Relevant bibliographies by topics / Proteomic pattern

Academic literature on the topic 'Proteomic pattern'

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Published: 6 September 2023

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Journal articles on the topic "Proteomic pattern"

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Mischak, Harald, Eric Schiffer, Petra Zürbig, Mohammed Dakna, and Jochen Metzger. "Urinary Proteome Analysis using Capillary Electrophoresis Coupled to Mass Spectrometry: A Powerful Tool in Clinical Diagnosis, Prognosis and Therapy Evaluation." Journal of Medical Biochemistry 28, no. 4 (October 1, 2009): 223–34. http://dx.doi.org/10.2478/v10011-009-0020-0.

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Urinary Proteome Analysis using Capillary Electrophoresis Coupled to Mass Spectrometry: A Powerful Tool in Clinical Diagnosis, Prognosis and Therapy EvaluationProteome analysis has emerged as a powerful tool to decipher (patho) physiological processes, resulting in the establishment of the field of clinical proteomics. One of the main goals is to discover biomarkers for diseases from tissues and body fluids. Due to the enormous complexity of the proteome, a separation step is required for mass spectrometry (MS)-based proteome analysis. In this review, the advantages and limitations of protein separation by two-dimensional gel electrophoresis, liquid chromatography, surface-enhanced laser desorption/ionization and capillary electrophoresis (CE) for proteomic analysis are described, focusing on CE-MS. CE-MS enables separation and detection of the small molecular weight proteome in biological fluids with high reproducibility and accuracy in one single processing step and in a short time. As sensitive and specific single biomarkers generally may not exist, a strategy to overcome this diagnostic void is shifting from single analyte detection to simultaneous analysis of multiple analytes that together form a disease-specific pattern. Such approaches, however, are accompanied with additional challenges, which we will outline in this review. Besides the choice of adequate technological platforms, a high level of standardization of proteomic measurements and data processing is also necessary to establish proteomic profiling. In this regard, demands concerning study design, choice of specimens, sample preparation, proteomic data mining, and clinical evaluation should be considered before performing a proteomic study.
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Baumann, Sven, Uta Ceglarek, Georg Martin Fiedler, Jan Lembcke, Alexander Leichtle, and Joachim Thiery. "Standardized Approach to Proteome Profiling of Human Serum Based on Magnetic Bead Separation and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry." Clinical Chemistry 51, no. 6 (June 1, 2005): 973–80. http://dx.doi.org/10.1373/clinchem.2004.047308.

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Abstract Background: Magnetic bead purification for the analysis of low-abundance proteins in body fluids facilitates the identification of potential new biomarkers by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The aims of our study were to establish a proteome fractionation technique and to validate a standardized blood sampling, processing, and storage procedure for proteomic pattern analysis. Methods: We used magnetic bead separation for proteome profiling of human blood by MALDI-TOF MS (mass range, 1000–10 000 Da) and studied the effects on the quality and reproducibility of the proteome analysis of anticoagulants, blood clotting, time and temperature of sample storage, and the number of freeze–thaw cycles of samples. Results: The proteome pattern of human serum was characterized by ∼350 signals in the mass range of 1000–10 000 Da. The proteome profile showed time-dependent dynamic changes before and after centrifugation of the blood samples. Serum mass patterns differed between native samples and samples frozen once. The best reproducibility of proteomic patterns was with a single thawing of frozen serum samples. Conclusion: Application of the standardized preanalytical blood sampling and storage procedure in combination with magnetic bead-based fractionation decreases variability of proteome patterns in human serum assessed by MALDI-TOF MS.
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Yu, Li-Rong, Ming Zhou, Thomas P. Conrads, and Timothy D. Veenstra. "Diagnostic Proteomics: Serum Proteomic Patterns for the Detection of Early Stage Cancers." Disease Markers 19, no. 4-5 (2004): 209–18. http://dx.doi.org/10.1155/2004/612071.

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The ability to interrogate thousands of proteins found in complex biological samples using proteomic technologies has brought the hope of discovering novel disease-specific biomarkers. While most proteomic technologies used to discover diagnostic biomarkers are quite sophisticated, "proteomic pattern analysis" has emerged as a simple, yet potentially revolutionary, method for the early diagnosis of diseases. Utilizing this technology, hundreds of clinical samples can be analyzed per day and several preliminary studies suggest proteomic pattern analysis has the potential to be a novel, highly sensitive diagnostic tool for the early detection of cancer.
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Zhan, Xianquan, Biao Li, Xiaohan Zhan, Hartmut Schlüter, Peter R. Jungblut, and Jens R. Coorssen. "Innovating the Concept and Practice of Two-Dimensional Gel Electrophoresis in the Analysis of Proteomes at the Proteoform Level." Proteomes 7, no. 4 (October 30, 2019): 36. http://dx.doi.org/10.3390/proteomes7040036.

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Two-dimensional gel electrophoresis (2DE) is an important and well-established technical platform enabling extensive top-down proteomic analysis. However, the long-held but now largely outdated conventional concepts of 2DE have clearly impacted its application to in-depth investigations of proteomes at the level of protein species/proteoforms. It is time to popularize a new concept of 2DE for proteomics. With the development and enrichment of the proteome concept, any given “protein” is now recognized to consist of a series of proteoforms. Thus, it is the proteoform, rather than the canonical protein, that is the basic unit of a proteome, and each proteoform has a specific isoelectric point (pI) and relative mass (Mr). Accordingly, using 2DE, each proteoform can routinely be resolved and arrayed according to its different pI and Mr. Each detectable spot contains multiple proteoforms derived from the same gene, as well as from different genes. Proteoforms derived from the same gene are distributed into different spots in a 2DE pattern. High-resolution 2DE is thus actually an initial level of separation to address proteome complexity and is effectively a pre-fractionation method prior to analysis using mass spectrometry (MS). Furthermore, stable isotope-labeled 2DE coupled with high-sensitivity liquid chromatography-tandem MS (LC-MS/MS) has tremendous potential for the large-scale detection, identification, and quantification of the proteoforms that constitute proteomes.
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Walker, Maura E., Rebecca J. Song, Xiang Xu, Robert E. Gerszten, Debby Ngo, Clary B. Clish, Laura Corlin, et al. "Proteomic and Metabolomic Correlates of Healthy Dietary Patterns: The Framingham Heart Study." Nutrients 12, no. 5 (May 19, 2020): 1476. http://dx.doi.org/10.3390/nu12051476.

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Data on proteomic and metabolomic signatures of healthy dietary patterns are limited. We evaluated the cross-sectional association of serum proteomic and metabolomic markers with three dietary patterns: the Alternative Healthy Eating Index (AHEI), the Dietary Approaches to Stop Hypertension (DASH) diet; and a Mediterranean-style (MDS) diet. We examined participants from the Framingham Offspring Study (mean age; 55 years; 52% women) who had complete proteomic (n = 1713) and metabolomic (n = 2284) data; using food frequency questionnaires to derive dietary pattern indices. Proteins and metabolites were quantified using the SomaScan platform and liquid chromatography/tandem mass spectrometry; respectively. We used multivariable-adjusted linear regression models to relate each dietary pattern index (independent variables) to each proteomic and metabolomic marker (dependent variables). Of the 1373 proteins; 103 were associated with at least one dietary pattern (48 with AHEI; 83 with DASH; and 8 with MDS; all false discovery rate [FDR] ≤ 0.05). We identified unique associations between dietary patterns and proteins (17 with AHEI; 52 with DASH; and 3 with MDS; all FDR ≤ 0.05). Significant proteins enriched biological pathways involved in cellular metabolism/proliferation and immune response/inflammation. Of the 216 metabolites; 65 were associated with at least one dietary pattern (38 with AHEI; 43 with DASH; and 50 with MDS; all FDR ≤ 0.05). All three dietary patterns were associated with a common signature of 24 metabolites (63% lipids). Proteins and metabolites associated with dietary patterns may help characterize intermediate phenotypes that provide insights into the molecular mechanisms mediating diet-related disease. Our findings warrant replication in independent populations
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Mischak-Weissinger, Eva M., Jochen Metzger, Annika Krons, Julia Kontsendorn, Jürgen Krauter, Michael Stadler, Harald Mischak, and Arnold Ganser. "Prospective Evaluation of Proteomic Screening with An Agvhd-Specific Proteomic Pattern MS-17." Blood 114, no. 22 (November 20, 2009): 2246. http://dx.doi.org/10.1182/blood.v114.22.2246.2246.

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Abstract Abstract 2246 Poster Board II-223 Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is the only curative treatment for many hematologic malignancies or hematopoietic dysfunction syndromes in adults, but the application is still limited due to major complications, such as severe graft versus host disease (GvHD) and infectious complications. Diagnosis GvHD is based on clinical features and biopsies, a non-invasive, unbiased laboratory test using proteomics was published previously and evaluated in a multicenter setting (Weissinger et al., 2007). In order to maintain good quality data of the proteomic pattern data and due to the fact that the electrospray ionization time of flight mass spectrometer (ESI-TOF) from ABI (mariner) is no longer produced, we applied a more sensitive mass spectrometer (MS; ESI-TOF/Bruker). In order to validate the quality of the data produced with the Bruker, ESI-TOF was used since December 2007 in parallel to the mariner. Our first and previously published “aGvHD-specific pattern” (Weissinger et al., 2007) was used to evaluate and improve the pattern with the more sensitive decreased (6) or increased (11) signal intensity in patients with GvHD grade II to IV. Patients post HSCT and patients with GvHD grade I have the same pattern. In addition, the MS-17-pattern yielded at least comparable if not superior results to the previous one yielding sensitivities around 95% and specificity about 80%. To date the proteomic pattern specific for aGvHD MS17 was evaluated blindly on 400 samples collected from about 90 patients undergoing allo-HSCT at MHH since Dec. 2007. The peptide pattern MS-17 consists of 17 peptides - either absent/decreased (6) or present /increased (11) in aGvHD grade II to IV when compared to patients with clinical aGvHD grade I or without GvHD. Prospective and blinded evaluation of the patients included in this parallel diagnostic study revealed the correct classification of patients developing aGvHD about 7 days prior to the development of clinical signs and symptoms for aGVHD with a sensitivity and specificity of about 85%. Sequencing 3 of the 17 markers yielded the following results: Peptide No 5: Albumine fragment (N-terminus); Peptide No 7: ψ2 microglobulin; Peptide No 10: fragment of CD99 (MIC2; a single-chain type-1 glycoprotein). CD99 and β-2 microglobulin are particulary interesting because of their involvement in immune responses, both being expressed on leukocytes and CD 99 especially on thymocytes with involvement in apoptosis of double positive T-cells and binding cyclosporin A. Data on the pattern, signal intensity (3 dimension, mass and charge are shown in Figure 1) Disclosures: Metzger: mosaiques-diagnostics GmbH: Employment. Krons:mosaiques-diagnostics GmbH: Employment. Mischak:mosaiques-diagnostics GmbH: Patents & Royalties, coowner and founder of mosaiques-diagnostics.
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Gillette, Michael A., D. R. Mani, and Steven A. Carr. "Place of Pattern in Proteomic Biomarker Discovery†." Journal of Proteome Research 4, no. 4 (August 2005): 1143–54. http://dx.doi.org/10.1021/pr0500962.

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Müller, Ute, Günther Ernst, Christian Melle, Reinhard Guthke, and Ferdinand von Eggeling. "Convergence of the proteomic pattern in cancer." Bioinformatics 22, no. 11 (March 7, 2006): 1293–96. http://dx.doi.org/10.1093/bioinformatics/btl077.

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Conrads, T. P., V. A. Fusaro, S. Ross, D. Johann, V. Rajapakse, B. A. Hitt, S. M. Steinberg, et al. "High-resolution serum proteomic features for ovarian cancer detection." Endocrine-related cancer 11, no. 2 (June 2004): 163–78. http://dx.doi.org/10.1677/erc.0.0110163.

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Serum proteomic pattern diagnostics is an emerging paradigm employing low-resolution mass spectrometry (MS) to generate a set of biomarker classifiers. In the present study, we utilized a well-controlled ovarian cancer serum study set to compare the sensitivity and specificity of serum proteomic diagnostic patterns acquired using a high-resolution versus a low-resolution MS platform. In blinded testing sets, the high-resolution mass spectral data contained multiple diagnostic signatures that were superior to the low-resolution spectra in terms of sensitivity and specificity (P<0.00001) throughout the range of modeling conditions. Four mass spectral feature set patterns acquired from data obtained exclusively with the high-resolution mass spectrometer were 100% specific and sensitive in their diagnosis of serum samples as being acquired from either unaffected patients or those suffering from ovarian cancer. Important to the future of proteomic pattern diagnostics is the ability to recognize inferior spectra statistically, so that those resulting from a specific process error are recognized prior to their potentially incorrect (and damaging) diagnosis. To meet this need, we have developed a series of quality-assurance and in-process control procedures to (a) globally evaluate sources of sample variability, (b) identify outlying mass spectra, and (c) develop quality-control release specifications. From these quality-assurance and control (QA/QC) specifications, we identified 32 mass spectra out of the total 248 that showed statistically significant differences from the norm. Hence, 216 of the initial 248 high-resolution mass spectra were determined to be of high quality and were remodeled by pattern-recognition analysis. Again, we obtained four mass spectral feature set patterns that also exhibited 100% sensitivity and specificity in blinded validation tests (68/68 cancer: including 18/18 stage I, and 43/43 healthy). We conclude that (a) the use of high-resolution MS yields superior classification patterns as compared with those obtained with lower resolution instrumentation; (b) although the process error that we discovered did not have a deleterious impact on the present results obtained from proteomic pattern analysis, the major source of spectral variability emanated from mass spectral acquisition, and not bias at the clinical collection site; (c) this variability can be reduced and monitored through the use of QA/QC statistical procedures; (d) multiple and distinct proteomic patterns, comprising low molecular weight biomarkers, detected by high-resolution MS achieve accuracies surpassing individual biomarkers, warranting validation in a large clinical study.
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Pouliquen, Daniel L., Alice Boissard, Cécile Henry, Stéphanie Blandin, Olivier Coqueret, and Catherine Guette. "Lymphoid Organ Proteomes Identify Therapeutic Efficacy Biomarkers following the Intracavitary Administration of Curcumin in a Highly Invasive Rat Model of Peritoneal Mesothelioma." International Journal of Molecular Sciences 22, no. 16 (August 9, 2021): 8566. http://dx.doi.org/10.3390/ijms22168566.

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This study aimed to identify the proteomic changes produced by curcumin treatment following stimulation of the host immune system in a rat model of malignant mesothelioma. We analyzed the proteomes of secondary lymphoid organs from four normal rats, four untreated tumor-bearing rats, and four tumor-bearing rats receiving repeated intraperitoneal administrations of curcumin. Cross-comparing proteome analyses of histological sections of the spleen from the three groups first identified a list of eighty-three biomarkers of interest, thirteen of which corresponded to proteins already reported in the literature and involved in the anticancer therapeutic effects of curcumin. In a second step, comparing these data with proteomic analyses of histological sections of mesenteric lymph nodes revealed eight common biomarkers showing a similar pattern of changes in both lymphoid organs. Additional findings included a partial reduction of the increase in spleen-circulating biomarkers, a decrease in C-reactive protein and complement C3 in the spleen and lymph nodes, and an increase in lymph node purine nucleoside phosphorylase previously associated with liver immunodeficiency. Our results suggest some protein abundance changes could be related to the systemic, distant non-target antitumor effects produced by this phytochemical.
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Dissertations / Theses on the topic "Proteomic pattern"

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Komori, Mika. "Proteomic pattern analysis discriminates among multiple sclerosis-related disorders." Kyoto University, 2012. http://hdl.handle.net/2433/152501.

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Liu, Yiding. "Technologies for Proteomic and Genomic Biomarker Analysis." Cleveland State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=csu1229461302.

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Agatea, Lisa. "An integrated proteomic and genomic approach to study FAP patients without APC and MutHY mutations." Doctoral thesis, Università degli studi di Padova, 2016. http://hdl.handle.net/11577/3424509.

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Familial Adenomatous Polyposis (FAP) is one of the most important clinical forms of inherited susceptibility to colorectal cancer, that is characterized by the development of hundreds to thousands of adenomas in the colon and rectum during the second decade of life. FAP is due to a germline mutation in the APC gene or to biallelic variations of MutYH gene. Almost all patients will develop cancer if the disease is not identified and surgically treated at an early stage. The aim of this study was to characterize, by peptidomic and genetic approaches, 4 pa-tients that, although at the colonoscopy showed many polyps, they did not present any mutations of APC and MutYH genes (defined here unresolved FAP). Regarding the peptidomic study, MALDI-TOF analysis was performed on mutated and unresolved FAP patients. These data were compared with the one from adenoma patients, CRC patients and healthy control subjects. The peptide fingerprint of mutated FAP patients was obtained after performing statistical analysis. A subset of 45 ionic species was found differently expressed in the four groups considered, 12 of them peculiar of FAP patients. Four ionic species were found significantly different in the switch between adenoma and malignant carcinoma. In this study, the potentially prognostic peptides identified derive mainly from circulating proteins and some of them are involved in the inflammatory response. In particular, proteins such as Complement C3 and C4 are known to be cleaved by exoproteases that seem pathology-related. In the case of unresolved FAP patients, in order to better define a specific pattern, the data from MALDI-TOF were combined with whole exome sequencing. The peptidomics data clearly mark a substantial difference between mutated and unresolved FAP patients. Indeed, unresolved FAP patients have characteristics similar to the control subjects, adenoma patients, CRC patients but not to mutated FAP patients. To understand the possible molecular pathway involved in the unresolved FAP cases, the whole exome sequencing (WES) was performed. From WES data analysis, 285 genes present in all the four unresolved FAP patients were filtered and selected. Among them, the O-linked glycans pathway of the mucins was the most represented. In conclusion, in this study it was defined for the first time a specific panel of peptides for mutated FAP patients, that could be useful to monitor and predict the pathological evolution of adenocarcinoma malignancy. Furthermore, it was possible to characterize a preliminary genetic variations pattern for unresolved FAP patients, in which mucin genes might represent the key of the molecular pathway involved. However, further study are necessary to relate the identified mucin gene variations to their possible causative role in the polyposis. Future analysis of this pattern will be helpful, indeed, to better understand the interatome (the biological network that in-cludes the whole set of direct and indirect molecular interactions in a cell) of these un-resolved FAP patients.
La poliposi adenomatosa familiare (FAP) è una delle più importanti forme cliniche di cancro colo-rettale ereditario ed è caratterizzata dallo sviluppo di centinaia/migliaia di polipi adenomatosi nel colon e nel retto durante la seconda decade di vita. La FAP è causata da una mutazione germinale del gene APC o da varianti bialleliche del gene MutYH. Quasi tutti i pazienti FAP sviluppano il cancro se la patologia non viene precocemente identificata e trattata chirurgicamente. Lo scopo di questo lavoro è stato caratterizzare 4 pazienti in cui, nonostante l’esame colonscopico presentasse una poliposi conclamata, non risultavano mutazioni nei gene APC e MutYH (in questa tesi definiti pazienti FAP irrisolti) utilizzando un approccio integrato di peptidomica e genomica. Riguardo la peptidomica, il MALDI-TOF è stato utilizzato per studiare il profilo peptidico plasmatico di pazienti FAP mutati ed irrisolti comparando i dati ottenuti con quelli derivanti dallo studio di pazienti con adenoma, cancro colo-rettale e soggetti sani di controllo. Dopo analisi statistica è stato ottenuto il fingerprint peptidico dei pazienti FAP mutati. Sono state ottenute 45 specie ioniche differentemente espresse nei quattro gruppi considerati, 12 delle quali peculiari per i pazienti FAP. L’intensità di segnale di quattro di queste specie ioniche è stata trovata statisticamente alterata nello switch tra adenoma e carcinoma maligno. I peptidi potenzialmente prognostici identificati in questo studio derivano principalmente da proteine circolanti, alcune delle quali implicate nella risposta infiammatoria. In particolare è noto dalla letteratura che proteine del sistema del complemento come C3 e C4 vengono tagliate da esoproteasi che sembrano essere patologia correlate. Riguardo ai pazienti FAP irrisolti, per definirne un pattern specifico, i dati derivanti dall’analisi con il MALDI-TOF sono stati combinati con quelli ottenuti dal sequenzia-mento dell’esoma. I dati di peptidomica hanno chiaramente evidenziato le differenze tra pazienti FAP mutati e FAP irrisolti. Infatti i pazienti FAP irrisolti presentano caratteristiche simili a quelle dei soggetti di controllo, dei pazienti con adenoma e cancro colo rettale ma non a quelle dei pazienti FAP mutati. Allo scopo di capire la via di trasduzione del segnale implicata, è stato quindi eseguito il sequenziamento dell'esoma dei pazienti FAP irrisolti. Da questa analisi sono stati selezionati 285 geni variati in tutti i pazienti e tra questi la via di trasduzione del segnale della O-glicosilazione delle mucine è risultata la più rappresentata. In conclusione, in questo studio è stato definito per la prima volta un set peptidico specifico per i pazienti FAP mutati che potrebbe essere utilizzato per monitorare e predire l’evoluzione patologica della malattia. Inoltre è stato possibile caratterizzare un pattern preliminare per i pazienti FAP irrisolti in cui i geni delle mucine potrebbero rappresentare la chiave della via di trasduzione del segnale implicata. Ulteriori studi saranno necessari per correlare i geni delle mucine con la poliposi e costruire l'interatoma (network biologico definito come l’insieme di tutte le interazioni molecolari dirette e indirette che ci sono all'interno di una cellula e di un organismo) di questi pazienti FAP irrisolti.
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Wibom, Carl. "Multivariate analyses of proteomic and metabolomic patterns in brain tumors." Doctoral thesis, Umeå universitet, Onkologi, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-25670.

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Glioblastoma multiforme (GBM) is the most common primary brain tumor. Given the current standard of care, the prognosis for patients diagnosed with this disease is still poor. There consequently exists a need to improve current treatments, as well as to develop new ones. Many obstacles however need to be overcome to facilitate this effort and one of these involves the development of improved methods to monitor treatment effects. At present, the effects of treatment are typically assessed by radiological means several months after its initiation, which is unsatisfactory for a fast growing tumor like GBM. It is however likely that treatment effects can be detected on a molecular level long before radiological response, especially considering many of the targeted therapies that are currently being developed. Biomarkers for treatment efficacy may be of great importance in the future individualization of brain tumor treatment. The work presented herein was primarily focused on detecting early effects of GBM treatment. To this end, we designed experiments in the BT4C rat glioma model in which we studied effects of both conventional radiotherapy and an experimental angiogenesis inhibitor, vandetanib. Brain tissue samples were analyzed using a high throughput mass spectrometry (MS) based screening, known as Surface Enhanced Laser Desorption/Ionization - Time of Flight - Mass Spectrometry (SELDI-TOF-MS). The vast amounts of data generated were subsequently analyzed by established multivariate statistical methods, such as Principal Component Analysis (PCA), Partial Least Squares (PLS), and Orthogonal Partial Least Squares (OPLS), developed for analysis of large and complex datasets. In the radiotherapy study we detected a protein spectrum pattern clearly related to tumor progression. We notably observed how this progression pattern was hampered by radiotherapy. The vandetanib study also revealed significant alterations of protein expression following treatment of different durations, both in tumor tissue and in normal brain contralateral to the tumor. In an effort to further elucidate the pathophysiology of GBM, particularly in relation to treatment, we collected extracellular fluid (ECF) samples from 11 patients diagnosed with inoperable GBM. The samples were collected by means of stereotactic microdialysis, both from within the contrast enhancing tumor and the brain adjacent to tumor (BAT). Samples were collected longitudinally from each patient in a time span of up to two weeks, during which the patient received the first five fractions of radiotherapy. The ECF samples were then analyzed by Gas Chromatography Mass Spectrometry (GC-MS) to screen them with respect to concentrations of low molecular weight compounds (metabolites). Suitable multivariate analysis strategies enabled us to extract patterns of varying metabolite concentrations distinguishing between samples collected at different locations in the brain as well as between samples collected at different time points in relation to treatment. In a separate study, we also applied SELDI-TOF-MS and multivariate statistical methods to unravel possible differences in protein spectra between invasive and non-invasive WHO grade I meningiomas. This type of tumor can usually be cured by surgical resection however sometimes it grows invasively into the bone, ultimately causing clinical problems. This study revealed the possibility to differentiate between invasive and non-invasive benign meningioma based on the expression pattern of a few proteins. Our approach, which includes sample analysis and data handling, is applicable to a wide range of screening studies. In this work we demonstrated that the combination of MS screening and multivariate analyses is a powerful tool in the search for patterns related to treatment effects and diagnostics in brain tumors.
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Cerjan, Dijana. "INTRACELLULAR DISTRIBUTION PATTERNS OF ORGANELL SPECIFIC PROTEINS USING IMMUNOHISTOCHEMICAL STAINING OF TISSUE MICRO ARRAYS." Thesis, Uppsala University, Department of Medical Biochemistry and Microbiology, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6154.

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The knowledge of the human genome sequence, as revealed in the HUGO project, has created exciting new possibilities for biomedical research. The Swedish Human Proteome Resource (HPR) program aims to make use of this information to gain further insight into the human proteome. Recombinant proteins are generated from coding sequences identified from the human genome sequence and used to produce specific antibodies to target proteins. Antibodies are subsequently utilized for functional analysis of the corresponding proteins using tissue micro arrays. The aim of my project was to investigate the possibility of distinguishing characteristic distribution patterns of intracellular proteins in the resolution capacity offered by light microscopy. A map of representative distribution patterns was created using immunohistological staining with commercially available antibodies toward well-characterised proteins in the cell. Such a map could then aid in interpreting the results of immunohistological staining of intracellular proteins using antibodies produced within the Human Proteome Resource program. Proteins manifested in nucleus, nuclear membrane and plasma membrane were clearly visible at the expected location. Proteins manifested in different organelles in the cytoplasm however, showed all a similar staining pattern, making determination of exact protein location uncertain. A possible explanation is the resolution of the light microscope not being sufficient to visualize certain proteins specific to organelles in the cytoplasm. Results may also have been influenced by the choice of secondary antibody, where the strenghtened signal generated by an enzyme labelled polymer may have a negative effect on depiction of details in the image generated.

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Sabounchi, Schütt Fariba. "Bronchoalveolar lavage and serum protein patterns in healthy individuals and sarcoidosis patients : a proteomics approach /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-790-8/.

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Öztürk, Özgür. "Feature extraction and similarity-based analysis for proteome and genome databases." Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1190138805.

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Lindskog, Bergström Cecilia. "Tissue Microarrays for Analysis of Expression Patterns." Doctoral thesis, Uppsala universitet, Molekylär och morfologisk patologi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-186272.

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Proteins are essential building blocks in every living cell, and since the complete human genome was sequenced in 2004, researchers have attempted to map the human proteome, which is the functional representation of the genome. One such initiative is the Human Protein Atlas programme (HPA), which generates monospecific antibodies towards all human proteins and uses these for high-throughput tissue profiling on tissue microarrays (TMAs). The results are publically available at the website www.proteinatlas.org. In this thesis, TMAs were used for analysis of expression patterns in various research areas. Different search queries in the HPA were tested and evaluated, and a number of potential biomarkers were identified, e.g. proteins exclusively expressed in islets of Langerhans, but not in exocrine glandular cells or other abdominal organs close to pancreas. The identified candidates were further analyzed on TMAs with pancreatic tissues from normal and diabetic individuals, and colocalization studies with insulin and glucagon revealed that several of the investigated proteins (DGCR2, GBF1, GPR44 and SerpinB10) appeared to be beta cell specific. Moreover, a set of proteins differentially expressed in lung cancer stroma was further analyzed on a clinical lung cancer cohort in the TMA format, and one protein (CD99) was significantly associated with survival. In addition, TMAs with tissue samples from different species were generated, e.g. for mapping of influenza virus attachment in various human and avian tissues. The results showed that the gull influenza virus H16N3 attached to human respiratory tract and eye, suggesting possible transmission of the virus between gull and human. TMAs were also used for analysis of protein expression differences between humans and other primates, and two proteins (TCF3 and SATB2) proved to be significantly differentially expressed on the human lineage at both the protein level and the RNA level.   In conclusion, this thesis exemplifies the potential of the TMA technology, which can be used for analysis of expression patterns in a large variety of research fields, such as biomarker discovery, influenza virus research or further understanding of human evolution.
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Göbel, Thomas. "Identifizierung von Proteom Pattern und Proteinmarkern durch SELDI-TOF MS bei Patienten mit chronischer Hepatitis C." Düsseldorf, 2008. http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&doc_number=016540450&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA.

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Pajak, Maciej. "Evolutionary conservation and diversification of complex synaptic function in human proteome." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/31108.

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The evolution of synapses from early proto-synaptic protein complexes in unicellular eukaryotes to sophisticated machines comprising thousands of proteins parallels the emergence of finely tuned synaptic plasticity, a molecular correlate for memory and learning. Phenotypic change in organisms is ultimately the result of evolution of their genotype at the molecular level. Selection pressure is a measure of how changes in genome sequence that arise though naturally occurring processes in populations are fixed or eliminated in subsequent generations. Inferring phylogenetic information about proteins such as the variation of selection pressure across coding sequences can provide valuable information not only about the origin of proteins, but also the contribution of specific sites within proteins to their current roles within an organism. Recent evolutionary studies of synaptic proteins have generated attractive hypotheses about the emergence of finely-tuned regulatory mechanisms in the post-synaptic proteome related to learning, however, these analyses are relatively superficial. In this thesis, I establish a scalable molecular phylogenetic modelling framework based on three new inference methodologies to investigate temporal and spatial aspects of selection pressure changes for the whole human proteome using protein orthologs from up to 68 taxa. Temporal modelling of evolutionary selection pressure reveals informative features and patterns for the entire human proteome and identifies groups of proteins that share distinct diversification timelines. Multi-ontology enrichment analysis of these gene cohorts was used to aid biological interpretation, but these approaches are statistically under powered and do not capture a clear picture of the emergence of synaptic plasticity. Subsequent pathway-centric analysis of key synaptic pathways extends the interpretation of temporal data and allows for revision of previous hypotheses about the evolution of complex synaptic function. I proceed to integrate inferred selection pressure timeline information in the context of static protein-protein interaction data. A network analysis of the full human proteome reveals systematic patterns linking the temporal profile of proteins’ evolution and their topological role in the interaction graph. These graphs were used to test a mechanistic hypothesis that proposed a propagating diversification signal between interactors using the temporal modelling data and network analysis tools. Finally, I analyse the data of amino-acid level spatial modelling of selection pressure events in Arc, one of the master regulators of synaptic plasticity, and its interactors for which detailed experimental data is available. I use the Arc interactome as an example to discuss episodic and localised diversifying selection pressure events in tightly coupled complexes of protein and showcase potential for a similar systematic analysis of larger complexes of proteins using a pathway-centric approach. Through my work I revised our understanding of temporal evolutionary patterns that shaped contemporary synaptic function through profiling of emergence and refinement of proteins in multiple pathways of the nervous system. I also uncovered systematic effects linking dependencies between proteins with their active diversification, and hypothesised about their extension to domain level selection pressure events.
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Books on the topic "Proteomic pattern"

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Grant, Seth G. N. Synaptic Mechanisms of Psychotic Disorders. Edited by Dennis S. Charney, Eric J. Nestler, Pamela Sklar, and Joseph D. Buxbaum. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190681425.003.0017.

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Synapses are the hallmark of the neuroanatomy of the brain. The million billion synapses of the human brain connect the nerve cells into the networks that underpin all behavior. The molecular anatomy of synapses is also remarkably complicated with ~2000 proteins in the synapse proteome. The proteins are physically organized into a hierarchy of molecular machines that control synapse biology. These proteins integrate and compute the information in patterns of nerve cell activity. Mutations in hundreds of genes that encode synaptic proteins contribute to over one hundred brain diseases, including common mental disorders. The synapse proteome is of fundamental importance to mental illness.
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Suffredini, Anthony F., and J. Perren Cobb. Genetic and molecular expression patterns in critical illness. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780199600830.003.0031.

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Investigators who study RNA, proteins, or metabolites use analytic platforms that simultaneously measure changes in the relative abundance of thousands of molecules in a single biological sample. Over the last decade, the application of these high-throughput, genome-wide platforms to study critical illness and injury has generated huge quantities of data that require specialized computational skills for analysis. These investigations hold promise for improving our understanding of the host response, thereby transforming the practice of intensive care. This chapter summarizes recent technological and computational approaches used in genomics, proteomics, and metabolomics. While major advances have been made with these approaches when applied to chronic diseases, the acute nature of critical illness and injury has unique challenges. The rapidity of initiating events, the trajectory of inflammation that follows injury or infection and the interplay of host responses to a replicating infection, all have major effects on changes in gene and molecular expression. This complexity is further accentuated by measurement that may vary with the timing and type of tissue sampled after the critical event. In addition, the hunt for novel molecular markers holds promise for identifying patients at risk for severe illness and for enabling more individualized therapy.
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Book chapters on the topic "Proteomic pattern"

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Taguchi, Y. h., and Akira Okamoto. "Principal Component Analysis for Bacterial Proteomic Analysis." In Pattern Recognition in Bioinformatics, 141–52. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-34123-6_13.

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Harris, Keith, Mark Girolami, and Harald Mischak. "Definition of Valid Proteomic Biomarkers: A Bayesian Solution." In Pattern Recognition in Bioinformatics, 137–49. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-04031-3_13.

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Deusdado, Sérgio, and Paulo Carvalho. "Efficient Exact Pattern-Matching in Proteomic Sequences." In Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living, 1178–86. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-02481-8_178.

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Jong, Kees, Elena Marchiori, and Aad van der Vaart. "Analysis of Proteomic Pattern Data for Cancer Detection." In Lecture Notes in Computer Science, 41–51. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-24653-4_5.

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Arnau, Vicente, and Ignacio Marín. "A Hierarchical Clustering Strategy and Its Application to Proteomic Interaction Data." In Pattern Recognition and Image Analysis, 62–69. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-540-44871-6_8.

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Kim, Jung-Ja, Young-Ho Kim, and Yonggwan Won. "Proteomic Pattern Classification Using Bio-markers for Prostate Cancer Diagnosis." In Computational and Information Science, 631–38. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-30497-5_99.

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Somorjai, Ray L. "Pattern Recognition Approaches for Classifying Proteomic Mass Spectra of Biofluids." In Methods in Molecular Biology™, 383–95. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-117-8_20.

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Carpentier, Sebastien C. "Multiple Testing and Pattern Recognition in 2-DE Proteomics." In Methods in Molecular Biology, 215–35. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3255-9_13.

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Ng, Julio, Amihood Amir, and Pavel A. Pevzner. "Blocked Pattern Matching Problem and Its Applications in Proteomics." In Lecture Notes in Computer Science, 298–319. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-20036-6_27.

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Luo, Zhiyuan, Tony Bellotti, and Alex Gammerman. "Qualified Predictions for Proteomics Pattern Diagnostics with Confidence Machines." In Lecture Notes in Computer Science, 46–51. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-28651-6_7.

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Conference papers on the topic "Proteomic pattern"

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LIU, YING. "SERUM PROTEOMIC PATTERN ANALYSIS FOR EARLY CANCER DETECTION." In Proceedings of the International Conference. WORLD SCIENTIFIC, 2005. http://dx.doi.org/10.1142/9789812702098_0015.

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Kim, Young Bun, Jean Gao, Ying Dong, and Chin-Rang Yang. "Functional Proteomic Pattern Identification under Low Dose Ionizing Radiation." In 2008 IEEE International Conference on Bioinformatics and Biomedicine. IEEE, 2008. http://dx.doi.org/10.1109/bibm.2008.50.

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Szasz, A., A. Szasz, A. Szasz, M. Micsinai, A. Tokes, A. Tokes, L. Madaras, T. Krenacs, and J. Kulka. "Proteomic Profiling of Breast Carcinomas Based on Claudin Expression Pattern." In Abstracts: Thirty-Second Annual CTRC‐AACR San Antonio Breast Cancer Symposium‐‐ Dec 10‐13, 2009; San Antonio, TX. American Association for Cancer Research, 2009. http://dx.doi.org/10.1158/0008-5472.sabcs-09-6123.

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Meng, Yan. "A Swarm Intelligence Based Algorithm for Proteomic Pattern Detection of Ovarian Cancer." In 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology. IEEE, 2006. http://dx.doi.org/10.1109/cibcb.2006.331010.

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Xu, Q., S. S. Mohamed, M. M. A. Salama, M. Kamel, and K. Rizkalla. "Mass spectrometry-based proteomic pattern analysis for prostate cancer detection using neural networks with statistical significance test-based feature selection." In 2009 IEEE Toronto International Conference - Science and Technology for Humanity (TIC-STH 2009). IEEE, 2009. http://dx.doi.org/10.1109/tic-sth.2009.5444384.

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Martens, William L., Philip Poronnik, and Darren Saunders. "Hypothesis-Driven Sonification of Proteomic Data Distributions Indicating Neurodegredation in Amyotrophic Lateral Sclerosis." In The 22nd International Conference on Auditory Display. Arlington, Virginia: The International Community for Auditory Display, 2016. http://dx.doi.org/10.21785/icad2016.024.

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Three alternative sonifications of proteomic data distributions were compared as a means to indicate the neuropathology associated with Amyotrophic Lateral Sclerosis (ALS) via auditory display (through exploration of the differentiation of induced pluripotent stem cell derived neurons). Pure visual displays of proteomic data often result in ”visual overload” such that detailed or subtle data important to describe ALS neurodegradation may be glossed over, and so three competing approaches to the sonification of proteomic data were designed to capitalize upon human auditory capacities that complement the visual capacities engaged by more conventional graphic representations. The auditory displays resulting from hypothesis-driven design of three alternative sonifications were evaluated by naïve listeners, who were instructed to listen for differences between the sonifications produce from proteomic data associated with three different types of cells. One of the sonifications was based upon the hypothesis that auditory sensitivity to regularities and irregularities in spatio-temporal patterns in the data could be heard through spatial distribution of sonification components. The design of a second sonification was based upon the hypothesis that variation in timbral components might create a distinguishable sound for each of three types of cells. A third sonification was based upon the hypothesis that redundant variation in both spatial and timbral components would be even more powerful as a means for identifying spatio-temporal patterns in the dynamic, multidimensional data generated in current proteomic studies of ALS.
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Manole, Sagi, Amit Golander, and Shlomo Weiss. "Workload optimization of proteomics pattern matching using embedded accelerator." In Electronics Engineers in Israel (IEEEI 2010). IEEE, 2010. http://dx.doi.org/10.1109/eeei.2010.5662102.

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Nolasco Jauregui, Oralia. "A Machine Learning approach to Neural Information Decoding of Spike Train Distances in the Peripheral Nervous System." In LatinX in AI at Neural Information Processing Systems Conference 2019. Journal of LatinX in AI Research, 2019. http://dx.doi.org/10.52591/lxai2019120817.

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Decoding the neural signal has proved to be an elusive goal. We explore the use of sequence analysis algorithms to identify repeating patterns of spike train distances and found that they could be associated to the stimulus in the rat peripheral system with good results. The use of these algorithms is very common in genomics and proteomics for genetic sequence analysis but rarely applied to neural systems analysis. We are convinced that with proper tuning they could yield useful results.
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Kordy, Hussain Montazery. "A hybrid wavelet based feature extraction approach to analysis of high dimensional proteomic patterns." In 2011 International Conference on Electrical and Control Engineering (ICECE). IEEE, 2011. http://dx.doi.org/10.1109/iceceng.2011.6057914.

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Zhang, Xuegong. "Pattern Recognition in Mining High-Throughput Genomics/Proteomics Data: The New Challenges in Old Questions." In 2007 International Conference on Computing: Theory and Applications (ICCTA'07). IEEE, 2007. http://dx.doi.org/10.1109/iccta.2007.103.

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Reports on the topic "Proteomic pattern"

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Avni, Adi, and Gitta L. Coaker. Proteomic investigation of a tomato receptor like protein recognizing fungal pathogens. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600030.bard.

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Maximizing food production with minimal negative effects on the environment remains a long-term challenge for sustainable food production. Microbial pathogens cause devastating diseases, minimizing crop losses by controlling plant diseases can contribute significantly to this goal. All plants possess an innate immune system that is activated after recognition of microbial-derived molecules. The fungal protein Eix induces defense responses in tomato and tobacco. Plants recognize Eix through a leucine-rich-repeat receptor- like-protein (LRR-RLP) termed LeEix. Despite the knowledge obtained from studies on tomato, relatively little is known about signaling initiated by RLP-type immune receptors. The focus of this grant proposal is to generate a foundational understanding of how the tomato xylanase receptor LeEix2 signals to confer defense responses. LeEix2 recognition results in pattern triggered immunity (PTI). The grant has two main aims: (1) Isolate the LeEix2 protein complex in an active and resting state; (2) Examine the biological function of the identified proteins in relation to LeEix2 signaling upon perception of the xylanase elicitor Eix. We used two separate approaches to isolate receptor interacting proteins. Transgenic tomato plants expressing LeEix2 fused to the GFP tag were used to identify complex components at a resting and activated state. LeEix2 complexes were purified by mass spectrometry and associated proteins identified by mass spectrometry. We identified novel proteins that interact with LeEix receptor by proteomics analysis. We identified two dynamin related proteins (DRPs), a coiled coil – nucleotide binding site leucine rich repeat (SlNRC4a) protein. In the second approach we used the split ubiquitin yeast two hybrid (Y2H) screen system to identified receptor-like protein kinase At5g24010-like (SlRLK-like) (Solyc01g094920.2.1) as an interactor of LeEIX2. We examined the role of SlNRC4a in plant immunity. Co-immunoprecipitation demonstrates that SlNRC4a is able to associate with different PRRs. Physiological assays with specific elicitors revealed that SlNRC4a generally alters PRR-mediated responses. SlNRC4a overexpression enhances defense responses while silencing SlNRC4 reduces plant immunity. We propose that SlNRC4a acts as a non-canonical positive regulator of immunity mediated by diverse PRRs. Thus, SlNRC4a could link both intracellular and extracellular immune perception. SlDRP2A localizes at the plasma membrane. Overexpression of SlDRP2A increases the sub-population of LeEIX2 inVHAa1 endosomes, and enhances LeEIX2- and FLS2-mediated defense. The effect of SlDRP2A on induction of plant immunity highlights the importance of endomembrane components and endocytosis in signal propagation during plant immune . The interaction of LeEIX2 with SlRLK-like was verified using co- immunoprecipitation and a bimolecular fluorescence complementation assay. The defence responses induced by EIX were markedly reduced when SlRLK-like was over-expressed, and mutation of slrlk-likeusing CRISPR/Cas9 increased EIX- induced ethylene production and SlACSgene expression in tomato. Co-expression of SlRLK-like with different RLPs and RLKs led to their degradation, apparently through an endoplasmic reticulum-associated degradation process. We provided new knowledge and expertise relevant to expression of specific be exploited to enhance immunity in crops enabling the development of novel environmentally friendly disease control strategies.
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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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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.

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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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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.

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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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Epel, Bernard, and Roger Beachy. Mechanisms of intra- and intercellular targeting and movement of tobacco mosaic virus. United States Department of Agriculture, November 2005. http://dx.doi.org/10.32747/2005.7695874.bard.

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To cause disease, plant viruses must replicate and spread locally and systemically within the host. Cell-to-cell virus spread is mediated by virus-encoded movement proteins (MPs), which modify the structure and function of plasmodesmata (Pd), trans-wall co-axial membranous tunnels that interconnect the cytoplasm of neighboring cells. Tobacco mosaic virus (TMV) employ a single MP for cell- cell spread and for which CP is not required. The PIs, Beachy (USA) and Epel (Israel) and co-workers, developed new tools and approaches for study of the mechanism of spread of TMV that lead to a partial identification and molecular characterization of the cellular machinery involved in the trafficking process. Original research objectives: Based on our data and those of others, we proposed a working model of plant viral spread. Our model stated that MPᵀᴹⱽ, an integral ER membrane protein with its C-terminus exposed to the cytoplasm (Reichel and Beachy, 1998), alters the Pd SEL, causes the Pd cytoplasmic annulus to dilate (Wolf et al., 1989), allowing ER to glide through Pd and that this gliding is cytoskeleton mediated. The model claimed that in absence of MP, the ER in Pd (the desmotubule) is stationary, i.e. does not move through the Pd. Based on this model we designed a series of experiments to test the following questions: -Does MP potentiate ER movement through the Pd? - In the presence of MP, is there communication between adjacent cells via ER lumen? -Does MP potentiate the movement of cytoskeletal elements cell to cell? -Is MP required for cell-to-cell movement of ER membranes between cells in sink tissue? -Is the binding in situ of MP to RNA specific to vRNA sequences or is it nonspecific as measured in vitro? And if specific: -What sequences of RNA are involved in binding to MP? And finally, what host proteins are associated with MP during intracellular targeting to various subcellular targets and what if any post-translational modifications occur to MP, other than phosphorylation (Kawakami et al., 1999)? Major conclusions, solutions and achievements. A new quantitative tool was developed to measure the "coefficient of conductivity" of Pd to cytoplasmic soluble proteins. Employing this tool, we measured changes in Pd conductivity in epidermal cells of sink and source leaves of wild-type and transgenic Nicotiana benthamiana (N. benthamiana) plants expressing MPᵀᴹⱽ incubated both in dark and light and at 16 and 25 ᵒC (Liarzi and Epel, 2005 (appendix 1). To test our model we measured the effect of the presence of MP on cell-to-cell spread of a cytoplasmic fluorescent probe, of two ER intrinsic membrane protein-probes and two ER lumen protein-probes fused to GFP. The effect of a mutant virus that is incapable of cell-to-cell spread on the spread of these probes was also determined. Our data shows that MP reduces SEL for cytoplasmic molecules, dilates the desmotubule allowing cell-cell diffusion of proteins via the desmotubule lumen and reduces the rate of spread of the ER membrane probes. Replicase was shown to enhance cell-cell spread. The data are not in support of the proposed model and have led us to propose a new model for virus cell-cell spread: this model proposes that MP, an integral ER membrane protein, forms a MP:vRNAER complex and that this ER-membrane complex diffuses in the lipid milieu of the ER into the desmotubule (the ER within the Pd), and spreads cell to cell by simple diffusion in the ER/desmotubule membrane; the driving force for spread is the chemical potential gradient between an infected cell and contingent non-infected neighbors. Our data also suggests that the virus replicase has a function in altering the Pd conductivity. Transgenic plant lines that express the MP gene of the Cg tobamovirus fused to YFP under the control the ecdysone receptor and methoxyfenocide ligand were generated by the Beachy group and the expression pattern and the timing and targeting patterns were determined. A vector expressing this MPs was also developed for use by the Epel lab . The transgenic lines are being used to identify and isolate host genes that are required for cell-to-cell movement of TMV/tobamoviruses. This line is now being grown and to be employed in proteomic studies which will commence November 2005. T-DNA insertion mutagenesis is being developed to identify and isolate host genes required for cell-to-cell movement of TMV.
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Blumwald, Eduardo, and Avi Sadka. Citric acid metabolism and mobilization in citrus fruit. United States Department of Agriculture, October 2007. http://dx.doi.org/10.32747/2007.7587732.bard.

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Abstract:
Accumulation of citric acid is a major determinant of maturity and fruit quality in citrus. Many citrus varieties accumulate citric acid in concentrations that exceed market desires, reducing grower income and consumer satisfaction. Citrate is accumulated in the vacuole of the juice sac cell, a process that requires both metabolic changes and transport across cellular membranes, in particular, the mitochondrial and the vacuolar (tonoplast) membranes. Although the accumulation of citrate in the vacuoles of juice cells has been clearly demonstrated, the mechanisms for vacuolar citrate homeostasis and the components controlling citrate metabolism and transport are still unknown. Previous results in the PIs’ laboratories have indicated that the expression of a large number of a large number of proteins is enhanced during fruit development, and that the regulation of sugar and acid content in fruits is correlated with the differential expression of a large number of proteins that could play significant roles in fruit acid accumulation and/or regulation of acid content. The objectives of this proposal are: i) the characterization of transporters that mediate the transport of citrate and determine their role in uptake/retrieval in juice sac cells; ii) the study of citric acid metabolism, in particular the effect of arsenical compounds affecting citric acid levels and mobilization; and iii) the development of a citrus fruit proteomics platform to identify and characterize key processes associated with fruit development in general and sugar and acid accumulation in particular. The understanding of the cellular processes that determine the citrate content in citrus fruits will contribute to the development of tools aimed at the enhancement of citrus fruit quality. Our efforts resulted in the identification, cloning and characterization of CsCit1 (Citrus sinensis citrate transporter 1) from Navel oranges (Citrus sinesins cv Washington). Higher levels of CsCit1 transcripts were detected at later stages of fruit development that coincided with the decrease in the juice cell citrate concentrations (Shimada et al., 2006). Our functional analysis revealed that CsCit1 mediates the vacuolar efflux of citrate and that the CsCit1 operates as an electroneutral 1CitrateH2-/2H+ symporter. Our results supported the notion that it is the low permeable citrateH2 - the anion that establishes the buffer capacity of the fruit and determines its overall acidity. On the other hand, it is the more permeable form, CitrateH2-, which is being exported into the cytosol during maturation and controls the citrate catabolism in the juice cells. Our Mass-Spectrometry-based proteomics efforts (using MALDI-TOF-TOF and LC2- MS-MS) identified a large number of fruit juice sac cell proteins and established comparisons of protein synthesis patterns during fruit development. So far, we have identified over 1,500 fruit specific proteins that play roles in sugar metabolism, citric acid cycle, signaling, transport, processing, etc., and organized these proteins into 84 known biosynthetic pathways (Katz et al. 2007). This data is now being integrated in a public database and will serve as a valuable tool for the scientific community in general and fruit scientists in particular. Using molecular, biochemical and physiological approaches we have identified factors affecting the activity of aconitase, which catalyze the first step of citrate catabolism (Shlizerman et al., 2007). Iron limitation specifically reduced the activity of the cytosolic, but not the mitochondrial, aconitase, increasing the acid level in the fruit. Citramalate (a natural compound in the juice) also inhibits the activity of aconitase, and it plays a major role in acid accumulation during the first half of fruit development. On the other hand, arsenite induced increased levels of aconitase, decreasing fruit acidity. We have initiated studies aimed at the identification of the citramalate biosynthetic pathway and the role(s) of isopropylmalate synthase in this pathway. These studies, especially those involved aconitase inhibition by citramalate, are aimed at the development of tools to control fruit acidity, particularly in those cases where acid level declines below the desired threshold. Our work has significant implications both scientifically and practically and is directly aimed at the improvement of fruit quality through the improvement of existing pre- and post-harvest fruit treatments.
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