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The Need for Biomarkers in the ALS-FTD Spectrum: A Clinical Point of View on the Role of Proteomics. ALS-FTD谱中对生物标志物的需求:蛋白质组学作用的临床观点
IF 3.3
Proteomes Pub Date : 2023-01-09 DOI: 10.3390/proteomes11010001
Francesca Vignaroli, Angelica Mele, Giacomo Tondo, Veronica De Giorgis, Marcello Manfredi, Cristoforo Comi, Letizia Mazzini, Fabiola De Marchi
{"title":"The Need for Biomarkers in the ALS-FTD Spectrum: A Clinical Point of View on the Role of Proteomics.","authors":"Francesca Vignaroli,&nbsp;Angelica Mele,&nbsp;Giacomo Tondo,&nbsp;Veronica De Giorgis,&nbsp;Marcello Manfredi,&nbsp;Cristoforo Comi,&nbsp;Letizia Mazzini,&nbsp;Fabiola De Marchi","doi":"10.3390/proteomes11010001","DOIUrl":"https://doi.org/10.3390/proteomes11010001","url":null,"abstract":"<p><p>Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are severely debilitating and progressive neurodegenerative disorders. A distinctive pathological feature of several neurodegenerative diseases, including ALS and FTD, is the deposition of aberrant protein inclusions in neuronal cells, which leads to cellular dysfunction and neuronal damage and loss. Despite this, to date, the biological process behind developing these protein inclusions must be better clarified, making the development of disease-modifying treatment impossible until this is done. Proteomics is a powerful tool to characterize the expression, structure, functions, interactions, and modifications of proteins of tissue and biological fluid, including plasma, serum, and cerebrospinal fluid. This protein-profiling characterization aims to identify disease-specific protein alteration or specific pathology-based mechanisms which may be used as markers of these conditions. Our narrative review aims to highlight the need for biomarkers and the potential use of proteomics in clinical practice for ALS-FTD spectrum disorders, considering the emerging rationale in proteomics for new drug development. Certainly, new data will emerge in the near future in this regard and support clinicians in the development of personalized medicine.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9844364/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10555101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Multi-Omics of Corynebacterium Pseudotuberculosis 12CS0282 and an In Silico Reverse Vaccinology Approach Reveal Novel Vaccine and Drug Targets. 假结核棒状杆菌12CS0282的多组学和计算机反向疫苗学方法揭示了新的疫苗和药物靶点。
IF 3.3
Proteomes Pub Date : 2022-11-23 DOI: 10.3390/proteomes10040039
Jens Möller, Mona Bodenschatz, Vartul Sangal, Jörg Hofmann, Andreas Burkovski
{"title":"Multi-Omics of <i>Corynebacterium Pseudotuberculosis</i> 12CS0282 and an In Silico Reverse Vaccinology Approach Reveal Novel Vaccine and Drug Targets.","authors":"Jens Möller,&nbsp;Mona Bodenschatz,&nbsp;Vartul Sangal,&nbsp;Jörg Hofmann,&nbsp;Andreas Burkovski","doi":"10.3390/proteomes10040039","DOIUrl":"https://doi.org/10.3390/proteomes10040039","url":null,"abstract":"<p><p><i>Corynebacterium pseudotuberculosis</i> is an important animal pathogen, which is also able to infect humans. An optimal treatment of infections with this pathogen is not available today and consequently, more research is necessary to understand the infection process. Here, we present a combined -omics and bioinformatics approach to characterize <i>C. pseudotuberculosis</i> 12CS0282. The genome sequence of strain 12CS0282 was determined, analyzed in comparison with the available 130 <i>C. pseudotuberculosis</i> sequences and used as a basis for proteome analyses. In a reverse vaccinology approach, putative vaccine and drug targets for 12CS0208 were identified. Mass spectrometry analyses revealed the presence of multiple virulence factors even without host contact. In macrophage interaction studies, <i>C. pseudotuberculosis</i> 12CS0282 was highly resistant against human phagocytes and even multiplied within human THP-1 cells. Taken together, the data indicate a high pathogenic potential of the strain.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"10 4","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9784263/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10427698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Impact of CHIKV Replication on the Global Proteome of Aedes albopictus Cells. CHIKV病毒复制对白纹伊蚊细胞整体蛋白质组的影响
IF 3.3
Proteomes Pub Date : 2022-11-10 DOI: 10.3390/proteomes10040038
Ramesh Kumar, Divya Mehta, Sakshi Chaudhary, Debasis Nayak, Sujatha Sunil
{"title":"Impact of CHIKV Replication on the Global Proteome of <i>Aedes albopictus</i> Cells.","authors":"Ramesh Kumar,&nbsp;Divya Mehta,&nbsp;Sakshi Chaudhary,&nbsp;Debasis Nayak,&nbsp;Sujatha Sunil","doi":"10.3390/proteomes10040038","DOIUrl":"https://doi.org/10.3390/proteomes10040038","url":null,"abstract":"<p><p>Arboviruses are some of the important causative agents of mosquito-mediated viral diseases. These viruses are transmitted between vector and host during the blood meal. Upon viral entry, host replication machinery is hijacked, supporting new virus particle production and thereby allowing viral survival in the host. In this process, host proteins interact with viral proteins to either facilitate viral replication, or they may provide antiviral defense mechanisms. In this study, we analyzed the impact of chikungunya virus (CHIKV) infection on the global proteome of Dicer active <i>Aedes albopictus</i> cells during the early and late time points of infection. We utilized a bottom-up approach of global proteomics analysis, and we used label-free quantitative mass spectrometry to identify the global protein signatures of <i>Ae. albopictus</i> at two different time points upon CHIKV infection. The mass spectrometry data analysis of the early time point revealed that proteins belonging to pathways such as translation, RNA processing, and cellular metabolic processes were less in abundance, whereas those belonging to pathways such as cellular catabolic process and organic substance transport were significantly abundant. At later time points, proteins belonging to pathways such as cellular metabolic processes, primary metabolic process, organonitrogen compound metabolic process, and organic substance metabolic process were found to be decreased in their presence, whereas those belonging to pathways such as RNA processing, gene expression, macromolecule metabolic processing, and nitrogen compound metabolic processing were found to be abundant during CHIKV infection, indicating that modulation in gene expression favoring cell survival occurs at a later time point, suggesting a survival strategy of <i>Aedes</i> cells to counter prolonged CHIKV infection.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"10 4","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9680348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10689970","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Salivary Biomarkers in Oral Squamous Cell Carcinoma: A Proteomic Overview. 口腔鳞状细胞癌的唾液生物标志物:蛋白质组学综述。
IF 3.3
Proteomes Pub Date : 2022-11-07 DOI: 10.3390/proteomes10040037
Gabriele Riccardi, Mario Giuseppe Bellizzi, Irene Fatuzzo, Federica Zoccali, Luca Cavalcanti, Antonio Greco, Marco de Vincentiis, Massimo Ralli, Marco Fiore, Carla Petrella, Antonio Minni, Christian Barbato
{"title":"Salivary Biomarkers in Oral Squamous Cell Carcinoma: A Proteomic Overview.","authors":"Gabriele Riccardi,&nbsp;Mario Giuseppe Bellizzi,&nbsp;Irene Fatuzzo,&nbsp;Federica Zoccali,&nbsp;Luca Cavalcanti,&nbsp;Antonio Greco,&nbsp;Marco de Vincentiis,&nbsp;Massimo Ralli,&nbsp;Marco Fiore,&nbsp;Carla Petrella,&nbsp;Antonio Minni,&nbsp;Christian Barbato","doi":"10.3390/proteomes10040037","DOIUrl":"https://doi.org/10.3390/proteomes10040037","url":null,"abstract":"<p><strong>Background: </strong>Oral squamous cell carcinoma (OSCC) is one of the most frequent cancers worldwide. Endoscopic methods may be useful in the evaluation of oral injuries even though the diagnostic gold standard is a biopsy. Targeted screenings could be considered the best way to prevent the occurrence of oral cancer. Aimed to elucidate the potential identification of specific biomarkers of OSCC, the use of saliva is convenient and noninvasive. Many studies reported more than a hundred putative saliva biomarkers for OSCC, and proteogenomic approaches were fundamental to disclosing this issue.</p><p><strong>Methods: </strong>Relevant literature published in the last few years was systematically searched on PubMed and we focused on articles about the use and study of salivary biomarkers in the diagnostics of head and neck cancer (n = 110). Thereafter, we performed a selection focusing on diagnosis with salivary proteomics in OSCC (n = 8).</p><p><strong>Results: </strong>Saliva proteomics can be a source of biomarkers for OSCC. We reviewed literature of biomarker proteins in saliva that could also be evaluated as probable targets for non-invasive screening of oral neoplasm such as cytokines, matrix metalloproteinases, and acute-phase response proteins.</p><p><strong>Conclusions: </strong>The measurement of salivary biomarkers is a highly hopeful technique for the diagnosis of OSCC. Proteogenomic approaches could permit an accurate and early diagnosis of OSCC. This review seeks to generate an up-to-date view on translational OSCC issues by raising awareness of researchers, physicians, and surgeons. Renewed clinical studies, which will validate the sensitivity and specificity of salivary biomarkers, are necessary to translate these results into possible strategies for early diagnosis of OSCC, thus improving patient outcomes.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"10 4","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9680331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10689972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
Mass Spectrometry-Based Proteomics of Human Milk to Identify Differentially Expressed Proteins in Women with Breast Cancer versus Controls. 基于质谱的人类乳汁蛋白质组学鉴定乳腺癌妇女与对照组中不同表达的蛋白质
IF 4
Proteomes Pub Date : 2022-10-28 DOI: 10.3390/proteomes10040036
Roshanak Aslebagh, Danielle Whitham, Devika Channaveerappa, Panashe Mutsengi, Brian T Pentecost, Kathleen F Arcaro, Costel C Darie
{"title":"Mass Spectrometry-Based Proteomics of Human Milk to Identify Differentially Expressed Proteins in Women with Breast Cancer versus Controls.","authors":"Roshanak Aslebagh, Danielle Whitham, Devika Channaveerappa, Panashe Mutsengi, Brian T Pentecost, Kathleen F Arcaro, Costel C Darie","doi":"10.3390/proteomes10040036","DOIUrl":"10.3390/proteomes10040036","url":null,"abstract":"<p><p>It is thought that accurate risk assessment and early diagnosis of breast cancer (BC) can help reduce cancer-related mortality. Proteomics analysis of breast milk may provide biomarkers of risk and occult disease. Our group works on the analysis of human milk samples from women with BC and controls to investigate alterations in protein patterns of milk that could be related to BC. In the current study, we used mass spectrometry (MS)-based proteomics analysis of 12 milk samples from donors with BC and matched controls. Specifically, we used one-dimensional (1D)-polyacrylamide gel electrophoresis (PAGE) coupled with nanoliquid chromatography tandem MS (nanoLC-MS/MS), followed by bioinformatics analysis. We confirmed the dysregulation of several proteins identified previously in a different set of milk samples. We also identified additional dysregulations in milk proteins shown to play a role in cancer development, such as Lactadherin isoform A, O-linked N-acetylglucosamine (GlcNAc) transferase, galactosyltransferase, recoverin, perilipin-3 isoform 1, histone-lysine methyltransferase, or clathrin heavy chain. Our results expand our current understanding of using milk as a biological fluid for identification of BC-related dysregulated proteins. Overall, our results also indicate that milk has the potential to be used for BC biomarker discovery, early detection and risk assessment in young, reproductively active women.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"10 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2022-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9680319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10672975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Viral Biomarker Detection and Validation Using MALDI Mass Spectrometry Imaging (MSI). 利用MALDI质谱成像(MSI)检测和验证病毒生物标志物。
IF 3.3
Proteomes Pub Date : 2022-09-13 DOI: 10.3390/proteomes10030033
Matthew B O'Rourke, Ben R Roediger, Christopher J Jolly, Ben Crossett, Matthew P Padula, Phillip M Hansbro
{"title":"Viral Biomarker Detection and Validation Using MALDI Mass Spectrometry Imaging (MSI).","authors":"Matthew B O'Rourke,&nbsp;Ben R Roediger,&nbsp;Christopher J Jolly,&nbsp;Ben Crossett,&nbsp;Matthew P Padula,&nbsp;Phillip M Hansbro","doi":"10.3390/proteomes10030033","DOIUrl":"https://doi.org/10.3390/proteomes10030033","url":null,"abstract":"<p><p>(1) Background: MALDI imaging is a technique that still largely depends on time of flight (TOF)-based instrument such as the Bruker UltrafleXtreme. While capable of performing targeted MS/MS, these instruments are unable to perform fragmentation while imaging a tissue section necessitating the reliance of MS1 values for peptide level identifications. With this premise in mind, we have developed a hybrid bioinformatic/image-based method for the identification and validation of viral biomarkers. (2) Methods: Formalin-Fixed Paraffin-Embedded (FFPE) mouse samples were sectioned, mounted and prepared for mass spectrometry imaging using our well-established methods. Peptide identification was achieved by first extracting confident images corresponding to theoretical viral peptides. Next, those masses were used to perform a Peptide Mmass Fingerprint (PMF) searched against known viral FASTA sequences against a background mouse FASTA database. Finally, a correlational analysis was performed with imaging data to confirm pixel-by-pixel colocalization and intensity of viral peptides. (3) Results: 14 viral peptides were successfully identified with significant PMF Scores and a correlational result of >0.79 confirming the presence of the virus and distinguishing it from the background mouse proteins. (4) Conclusions: this novel approach leverages the power of mass spectrometry imaging and provides confident identifications for viral proteins without requiring MS/MS using simple MALDI Time Of Flight/Time Of Flight (TOF/TOF) instrumentation.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"10 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9506211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10862284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Proteomics for Biomarker Discovery for Diagnosis and Prognosis of Kidney Transplantation Rejection. 蛋白质组学发现肾移植排斥反应诊断和预后的生物标志物。
IF 3.3
Proteomes Pub Date : 2022-07-02 DOI: 10.3390/proteomes10030024
Luís M Ramalhete, Rúben Araújo, Aníbal Ferreira, Cecília R C Calado
{"title":"Proteomics for Biomarker Discovery for Diagnosis and Prognosis of Kidney Transplantation Rejection.","authors":"Luís M Ramalhete,&nbsp;Rúben Araújo,&nbsp;Aníbal Ferreira,&nbsp;Cecília R C Calado","doi":"10.3390/proteomes10030024","DOIUrl":"https://doi.org/10.3390/proteomes10030024","url":null,"abstract":"<p><p>Renal transplantation is currently the treatment of choice for end-stage kidney disease, enabling a quality of life superior to dialysis. Despite this, all transplanted patients are at risk of allograft rejection processes. The gold-standard diagnosis of graft rejection, based on histological analysis of kidney biopsy, is prone to sampling errors and carries high costs and risks associated with such invasive procedures. Furthermore, the routine clinical monitoring, based on urine volume, proteinuria, and serum creatinine, usually only detects alterations after graft histologic damage and does not differentiate between the diverse etiologies. Therefore, there is an urgent need for new biomarkers enabling to predict, with high sensitivity and specificity, the rejection processes and the underlying mechanisms obtained from minimally invasive procedures to be implemented in routine clinical surveillance. These new biomarkers should also detect the rejection processes as early as possible, ideally before the 78 clinical outputs, while enabling balanced immunotherapy in order to minimize rejections and reducing the high toxicities associated with these drugs. Proteomics of biofluids, collected through non-invasive or minimally invasive analysis, e.g., blood or urine, present inherent characteristics that may provide biomarker candidates. The current manuscript reviews biofluids proteomics toward biomarkers discovery that specifically identify subclinical, acute, and chronic immune rejection processes while allowing for the discrimination between cell-mediated or antibody-mediated processes. In time, these biomarkers will lead to patient risk stratification, monitoring, and personalized and more efficient immunotherapies toward higher graft survival and patient quality of life.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"10 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9326686/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10704787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Integrative Proteomic and Phosphoproteomic Analyses of Hypoxia-Treated Pulmonary Artery Smooth Muscle Cells. 缺氧处理肺动脉平滑肌细胞的综合蛋白质组学和磷酸化蛋白质组学分析。
IF 3.3
Proteomes Pub Date : 2022-06-28 DOI: 10.3390/proteomes10030023
Ang Luo, Rongrong Hao, Xia Zhou, Yangfan Jia, Haiyang Tang
{"title":"Integrative Proteomic and Phosphoproteomic Analyses of Hypoxia-Treated Pulmonary Artery Smooth Muscle Cells.","authors":"Ang Luo,&nbsp;Rongrong Hao,&nbsp;Xia Zhou,&nbsp;Yangfan Jia,&nbsp;Haiyang Tang","doi":"10.3390/proteomes10030023","DOIUrl":"https://doi.org/10.3390/proteomes10030023","url":null,"abstract":"<p><p>Abnormal proliferation of pulmonary artery smooth muscle cells (PASMCs) is one of the main causes of pulmonary vascular remodeling in pulmonary arterial hypertension (PAH). Hypoxia is an important factor related to PAH and can induce the excessive proliferation of PASMCs and inhibit apoptosis. To explore the possible mechanism of hypoxia-related PAH, human PASMCs are exposed to hypoxia for 24 h and tandem mass tag (TMT)-based quantitative proteomic and phosphoproteomic analyses are performed. Proteomic analysis revealed 134 proteins are significantly changed (p < 0.05, |log2 (fold change)| > log2 [1.1]), of which 48 proteins are upregulated and 86 are downregulated. Some of the changed proteins are verified by using qRT-PCR and Western blotting. Phosphoproteomic analysis identified 404 significantly changed (p < 0.05, |log2 (fold change)| > log2 [1.1]) phosphopeptides. Among them, 146 peptides are upregulated while 258 ones are downregulated. The kinase-substrate enrichment analysis revealed kinases such as P21 protein-activated kinase 1/2/4 (PAK1/2/4), protein-kinase cGMP-dependent 1 and 2 (PRKG1/2), and mitogen-activated protein-kinase 4/6/7 (MAP2K4/6/7) are significantly enriched and activated. For all the significantly changed proteins or phosphoproteins, a comprehensive pathway analysis is performed. In general, this study furthers our understanding of the mechanism of hypoxia-induced PAH.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"10 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9326561/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10872396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Wheat Proteomics for Abiotic Stress Tolerance and Root System Architecture: Current Status and Future Prospects 小麦抗非生物胁迫蛋白质组学与根系结构研究现状与展望
IF 3.3
Proteomes Pub Date : 2022-05-22 DOI: 10.3390/proteomes10020017
T. Halder, M. Choudhary, Hui Liu, Yinglong Chen, G. Yan, K. Siddique
{"title":"Wheat Proteomics for Abiotic Stress Tolerance and Root System Architecture: Current Status and Future Prospects","authors":"T. Halder, M. Choudhary, Hui Liu, Yinglong Chen, G. Yan, K. Siddique","doi":"10.3390/proteomes10020017","DOIUrl":"https://doi.org/10.3390/proteomes10020017","url":null,"abstract":"Wheat is an important staple cereal for global food security. However, climate change is hampering wheat production due to abiotic stresses, such as heat, salinity, and drought. Besides shoot architectural traits, improving root system architecture (RSA) traits have the potential to improve yields under normal and stressed environments. RSA growth and development and other stress responses involve the expression of proteins encoded by the trait controlling gene/genes. Hence, mining the key proteins associated with abiotic stress responses and RSA is important for improving sustainable yields in wheat. Proteomic studies in wheat started in the early 21st century using the two-dimensional (2-DE) gel technique and have extensively improved over time with advancements in mass spectrometry. The availability of the wheat reference genome has allowed the exploration of proteomics to identify differentially expressed or abundant proteins (DEPs or DAPs) for abiotic stress tolerance and RSA improvement. Proteomics contributed significantly to identifying key proteins imparting abiotic stress tolerance, primarily related to photosynthesis, protein synthesis, carbon metabolism, redox homeostasis, defense response, energy metabolism and signal transduction. However, the use of proteomics to improve RSA traits in wheat is in its infancy. Proteins related to cell wall biogenesis, carbohydrate metabolism, brassinosteroid biosynthesis, and transportation are involved in the growth and development of several RSA traits. This review covers advances in quantification techniques of proteomics, progress in identifying DEPs and/or DAPs for heat, salinity, and drought stresses, and RSA traits, and the limitations and future directions for harnessing proteomics in wheat improvement.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47113422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 9
Applications of Proteomics in Ovarian Cancer: Dawn of a New Era 蛋白质组学在卵巢癌中的应用:一个新时代的黎明
IF 3.3
Proteomes Pub Date : 2022-05-09 DOI: 10.3390/proteomes10020016
Aruni Ghose, Srikar Gullapalli, Naila Chohan, A. Bolina, M. Moschetta, E. Rassy, S. Boussios
{"title":"Applications of Proteomics in Ovarian Cancer: Dawn of a New Era","authors":"Aruni Ghose, Srikar Gullapalli, Naila Chohan, A. Bolina, M. Moschetta, E. Rassy, S. Boussios","doi":"10.3390/proteomes10020016","DOIUrl":"https://doi.org/10.3390/proteomes10020016","url":null,"abstract":"The ability to identify ovarian cancer (OC) at its earliest stages remains a challenge. The patients present an advanced stage at diagnosis. This heterogeneous disease has distinguishable etiology and molecular biology. Next-generation sequencing changed clinical diagnostic testing, allowing assessment of multiple genes, simultaneously, in a faster and cheaper manner than sequential single gene analysis. Technologies of proteomics, such as mass spectrometry (MS) and protein array analysis, have advanced the dissection of the underlying molecular signaling events and the proteomic characterization of OC. Proteomics analysis of OC, as well as their adaptive responses to therapy, can uncover new therapeutic choices, which can reduce the emergence of drug resistance and potentially improve patient outcomes. There is an urgent need to better understand how the genomic and epigenomic heterogeneity intrinsic to OC is reflected at the protein level, and how this information could potentially lead to prolonged survival.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45972906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 51
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