EXSPub Date : 2007-01-01DOI: 10.1007/978-3-7643-7439-6_7
Sven Schuchardt, Albert Sickmann
{"title":"Protein identification using mass spectrometry: a method overview.","authors":"Sven Schuchardt, Albert Sickmann","doi":"10.1007/978-3-7643-7439-6_7","DOIUrl":"https://doi.org/10.1007/978-3-7643-7439-6_7","url":null,"abstract":"<p><p>With the introduction of soft ionization techniques such as Matrix Assisted Laser Desorption Ionization (MALDI), and Electrospray Ionization (ESI), proteins have become accessible to mass spectrometric analyses. Since then, mass spectrometry has become the method of choice for sensitive, reliable and inexpensive protein and peptide identification. With the increasing number of full genome sequences for a variety of organisms and the numerous protein databases constructed thereof, all the tools necessary for the high-throughput protein identification with mass spectrometry are in place. This chapter highlights the different mass spectrometric techniques currently applied in proteome research by giving a brief overview of methods for identification of posttranslational modifications and discussing their suitability of strategies for automated data analysis.</p>","PeriodicalId":77125,"journal":{"name":"EXS","volume":"97 ","pages":"141-70"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-3-7643-7439-6_7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26664609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EXSPub Date : 2007-01-01DOI: 10.1007/978-3-7643-7439-6_9
Lloyd W Sumner, David V Huhman, Ewa Urbanczyk-Wochniak, Zhentian Lei
{"title":"Methods, applications and concepts of metabolite profiling: secondary metabolism.","authors":"Lloyd W Sumner, David V Huhman, Ewa Urbanczyk-Wochniak, Zhentian Lei","doi":"10.1007/978-3-7643-7439-6_9","DOIUrl":"https://doi.org/10.1007/978-3-7643-7439-6_9","url":null,"abstract":"<p><p>Plants manufacture a vast array of secondary metabolites/natural products for protection against biotic or abiotic environmental challenges. These compounds provide increased fitness due to their antimicrobial, anti-herbivory, and/or alleopathic activities. Secondary metabolites also serve fundamental roles as key signaling compounds in mutualistic interactions and plant development. Metabolic profiling and integrated functional genomics are advancing the understanding of these intriguing biosynthetic pathways and the response of these pathways to environmental challenges. This chapter provides an overview of the basic methods, select applications, and future directions of metabolic profiling of secondary metabolism. The emphasis of the application section includes the combination of primary and secondary metabolic profiling. The future directions section describes the need for increased chromatographic and mass resolution, as well as the inevitable need and benefit of spatially and temporally resolved metabolic profiling.</p>","PeriodicalId":77125,"journal":{"name":"EXS","volume":"97 ","pages":"195-212"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-3-7643-7439-6_9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26664611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EXSPub Date : 2007-01-01DOI: 10.1007/978-3-7643-7439-6_10
Martine Dieuaide-Noubhani, Ana-Paula Alonso, Dominique Rolin, Wolfgang Eisenreich, Philippe Raymond
{"title":"Metabolic flux analysis: recent advances in carbon metabolism in plants.","authors":"Martine Dieuaide-Noubhani, Ana-Paula Alonso, Dominique Rolin, Wolfgang Eisenreich, Philippe Raymond","doi":"10.1007/978-3-7643-7439-6_10","DOIUrl":"https://doi.org/10.1007/978-3-7643-7439-6_10","url":null,"abstract":"<p><p>Isotopic tracers are used to both trace metabolic pathways and quantify fluxes through these pathways. The use of different labeling methods recently led to profound changes in our views of plant metabolism. Examples are taken from primary metabolism, with sugar interconversions, carbon partitioning between glycolysis and the pentose phosphate pathway, or metabolite inputs into the tricarboxylic acid (TCA) cycle, as well as from secondary metabolism with the relative contribution of the plastidial and cytosolic pathways to the biosynthesis of terpenoids. While labeling methods are often distinguished according to the instruments used for label detection, emphasis is put here on labeling duration. Short time labeling is adequate to study limited areas of the metabolic network. Long-term labeling, when designed to obtain metabolic and isotopic steady-state, allows to calculate various fluxes in large areas ofcentral metabolism. After longer labeling periods, large amounts of label accumulate in structural or storage compounds: their detailed study through the retrobiosynthetic method gives access to the biosynthetic pathways of otherwise undetectable precursors. This chapter presents the power and limits of the different methods, and illustrates how they can be associated with each other and with other methods of cell biology, to provide the information needed for a rational approach of metabolic engineering.</p>","PeriodicalId":77125,"journal":{"name":"EXS","volume":"97 ","pages":"213-43"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26664612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EXSPub Date : 2007-01-01DOI: 10.1007/978-3-7643-7439-6_12
Christian H Ahrens, Ulrich Wagner, Hubert K Rehrauer, Can Türker, Ralph Schlapbach
{"title":"Current challenges and approaches for the synergistic use of systems biology data in the scientific community.","authors":"Christian H Ahrens, Ulrich Wagner, Hubert K Rehrauer, Can Türker, Ralph Schlapbach","doi":"10.1007/978-3-7643-7439-6_12","DOIUrl":"https://doi.org/10.1007/978-3-7643-7439-6_12","url":null,"abstract":"<p><p>Today's rapid development and broad application of high-throughput analytical technologies are transforming biological research and provide an amount of data and analytical opportunities to understand the fundamentals of biological processes undreamt of in past years. To fully exploit the potential of the large amount of data, scientists must be able to understand and interpret the information in an integrative manner. While the sheer data volume and heterogeneity of technical platforms within each discipline already poses a significant challenge, the heterogeneity of platforms and data formats across disciplines makes the integrative management, analysis, and interpretation of data a significantly more difficult task. This challenge thus lies at the heart of systems biology, which aims at a quantitative understanding of biological systems to the extent that systemic features can be predicted. In this chapter, we discuss several key issues that need to be addressed in order to put an integrated systems biology data analysis and mining within reach.</p>","PeriodicalId":77125,"journal":{"name":"EXS","volume":"97 ","pages":"277-307"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26664614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EXSPub Date : 2006-01-01DOI: 10.1007/3-7643-7378-4_15
Assam El-Osta
{"title":"Mechanisms of abnormal gene expression in tumor cells.","authors":"Assam El-Osta","doi":"10.1007/3-7643-7378-4_15","DOIUrl":"https://doi.org/10.1007/3-7643-7378-4_15","url":null,"abstract":"<p><p>Epigenetic mechanisms are involved in critical nuclear processes such as transcriptional control, genome stability, replication and repair. Recent evidence suggests that changes in the epigenetic repertoire can drive tumorigenesis. This review examines the latest experimental evidence that questions the mechanisms underlying the consequence of epigenetic changes in gene regulation and cancer development.</p>","PeriodicalId":77125,"journal":{"name":"EXS","volume":" 96","pages":"351-61"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/3-7643-7378-4_15","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25775071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EXSPub Date : 2006-01-01DOI: 10.1007/3-7643-7417-9_3
Nicole Merten, Annette G Beck-Sickinger
{"title":"Molecular ligand-receptor interaction of the NPY/PP peptide family.","authors":"Nicole Merten, Annette G Beck-Sickinger","doi":"10.1007/3-7643-7417-9_3","DOIUrl":"https://doi.org/10.1007/3-7643-7417-9_3","url":null,"abstract":"","PeriodicalId":77125,"journal":{"name":"EXS","volume":" 95","pages":"35-62"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/3-7643-7417-9_3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25775172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EXSPub Date : 2006-01-01DOI: 10.1007/3-7643-7417-9_8
Giora Z Feuerstein, Edward W Lee
{"title":"Neuropeptide Y and the heart: implication for myocardial infarction and heart failure.","authors":"Giora Z Feuerstein, Edward W Lee","doi":"10.1007/3-7643-7417-9_8","DOIUrl":"https://doi.org/10.1007/3-7643-7417-9_8","url":null,"abstract":"","PeriodicalId":77125,"journal":{"name":"EXS","volume":" 95","pages":"113-22"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/3-7643-7417-9_8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25775177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EXSPub Date : 2006-01-01DOI: 10.1007/3-7643-7417-9_9
Joseph Winaver, Zaid Abassi
{"title":"Role of neuropeptide Y in the regulation of kidney function.","authors":"Joseph Winaver, Zaid Abassi","doi":"10.1007/3-7643-7417-9_9","DOIUrl":"https://doi.org/10.1007/3-7643-7417-9_9","url":null,"abstract":"<p><p>The presence in the mammalian kidney of NPY and at least one of its receptor subtypes has been proven by several independent methodologies. Also, numerous studies using physiological and pharmacological approaches indicated that this peptide has the capacity to alter renal function. In particular, these studies suggest that NPY may exert renal vasoconstrictor and tubular actions that are species dependent, and may also influence renin secretion by the kidney. The question whether NPY plays an important role in the physiological regulation of renal hemodynamics and electrolyte excretion, remains largely unanswered at present. No major impairments in renal function have been reported in genetically models deficient in NPY or its Y1 receptor. Thus, additional studies are required to elucidate the role of NPY in the physiological and pathophysiological regulation of renal function.</p>","PeriodicalId":77125,"journal":{"name":"EXS","volume":" 95","pages":"123-32"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/3-7643-7417-9_9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25775178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EXSPub Date : 2006-01-01DOI: 10.1007/978-3-7643-7772-4_2
Mohammad R Zarrindast
{"title":"Neurotransmitters and cognition.","authors":"Mohammad R Zarrindast","doi":"10.1007/978-3-7643-7772-4_2","DOIUrl":"https://doi.org/10.1007/978-3-7643-7772-4_2","url":null,"abstract":"","PeriodicalId":77125,"journal":{"name":"EXS","volume":"98 ","pages":"5-39"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-3-7643-7772-4_2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26291395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}