Enzyme annotation in UniProtKB using Rhea

Morgat, Anne; Lombardot, Thierry; Coudert, Elisabeth; Axelsen, Kristian; Neto, Teresa Batista; Géhant, Sébastien; Bansal, Parit; Bolleman, Jerven; Gasteiger, Elisabeth; Castro, Edouard de; Baratin, Delphine; Pozzato, Monica; Xénarios, Ioannis; Poux, Sylvain; Redaschi, Nicole; Bridge, Alan

doi:10.1093/bioinformatics/btz817

Cited by 85 publications

(79 citation statements)

References 40 publications

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“…b List of metabolites whose expressions were significantly changed (P < 0.05) in MET pups and were associated with the largest gene networks (≥5 gene/metabolite) c List of genes whose expressions were significantly changed (P < 0.05) in MET pups and were associated with the largest metabolite networks (≥5 metabolite/gene). d SAM-associated pathways involving genes whose levels were significantly changed (P < 0.05) in MET pups, using UniPort for identifying the metabolic reactions 86 . e NAD+-associated pathways involving genes whose levels were significantly changed in MET pups (P < 0.05) using UniPort for identifying the metabolic reactions 86 .…”

Section: Discussionmentioning

confidence: 99%

“…d SAM-associated pathways involving genes whose levels were significantly changed (P < 0.05) in MET pups, using UniPort for identifying the metabolic reactions 86 . e NAD+-associated pathways involving genes whose levels were significantly changed in MET pups (P < 0.05) using UniPort for identifying the metabolic reactions 86 . f Glutamate-associated pathways involving genes whose levels were significantly changed (P < 0.05) in MET pups.…”

Section: Discussionmentioning

confidence: 99%

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Metabolomic and transcriptomic signatures of prenatal excessive methionine support nature rather than nurture in schizophrenia pathogenesis

et al. 2020

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The imbalance of prenatal micronutrients may perturb one-carbon (C1) metabolism and increase the risk for neuropsychiatric disorders. Prenatal excessive methionine (MET) produces in mice behavioral phenotypes reminiscent of human schizophrenia. Whether in-utero programming or early life caregiving mediate these effects is, however, unknown. Here, we show that the behavioral deficits of MET are independent of the early life mother-infant interaction. We also show that MET produces in early life profound changes in the brain C1 pathway components as well as glutamate transmission, mitochondrial function, and lipid metabolism. Bioinformatics analysis integrating metabolomics and transcriptomic data reveal dysregulations of glutamate transmission and lipid metabolism, and identify perturbed pathways of methylation and redox reactions. Our transcriptomics Linkage analysis of MET mice and schizophrenia subjects reveals master genes involved in inflammation and myelination. Finally, we identify potential metabolites as early biomarkers for neurodevelopmental defects and suggest therapeutic targets for schizophrenia.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Metabolomic and transcriptomic signatures of prenatal excessive methionine support nature rather than nurture in schizophrenia pathogenesis

et al. 2020

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“…The primary sequence of Saccharomyces cerevisiae α-glucosidase (584 amino acids) was obtained from UniProtKB [27] with accession number P53341. The secondary structure prediction was performed using JPred [28], PORTER [29], Predict Protein [30], PSIPRED [31], SCRATCH [32] and YASPIN [33].…”

Section: Protein Structurementioning

confidence: 99%

Synthesis, In Vitro Evaluation and Molecular Docking of the 5-Acetyl-2-aryl-6-hydroxybenzo[b]furans against Multiple Targets Linked to Type 2 Diabetes

et al. 2020

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The 5-acetyl-2-aryl-6-hydroxybenzo[b]furans 2a-h have been evaluated through in vitro enzymatic assay against targets which are linked to type 2 diabetes (T2D), namely, α-glucosidase, protein tyrosine phosphatase 1B (PTP1B) and β-secretase. These compounds have also been evaluated for antioxidant activity using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) free-radical scavenging method. The most active compounds against α-glucosidase and/or PTP1B, namely, 4-fluorophenyl 2c, 4-methoxyphenyl 2g and 3,5-dimethoxyphenyl substituted 2h derivatives were also evaluated for potential anti-inflammatory properties against cyclooxygenase-2 activity. The Lineweaver-Burk and Dixon plots were used to determine the type of inhibition on compounds 2c and 2h against α-glucosidase and PTP1B receptors. The interactions were investigated in modelled complexes against α-glucosidase and PTP1B via molecular docking.

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“…Only clear electropherograms were considered in the observed variations of the SARS-CoV-2 sequences. The appropriate reading frame of the observed variants was aligned with its corresponding reference sequences within the viral surface glycoprotein using the UniProtKB server [21].…”

Section: Dna Sequencingmentioning

confidence: 99%

Unexpected Co-infection with Different Strains of SARS-CoV-2 in Patients with COVID-19

Hashim¹,

Mohammed²,

Mousa³

et al. 2020

Preprint

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There is a rising global concern for the ongoing outbreak of SARS-CoV-2 due to its high transmission rate and unavailability of treatment. Through the binding of its spike glycoprotein with angiotensin type 2 (ACE2), SARS-CoV-2 can efficiently get in the cells of patients and start its pandemic cycle. Herein, the biological diversity of SARS-CoV-2 infection was assessed in Babylon province of Iraq by investigating the possible genetic variations of the spike glycoprotein. A specific coding region of 795 bp within the viral spike (S) gene was amplified from 19 patients who suffered from obvious symptoms of SARS-CoV-2 infection. Sequencing results identified fifteen novel nucleic acid variations with a variety of distributions within the investigated samples. The electropherograms of all the identified variations showed obvious co-infections with at least two different viral strains per sample. Within these co-infections, the majority of samples exhibited three nonsense single nucleotide polymorphism (SNP)s, p.301Cdel, p.380Ydel, and p.436del, which yielded three truncated SARS-CoV-2 spike glycoproteins of 301, 380, and 436 amino acids length, respectively. The network and phylogenetic analyses indicated that for all viral infections were derived from multi-ancestral origins. Results inferred from the specific clade-based tree entailed that some viral strains were derived from European G-clade sequences. In conclusion, our data demonstrated the absence of any single strain infection among all investigated viral samples in the studied area, which may entail a higher risk of SARS-CoV-2 in this country. Through the identified high frequency of truncated spike proteins, we suggest that defective SARS-CoV-2 may depend on helper strains having intact spikes in its infection. Alternatively, another putative ACE2-independent route of viral infection way also suggested. To the best of our knowledge, this is the first report to describe the co-infection of multiple strains of SARS-CoV-2 in patients with COVID-19.

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Enzyme annotation in UniProtKB using Rhea

Cited by 85 publications

References 40 publications

Metabolomic and transcriptomic signatures of prenatal excessive methionine support nature rather than nurture in schizophrenia pathogenesis

Metabolomic and transcriptomic signatures of prenatal excessive methionine support nature rather than nurture in schizophrenia pathogenesis

Synthesis, In Vitro Evaluation and Molecular Docking of the 5-Acetyl-2-aryl-6-hydroxybenzo[b]furans against Multiple Targets Linked to Type 2 Diabetes

Unexpected Co-infection with Different Strains of SARS-CoV-2 in Patients with COVID-19

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