were discovered to increase cardiac output ex vivo, including the first-ever reported function for a crustacean hyperglycemic hormone precursor-related peptide (CPRP). Since CPRP (3.5 kDa) is co-released with crustacean hyperglycemic hormone (CHH) neuropeptide (8.5 kDa), an important neuropeptide that regulates glucose metabolism, we did not detect CHH in these hypoxia studies because its larger size prevented confident detection using typical neuropeptidomic MS workflow and data acquisition methods. Previous members of our research group have developed MS methods to sequence CHH, but limitations of those methods included requiring multiple MS instruments or reliance on targeted MS strategies in which information of potential novel neuropeptides is lost. I built upon those MS acquisition and data analysis methods and was able to sequence novel CHH isoforms and proteoforms, without assistance from genomic or transcriptomic-based sequence prediction, using a Thermo Orbitrap Fusion Lumos instrument. Additionally, I developed novel sample preparation methods to reduce the disulfide bonds and alkylate all six cysteine residues on CHH at high efficiency (83-89% labeling efficiency). While developing methods for CHH are beneficial for analyzing mid-size (8-10 kDa) peptides, I sought to also advance general neuropeptidomics data analysis pipeline. A novel concept for neuropeptide identification software, called HyPep, was created 10 years ago but was not finished and could not be used. To make the software usable, I incorporated features typically used in peptide-spectrum matching (PSM)-based algorithms in proteomics software, such as a false discovery rate. I optimized the software parameters which resulted in HyPep outperforming an analogous commercial software in identifying neuropeptides from four crustacean neuronal tissue types. Collectively, this dissertation is devoted to advancing sample preparation, data acquisition, and data analysis strategies for neuropeptidomics, and these methods are also potentially translatable to analyze other classes of endogenous peptides.
Download or read book Neuropeptide Signaling in Crustaceans Probed by Mass Spectrometry written by and published by . This book was released on 2016 with total page 564 pages. Available in PDF, EPUB and Kindle. Book excerpt: Neuropeptides are one of the most diverse classes of signaling molecules whose identities and functions are not yet fully understood. They have been implicated in the regulation of a wide range of physiological processes, including feeding-related and motivated behaviors, and also environmental adaptations. In this work, improved mass spectrometry-based analytical platforms were developed and applied to the crustacean systems to characterize signaling molecules. This dissertation begins with a review of mass spectrometry-based neuropeptide studies from both temporal- and spatial-domains. This review is then followed by several chapters detailing a few research projects related to the crustacean neuropeptidomic characterization and comparative analysis. The neuropeptidome of crayfish, Orconectes rusticus is characterized for the first time using mass spectrometry-based tools. In vivo microdialysis sampling technique offers the capability of direct sampling from extracellular space in a time-resolved manner. It is used to investigate the secreted neuropeptide and neurotransmitter content in Jonah crab, Cancer borealis, in this work. A new quantitation strategy using alternative mass spectrometry data acquisition approach is developed and applied for the first time to quantify neuropeptides. Coupling of this method with microdialysis enables the study of neuropeptide dynamics concurrent with different behaviors. Proof-of-principle experiments validating this approach have been carried out in Jonah crab, Cancer borealis to study feeding- and circadian rhythm-related neuropeptide changes using micoridialysis in a time-resolved manner. This permits a close correlation between behavioral and neurochemical changes, providing potential candidates for future validation of regulatory roles. In addition to providing spatial information, mass spectrometry imaging (MSI) technique enables the characterization of signaling molecules while preserving the temporal resolution. A novel MSI-based platform is developed by interfacing with microdialysis sample collection and is applied to the study of in vivo neuropeptide degradation profiles in an off-line ‘real-time’ fashion. This unique platform provides novel insights into neuropeptide inactivation/elimination process, which is an essential step to understand peptidegic signaling pathway. In addition to neuropeptides, this platform has been further modified to study secreted neurotransmitters, and small molecule metabolites that might interact with neuropeptides in crustacean for the first time. This work not only reports improvements upon neuropeptides identification and quantitation by developing improved analytical strategies, but also provides important evidence for the potential roles of several neuropeptides in regulating food intake and circadian rhythm behaviors. Novel platform that integrates MALDI-MSI with microdialysis in exploring neurochemical changes in dynamic biological events is also presented, which could be potentially applied to many other systems in future research. Collectively this dissertation research develops new analytical methods and improves our fundamental understanding of neuropeptide signaling.
Download or read book Neuropeptides in Crustaceans written by Chuanzi OuYang and published by . This book was released on 2016 with total page 341 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this thesis, multifaceted biological mass spectrometry (MS) based methods were developed and employed to enable comprehensive characterization of neuropeptides. Neuropeptides encompass the largest and most diverse group of signaling molecules in the nervous system. They are necessary for the initiation and regulation of numerous physiological processes such as feeding, reproduction and development. Due to the complexity and inaccessibility of human systems, many invertebrate model nervous systems have been utilized as test bed for neuropeptidome research. Of these, the decapod crustacean nervous system provides an excellent test bed to facilitate technology development and investigate the biological functions of neuropeptides. A review of the current status and progress in the field of invertebrate neuropeptide is included in this thesis. Among various MS based technologies, we focused on developing new methodologies in mass spectral imaging (MSI) to provide high throughput tools for multiplexed distribution characterization. Current development of MSI and microdialysis based MS approaches have been summarized as the background of MSI related projects. To this rapidly expanding body of literature, the work presented here contributes insight into the possible functionality of certain peptides by identifying neuropeptides found to be differentially expressed in correlation with food intake and changes of environmental conditions. This comparative peptidomic study utilized direct tissue analysis, MSI and stable isotopic labeling to provide comprehensive information regarding to peptide expression level changes under different physiological states. In addition, sample preparation method was developed to detect trace level of neuropeptides from crustacean circulating fluid hemolymph. Furthermore, optimized sample preparation for imaging mass spectrometry was developed to greatly increase the coverage of peptidome and the accuracy of identification. Finally, using established techniques, novel neuropeptides were identified from the neuroendocrine organs in Dungeness crab and rock crab, and their distribution was also investigated. Collectively, this body of work extends the capability of mass spectrometry as a bioanalytical tool for neuropeptide analysis and advances the basic understanding of neuronal signaling.
Download or read book A Mass Spectrometry based Neuropeptide Discovery Pipeline written by and published by . This book was released on 2013 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: Neuropeptides represent the most complex group of endogenous molecules in the nervous system that plays important roles in the regulation of physiological process. Elucidation of these signaling molecules is a crucial step towards understanding the underlying mechanism of neuromodulation. My thesis research focuses on development of an efficient peptide discovery pipeline that accelerates neuropeptidomic analysis in crustacean models. We established a high-definition MS approach for identification and characterization of large crustacean hyperglycemic hormone (CHH)-family neuropeptides, which was achieved by combining bottom-up, off-line top-down, and on-line top-down tandem MS methods. We further refined and incorporated this high-definition approach into a multi-scale strategy for simultaneous and confident sequence elucidation of various sizes of peptides in the crustacean nervous system. A wide range of neuropeptides with various molecular weights (0.9-8.2 kDa) were fully sequenced. The well-characterized primary sequences of neuropeptides provide opportunities for elucidation of their structural information. To rapidly and precisely localize D-amino acids in bioactive peptides, we developed a novel site-specific strategy by ion mobility spectrometry (IMS) analysis of MS-generated epimeric fragment ions. Our results indicate that the isomerization of L- to D-Phe occurs in the American lobster CHHs. In addition to characterization of conformational isomers of neuropeptides, our method allows elucidating structural isomers in gas phase. We report on a novel strategy for qualitative and quantitative analysis of b-type ion isomers by combining electron transfer dissociation, IMS and formaldehyde labeling. The analysis results provide evidence to support the proposed fragmentation mechanism of peptide sequence scrambling in gas phase. The final goal of our study is to understand the roles of neuropeptides play in neural circuits. To investigate if CHHs are involved in regulation of food intake, a new isotopic labeling-assisted top-down MS strategy was developed to directly monitor the abundance changes of endogenous large neuropeptides. Comparative analysis in unfed and fed crabs revealed that the CHH abundance in the sinus glands was significantly increased after food intake. In addition, label-free quantitative analysis reveals that the orcokinin and RFamide peptides were down-regulated after food intake, suggesting that the release of these neuropeptides might be altered by feeding behavior.
Download or read book Multi faceted Mass Spectrometric Approaches for the Analysis of Neuropeptides in Crustacean written by Ruibing Chen and published by . This book was released on 2009 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Neuroproteomics written by Oscar Alzate and published by CRC Press. This book was released on 2009-10-26 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this, the post-genomic age, our knowledge of biological systems continues to expand and progress. As the research becomes more focused, so too does the data. Genomic research progresses to proteomics and brings us to a deeper understanding of the behavior and function of protein clusters. And now proteomics gives way to neuroproteomics as we beg
Download or read book Peptidomics written by Mikhail Soloviev and published by John Wiley & Sons. This book was released on 2007-12-21 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Neuropeptide Systems as Targets for Parasite and Pest Control written by Timothy G. Geary and published by Springer Science & Business Media. This book was released on 2011-01-13 with total page 246 pages. Available in PDF, EPUB and Kindle. Book excerpt: The need to continually discover new agents for the control or treatment of invertebrate pests and pathogens is undeniable. Agriculture, both animal and plant, succeeds only to the extent that arthropod and helminth consumers, vectors and pathogens can be kept at bay. Humans and their companion animals are also plagued by invertebrate parasites. The deployment of chemical agents for these purposes inevitably elicits the selection of resistant populations of the targets of control, necessitating a regular introduction of new kinds of molecules. Experience in other areas of chemotherapy has shown that a thorough understanding of the biology of disease is an essential platform upon which to build a discovery program. Unfortunately, investment of research resources into understanding the basic physiology of invertebrates as a strategy to illuminate new molecular targets for pesticide and parasiticide discovery has been scarce, and the pace of introduction of new molecules for these indications has been slowed as a result. An exciting and so far unexploited area to explore in this regard is invertebrate neuropeptide physiology. This book was assembled to focus attention on this promising field by compiling a comprehensive review of recent research on neuropeptides in arthropods and helminths, with contributions from many of the leading laboratories working on these systems.
Download or read book Proteomics for Biological Discovery written by Timothy D. Veenstra and published by John Wiley & Sons. This book was released on 2006-06-12 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by recognized experts in the study of proteins, Proteomics for Biological Discovery begins by discussing the emergence of proteomics from genome sequencing projects and a summary of potential answers to be gained from proteome-level research. The tools of proteomics, from conventional to novel techniques, are then dealt with in terms of underlying concepts, limitations and future directions. An invaluable source of information, this title also provides a thorough overview of the current developments in post-translational modification studies, structural proteomics, biochemical proteomics, microfabrication, applied proteomics, and bioinformatics relevant to proteomics. Presents a comprehensive and coherent review of the major issues faced in terms of technology development, bioinformatics, strategic approaches, and applications Chapters offer a rigorous overview with summary of limitations, emerging approaches, questions, and realistic future industry and basic science applications Discusses higher level integrative aspects, including technical challenges and applications for drug discovery Accessible to the novice while providing experienced investigators essential information Proteomics for Biological Discovery is an essential resource for students, postdoctoral fellows, and researchers across all fields of biomedical research, including biochemistry, protein chemistry, molecular genetics, cell/developmental biology, and bioinformatics.
Download or read book From Guinea Pig to Computer Mouse written by Ursula Zinko and published by . This book was released on 1997 with total page 244 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Honeybee Neurobiology and Behavior written by C. Giovanni Galizia and published by Springer Science & Business Media. This book was released on 2011-11-25 with total page 500 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book is a sequel of a similar book, edited by Randolf Menzel and Alison Mercer, “Neurobiology and Behavior of Honeybees”, published in 1987. It is a “Festschrift” for the 70th birthday of Randolf Menzel, who devoted his life to the topic of the book. The book will include an open commentary for each section written by Randolf Menzel, and discussed with the authors. The written contributions take their inspiration from a symposium on the topic, with all the authors, that was held in Berlin in summer 2010
Download or read book Peptidomics written by Michael Schrader and published by Humana. This book was released on 2019-06-04 with total page 423 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume describes protocols for basic state-of-the-art approaches in the field of peptidomics. Most of these approaches are independent of the instruments used for analysis and can easily be adapted for equipment that is available in a typical proteomics facility. Chapters detail many of the basic techniques used to detect and identify peptides, methods for the relative quantitation of peptides between samples using isotopic labels or label-free approaches, and biological species as well as sample types. Written in the highly successful format of the Methods in Molecular Biology series, each chapter includes an introduction to the topic, a list of the necessary materials and reagents, reproducible step-by-step laboratory protocols, and tips on troubleshooting common problems and avoiding pitfalls. Authoritative and practical, Peptidomics: Methods and Strategies provides useful guidance for studies in the rapidly growing field of peptidomics.
Download or read book Advancements of Mass Spectrometry in Biomedical Research written by Alisa G. Woods and published by Springer. This book was released on 2016-09-24 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores the use of mass spectrometry for biomedical applications. Chapters focus on specific therapeutic areas such as oncology, infectious disease and psychiatry. Additional chapters focus on methodology as well as new technologies and instrumentation. This volume provides readers with a comprehensive and informative manual that will allow them to appreciate mass spectrometry and proteomic research but also to initiate and improve their own work. Thus the book acts as a technical guide but also a conceptual guide to the newest information in this exciting field. Mass spectrometry is the central tool used in proteomic research today and is rapidly becoming indispensable to the biomedical scientist. With the completion of the human genome project and the genomic revolution, the proteomic revolution has followed closely behind. Understanding the human proteome has become critical to basic and clinical biomedical research and holds the promise of providing comprehensive understanding of human physiological processes. In addition, proteomics and mass spectrometry are bringing unprecedented biomarker discovery and are helping to personalize medicine.
Download or read book Medicinal Chemistry written by Thomas Nogrady and published by Oxford University Press. This book was released on 2005-08-11 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fully updated and rewritten by a basic scientist who is also a practicing physician, the third edition of this popular textbook remains comprehensive, authoritative and readable. Taking a receptor-based, target-centered approach, it presents the concepts central to the study of drug action in a logical, mechanistic way grounded on molecular and principles. Students of pharmacy, chemistry and pharmacology, as well as researchers interested in a better understanding of drug design, will find this book an invaluable resource. Starting with an overview of basic principles, Medicinal Chemistry examines the properties of drug molecules, the characteristics of drug receptors, and the nature of drug-receptor interactions. Then it systematically examines the various families of receptors involved in human disease and drug design. The first three classes of receptors are related to endogenous molecules: neurotransmitters, hormones and immunomodulators. Next, receptors associated with cellular organelles (mitochondria, cell nucleus), endogenous macromolecules (membrane proteins, cytoplasmic enzymes) and pathogens (viruses, bacteria) are examined. Through this evaluation of receptors, all the main types of human disease and all major categories of drugs are considered. There have been many changes in the third edition, including a new chapter on the immune system. Because of their increasingly prominent role in drug discovery, molecular modeling techniques, high throughput screening, neuropharmacology and genetics/genomics are given much more attention. The chapter on hormonal therapies has been thoroughly updated and re-organized. Emerging enzyme targets in drug design (e.g. kinases, caspases) are discussed, and recent information on voltage-gated and ligand-gated ion channels has been incorporated. The sections on antihypertensive, antiviral, antibacterial, anti-inflammatory, antiarrhythmic, and anticancer drugs, as well as treatments for hyperlipidemia and peptic ulcer, have been substantially expanded. One new feature will enhance the book's appeal to all readers: clinical-molecular interface sections that facilitate understanding of the treatment of human disease at a molecular level.
Download or read book Nerve Cells and Insect Behavior written by Kenneth David Roeder and published by Harvard University Press. This book was released on 1998 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt: Insects are ideal subjects for neurophysiological studies. This classic volume relates the activities of nerve cells to the activities of insects, something that had never been attempted when the book first appeared in 1963. In several elegant experiments, Roeder shows how stimulus and behavior are related through the nervous system.
Download or read book Polarized Light and Polarization Vision in Animal Sciences written by Gábor Horváth and published by Springer. This book was released on 2014-10-30 with total page 652 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers advances made since the 2004 Springer volume “Polarized Light in Animal Vision” edited by Horvath and Varju, but also provides reviews and synopses of some areas. Part I examines polarization sensitivity across many animal taxa including vertebrates and invertebrates and details both terrestrial and aquatic life. Part II is devoted to the description of polarized light in nature and explores how the physics of light must be taken into account when understanding how polarized light is detected by the visual system. This includes underwater polarization due to scattering; polarization patterns reflected from freshwater bodies; polarization characteristics of forest canopies; normal and anomalous polarization patterns of the skies; skylight polarization transmitted through Snell’s window and both linearly and circularly polarized signals produced by terrestrial and aquatic animals. This Part also examines polarized “light pollution” induced by anthropogenic factors such as reflection off asphalt surfaces, glass panes, car bodies, and other man-made structures that are now known to form ecological traps for polarotactic insects. Part III surveys some of the practical applications of polarization vision including polarization-based traps for biting insects, ground-based polarimetric cloud detectors and an historical examination of the navigational abilities of Viking seafarers using the sky polarization compass. The deterrent qualities of ungulate pelage to polarization-sensitive biting insects is also examined in this section.
Download or read book Serum Plasma Proteomics written by Richard J Simpson and published by Humana Press. This book was released on 2016-05-01 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: Blood science has become a cornerstone of multiple disciplines. This book, contributed to by leading experts in the field, provides a comprehensive resource of protocols for areas, pre-analytical through to analytical, of plasma and serum proteomics.
