An in silico analysis of genome-wide expression profiles of the effects of exhaustive exercise identifies heat shock proteins as the key players

Meta Gene ◽  
2022 ◽  
pp. 101012
Author(s):  
Carlos A. Orozco ◽  
Yeimy González-Giraldo ◽  
Diego A. Bonilla ◽  
Diego A. Forero
Keyword(s):  
Heat Shock ◽  
Heat Shock Proteins ◽  
In Silico ◽  
Expression Profiles ◽  
In Silico Analysis ◽  
Genome Wide ◽  
Key Players ◽  
Shock Proteins ◽  
Genome Wide Expression ◽  
Silico Analysis

scholarly journals Comparative In Silico Analysis of Randomly Selected Heat Shock Proteins in Caenorhabditis elegans and Photorhabdus temperata

2020 ◽  
Vol 11 (4) ◽  
pp. 11418-11430
Keyword(s):  
Caenorhabditis Elegans ◽  
Heat Shock ◽  
Heat Shock Proteins ◽  
In Silico ◽  
Pearson Correlation ◽  
In Silico Analysis ◽  
Multivariate Techniques ◽  
Shock Proteins ◽  
Silico Analysis ◽  
Photorhabdus Temperata

Heat shock proteins (HSPs) such as HSP70A, HSP90 etc. (also known as Chaperons) play an important role in folding and unfolding of proteins, an assemblage of multiprotein complexes, transportation and sorting of proteins in subcellular compartments, cell cycle control, signaling pathways, protection against stress and programmed cell death. Studies have also linked heat shock proteins with a sudden rise in temperature, which can be related to anhydrobiosis in nematodes. Considering the significance of HSPs in nematodes and bacteria, the present study was designed for their in silico analysis in Caenorhabditis elegans and Photorhabdus temperata. The availability of a vast amount of sequence data generated through various bioinformatics tools, coupled with computational biology advancements, provides an ideal framework for silico gene expression and its analysis. A detailed in silico insight into these proteins include physicochemical properties, secondary structure prediction, homology modeling, and different models. The amino acid composition data were subjected to multivariate techniques, Pearson correlation, and phylogenetic analysis. In the present study, the authors characterized different HSPs according to different stability parameters and valid structures. A detailed in silico analysis of these proteins and prediction of their activity in different conditions can be very useful in both in vitro and in vivo experiments.

scholarly journals In Silico Analysis of the Age-Dependent Evolution of the Transcriptome of Mouse Skin Stem Cells

Cells ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 165
Author(s):  
L. Francisco Lorenzo-Martín ◽  
Xosé R. Bustelo
Keyword(s):  
Stem Cells ◽  
In Silico ◽  
Mouse Skin ◽  
In Silico Analysis ◽  
Time Points ◽  
The Core ◽  
Genome Wide ◽  
Age Dependent ◽  
Genome Wide Expression ◽  
Silico Analysis

The stem cells located in the hair follicle bulge area are critical for skin regeneration and repair. To date, little is known about the evolution of the transcriptome of these cells across time. Here, we have combined genome-wide expression analyses and a variety of in silico tools to determine the age-dependent evolution of the transcriptome of those cells. Our results reveal that the transcriptome of skin stem cells fluctuates extensively along the lifespan of mice. The use of both unbiased and pathway-centered in silico approaches has also enabled the identification of biological programs specifically regulated at those specific time-points. It has also unveiled hubs of highly transcriptionally interconnected genes and transcriptional factors potentially located at the core of those age-specific changes.

Distinctive heat-shock response of bioleaching microorganismAcidithiobacillus ferrooxidansobserved using genome-wide microarray

2012 ◽  
Vol 58 (5) ◽  
pp. 628-636 ◽  
Author(s):  
Huaqun Yin ◽  
Min Tang ◽  
Zhijun Zhou ◽  
Xian Fu ◽  
Li Shen ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Response ◽  
Heterotrophic Bacteria ◽  
Expression Profiles ◽  
Central Carbon Metabolism ◽  
Autotrophic Bacteria ◽  
Genome Wide ◽  
Shock Response ◽  
Shock Proteins ◽  
Genome Wide Expression

Temperature plays an important role in the heap bioleaching. The maldistribution of ventilation in the heap leads to local hyperthermia, which does exert a tremendous stress on bioleaching microbes. In this study, the genome-wide expression profiles of Acidithiobacillus ferrooxidans at 40 °C were detected using the microarray. The results showed that some classic proteases like Lon and small heat-shock proteins were not induced, and heat-inducible membrane proteins were suggested to be under the control of σE. Moreover, expression changes of energy metabolism are noteworthy, which is different from that in heterotrophic bacteria upon heat stress. The induced enzymes catalyzed the central carbon metabolism pathway that might mainly provide precursors of amino acids for protein synthesis. These results will deepen the understanding of the mechanisms of heat-shock response on autotrophic bacteria.

scholarly journals Exosomal Heat Shock Proteins as New Players in Tumour Cell-to-Cell Communication

2014 ◽  
Vol 3 (1) ◽  
Author(s):  
Claudia Campanella ◽  
Celeste Caruso Bavisotto ◽  
Antonella Marino Gammazza ◽  
Dragana Nikolic ◽  
Francesca Rappa ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Heat Shock ◽  
Heat Shock Proteins ◽  
Cell Communication ◽  
Clinical Applications ◽  
Cancer Development ◽  
Pathological Conditions ◽  
Key Players ◽  
Novel Biomarkers ◽  
Shock Proteins

Exosomes have recently been proposed as novel elements in the study of intercellular communication in normal and pathological conditions. The biomolecular composition of exosomes reflects the specialized functions of the original cells. Heat shock proteins (Hsps) are a group of chaperone proteins with diverse biological roles. In recent years, many studies have focused on the extracellular roles played by Hsps that appear to be involved in cancer development and immune system stimulation. Hsps localized on the surface of exosomes, secreted by normal and tumour cells, could be key players in intercellular cross-talk, particularly during the course of different diseases, such as cancer. Exosomal Hsps offer significant opportunities for clinical applications, including their use as potential novel biomarkers for the diagnoses or prognoses of different diseases, or for therapeutic applications and drug delivery.

scholarly journals Computational genome-wide identification of heat shock protein genes in the bovine genome

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1504 ◽  
Author(s):  
Oyeyemi O. Ajayi ◽  
Sunday O. Peters ◽  
Marcos De Donato ◽  
Sunday O. Sowande ◽  
Fidalis D.N. Mujibi ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Proteins ◽  
Bovine Genome ◽  
Protein Family ◽  
Evolutionary Trace ◽  
Sequence Identity ◽  
Genome Wide ◽  
Physico Chemical ◽  
Small Hsp ◽  
Shock Proteins

Background: Heat shock proteins (HSPs) are molecular chaperones known to bind and sequester client proteins under stress. Methods: To identify and better understand some of these proteins, we carried out a computational genome-wide survey of the bovine genome. For this, HSP sequences from each subfamily (sHSP, HSP40, HSP70 and HSP90) were used to search the Pfam (Protein family) database, for identifying exact HSP domain sequences based on the hidden Markov model. ProtParam tool was used to compute potential physico-chemical parameters detectable from a protein sequence. Evolutionary trace (ET) method was used to extract evolutionarily functional residues of a homologous protein family. Results: We computationally identified 67 genes made up of 10, 43, 10 and 4 genes belonging to small HSP, HSP40, HSP70 and HSP90 families respectively. These genes were widely dispersed across the bovine genome, except in chromosomes 24, 26 and 27, which lack bovine HSP genes. We found an uncharacterized outer dense fiber (ODF1) gene in cattle with an intact alpha crystallin domain, like other small HSPs. Physico-chemical characteristic of aliphatic index was higher in HSP70 and HSP90 gene families, compared to small HSP and HSP40. Grand average hydropathy showed that small HSP (sHSP), HSP40, HSP70 and HSP90 genes had negative values except for DNAJC22, a member of HSP40 gene family. The uniqueness of DNAJA3 and DNAJB13 among HSP40 members, based on multiple sequence alignment, evolutionary trace analysis and sequence identity dendrograms, suggests evolutionary distinct structural and functional features, with unique roles in substrate recognition and chaperone functions. The monophyletic pattern of the sequence identity dendrograms of cattle, human and mouse HSP sequences suggests functional similarities. Conclusions: Our computational results demonstrate the first-pass in-silico identification of heat shock proteins and calls for further investigation to better understand their functional roles and mechanisms in Bovidae.

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