Academic literature on the topic 'Proteomics research'
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Journal articles on the topic "Proteomics research"
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Krieg, Rene C., Cloud P. Paweletz, Lance A. Liotta, and Emanuel F. Petricoin. "Clinical Proteomics for Cancer Biomarker Discovery and Therapeutic Targeting." Technology in Cancer Research & Treatment 1, no. 4 (August 2002): 263–72. http://dx.doi.org/10.1177/153303460200100407.
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As we emerge into the post-genome era, proteomics finds itself as the driving force field as we translate the nucleic acid information archive into understanding how the cell actually works and how disease processes operate. Even so, the traditionally held view of proteomics as simply cataloging and developing lists of the cellular protein repertoire of a cell are now changing, especially in the sub-discipline of clinical proteomics. The most relevant information archive to clinical applications and drug development involves the elucidation of the information flow of the cell; the “software” of protein pathway networks and circuitry. The deranged circuitry of the cell as the drug target itself as well as the effect of the drug on not just the target, but also the entire network, is what we now are striving towards. Clinical proteomics, as a new and most exciting sub-discipline of proteomics, involves the bench-to-bedside clinical application of proteomic tools. Unlike the genome, there are potentially thousands of proteomes: each cell type has its own unique proteome. Moreover, each cell type can alter its proteome depending on the unique tissue microenvironment in which it resides, giving rise to multiple permutations of a single proteome. Since there is no polymerase chain reaction equivalent to proteomics- identifying and discovering the “wiring diagram” of a human diseased cell in a biopsy specimen remains a daunting challenge. New micro-proteomic technologies are being and still need to be developed to drill down into the proteomes of clinically relevant material. Cancer, as a model disease, provides a fertile environment to study the application of proteomics at the bedside. The promise of clinical proteomics and the new technologies that are developed is that we will detect cancer earlier through discovery of biomarkers, we will discover the next generation of targets and imaging biomarkers, and we can then apply this knowledge to patient-tailored therapy.
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Sadeesh, Nithin, Mauro Scaravilli, and Leena Latonen. "Proteomic Landscape of Prostate Cancer: The View Provided by Quantitative Proteomics, Integrative Analyses, and Protein Interactomes." Cancers 13, no. 19 (September 27, 2021): 4829. http://dx.doi.org/10.3390/cancers13194829.
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Prostate cancer is the second most frequent cancer of men worldwide. While the genetic landscapes and heterogeneity of prostate cancer are relatively well-known already, methodological developments now allow for studying basic and dynamic proteomes on a large scale and in a quantitative fashion. This aids in revealing the functional output of cancer genomes. It has become evident that not all aberrations at the genetic and transcriptional level are translated to the proteome. In addition, the proteomic level contains heterogeneity, which increases as the cancer progresses from primary prostate cancer (PCa) to metastatic and castration-resistant prostate cancer (CRPC). While multiple aspects of prostate adenocarcinoma proteomes have been studied, less is known about proteomes of neuroendocrine prostate cancer (NEPC). In this review, we summarize recent developments in prostate cancer proteomics, concentrating on the proteomic landscapes of clinical prostate cancer, cell line and mouse model proteomes interrogating prostate cancer-relevant signaling and alterations, and key prostate cancer regulator interactomes, such as those of the androgen receptor (AR). Compared to genomic and transcriptomic analyses, the view provided by proteomics brings forward changes in prostate cancer metabolism, post-transcriptional RNA regulation, and post-translational protein regulatory pathways, requiring the full attention of studies in the future.
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Geng, Ruihui, Zhaoshen Li, Shude Li, and Jun Gao. "Proteomics in Pancreatic Cancer Research." International Journal of Proteomics 2011 (August 14, 2011): 1–5. http://dx.doi.org/10.1155/2011/365350.
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Pancreatic cancer is a highly aggressive malignancy with a poor prognosis and deeply affects the life of people. Therefore, the earlier diagnosis and better treatments are urgently needed. In recent years, the proteomic technologies are well established and growing rapidly and have been widely applied in clinical applications, especially in pancreatic cancer research. In this paper, we attempt to discuss the development of current proteomic technologies and the application of proteomics to the field of pancreatic cancer research. This will explore the potential perspective in revealing pathogenesis, making the diagnosis earlier and treatment.
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Janech, Michael G., John R. Raymond, and John M. Arthur. "Proteomics in renal research." American Journal of Physiology-Renal Physiology 292, no. 2 (February 2007): F501—F512. http://dx.doi.org/10.1152/ajprenal.00298.2006.
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Proteomic technologies are used with increasing frequency in the renal community. In this review, we highlight the use in renal research of a number of available techniques including two-dimensional gel electrophoresis, liquid chromatography/mass spectrometry, surface-enhanced laser desorption/ionization, capillary electrophoresis/mass spectrometry, and antibody and tissue arrays. These techniques have been used to identify proteins or changes in proteins specific to regions of the kidney or associated with renal diseases or toxicity. They have also been used to examine protein expression changes and posttranslational modifications of proteins during signaling. A number of studies have used proteomic methodologies to look for diagnostic biomarkers in body fluids. The rapid rate of development of the technologies along with the combination of classic physiological and biochemical techniques with proteomics will enable new discoveries.
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Ji, Qing, Fangshi Zhu, Xuan Liu, Qi Li, and Shi-bing Su. "Recent Advance in Applications of Proteomics Technologies on Traditional Chinese Medicine Research." Evidence-Based Complementary and Alternative Medicine 2015 (2015): 1–13. http://dx.doi.org/10.1155/2015/983139.
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Proteomics technology, a major component of system biology, has gained comprehensive attention in the area of medical diagnosis, drug development, and mechanism research. On the holistic and systemic theory, proteomics has a convergence with traditional Chinese medicine (TCM). In this review, we discussed the applications of proteomic technologies in diseases-TCM syndrome combination researches. We also introduced the proteomic studies on thein vivoandin vitroeffects and underlying mechanisms of TCM treatments using Chinese herbal medicine (CHM), Chinese herbal formula (CHF), and acupuncture. Furthermore, the combined studies of proteomics with other “-omics” technologies in TCM were also discussed. In summary, this report presents an overview of the recent advances in the application of proteomic technologies in TCM studies and sheds a light on the future global and further research on TCM.
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Vítámvás, P., K. Kosová, and I. T. Prášil. "Proteome analysis in plant stress research: a review." Czech Journal of Genetics and Plant Breeding 43, No. 1 (January 7, 2008): 1–6. http://dx.doi.org/10.17221/1903-cjgpb.
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Proteomic techniques that allow the identification and quantification of stress-related proteins, mapping of dynamics of their expression and posttranslational modifications represent an important approach in the research of plant stresses. In this review, we show an outline of proteomics methods and their applications in the research of plant resistance to various types of stresses.
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Mahajan, R., and P. Gupta. "Proteomics: taking over where genomics leaves off." Czech Journal of Genetics and Plant Breeding 46, No. 2 (June 29, 2010): 47–53. http://dx.doi.org/10.17221/34/2009-cjgpb.
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The proteomic studies are simultaneously developed in several directions and significantly influence our notions on the capabilities of biological sciences. The need for proteomics research is necessary as there are certain genes in a cell that encode proteins with specific functions. Using a variety of techniques, proteomics can be used to study how proteins interact within a system or how the protein expression changes in different parts of the body, in different stages of its life cycle and in different environmental conditions as every individual has one genome and many proteomes. Besides the qualitative and quantitative description of the expressed proteins, proteomics also deals with the analysis of mutual interactions of proteins. Thereby, candidate proteins can be identified which may be used as starting-points for diagnostic or even therapeutic approaches.
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Jain, K. K. "Oncoproteomics: State-of-the-Art." Technology in Cancer Research & Treatment 1, no. 4 (August 2002): 219–20. http://dx.doi.org/10.1177/153303460200100401.
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Proteomics is a promising approach in the identification of proteins and biochemical pathways involved in carcinogenesis. Proteomic technologies are now being incorporated in oncology in the post-genomic era. Cancer involves alterations in protein expression and provides a good model not only for detection of biomarkers but also their use in drug discovery. Proteomics has an impact on diagnostics as well as drug discovery. Genomics still remains an important approach but the value of proteomics lies in the fact that most of the diagnostics and drugs target proteins. The importance of application of proteomics in oncology is recognized by the publication of this special issue of TRCT.
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Li, Shi-Sheng. "Commentary — The Proteomics: A New Tool for Chinese Medicine Research." American Journal of Chinese Medicine 35, no. 06 (January 2007): 923–28. http://dx.doi.org/10.1142/s0192415x07005387.
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Proteomics technology is based on the vast analytical power for protein/peptide identification and quantification offered by modern mass spectrometry coupled with hyphenated separation techniques such as two-dimensional gel electrophoresis (2DE) and micro- or nano-scale multidimensional liquid chromatography. The rapid growth of proteomics field provides an array of new tools for the integration of traditional Chinese medicine (TCM) with modern technology and systems biology, and is potentially advancing the progress of modernization and internationalization of TCM. Cho, in this issue of the American Journal of Chinese Medicine, highlights the recent application of 2DE-based and bottom-up proteomics in Chinese medicine research, including the exploration of pharmacological mechanisms of the actions of TCM, the facilitation of herb authentication and identification, and the profiling of protein expression following acupuncture treatment in animal models. Recent development in proteomics has provided further refinement on the analysis of proteins posttranslational modifications as well as quantitative comparison of different proteomes, and enabled the study of proteomes of specific diseases or biological processes under clinically relevant conditions. It is conceivable that the application of technologies developed in proteomics, genomics and metabonomics in the clinical practice and basic research of Chinese medicine will eventually lead to the reconciliation and integration of TCM and contemporary medicine. Chinese medicine is fundamentally a highly personalized medicine; perhaps it is time to embrace the arrival of TCM OMICS era in Chinese medicine research.
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KOLCH, Walter, Harald MISCHAK, and Andrew R. PITT. "The molecular make-up of a tumour: proteomics in cancer research." Clinical Science 108, no. 5 (April 22, 2005): 369–83. http://dx.doi.org/10.1042/cs20050006.
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The enormous progress in proteomics, enabled by recent advances in MS (mass spectrometry), has brought protein analysis back into the limelight of cancer research, reviving old areas as well as opening new fields of study. In this review, we discuss the basic features of proteomic technologies, including the basics of MS, and we consider the main current applications and challenges of proteomics in cancer research, including (i) protein expression profiling of tumours, tumour fluids and tumour cells; (ii) protein microarrays; (iii) mapping of cancer signalling pathways; (iv) pharmacoproteomics; (v) biomarkers for diagnosis, staging and monitoring of the disease and therapeutic response; and (vi) the immune response to cancer. All these applications continue to benefit from further technological advances, such as the development of quantitative proteomics methods, high-resolution, high-speed and high-sensitivity MS, functional protein assays, and advanced bioinformatics for data handling and interpretation. A major challenge will be the integration of proteomics with genomics and metabolomics data and their functional interpretation in conjunction with clinical results and epidemiology.
Dissertations / Theses on the topic "Proteomics research"
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Eriksson, Cecilia. "Affinity based proteomics research tools /." Stockholm : Skolan för bioteknologi, Kungliga Tekniska högskolan, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-11184.
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Falk, Ronny. "Systems enabling antibody-mediated proteomics research." Doctoral thesis, Stockholm, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4025.
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Hoffman, Melissa. "Quantitative Proteomics to Support Translational Cancer Research." Scholar Commons, 2018. https://scholarcommons.usf.edu/etd/7303.
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Altered signaling pathways, which are mediated by post-translational modifications and changes in protein expression levels, are key regulators of cancer initiation, progression, and therapeutic escape. Many aspects of cancer progression, including early carcinogenesis and immediate response to drug treatment, are beyond the scope of genetic profiling and non-invasive monitoring techniques. Global protein profiling of cancer cell line models, tumor tissues, and biofluids (e.g. serum or urine) using mass spectrometry-based proteomics produces novel biological insights, which support improved patient outcomes. Recent technological advances resulting in next-generation mass spectrometry instrumentation and improved bioinformatics workflows have led to unprecedented measurement reproducibility as well as increased depth and coverage of the human proteome. It is now possible to interrogate the cancer proteome with quantitative proteomics to identify prognostic cancer biomarkers, stratify patients for treatment, identify new therapeutic targets, and elucidate drug resistance mechanisms. There are, however, numerous challenges associated with protein measurements. Biological samples have a high level of complexity and wide dynamic range, which is even more pronounced in samples used for non-invasive disease monitoring, such as serum. Cancer biomarkers are generally found in low abundance compared to other serum proteins, particularly at early stages of disease where cancer detection would make the biggest impact on improving patient survival. Additionally, the large-scale datasets generally require bioinformatics expertise to produce useful biological insights. These difficulties converge to create obstacles for down-stream clinical translation. This dissertation research demonstrates how proteomics is applied to develop new resources and generate novel workflows to improve protein quantification in complex biosamples, which could improve translation of cancer research to benefit patient care. The studies described in this dissertation move from assessment of quantitative mass spectrometry platforms, to analytical assay development and validation, and ending with personalized biomarker development applied to patient samples.
As an example, four different quantitative mass spectrometry acquisition platforms are explored and comparisons of their ability to quantify low abundance peptides in a complex background are explored. Lung cancers frequently have aberrant signaling resulting in increased kinase activity and targetable signaling hubs; kinase inhibitors have been successfully developed and implemented clinically. Therefore, changes in amounts of kinase peptides in the complex background of peptides from all ATP-utilizing enzymes in a lung cancer cell line model after kinase inhibitor treatment was selected as a model system. Traditional mass spectrometry platforms, data dependent acquisition and multiple reaction monitoring, are compared to the two newer methods, data independent acquisition and parallel reaction monitoring. Relative quantification is performed across the four methods and analytical performance as well as downstream applications, including drug target identification and elucidation of signaling changes. Liquid chromatography – multiple reaction monitoring (LC-MRM) was selected for development of multiplexed quantitative assays based on superior sensitivity and fast analysis times, allowing for larger peptide panels. Method comparison results also provide guidelines for quantitative proteomics platform selection for translational cancer researchers.
Next, a multiplexed quantitative LC-MRM assay targeting a panel of 30 RAS signaling proteins was developed and described. Over 30% of all human cancers have a RAS mutation and these cancers are generally aggressive and limited treatment options, leading to poor patient prognosis. Many targeted inhibitors have successfully shut down RAS signaling, leading to tumor regression, however, acquired drug resistance is common. The multiplexed LC-MRM assays characterized and validated are a publically available resource for cancer researchers to interrogate the RAS signal transduction network. Feasibility has been demonstrated in cell line models in order to identify signaling changes that confer BRAF inhibitor resistance and biomarkers of sensitivity to treatment. This analytical LC-MRM panel could support meaningful development of new therapeutic options and identification of companion biomarkers, with the end goal of improving patient outcomes.
Multiplexed LC-MRM assays developed for personalized disease biomarkers using an integrated multi-omics approach are described for Multiple Myeloma, an incurable malignancy with poor patient outcomes. This disease is characterized by clonal expansion of the plasma cells in the bone marrow, which secrete a monoclonal immunoglobulin, or M-protein. Clinical treatment decisions are based on multiple semi-quantitative assays that require manual evaluation. In the clinic, minimal residual disease quantification methods, including multi-parameter flow cytometry and immunohistochemistry, are applied to bone marrow aspirates, which is a highly invasive technique that does not provide a systemic evaluation of the disease. To address these issues, we hypothesized that unique variable region peptides could be identified and LC-MRM assays developed specific to each patient’s M-protein to improve specificity and sensitivity in non-invasive disease monitoring. A proteogenomics approach was used to design personalized assays for each patient to monitor their disease progression, which demonstrate improved specificity and up to a 500-fold increase in sensitivity compared to current clinical methods. Assays can be developed from marrow aspirates collected when the patient was at residual disease stage, which is useful if no sample with high disease burden is available. The patient-specific tests are also multiplexed with constant region peptide assays that monitor all immunoglobulin heavy and light chain classes, which could reduce analysis to a single test. In conclusion, highly sensitive patient-specific assays have been developed that could change the paradigm for patient evaluation and clinical decision-making, increasing the ability of clinicians to continue first line therapy in the hopes of achieving a cure, or to intervene at an earlier time point in disease recurrence. This study also provides a blueprint for future development of personalized diagnostics, which could be applied to biomarkers of other cancer types.
Overall, these studies demonstrate how quantitative proteomics can be used to support translational cancer research, from the impact of different mass spectrometry platforms on elucidating signaling changes and drug targets to the characterization of multiplexed LC-MRM assays applied to cell line models for translational research purposes and in patient serum samples optimized for clinical translation. We believe that mass spectrometry-based proteomics is poised to play a pivotal role in personalized diagnostics to support implementation of precision medicine, an effort that will improve the quality and efficiency of patient care.
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Gibson, Frank. "The development of standards for proteomics research and a proteomics investigation of diabetic adipocyte models." Thesis, University of Newcastle Upon Tyne, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.445541.
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Larsson, Karin. "Generation and characterization of antibodies for proteomics research." Doctoral thesis, Stockholm : Skolan för bioteknologi, Kungliga Tekniska högskolan, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-11425.
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Pujari, Goutam. "Current and future trends in proteomics (SELDI-TOF) in clinical diagnosis and clinical research." Thesis, Click to view the E-thesis via HKUTO, 2004. http://sunzi.lib.hku.hk/hkuto/record/B31972111.
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Muir, Matthew Stewart. "Proteomics of the ovine cataract." Diss., Lincoln University, 2008. http://hdl.handle.net/10182/792.
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The lens of the eye needs to be completely transparent in order to allow all light entering the eye to reach the retina. This transparency is maintained by the highly ordered structure of the lens proteins the crystallins. Any disruption to the lens proteins can cause an opacity to develop which is known as cataract. During cortical cataract formation there is increased truncation of the lens crystallins. It is believed that overactivation of calcium-dependent cysteine proteases, the calpains, is responsible for the increased proteolysis of the crystallins seen during cataractogenesis. Within the ovine lens there are three calpains, calpain 1, 2 and the lens specific calpain Lp82. The aim of this thesis was to determine the changes in the lens proteins during ageing and cataractogenesis, and to establish the role of the calpains in these processes. Calpain 1 and 2 were purified from ovine lung and Lp82 was purified from lamb lenses using chromatography. Activity and presence of the calpains was determined by using the BODIPY-FL casein assay, gel electrophoresis, Western blot and casein zymography. Changes in the lens proteins, specifically the crystallins, were visualised using two-dimensional electrophoresis (2DE). Lenses from fetal, 6 month old and 8 year old sheep were collected, as well as stage 0, 1, 3 and 6 cataractous ovine lenses. The proteins from the lenses were separated into the water soluble and urea soluble fractions and analysed by 2DE. Mass spectrometry was used to determine the masses and therefore modifications of the crystallins. Finally, the individual crystallins were separated using gel filtration chromatography and incubated with the purified calpains in the presence of calcium. The extent of the proteolysis was visualised using 2DE and truncation sites determined by mass spectrometry. Purification of the calpains resulted in samples that were specific for each calpain and could be used in further experiments. 2DE analysis showed that there were changes to the crystallins during maturation of the lens. The α-crystallins become increasingly phosphorylated as the lens ages and a small amount becomes truncated. The β-crystallins were also modified during ageing by truncation and deamidation. When crystallins from cataractous lenses were compared using 2DE there were changes to both the α- and β-crystallins. The α-crystallins were found to be extensively truncated at their C-terminal tail. Four of the seven β-crystallins, βB1, βB3, βB2 and βA3, showed increased truncation of their N-terminal extensions during cataract formation. All three calpains truncated αA and αB-crystallin at their C-terminal ends after incubation. Calpain 2 and Lp82 each produced unique αA-crystallin truncations. All three calpains truncated βB1 and βA3 and calpain 2 also truncated βB3. When the truncations from the calpain incubations were compared to those seen during cataract formation, many of the truncations were found to be similar. Both the unique truncations from calpain 2 and Lp82 were found in cataractous lenses, with the Lp82 more obvious in the 2DE. The β-crystallin truncations found after incubation with the calpains were similar to those found during cataractogenesis. In conclusion this study documents the changes to the ovine lens during maturation and cataractogenesis and indicates a role for the calpain family in the increased proteolysis observed in the ovine cataract.
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Spicka, Kevin James. "Design and synthesis of fluorescent dyes for use in proteomic research." Thesis, Montana State University, 2008. http://etd.lib.montana.edu/etd/2008/spicka/SpickaK0808.pdf.
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Proteomics is a rapidly developing field requiring powerful new technology in order to be able to detect proteins at increasingly lower concentrations. To aid in the detection of proteins at lower concentrations, DIGE dyes, a family of spectrally resolved fluorescent dyes, are currently available to proteomic researchers for 2D gel analysis. However, the demands of protein detection dictate that dyes that are even more sensitive and versatile be created. The syntheses of highly sensitive, water soluble BODIPY fluorophore dyes are described. These dyes are proposed to have the necessary sensitivity to allow for detection of proteins in much lower concentrations, providing an improvement over current protein detection limits. The BODIPY dyes that have been synthesized are available in a variety of absorbances and emissions. While fluorescent dyes that are amine-reactive are the most popular covalently binding protein labeling markers being used in today's proteomic research, thiol-reactive fluorescent markers are gaining importance in proteomic research. Since thiol residues are less common in proteins compared to their amine counterparts, saturation labeling and quantification are more easily achieved. The syntheses of sensitive thiol- reactive fluorescent dyes are described. These syntheses allow for quick generation of thiol-reactive fluorescent markers to be used in proteomic research.
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Balluff, Benjamin. "MALDI imaging mass spectrometry in clinical proteomics research of gastric cancer tissues." Diss., lmu, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-155986.
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Zhang, Songya [Verfasser], Andreas [Akademischer Betreuer] Bechthold, and Irmgard [Akademischer Betreuer] Merfort. "Genomics, proteomics and secondary metabolites biosynthesis research on Streptomyces asterosporus DSM 41452." Freiburg : Universität, 2018. http://d-nb.info/115950511X/34.
Full textBooks on the topic "Proteomics research"
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Anscomb, Anne. The Kalorama proteomics 50: Competing technologies and alliances. New York: Kalorama Information, 2001.
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Sensen, C. W. Handbook of genome research: Genomics, proteomics, metabolomics, bioinformatics, ethical, and legal issues. Weinheim: Wiley-VCH, 2005.
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Proteomics of biological systems: Protein phosphorylation using mass spectrometry techniques. Hoboken, N.J: John Wiley & Sons, 2012.
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Dassanayake, Ranil S. Genomic and proteomic techniques: In post genomics era. Oxford: Alpha Science International, 2011.
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Introduction to proteomics: Tools for the new biology. Totowa, NJ: Humana Press, 2002.
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Kenneth, Blum, and Madigan Margaret A, eds. OMICS: Biomedical perspectives and applications. Boca Raton: Taylor & Francis, 2012.
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Guest, Paul C., ed. Proteomic Methods in Neuropsychiatric Research. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-52479-5.
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Bioinformatics: The impact of accurate quantification on proteomic and genetic analysis and research. Toronto: Apple Academic Press, 2014.
Find full textBook chapters on the topic "Proteomics research"
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Klocke, Rainer, Sergiu Scobioala, and Sigrid Nikol. "Cardiovascular Proteomics." In Cardiovascular Research, 65–74. Boston, MA: Springer US, 2006. http://dx.doi.org/10.1007/0-387-23329-6_3.
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Ahmed, Meftun. "Proteomics Proteomics and Islet Research." In Islets of Langerhans, 1131–63. Dordrecht: Springer Netherlands, 2014. http://dx.doi.org/10.1007/978-94-007-6686-0_12.
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Langen, Hanno, and Peter Berndt. "Proteomics Databases." In Proteome Research: Mass Spectrometry, 229–57. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-56895-4_12.
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Gupta, Manoj Kumar, Gayatri Gouda, S. Sabarinathan, Ravindra Donde, Pallabi Pati, Sushil Kumar Rathore, Ramakrishna Vadde, and Lambodar Behera. "Structural Proteomics." In Bioinformatics in Rice Research, 239–56. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-3993-7_11.
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Ashman, Keith, Greg Rice, and Murray Mitchell. "Proteomics Methods." In Molecular Pathology in Cancer Research, 219–37. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6643-1_10.
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Sanchez, Jean-Charles, Yohann Couté, Laure Allard, Pierre Lescuyer, and Denis F. Hochstrasser. "Biomedical Applications of Proteomics." In Proteome Research, 193–221. Berlin, Heidelberg: Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/978-3-540-72910-5_9.
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Gupta, Archana P., Zbynek Bozdech, and Peter R. Preiser. "Transcriptomics and proteomics." In Advances in Malaria Research, 197–217. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2016. http://dx.doi.org/10.1002/9781118493816.ch8.
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Ahmed, Meftun. "Proteomics and Islet Research." In Advances in Experimental Medicine and Biology, 363–90. Dordrecht: Springer Netherlands, 2010. http://dx.doi.org/10.1007/978-90-481-3271-3_16.
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Ahmed, Meftun. "Proteomics and Islet Research." In Islets of Langerhans, 2. ed., 1–31. Dordrecht: Springer Netherlands, 2013. http://dx.doi.org/10.1007/978-94-007-6884-0_12-1.
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Villar, Elena Lopez, and William Chi-Shing Cho. "Proteomics and Cancer Research." In Translational Bioinformatics, 75–101. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-5811-7_4.
Full textConference papers on the topic "Proteomics research"
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Evans, Caroline. "Application of Proteomics to Biomedical Research." In University of Sheffield Engineering Symposium. USES, 2015. http://dx.doi.org/10.15445/01022014.23.
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Ouyang, Jingying. "Research techniques and applications of proteomics." In 4TH INTERNATIONAL CONFERENCE ON FRONTIERS OF BIOLOGICAL SCIENCES AND ENGINEERING (FBSE 2021). AIP Publishing, 2022. http://dx.doi.org/10.1063/5.0094305.
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Hashim, O. "Proteomics Approach To Cancer Studies." In 2nd International University of Malaya Research Imaging Symposium (UMRIS) 2005: Fundamentals of Molecular Imaging. Kuala Lumpur, Malaysia: Department of Biomedical Imaging, University of Malaya, 2005. http://dx.doi.org/10.2349/biij.1.1.e7-41.
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Massion, Pierre. "Abstract CN14-02: Proteomics strategies for lung cancer diagnostics." In Abstracts: Frontiers in Cancer Prevention Research 2008. American Association for Cancer Research, 2008. http://dx.doi.org/10.1158/1940-6207.prev-08-cn14-02.
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Ding, Jianchen. "Proteomics and Radiomics in Diagnosis of Nasopharyngeal Carcinoma." In ICBRA 2021: 2021 8th International Conference on Bioinformatics Research and Applications. New York, NY, USA: ACM, 2021. http://dx.doi.org/10.1145/3487027.3487030.
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Li, KC. "New Clinical Approaches Combining Genomics And Proteomics With Imaging." In 2nd International University of Malaya Research Imaging Symposium (UMRIS) 2005: Fundamentals of Molecular Imaging. Kuala Lumpur, Malaysia: Department of Biomedical Imaging, University of Malaya, 2005. http://dx.doi.org/10.2349/biij.1.1.e7-54.
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Wang, Zhen, Jiyang Zhang, Yunping Zhu, and Hongwei Xie. "Research on Efficient Algorithm of Peptide Identification and Quantification in Proteomics." In International Conference on Biomedical and Biological Engineering. Paris, France: Atlantis Press, 2016. http://dx.doi.org/10.2991/bbe-16.2016.22.
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Aoki, Fujiko, Kenshi Haraguchi, Arata Shiraishi, Takeo Yoshimura, and Shokichi Ohuchi. "Microwave assisted trypsin digestion with cavity type resonator reactor as an innovative proteomics technology." In 2016 Progress in Electromagnetic Research Symposium (PIERS). IEEE, 2016. http://dx.doi.org/10.1109/piers.2016.7735585.
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Vickers, Sofia Lage, Juan Antonio Bizzotto, Alejandra Paez, Javier Cotignola, Carlos Scorticati, Osvaldo Mazza, Pia Valacco, Geraldine Gueron, and Elba Vazquez. "Abstract A058: Integrative prostate cancer tissue proteomics dissects clear and distinct proteomes for human prostate cancer and benign prostatic hyperplasia." In Abstracts: AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; December 2-5, 2017; Orlando, Florida. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.prca2017-a058.
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Dubois, Etienne, Antonio Nunez Galindo, Loic Dayon, and Ornella Cominetti. "Comparison of normalization methods in clinical research applications of mass spectrometry-based proteomics." In 2020 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2020. http://dx.doi.org/10.1109/cibcb48159.2020.9277702.
Full textReports on the topic "Proteomics research"
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Heifetz, Yael, and Michael Bender. Success and failure in insect fertilization and reproduction - the role of the female accessory glands. United States Department of Agriculture, December 2006. http://dx.doi.org/10.32747/2006.7695586.bard.
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The research problem. Understanding of insect reproduction has been critical to the design of insect pest control strategies including disruptions of mate-finding, courtship and sperm transfer by male insects. It is well known that males transfer proteins to females during mating that profoundly affect female reproductive physiology, but little is known about the molecular basis of female mating response and no attempts have yet been made to interfere with female post-mating responses that directly bear on the efficacy of fertilization. The female reproductive tract provides a crucial environment for the events of fertilization yet thus far those events and the role of the female tract in influencing them are poorly understood. For this project, we have chosen to focus on the lower reproductive tract because it is the site of two processes critical to reproduction: sperm management (storage, maintenance, and release from storage) and fertilization. E,fforts during this project period centered on the elucidation of mating responses in the female lower reproductive tract The central goals of this project were: 1. To identify mating-responsive genes in the female lower reproductive tract using DNA microarray technology. 2. In parallel, to identify mating-responsive genes in these tissues using proteomic assays (2D gels and LC-MS/MS techniques). 3. To integrate proteomic and genomic analyses of reproductive tract gene expression to identify significant genes for functional analysis. Our main achievements were: 1. Identification of mating-responsive genes in the female lower reproductive tract. We identified 539 mating-responsive genes using genomic and proteomic approaches. This analysis revealed a shift from gene silencing to gene activation soon after mating and a peak in differential gene expression at 6 hours post-mating. In addition, comparison of the two datasets revealed an expression pattern consistent with the model that important reproductive proteins are pre-programmed for synthesis prior to mating. This work was published in Mack et al. (2006). Validation experiments using real-time PCR techniques suggest that microarray assays provide a conservativestimate of the true transcriptional activity in reproductive tissues. 2.lntegration of proteomics and genomics data sets. We compared the expression profiles from DNA microarray data with the proteins identified in our proteomic experiments. Although comparing the two data sets poses analyical challenges, it provides a more complete view of gene expression as well as insights into how specific genes may be regulated. This work was published in Mack et al. (2006). 3. Development of primary reproductive tract cell cultures. We developed primary cell cultures of dispersed reproductive tract cell types and determined conditions for organ culture of the entire reproductive tract. This work will allow us to rapidly screen mating-responsive genes for a variety of reproductive-tract specifi c functions. Scientific and agricultural significance. Together, these studies have defined the genetic response to mating in a part of the female reproductive tract that is critical for successful fertllization and have identified alarge set of mating-responsive genes. This work is the first to combine both genomic and proteomic approaches in determining female mating response in these tissues and has provided important insights into insect reproductive behavior.
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Chen, Xiaole, Peng Wang, Yunquan Luo, Yi-Yu Lu, Wenjun Zhou, Mengdie Yang, Jian Chen, Zhi-Qiang Meng, and Shi-Bing Su. Therapeutic Efficacy Evaluation and Underlying Mechanisms Prediction of Jianpi Liqi Decoction for Hepatocellular Carcinoma. Science Repository, September 2021. http://dx.doi.org/10.31487/j.jso.2021.02.04.sup.
Full textAbstract:
Objective: The aim of this study was to assess the therapeutic effects of Jianpi Liqi decoction (JPLQD) in hepatocellular carcinoma (HCC) and explore its underlying mechanisms. Methods: The characteristics and outcomes of HCC patients with intermediate stage B who underwent sequential conventional transcatheter arterial chemoembolization (cTACE) and radiofrequency ablation (RFA) only or in conjunction with JPLQD were analysed retrospectively. The plasma proteins were screened using label-free quantitative proteomics analysis. The effective mechanisms of JPLQD were predicted through network pharmacology approach and partially verified by ELISA. Results: Clinical research demonstrated that the Karnofsky Performance Status (KPS), traditional Chinese medicine (TCM) syndrome scores, neutropenia and bilirubin, median progression-free survival (PFS), and median overall survival (OS) in HCC patients treated with JPLQD were superior to those in patients not treated with JPLQD (all P<0.05). The analysis of network pharmacology, combined with proteomics, suggested that 52 compounds targeted 80 potential targets, which were involved in the regulation of multiple signaling pathways, especially affecting the apoptosis-related pathways including TNF, p53, PI3K-AKT, and MAPK. Plasma IGFBP3 and CA2 were significantly up-regulated in HCC patients with sequential cTACE and RFA therapy treated with JPLQD than those in patients not treated with JPLQD (P<0.001). The AUC of the IGFBP3 and CA2 panel, estimated using ROC analysis for JPLQD efficacy evaluation, was 0.867. Conclusion: These data suggested that JPLQD improves the quality of life, prolongs the overall survival, protects liver function in HCC patients, and exhibits an anticancer activity against HCC. IGFBP3 and CA2 panels may be potential therapeutic targets and indicators in the efficacy evaluation for JPLQD treatment, and the effective mechanisms involved in the regulation of multiple signaling pathways, possibly affected the regulation of apoptosis.
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Ghanim, Murad, Joe Cicero, Judith K. Brown, and Henryk Czosnek. Dissection of Whitefly-geminivirus Interactions at the Transcriptomic, Proteomic and Cellular Levels. United States Department of Agriculture, February 2010. http://dx.doi.org/10.32747/2010.7592654.bard.
Full textAbstract:
Our project focuses on gene expression and proteomics of the whitefly Bemisia tabaci (Gennadius) species complex in relation to the internal anatomy and localization of expressed genes and virions in the whitefly vector, which poses a major constraint to vegetable and fiber production in Israel and the USA. While many biological parameters are known for begomovirus transmission, nothing is known about vector proteins involved in the specific interactions between begomoviruses and their whitefly vectors. Identifying such proteins is expected to lead to the design of novel control methods that interfere with whitefly-mediated begomovirus transmission. The project objectives were to: 1) Perform gene expression analyses using microarrays to study the response of whiteflies (B, Q and A biotypes) to the acquisition of begomoviruses (Tomato yellow leaf curl (TYLCV) and Squash leaf curl (SLCV). 2) Construct a whitefly proteome from whole whiteflies and dissected organs after begomovirus acquisition. 3) Validate gene expression by q-RTPCR and sub-cellular localization of candidate ESTs identified in microarray and proteomic analyses. 4) Verify functionality of candidate ESTs using an RNAi approach, and to link these datasets to overall functional whitefly anatomical studies. During the first and second years biological experiments with TYLCV and SLCV acquisition and transmission were completed to verify the suitable parameters for sample collection for microarray experiments. The parameters were generally found to be similar to previously published results by our groups and others. Samples from whole whiteflies and midguts of the B, A and Q biotypes that acquired TYLCV and SLCV were collected in both the US and Israel and hybridized to B. tabaci microarray. The data we analyzed, candidate genes that respond to both viruses in the three tested biotypes were identified and their expression that included quantitative real-time PCR and co-localization was verified for HSP70 by the Israeli group. In addition, experiments were undertaken to employ in situ hybridization to localize several candidate genes (in progress) using an oligonucleotide probe to the primary endosymbiont as a positive control. A proteome and corresponding transcriptome to enable more effective protein identification of adult whiteflies was constructed by the US group. Further validation of the transmission route of begomoviruses, mainly SLCV and the involvement of the digestive and salivary systems was investigated (Cicero and Brown). Due to time and budget constraints the RNAi-mediated silencing objective to verify gene function was not accomplished as anticipated. HSP70, a strong candidate protein that showed over-expression after TYLCV and SLCV acquisition and retention by B. tabaci, and co-localization with TYLCV in the midgut, was further studies. Besides this protein, our joint research resulted in the identification of many intriguing candidate genes and proteins that will be followed up by additional experiments during our future research. To identify these proteins it was necessary to increase the number and breadth of whitefly ESTs substantially and so whitefly cDNAs from various libraries made during the project were sequenced (Sanger, 454). As a result, the proteome annotation (ID) was far more successful than in the initial attempt to identify proteins using Uniprot or translated insect ESTs from public databases. The extent of homology shared by insects in different orders was surprisingly low, underscoring the imperative need for genome and transcriptome sequencing of homopteran insects. Having increased the number of EST from the original usable 5500 generated several years ago to >600,000 (this project+NCBI data mining), we have identified about one fifth of the whitefly proteome using these new resources. Also we have created a database that links all identified whitefly proteins to the PAVEdb-ESTs in the database, resulting in a useful dataset to which additional ESTS will be added. We are optimistic about the prospect of linking the proteome ID results to the transcriptome database to enable our own and other labs the opportunity to functionally annotate not only genes and proteins involved in our area of interest (whitefly mediated transmission) but for the plethora of other functionalities that will emerge from mining and functionally annotating other key genes and gene families in whitefly metabolism, development, among others. This joint grant has resulted in the identification of numerous candidate proteins involved in begomovirus transmission by B. tabaci. A next major step will be to capitalize on validated genes/proteins to develop approaches to interfere with the virus transmission.
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Manulis, Shulamit, Christine D. Smart, Isaac Barash, Guido Sessa, and Harvey C. Hoch. Molecular Interactions of Clavibacter michiganensis subsp. michiganensis with Tomato. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7697113.bard.
Full textAbstract:
Clavibacter michiganensis subsp. michiganensis (Cmm), the causal agent of bacterial wilt and canker of tomato, is the most destructive bacterial disease of tomato causing substantial economic losses in Israel, the U.S.A. and worldwide. The molecular strategies that allow Cmm, a Gram-positive bacterium, to develop a successful infection in tomato plants are largely unknown. The goal of the project was to elucidate the molecular interactions between Cmmand tomato. The first objective was to analyze gene expression profiles of susceptible tomato plants infected with pathogenic and endophytic Cmmstrains. Microarray analysis identified 122 genes that were differentially expressed during early stages of infection. Cmm activated typical basal defense responses in the host including induction of defense-related genes, production of scavenging of free oxygen radicals, enhanced protein turnover and hormone synthesis. Proteomic investigation of the Cmm-tomato interaction was performed with Multi-Dimensional Protein Identification Technology (MudPIT) and mass spectroscopy. A wide range of enzymes secreted by Cmm382, including cell-wall degrading enzymes and a large group of serine proteases from different families were identified in the xylem sap of infected tomato. Based on proteomic results, the expression pattern of selected bacterial virulence genes and plant defense genes were examined by qRT-PCR. Expression of the plasmid-borne cellulase (celA), serine protease (pat-1) and serine proteases residing on the chp/tomA pathogenicity island (chpCandppaA), were significantly induced within 96 hr after inoculation. Transcription of chromosomal genes involved in cell wall degradation (i.e., pelA1, celB, xysA and xysB) was also induced in early infection stages. The second objective was to identify by VIGS technology host genes affecting Cmm multiplication and appearance of disease symptoms in plant. VIGS screening showed that out of 160 tomato genes, which could be involved in defense-related signaling, suppression of 14 genes led to increase host susceptibility. Noteworthy are the genes Snakin-2 (inhibitor of Cmm growth) and extensin-like protein (ELP) involved in cell wall fortification. To further test the significance of Snakin -2 and ELP in resistance towards Cmm, transgenic tomato plants over-expressing the two genes were generated. These plants showed partial resistance to Cmm resulting in a significant delay of the wilt symptoms and reduction in size of canker lesion compared to control. Furthermore, colonization of the transgenic plants was significantly lower. The third objective was to assess the involvement of ethylene (ET), jasmonate (JA) and salicylic acid (SA) in Cmm infection. Microarray and proteomic studies showed the induction of enzymes involved in ET and JA biosynthesis. Cmm promoted ET production 8 days after inoculation and SIACO, a key enzyme of ET biosynthesis, was upregulated. Inoculation of the tomato mutants Never ripe (Nr) impaired in ET perception and transgenic plants with reduced ET synthesis significantly delayed wilt symptoms as compared to the wild-type plants. The retarded wilting in Nr plants was shown to be a specific effect of ET insensitivity and was not due to altered expression of defense related genes, reduced bacterial population or decrease in ethylene biosynthesis . In contrast, infection of various tomato mutants impaired in JA biosynthesis (e.g., def1, acx1) and JA insensitive mutant (jai1) yielded unequivocal results. The fourth objective was to determine the role of cell wall degrading enzymes produced by Cmm in xylem colonization and symptoms development. A significance increase (2 to 7 fold) in expression of cellulases (CelA, CelB), pectate lyases (PelA1, PelA2), polygalacturonase and xylanases (XylA, XylB) was detected by qRT-PCR and by proteomic analysis of the xylem sap. However, with the exception of CelA, whose inactivation led to reduced wilt symptoms, inactivation of any of the other cell wall degrading enzymes did not lead to reduced virulence. Results achieved emphasized the complexity involved in Cmm-tomato interactions. Nevertheless they provide the basis for additional research which will unravel the mechanism of Cmm pathogenicity and formulating disease control measures.
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Ron, Eliora, and Eugene Eugene Nester. Global functional genomics of plant cell transformation by agrobacterium. United States Department of Agriculture, March 2009. http://dx.doi.org/10.32747/2009.7695860.bard.
Full textAbstract:
The aim of this study was to carry out a global functional genomics analysis of plant cell transformation by Agrobacterium in order to define and characterize the physiology of Agrobacterium in the acidic environment of a wounded plant. We planed to study the proteome and transcriptome of Agrobacterium in response to a change in pH, from 7.2 to 5.5 and identify genes and circuits directly involved in this change. Bacteria-plant interactions involve a large number of global regulatory systems, which are essential for protection against new stressful conditions. The interaction of bacteria with their hosts has been previously studied by genetic-physiological methods. We wanted to make use of the new capabilities to study these interactions on a global scale, using transcription analysis (transcriptomics, microarrays) and proteomics (2D gel electrophoresis and mass spectrometry). The results provided extensive data on the functional genomics under conditions that partially mimic plant infection and – in addition - revealed some surprising and significant data. Thus, we identified the genes whose expression is modulated when Agrobacterium is grown under the acidic conditions found in the rhizosphere (pH 5.5), an essential environmental factor in Agrobacterium – plant interactions essential for induction of the virulence program by plant signal molecules. Among the 45 genes whose expression was significantly elevated, of special interest is the two-component chromosomally encoded system, ChvG/I which is involved in regulating acid inducible genes. A second exciting system under acid and ChvG/Icontrol is a secretion system for proteins, T6SS, encoded by 14 genes which appears to be important for Rhizobium leguminosarum nodule formation and nitrogen fixation and for virulence of Agrobacterium. The proteome analysis revealed that gamma aminobutyric acid (GABA), a metabolite secreted by wounded plants, induces the synthesis of an Agrobacterium lactonase which degrades the quorum sensing signal, N-acyl homoserine lactone (AHL), resulting in attenuation of virulence. In addition, through a transcriptomic analysis of Agrobacterium growing at the pH of the rhizosphere (pH=5.5), we demonstrated that salicylic acid (SA) a well-studied plant signal molecule important in plant defense, attenuates Agrobacterium virulence in two distinct ways - by down regulating the synthesis of the virulence (vir) genes required for the processing and transfer of the T-DNA and by inducing the same lactonase, which in turn degrades the AHL. Thus, GABA and SA with different molecular structures, induce the expression of these same genes. The identification of genes whose expression is modulated by conditions that mimic plant infection, as well as the identification of regulatory molecules that help control the early stages of infection, advance our understanding of this complex bacterial-plant interaction and has immediate potential applications to modify it. We expect that the data generated by our research will be used to develop novel strategies for the control of crown gall disease. Moreover, these results will also provide the basis for future biotechnological approaches that will use genetic manipulations to improve bacterial-plant interactions, leading to more efficient DNA transfer to recalcitrant plants and robust symbiosis. These advances will, in turn, contribute to plant protection by introducing genes for resistance against other bacteria, pests and environmental stress.
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Blumwald, Eduardo, and Avi Sadka. Sugar and Acid Homeostasis in Citrus Fruit. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7697109.bard.
Full textAbstract:
Citrus fruit quality standards have been determined empirically, depending on species and on the particular growing regions. In general, the TSS (total soluble solids) to total acidity (TA) ratio determines whether citrus fruit can be marketed. Soluble sugars account for most of the TSS during harvest while TA is determined almost solely by the citric acid content, which reaches levels of 1-5% by weight in many cultivated varieties. Acid and sugar homeostasis in the fruit is critical for the management of existing cultivars, the development of new cultivars, the improvement of pre- and post-harvest strategies and the control of fruit quality and disorders. The current proposal (a continuation of a previous proposal) aimed at: (1) completing the citrus fruit proteome and metabolome, and establish a citrus fruit functional database, (2) further characterization of the control of fruit acidity by studying the regulation of key steps affecting citrate metabolism, and determine the fate of citrate during acid decline stage, and (3) Studying acid and sugar homeostasis in citrus fruits by characterizing transport mechanisms across membranes. These aims were completed as the following: (1) Our initial efforts were aimed at the characterization and identification of citric acid transporters in citrus juice cells. The identification of citrate transporters at the vacuole of the citrus juice cell indicated that the steady-state citrate cytosolic concentration and the action of the cytosolic aconitase were key elements in establishing the pH homeostat in the cell that regulates the metabolic shift towards carbon usage in the fruit during the later stages of fruit development. We focused on the action of aconitase, the enzyme mediating the metabolic use of citric acid in the cells, and identified processes that control carbon fluxes in developing citrus fruits that control the fruit acid load; (2) The regulation of aconitase, catalyzing a key step in citrate metabolism, was further characterized by using two inhibitors, citramalte and oxalomalte. These compounds significantly increased citrate content and reduced the enzyme’s activity. Metabolite profiling and changes of amino-acid metabolizing enzymes in oxalomalate- treated cells suggested that the increase in citrate, caused by aconitase inhibition, induces amino acid synthesis and the GABA shunt, in accordance with the suggested fate of citrate during the acid decline stage in citrus fruit. (3) We have placed a considerable amount of time on the development of a citrus fruit proteome that will serve to identify all of the proteins in the juice cells and will also serve as an aid to the genomics efforts of the citrus research community (validating the annotation of the fruit genes and the different ESTs). Initially, we identified more than 2,500 specific fruit proteins and were able to assign a function to more than 2,100 proteins (Katz et al., 2007). We have now developed a novel Differential Quantitative LC-MS/MS Proteomics Methodology for the identification and quantitation of key biochemical pathways in fruits (Katz et al., 2010) and applied this methodology to identify determinants of key traits for fruit quality (Katz et al., 2011). We built “biosynthesis maps” that will aid in defining key pathways associated with the development of key fruit quality traits. In addition, we constructed iCitrus (http://wiki.bioinformatics.ucdavis.edu/index.php/ICitrus), a “functional database” that is essentially a web interface to a look-up table that allows users to use functional annotations in the web to identify poorly annotated citrus proteins. This resource will serve as a tool for growers and field extension specialists.
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Schaffer, Arthur A., and Jocelyn Rose. Understanding Cuticle Development in Tomato through the Study of Novel Germplasm with Malformed Cuticles. United States Department of Agriculture, June 2013. http://dx.doi.org/10.32747/2013.7593401.bard.
Full textAbstract:
Plant cuticle development and metabolism are still poorly understood, partly due to the chemical complexity of the cuticular layer. The overall research objective was to broaden and deepen our understanding of tomato fruit cuticle development by analyzing novel germplasm with cuticular malformations and by studying the transcriptome and proteome of the fruit epidermal tissues, as strategies to overcome the challenges posed by the recalcitrance of the biological system. During the project we succeeded in identifying two genes with major impact on cuticle development. One of these encoded the first cutin synthase to be identified in plants, a metabolic step that had been a black box in cutin synthesis. In addition genes controlling the triterpenoid components of the cuticle were identified and, most interestingly, genetic variability for this component was identified among the wild tomato species germplasm. Additional germplasm was developed based on interspecific crosses that will allow for the future characterization of modifier genes that interact with the microfissuring gene (CWP) to promote or inhibit fruit cracking. One of the major accomplishments of the joint project was the integrated transcriptomic and proteomic analysis of the fruit cuticle and underlying tissues which allows for the identification of the pericarp cell layers responsible for the extracellular, cuticle-localized protein component. The results of the project have expanded our understanding of tomato fruit cuticle development and its genetic control. In addition, germplasm developed will be useful in developing tomato varieties resistant to cracking, on the one hand, and varieties useful for the dehydration industry on the other.
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Manulis-Sasson, Shulamit, Christine D. Smart, Isaac Barash, Laura Chalupowicz, Guido Sessa, and Thomas J. Burr. Clavibacter michiganensis subsp. michiganensis-tomato interactions: expression and function of virulence factors, plant defense responses and pathogen movement. United States Department of Agriculture, February 2015. http://dx.doi.org/10.32747/2015.7594405.bard.
Full textAbstract:
Clavibactermichiganensissubsp. michiganensis(Cmm), the causal agent of bacterial wilt and canker of tomato, is the most destructive bacterial disease of tomato causing substantial economic losses in Israel, the U.S.A. and worldwide. The goal of the project was to unravel the molecular strategies that allow Cmm, a Gram-positive bacterium, to develop a successful infection in tomato. The genome of Cmm contains numerous genes encoding for extracellular serine proteases and cell wall degrading enzymes. The first objective was to elucidate the role of secreted serine proteases in Cmm virulence. Mutants of nine genes encoding serine proteases of 3 different families were tested for their ability to induce wilting, when tomato stems were puncture-inoculated, as compared to blisters formation on leaves, when plants were spray-inoculated. All the mutants showed reduction in wilting and blister formation as compared to the wild type. The chpCmutant displayed the highest reduction, implicating its major role in symptom development. Five mutants of cell wall degrading enzymes and additional genes (i.e. perforin and sortase) caused wilting but were impaired in their ability to form blisters on leaves. These results suggest that Cmm differentially expressed virulence genes according to the site of penetration. Furthermore, we isolated and characterized two Cmmtranscriptional activators, Vatr1 and Vatr2 that regulate the expression of virulence factors, membrane and secreted proteins. The second objective was to determine the effect of bacterial virulence genes on movement of Cmm in tomato plants and identify the routes by which the pathogen contaminates seeds. Using a GFP-labeledCmm we could demonstrate that Cmm extensively colonizes the lumen of xylem vessels and preferentially attaches to spiral secondary wall thickening of the protoxylem and formed biofilm-like structures composed of large bacterial aggregates. Our findings suggest that virulence factors located on the chp/tomAPAI or the plasmids are required for effective movement of the pathogen in tomato and for the formation of cellular aggregates. We constructed a transposon plasmid that can be stably integrated into Cmm chromosome and express GFP, in order to follow movement to the seeds. Field strains from New York that were stably transformed with this construct, could not only access seeds systemically through the xylem, but also externally through tomato fruit lesions, which harbored high intra-and intercellular populations. Active movement and expansion of bacteria into the fruit mesocarp and nearby xylem vessels followed, once the fruit began to ripen. These results highlight the ability of Cmm to invade tomato fruit and seed through multiple entry routes. The third objective was to assess correlation between disease severity and expression levels of Cmm virulence genes and tomato defense genes. The effect of plant age on expression of tomato defense related proteins during Cmm infection was analyzed by qRT-PCR. Five genes out of eleven showed high induction at early stages of infection of plants with 19/20 leaves compared to young plants bearing 7/8 leaves. Previous results showed that Cmm virulence genes were expressed at early stages of infection in young plants compared to older plants. Results of this study suggest that Cmm virulence genes may suppress expression of tomato defense-related genes in young plants allowing effective disease development. The possibility that chpCis involved in suppression of tomato defense genes is currently under investigation by measuring the transcript level of several PR proteins, detected previously in our proteomics study. The fourth objective was to define genome location and stability of virulence genes in Cmm strains. New York isolates were compared to Israeli, Serbian, and NCPPB382 strains. The plasmid profiles of New York isolates were diverse and differed from both Israeli and Serbian strains. PCR analysis indicated that the presence of putative pathogenicity genes varied between isolates and highlighted the ephemeral nature of pathogenicity genes in field populations of Cmm. Results of this project significantly contributed to the understanding of Cmm virulence, its movement within tomato xylem or externally into the seeds, the role of serine proteases in disease development and initiated research on global regulation of Cmm virulence. These results form a basis for developing new strategies to combat wilt and canker disease of tomato.
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Harman, Gary E., and Ilan Chet. Enhancement of plant disease resistance and productivity through use of root symbiotic fungi. United States Department of Agriculture, July 2008. http://dx.doi.org/10.32747/2008.7695588.bard.
Full textAbstract:
The objectives of the project were to (a) compare effects ofT22 and T-203 on growth promotion and induced resistance of maize inbred line Mol7; (b) follow induced resistance of pathogenesis-related proteins through changes in gene expression with a root and foliar pathogen in the presence or absence of T22 or T-203 and (c) to follow changes in the proteome of Mol? over time in roots and leaves in the presence or absence of T22 or T-203. The research built changes in our concepts regarding the effects of Trichoderma on plants; we hypothesized that there would be major changes in the physiology of plants and these would be reflected in changes in the plant proteome as a consequence of root infection by Trichoderma spp. Further, Trichoderma spp. differ in their effects on plants and these changes are largely a consequence of the production of different elicitors of elicitor mixtures that are produced in the zone of communication that is established by root infection by Trichoderma spp. In this work, we demonstrated that both T22 and T-203 increase growth and induce resistance to pathogens in maize. In Israel, it was shown that a hydrophobin is critical for root colonization by Trichoderma strains, and that peptaibols and an expansin-like protein from Ttrichoderma probably act as elicitors of induced resistance in plants. Further, this fungus induces the jasmonate/ethylene pathway of disease resistance and a specific cucumber MAPK is required for transduction of the resistance signal. This is the first such gene known to be induced by fungal systems. In the USA, extensive proteomic analyses of maize demonstrated a number of proteins are differentially regulated by T. harzianum strain T22. The pattern of up-regulation strongly supports the contention that this fungus induces increases in plant disease resistance, respiratory rates and photosynthesis. These are all very consistent with the observations of effects of the fungus on plants in the greenhouse and field. In addition, the chitinolytic complex of maize was examined. The numbers of maize genes encoding these enzymes was increased about 3-fold and their locations on maize chromosomes determined by sequence identification in specific BAC libraries on the web. One of the chitinolytic enzymes was determined to be a heterodimer between a specific exochitinase and different endochitinases dependent upon tissue differences (shoot or root) and the presence or absence of T. harzianum. These heterodimers, which were discovered in this work, are very strongly antifungal, especially the one from shoots in the presence of the biocontrol fungus. Finally, RNA was isolated from plants at Cornell and sent to Israel for transcriptome assessment using Affymetrix chips (the chips became available for maize at the end of the project). The data was sent back to Cornell for bioinformatic analyses and found, in large sense, to be consistent with the proteomic data. The final assessment of this data is just now possible since the full annotation of the sequences in the maize Affy chips is just now available. This work is already being used to discover more effective strains of Trichoderma. It also is expected to elucidate how we may be able to manipulate and breed plants for greater disease resistance, enhanced growth and yield and similar goals. This will be possible since the changes in gene and protein expression that lead to better plant performance can be elucidated by following changes induced by Trichoderma strains. The work was in, some parts, collaborative but in others, most specifically transcriptome analyses, fully synergistic.
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Ginzberg, Idit, and Walter De Jong. Molecular genetic and anatomical characterization of potato tuber skin appearance. United States Department of Agriculture, September 2008. http://dx.doi.org/10.32747/2008.7587733.bard.
Full textAbstract:
Potato (Solanum tuberosum L.) skin is composed of suberized phellem cells, the outer component of the tuber periderm. The focus of the proposed research was to apply genomic approaches to identify genes that control tuber skin appearance - smooth and shiny skin is highly preferred by the customers while russeted/netted skin potatoes are rejected. The breeding program (at Cornell University) seeks to develop smooth-skin varieties but has encountered frequent difficulties as inheritance of russeting involves complementary action by independently segregating genes, where a dominant allele at each locus is required for any degree of skin russeting. On the other hand, smooth-skin varieties frequently develop unsightly russeting in response to stress conditions, mainly high soil temperatures. Breeding programs in Israel aimed towards the improvement of heat tolerant varieties include skin quality as one of the desired characteristics. At the initiation of the present project it was unclear whether heat induced russeting and genetically inherited russeting share the same genes and biosynthesis pathways. Nevertheless, it has been suggested that russeting might result from increased periderm thickness, from strong cohesion between peridermal cells that prevents the outer layers from sloughing off, or from altered suberization processes in the skin. Hence, the original objectives were to conduct anatomical study of russet skin development, to isolate skin and russeting specific genes, to map the loci that determine the russet trait, and to compare with map locations the candidate russet specific genes, as well as to identify marker alleles that associated with russet loci. Anatomical studies suggested that russet may evolve from cracking at the outer layers of the skin, probably when skin development doesn’t meet the tuber expansion rate. Twodimensional gel electrophoresis and transcript profiling (cDNA chip, potato functional genomic project) indicated that in comparison to the parenchyma tissue, the skin is enriched with proteins/genes that are involved in the plant's responses to biotic and abiotic stresses and further expand the concept of the skin as a protective tissue containing an array of plantdefense components. The proteomes of skin from heat stressed tubers and native skin didn’t differ significantly, while transcript profiling indicated heat-related increase in three major functional groups: transcription factors, stress response and protein degradation. Exceptional was ACC synthase isogene with 4.6 fold increased level in the heat stressed skin. Russeting was mapped to two loci: rusB on chromosome 4 and rusC on chromosome 11; both required for russeting. No evidence was found for a third locus rusA that was previously proposed to be required for russeting. In an effort to find a link between the russeting character and the heat-induced russeting an attempt was made to map five genes that were found in the microarray experiment to be highly induced in the skin under heat stress in the segregating russet population. Only one gene was polymorphic; however it was localized to chromosome 2, so cannot correspond to rusB or rusC. Evaluation of AFLP markers tightly linked to rusB and rusC showed that these specific alleles are not associated with russeting in unrelated germplasm, and thus are not useful for MAS per se. To develop markers useful in applied breeding, it will be necessary to screen alleles of additional tightly linked loci, as well as to identify additional russet (heat-induced and/or native) related genes.