scholarly journals Quantitative proteomics and bioinformatic analysis provide new insight into the dynamic response of porcine intestine to Salmonella Typhimurium

2015 ◽  
Vol 5 ◽  
Author(s):  
Melania Collado-Romero ◽  
Carmen Aguilar ◽  
Cristina Arce ◽  
Concepción Lucena ◽  
Marius C. Codrea ◽  
...  
Keyword(s):  
Dynamic Response ◽  
Salmonella Typhimurium ◽  
Quantitative Proteomics ◽  
Bioinformatic Analysis ◽  
Insight Into

Quantitative proteomics and bioinformatic analysis provide new insight into protein function during avian eggshell biomineralization

2015 ◽  
Vol 113 ◽  
pp. 178-193 ◽  
Author(s):  
Pauline Marie ◽  
Valérie Labas ◽  
Aurélien Brionne ◽  
Grégoire Harichaux ◽  
Christelle Hennequet-Antier ◽  
...  
Keyword(s):  
Protein Function ◽  
Quantitative Proteomics ◽  
Bioinformatic Analysis ◽  
Insight Into

scholarly journals A new insight into role of phosphoketolase pathway in Synechocystis sp. PCC 6803

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Anushree Bachhar ◽  
Jiri Jablonsky
Keyword(s):  
In Silico Analysis ◽  
Bioinformatic Analysis ◽  
Phosphoglycerate Mutase ◽  
Phosphoketolase Pathway ◽  
Multi Level ◽  
Silico Analysis ◽  
Insight Into ◽  
Synechocystis Sp ◽  
Pcc 6803

AbstractPhosphoketolase (PKET) pathway is predominant in cyanobacteria (around 98%) but current opinion is that it is virtually inactive under autotrophic ambient CO2 condition (AC-auto). This creates an evolutionary paradox due to the existence of PKET pathway in obligatory photoautotrophs. We aim to answer the paradox with the aid of bioinformatic analysis along with metabolic, transcriptomic, fluxomic and mutant data integrated into a multi-level kinetic model. We discussed the problems linked to neglected isozyme, pket2 (sll0529) and inconsistencies towards the explanation of residual flux via PKET pathway in the case of silenced pket1 (slr0453) in Synechocystis sp. PCC 6803. Our in silico analysis showed: (1) 17% flux reduction via RuBisCO for Δpket1 under AC-auto, (2) 11.2–14.3% growth decrease for Δpket2 in turbulent AC-auto, and (3) flux via PKET pathway reaching up to 252% of the flux via phosphoglycerate mutase under AC-auto. All results imply that PKET pathway plays a crucial role under AC-auto by mitigating the decarboxylation occurring in OPP pathway and conversion of pyruvate to acetyl CoA linked to EMP glycolysis under the carbon scarce environment. Finally, our model predicted that PKETs have low affinity to S7P as a substrate.

scholarly journals Comparative Proteomics Analysis of Mouse Habu Nephritis Models with and without Unilateral Nephrectomy

2016 ◽  
Vol 39 (5) ◽  
pp. 1761-1776 ◽  
Author(s):  
Lei Chen ◽  
Yang Lu ◽  
Jun Wen ◽  
Xu Wang ◽  
Lingling Wu ◽  
...  
Keyword(s):  
Renal Injury ◽  
Quantitative Proteomics ◽  
Mesangial Cells ◽  
Unilateral Nephrectomy ◽  
Label Free ◽  
Proteomics Analysis ◽  
Single Kidney ◽  
Regulation Of Actin Cytoskeleton ◽  
Insight Into

Background/Aims: Individuals possessing a single kidney are at greater risk of renal injury upon exposure to harmful stimuli. This study aimed to explore the pathogenesis of renal injury in glomerulonephritis with versus without unilateral nephrectomy (UNX). Methods: Histological analysis and label-free quantitative proteomics were performed on two models—the Habu snake venom-induced glomerulonephritis model with versus without UNX (HabuU and Habu models, respectively). The role of villin 1, a differentially expressed protein (DEP) in mouse mesangial cells, was investigated. Results: Persistent mesangiolysis and focal hypercellularity together with reduced activation of cell proliferation in the HabuU model induced more serious renal injury compared with that in the Habu model. The DEPs between the two models were identified by label-free liquid chromatography-mass spectrometry. The KEGG pathway results indicated that regulation of actin cytoskeleton and focal adhesion were specifically enriched in the HabuU model. The cytoskeleton regulation protein villin 1 was downregulated in the HabuU model, but unchanged in the Habu model. Knockdown of villin 1 promoted apoptosis and inhibited the proliferation of mouse mesangial cells, suggesting villin 1 to be involved in qlomerular lesion self-repair insufficiency. Conclusion: By assessing the proteomic profiles of the two models, this study identified several important differences, particularly villin 1 expression, in regulatory mechanisms between the two models. Our findings provide novel insight into the mechanism of serious renal injury in glomerulonephritis with UNX.

scholarly journals The role of phagocytosis-dependent activation of TFEB in the clearance of salmonella

2021 ◽  
Author(s):  
Erika Ospina Escobar
Keyword(s):  
Transcription Factor ◽  
Salmonella Typhimurium ◽  
Nuclear Translocation ◽  
Steady Increase ◽  
Phagosome Maturation ◽  
Salmonella Infection ◽  
Complex Interplay ◽  
Transcription Factor Eb ◽  
Insight Into

During phagocytosis, macrophages engulf and sequester pathogens into phagosomes. Phagosomes then fuse with acidic and degradative lysosomes to degrade the internalized pathogen. We previously demonstrated that phagocytosis of IgG-opsonized particles and non-opsonized E.coli causes activation of the Transcription Factor EB (TFEB), which enhances the expression of lysosomal genes, increases the degradative capacity of lysosomes and boosts bactericidal activity. However, pathogens like Salmonella typhimurium have evolved mechanisms to evade and/or alter phagosome maturation to promote their own survival. We investigated: i) whether pathogens like Salmonella can alter TFEB activation and ii) whether phagocytosis-dependent activation of TFEB can counteract the pathogenicity of microorganisms. Here, we show that non-viable (heat-killed) S. typhimurium, pathogenic (EHEC and UPEC) and non-pathogenic E.coli (DH5α) all caused TFEB nuclear translocation in RAW macrophages, while strikingly live S. typhimurium maintained TFEB in the cytosol in the first hours post-infection. By contrast, Salmonella mutants for ΔsifA, ΔsopD2, ΔphoP all triggered TFEB activation in the first hour of infection. However, Salmonella infection eventually triggered a steady increase in nuclear TFEB after 4 h of infection, suggesting a more complex interplay between TFEB and Salmonella infection. We dissected the importance of TFEB activation towards Salmonella survivability by pre-activating TFEB before infection within WT macrophages and macrophages with a CRISPR-based deletion of TFEB. Our work suggests that Salmonella actively interferes with TFEB signaling in order to enhance its own survival. These results could provide insight into using TFEB as a target for the clearance of infections.

scholarly journals Multisystem proteinopathy due to a homozygous p.Arg159His VCP mutation

Neurology ◽  
2019 ◽  
Vol 94 (8) ◽  
pp. e785-e796 ◽  
Author(s):  
Willem De Ridder ◽  
Abdelkrim Azmi ◽  
Christoph S. Clemen ◽  
Ludwig Eichinger ◽  
Andreas Hofmann ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Disease Onset ◽  
Index Patient ◽  
Bioinformatic Analysis ◽  
Muscle Involvement ◽  
Proteomic Data ◽  
Disease Characteristics ◽  
Whole Exome ◽  
Disease Signatures ◽  
Muscle Biopsies

ObjectiveTo assess the clinical, radiologic, myopathologic, and proteomic findings in a patient manifesting a multisystem proteinopathy due to a homozygous valosin-containing protein gene (VCP) mutation previously reported to be pathogenic in the heterozygous state.MethodsWe studied a 36-year-old male index patient and his father, both presenting with progressive limb-girdle weakness. Muscle involvement was assessed by MRI and muscle biopsies. We performed whole-exome sequencing and Sanger sequencing for segregation analysis of the identified p.Arg159His VCP mutation. To dissect biological disease signatures, we applied state-of-the-art quantitative proteomics on muscle tissue of the index case, his father, 3 additional patients with VCP-related myopathy, and 3 control individuals.ResultsThe index patient, homozygous for the known p.Arg159His mutation in VCP, manifested a typical VCP-related myopathy phenotype, although with a markedly high creatine kinase value and a relatively early disease onset, and Paget disease of bone. The father exhibited a myopathy phenotype and discrete parkinsonism, and multiple deceased family members on the maternal side of the pedigree displayed a dementia, parkinsonism, or myopathy phenotype. Bioinformatic analysis of quantitative proteomic data revealed the degenerative nature of the disease, with evidence suggesting selective failure of muscle regeneration and stress granule dyshomeostasis.ConclusionWe report a patient showing a multisystem proteinopathy due to a homozygous VCP mutation. The patient manifests a severe phenotype, yet fundamental disease characteristics are preserved. Proteomic findings provide further insights into VCP-related pathomechanisms.

Gene co-expression network analysis provides a novel insight into the dynamic response of wheat to powdery mildew stress

2020 ◽  
Vol 99 (1) ◽  
Author(s):  
Weiguo Hu ◽  
Qiaohui Wang ◽  
Siwen Wang ◽  
Mengmeng Wang ◽  
Changyou Wang ◽  
...  
Keyword(s):  
Network Analysis ◽  
Powdery Mildew ◽  
Dynamic Response ◽  
Insight Into

Insight into the antibacterial property of chitosan nanoparticles against Escherichia coli and Salmonella Typhimurium and their application as vegetable wash disinfectant

Food Control ◽  
2018 ◽  
Vol 86 ◽  
pp. 294-301 ◽  
Author(s):  
Pathompong Paomephan ◽  
Apinya Assavanig ◽  
Soraya Chaturongakul ◽  
Nathaniel C. Cady ◽  
Magnus Bergkvist ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Salmonella Typhimurium ◽  
Antibacterial Property ◽  
Chitosan Nanoparticles ◽  
Insight Into

scholarly journals Systematically quantitative proteomics and metabolite profiles offer insight into fruit ripening behavior in Fragaria × ananassa

RSC Advances ◽  
2019 ◽  
Vol 9 (25) ◽  
pp. 14093-14108 ◽  
Author(s):  
Li Li ◽  
Qiong Wu ◽  
Youyong Wang ◽  
Morteza Soleimani Aghdam ◽  
Zhaojun Ban ◽  
...  
Keyword(s):  
Fruit Ripening ◽  
Quantitative Proteomics ◽  
Fragaria Ananassa ◽  
Metabolite Profiles ◽  
Insight Into

Proteome and metabolite profiles of fruit ripening behavior in Fragaria × ananassa Duch. ‘Benihoppe’.

Sign in / Sign up

Export Citation Format

Share Document