Using Mechanistic Models for Analysis of Proteomic Data

2019 ◽  
pp. 265-270
Author(s):  
Lily A. Chylek
Keyword(s):  
Mechanistic Models ◽  
Proteomic Data

Proteomics: Opportunities and Challenges

2011 ◽  
Vol 3 (4) ◽  
pp. 1165-1172 ◽  
Author(s):  
Parag A Pathade ◽  
Vinod A Bairagi ◽  
Yogesh S. Ahire ◽  
Neela M Bhatia
Keyword(s):  
Biomedical Research ◽  
Therapy Monitoring ◽  
Dynamic State ◽  
Data Sets ◽  
Protein Markers ◽  
Drug Target Discovery ◽  
Proteomic Data ◽  
Cell Tissue ◽  
A Cell ◽  
Analytical Tools

‘‘Proteomics’’, is the emerging technology leading to high-throughput identification and understanding of proteins. Proteomics is the protein equivalent of genomics and has captured the imagination of biomolecular scientists, worldwide. Because proteome reveals more accurately the dynamic state of a cell, tissue, or organism, much is expected from proteomics to indicate better disease markers for diagnosis and therapy monitoring. Proteomics is expected to play a major role in biomedical research, and it will have a significant impact on the development of diagnostics and therapeutics for cancer, heart ailments and infectious diseases, in future. Proteomics research leads to the identification of new protein markers for diagnostic purposes and novel molecular targets for drug discovery.  Though the potential is great, many challenges and issues remain to be solved, such as gene expression, peptides, generation of low abundant proteins, analytical tools, drug target discovery and cost. A systematic and efficient analysis of vast genomic and proteomic data sets is a major challenge for researchers, today. Nevertheless, proteomics is the groundwork for constructing and extracting useful comprehension to biomedical research. This review article covers some opportunities and challenges offered by proteomics.   

scholarly journals Differential proteomic analysis by SWATH-MS unravels the most dominant mechanisms underlying yeast adaptation to non-optimal temperatures under anaerobic conditions

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Tânia Pinheiro ◽  
Ka Ying Florence Lip ◽  
Estéfani García-Ríos ◽  
Amparo Querol ◽  
José Teixeira ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Temperature Response ◽  
Laboratory Strain ◽  
Temperature Tolerance ◽  
Anaerobic Conditions ◽  
Cold Response ◽  
Proteomic Data ◽  
Response To Temperature

AbstractElucidation of temperature tolerance mechanisms in yeast is essential for enhancing cellular robustness of strains, providing more economically and sustainable processes. We investigated the differential responses of three distinct Saccharomyces cerevisiae strains, an industrial wine strain, ADY5, a laboratory strain, CEN.PK113-7D and an industrial bioethanol strain, Ethanol Red, grown at sub- and supra-optimal temperatures under chemostat conditions. We employed anaerobic conditions, mimicking the industrial processes. The proteomic profile of these strains in all conditions was performed by sequential window acquisition of all theoretical spectra-mass spectrometry (SWATH-MS), allowing the quantification of 997 proteins, data available via ProteomeXchange (PXD016567). Our analysis demonstrated that temperature responses differ between the strains; however, we also found some common responsive proteins, revealing that the response to temperature involves general stress and specific mechanisms. Overall, sub-optimal temperature conditions involved a higher remodeling of the proteome. The proteomic data evidenced that the cold response involves strong repression of translation-related proteins as well as induction of amino acid metabolism, together with components related to protein folding and degradation while, the high temperature response mainly recruits amino acid metabolism. Our study provides a global and thorough insight into how growth temperature affects the yeast proteome, which can be a step forward in the comprehension and improvement of yeast thermotolerance.

scholarly journals Physiological and Proteomic Responses of Pitaya to PEG-Induced Drought Stress

Agriculture ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 632
Author(s):  
Aihua Wang ◽  
Chao Ma ◽  
Hongye Ma ◽  
Zhilang Qiu ◽  
Xiaopeng Wen
Keyword(s):  
Drought Stress ◽  
Energy Metabolism ◽  
Metabolic Pathways ◽  
Treatment Time ◽  
Soluble Sugar ◽  
Antioxidant Systems ◽  
Antioxidant Enzyme Activities ◽  
Proteomic Data ◽  
Proteome Profile ◽  
Proteomic Responses

Pitaya (Hylocereus polyrhizus L.) is highly tolerant to drought stress. Elucidating the response mechanism of pitaya to drought will substantially contribute to improving crop drought tolerance. In the present study, the physiological and proteomic responses of the pitaya cultivar ‘Zihonglong’ were compared between control seedlings and seedlings exposed to drought stress (−4.9 MPa) induced by polyethylene glycol for 7 days. Drought stress obviously enhanced osmolyte accumulation, lipid peroxidation, and antioxidant enzyme activities. Proteomic data revealed drought stress activated several pathways in pitaya, including carbohydrate and energy metabolism at two drought stress treatment time-points (6 h and 3 days). Other metabolic pathways, including those related to aspartate, glutamate, glutathione, and secondary metabolites, were induced more at 3 days than at 6 h, whereas photosynthesis and arginine metabolism were induced exclusively at 6 h. Overall, protein expression changes were consistent with the physiological responses, although there were some differences in the timing. The increases in soluble sugar contents mainly resulted from the degradation and transformation of insoluble carbohydrates. Differentially accumulated proteins in amino acid metabolism may be important for the conversion and accumulation of amino acids. GSH and AsA metabolism and secondary metabolism may play important roles in pitaya as enzymatic and nonenzymatic antioxidant systems. The enhanced carbohydrate and energy metabolism may provide the energy necessary for initiating the above metabolic pathways. The current study provided the first proteome profile of this species exposed to drought stress, and may clarify the mechanisms underlying the considerable tolerance of pitaya to drought stress.

scholarly journals Tear Proteomics Study of Dry Eye Disease: Which Eye Do You Adopt as the Representative Eye for the Study?

2021 ◽  
Vol 22 (1) ◽  
pp. 422
Author(s):  
Ming-Tse Kuo ◽  
Po-Chiung Fang ◽  
Shu-Fang Kuo ◽  
Alexander Chen ◽  
Yu-Ting Huang
Keyword(s):  
Dry Eye ◽  
Ocular Surface ◽  
Tear Film ◽  
Dry Eye Disease ◽  
Eye Disease ◽  
Mechanistic Studies ◽  
Clinical Tests ◽  
Tear Proteins ◽  
Proteomic Data ◽  
Surface Performance

Most studies about dry eye disease (DED) chose unilateral eye for investigation and drew conclusions based on monocular results, whereas most studies involving tear proteomics were based on the results of pooling tears from a group of DED patients. Patients with DED were consecutively enrolled for binocular clinical tests, tear biochemical markers of DED, and tear proteome. We found that bilateral eyes of DED patients may have similar but different ocular surface performance and tear proteome. Most ocular surface homeostatic markers and tear biomarkers were not significantly different in the bilateral eyes of DED subjects, and most clinical parameters and tear biomarkers were correlated significantly between bilateral eyes. However, discrepant binocular presentation in the markers of ocular surface homeostasis and the associations with tear proteins suggested that one eye’s performance cannot represent that of the other eye or both eyes. Therefore, in studies for elucidating tear film homeostasis of DED, we may lose some important messages hidden in the fellow eye if we collected clinical and proteomic data only from a unilateral eye. For mechanistic studies, it is recommended that researchers collect tear samples from the eye with more severe DED under sensitive criteria for identifying the more severe eye and evaluating the tear biochemical and proteomic markers with binocular concordance drawn in prior binocular studies.

scholarly journals Production of nonulosonic acids in the extracellular polymeric substances of “Candidatus Accumulibacter phosphatis”

2021 ◽  
Author(s):  
Sergio Tomás-Martínez ◽  
Hugo B.C. Kleikamp ◽  
Thomas R. Neu ◽  
Martin Pabst ◽  
David G. Weissbrodt ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Pathogenic Bacteria ◽  
Extracellular Polymeric Substances ◽  
Lectin Binding ◽  
Wide Distribution ◽  
Sialic Acids ◽  
Animal Cells ◽  
Microbial Life ◽  
Proteomic Data ◽  
Accumulibacter Phosphatis

Abstract Nonulosonic acids (NulOs) are a family of acidic carbohydrates with a nine-carbon backbone, which include different related structures, such as sialic acids. They have mainly been studied for their relevance in animal cells and pathogenic bacteria. Recently, sialic acids have been discovered as an important compound in the extracellular matrix of virtually all microbial life and in “Candidatus Accumulibacter phosphatis”, a well-studied polyphosphate-accumulating organism, in particular. Here, bioaggregates highly enriched with these bacteria (approx. 95% based on proteomic data) were used to study the production of NulOs in an enrichment of this microorganism. Fluorescence lectin-binding analysis, enzymatic quantification, and mass spectrometry were used to analyze the different NulOs present, showing a wide distribution and variety of these carbohydrates, such as sialic acids and bacterial NulOs, in the bioaggregates. Phylogenetic analysis confirmed the potential of “Ca. Accumulibacter” to produce different types of NulOs. Proteomic analysis showed the ability of “Ca. Accumulibacter” to reutilize and reincorporate these carbohydrates. This investigation points out the importance of diverse NulOs in non-pathogenic bacteria, which are normally overlooked. Sialic acids and other NulOs should be further investigated for their role in the ecology of “Ca. Accumulibacter” in particular, and biofilms in general. Key Points •“Ca. Accumulibacter” has the potential to produce a range of nonulosonic acids. •Mass spectrometry and lectin binding can reveal the presence and location of nonulosonic acids. •The role of nonulosonic acid in non-pathogenic bacteria needs to be studied in detail.

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