scholarly journals Differential protein profile in sexed bovine semen: shotgun proteomics investigation

2014 ◽  
Vol 10 (6) ◽  
pp. 1264-1271 ◽  
Author(s):  
Michele De Canio ◽  
Alessio Soggiu ◽  
Cristian Piras ◽  
Luigi Bonizzi ◽  
Andrea Galli ◽  
...  
Keyword(s):  
Protein Profile ◽  
Shotgun Proteomics ◽  
Differential Protein ◽  
Bovine Semen

scholarly journals Insights into the physiology of Methylotenera mobilis as revealed by metagenome-based shotgun proteomic analysis

Microbiology ◽  
2009 ◽  
Vol 155 (4) ◽  
pp. 1103-1110 ◽  
Author(s):  
Gundula Bosch ◽  
Tiansong Wang ◽  
Ekaterina Latypova ◽  
Marina G. Kalyuzhnaya ◽  
Murray Hackett ◽  
...  
Keyword(s):  
Large Scale ◽  
Protein Profile ◽  
Shotgun Proteomics ◽  
Metagenomic Sequencing ◽  
Sequence Coverage ◽  
Metagenomic Sequence ◽  
The Family ◽  
Proteomics Approach ◽  
Sequence Quality ◽  
Environmental Microbes

While the shotgun proteomics approach is gaining momentum in understanding microbial physiology, it remains limited by the paucity of high-quality genomic data, especially when it comes to poorly characterized newly identified phyla. At the same time, large-scale metagenomic sequencing projects produce datasets representing genomes of a variety of environmental microbes, although with lower sequence coverage and sequence quality. In this work we tested the utility of a metagenomic dataset enriched in sequences of environmental strains of Methylotenera mobilis, to assess the protein profile of a laboratory-cultivated strain, M. mobilis JLW8, as a proof of principle. We demonstrate that a large portion of the proteome predicted from the metagenomic sequence (approx. 20 %) could be identified with high confidence (three or more peptide sequences), thus gaining insights into the physiology of this bacterium, which represents a new genus within the family Methylophilaceae.

Organic mineral supplementation on differential protein profile of Osmanabadi bucks (Capra hircus)

2021 ◽  
Vol 21 (3) ◽  
pp. 100533
Author(s):  
Backialakshmi Sekar ◽  
Arunachalam Arangasamy ◽  
Sharanya Jeevendra Naidu ◽  
Ippala Janardhan Reddy ◽  
Raghavendra Bhatta
Keyword(s):  
Protein Profile ◽  
Capra Hircus ◽  
Differential Protein ◽  
Mineral Supplementation ◽  
Organic Mineral

scholarly journals Differential Protein Abundance in Dark-Cutting and Normal-pH Beef

2019 ◽  
Vol 3 (2) ◽  
Author(s):  
F. Kiyimba ◽  
S. Hartson ◽  
J. Rogers ◽  
G. Mafi ◽  
D. VanOverbeke ◽  
...  
Keyword(s):  
Protein Expression ◽  
Pathway Analysis ◽  
Solid Phase ◽  
Muscle Protein ◽  
Expression Profiles ◽  
Protein Profile ◽  
Differentially Expressed ◽  
Cutting Condition ◽  
Differentially Expressed Proteins ◽  
Differential Protein

ObjectivesDark-cutting beef is a meat quality defect in which meat does not display the marketable bright-red color. Although previous studies have indicated that the ultimate pH of dark-cutting beef is greater than normal, the mechanistic basis for the occurrence is not clear. Various mitochondrial and glycolytic enzymes/proteins are involved in muscle metabolism and lowering of pH. However, limited knowledge is currently available on the muscle protein profile differences between dark-cutting and normal-pH beef. The objective of the current study was to identify proteins related to the development of the dark-cutting condition by comparing the protein expression differences between dark-cutting and normal-pH beef.Materials and MethodsDark-cutting and normal-pH beef samples were collected from six (n = 6) different animals after slaughter. Tissue samples (0.5 g) were digested in 5 mL of lysis buffer. Tissue lysates were homogenized, boiled, sonicated using a bioruptor and centrifuged at 10,000 g for 10 min. Samples were digested with trypsin/Lys-C overnight at 37°C, after which additional 2 µg/mL of protease was added and digestion was continued for another 8h. The resulting trypsinolytic peptides were acidified to 1% trifluoroacetic acid and purified by solid phase extraction with C18 affinity media. Protein expression profiles of both dark-cutting and normal-pH beef samples were determined using LC-MS/MS mass spectrometry-based proteomics. Collected raw data instrument files were searched against a bovine proteome database of 23,968 bovine proteome sequences using MaxQuant (V.1.5.3.8). Differential protein expression analysis was done in Perseus (V.1.5.1.3). Ingenuity pathway analysis (IPA) was utilized to determine the significant pathways of the differentially expressed proteins in dark-cutting and normal-pH beef. Gene ontology enrichment pathway analysis was performed to determine the main functions of the differentially expressed proteins in dark-cutting and normal-pH beef identified in our samples.ResultsMass spectrometry analysis identified 1148 proteins, and 97 of these proteins were differentially expressed between normal-pH and dark-cutting beef (P < 0.05). Fold change of 1.5 was observed for 29 proteins. Dark-cutting beef had 19 abundant proteins, while normal-pH beef had 10 abundant proteins. The majority of the upregulated proteins in dark-cutting beef were involved in mitochondrial functioning and metabolism, while the majority of the downregulated proteins were important in glycogen degradation, calcium signaling, α-adrenergic signaling, n-NOS-signaling and the proteasome pathways.ConclusionThe results identify new protein biomarkers associated with dark-cutting and suggest new mechanistic explanations for the dark-cutting phenotype.

scholarly journals Peripheral blood proteomic profiling of idiopathic pulmonary fibrosis biomarkers in the multicentre IPF-PRO Registry

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jamie L. Todd ◽  
◽  
Megan L. Neely ◽  
Robert Overton ◽  
Katey Durham ◽  
...  
Keyword(s):  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Protein Expression ◽  
Lung Disease ◽  
Disease Severity ◽  
Protein Profile ◽  
Receiver Operating Curve ◽  
Intercellular Adhesion Molecule ◽  
Differential Protein Expression ◽  
Differential Protein

Abstract Background Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease for which diagnosis and management remain challenging. Defining the circulating proteome in IPF may identify targets for biomarker development. We sought to quantify the circulating proteome in IPF, determine differential protein expression between subjects with IPF and controls, and examine relationships between protein expression and markers of disease severity. Methods This study involved 300 patients with IPF from the IPF-PRO Registry and 100 participants without known lung disease. Plasma collected at enrolment was analysed using aptamer-based proteomics (1305 proteins). Linear regression was used to determine differential protein expression between participants with IPF and controls and associations between protein expression and disease severity measures (percent predicted values for forced vital capacity [FVC] and diffusion capacity of the lung for carbon monoxide [DLco]; composite physiologic index [CPI]). Multivariable models were fit to select proteins that best distinguished IPF from controls. Results Five hundred fifty one proteins had significantly different levels between IPF and controls, of which 47 showed a |log2(fold-change)| > 0.585 (i.e. > 1.5-fold difference). Among the proteins with the greatest difference in levels in patients with IPF versus controls were the glycoproteins thrombospondin 1 and von Willebrand factor and immune-related proteins C-C motif chemokine ligand 17 and bactericidal permeability-increasing protein. Multivariable classification modelling identified nine proteins that, when considered together, distinguished IPF versus control status with high accuracy (area under receiver operating curve = 0.99). Among participants with IPF, 14 proteins were significantly associated with FVC % predicted, 23 with DLco % predicted, 14 with CPI. Four proteins (roundabout homolog-2, spondin-1, polymeric immunoglobulin receptor, intercellular adhesion molecule 5) demonstrated the expected relationship across all three disease severity measures. When considered in pathways analyses, proteins associated with the presence or severity of IPF were enriched in pathways involved in platelet and haemostatic responses, vascular or platelet derived growth factor signalling, immune activation, and extracellular matrix organisation. Conclusions Patients with IPF have a distinct circulating proteome and can be distinguished using a nine-protein profile. Several proteins strongly associate with disease severity. The proteins identified may represent biomarker candidates and implicate pathways for further investigation. Trial registration ClinicalTrials.gov (NCT01915511).

scholarly journals 153 DETERMINATION OF A DIFFERENTIAL PROTEIN PROFILE IN THE SYNOVIAL FLUID OF PATIENTS WITH RHEUMATOID ARTHRITIS AND OSTEOARTHRITIS

2011 ◽  
Vol 19 ◽  
pp. S78
Author(s):  
J. Mateos ◽  
P. Fernández-Puente ◽  
V. Calamia ◽  
L. Lourido ◽  
C. Fernández-López ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Synovial Fluid ◽  
Protein Profile ◽  
Differential Protein

Cellular alteration and differential protein profile explain effects of GA 3 and ABA and their inhibitor on Trichocline catharinensis (Asteraceae) seed germination

2020 ◽  
Vol 169 (2) ◽  
pp. 258-275
Author(s):  
Ana P. Lando ◽  
Willian G. Viana ◽  
Ellen M. Vale ◽  
Marisa Santos ◽  
Vanildo Silveira ◽  
...  
Keyword(s):  
Seed Germination ◽  
Protein Profile ◽  
Differential Protein ◽  
Cellular Alteration
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