Project description:We aimed to identify genes with considerable expression changes between male and female patients with idiopathic carpal tunnel syndrome (ICTS). For this purpose, we collected subsynovial connective tissues from 6 male and 6 female patients diagnosed with idiopathic carpal tunnel syndrome during surgery. We extracted the total RNA from the collected specimens and performed a comprehensive gene expression analysis using RNA sequencing by comparing between male and female patients. We analyzed the changes in gene expression in male patients relative to that in female patients, and as a result, 26 genes were extracted. In the RNAseq analysis, the expression of these genes (IGF1, COL1A1, and COL3A1) was upregulated in the male patient group.
Project description:Continuous translation elongation, irrespective of amino acid sequences, is a prerequisite for living organisms to produce their proteomes. However, the risk of elongation abortion is concealed within nascent polypeptide products. For example, negatively charged sequences with occasional intermittent prolines, termed intrinsic ribosome destabilization (IRD) sequences, destabilizes the translating ribosomal complex. Thus, some nascent chain sequences lead to premature translation cessation. Here, we show that most potential IRD sequences in the middle of open reading frames remain cryptic by two mechanisms: the nascent polypeptide itself that spans the exit tunnel and its bulky amino acid residues that occupy the tunnel entrance region. Thus, nascent polypeptide products have a built-in ability to ensure elongation continuity by serving as a bridge and thus by protecting the large and small ribosomal subunits from dissociation.
Project description:Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.
Project description:Full title: Environmental transcriptome analysis of LfeRT32a in its natural microbial community comparing the biofilm and planktonic modes of life. Extreme acidic environments are characterized among other features by the high metal content and the lack of nutrients (oligotrophy). Macroscopic biofilms and filaments usually grow on the water-air interface or under the stream attached to solid substrates (streamers). In the Tinto River (Spain), brown filaments develop under the water stream where the Gram-negative iron-oxidizing bacteria Leptospirillum ferrooxidans and Acidithiobacillus ferrooxidans are abundant. Both microorganisms play a critical role in bioleaching processes for industrial (biominery) and environmental applications (acid mine drainage, bioremediation). The aim of this study was to investigate the physiological differences between the free living (planktonic) and the sessile (biofilm associated) lifestyles of L. ferrooxidans as part of a natural extremely acidophilic community.
Project description:Comparison of gene expression profiles from Nothobranchius furzeri (strain: MZM-04/10p) liver for 2 age groups after physical exercise (swim-tunnel). For physical exercise, fish were placed in swim-tunnel for 4 weeks and were swimming 6 times per day for 5 min duration (water velocity 14 cm/s).The RNA-seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)
Project description:Comparison of gene expression profiles from Nothobranchius furzeri (strain: MZM-04/10p) brain for 2 age groups after physical exercise (swim-tunnel). For physical exercise, fish were placed in swim-tunnel for 4 weeks and were swimming 6 times per day for 5 min duration (water velocity 14 cm/s). The RNA-seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)
Project description:Comparison of gene expression profiles from Nothobranchius furzeri (strain: MZM-04/10p) skin for 2 age groups after physical exercise (swim-tunnel). For physical exercise, fish were placed in swim-tunnel for 4 weeks and were swimming 6 times per day for 5 min duration (water velocity 14 cm/s). The RNA-seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)
Project description:Comparison of gene expression profiles from Nothobranchius furzeri (strain: MZM-04/10p) muscle for 2 age groups after physical exercise (swim-tunnel). For physical exercise, fish were placed in swim-tunnel for 4 weeks and were swimming 6 times per day for 5 min duration (water velocity 14 cm/s). The RNA-seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)
