UniProt Protein Knowledgebase

Pundir, Sangya; Martin, Maria Jesus; O′Donovan, Claire

doi:10.1007/978-1-4939-6783-4_2

Cited by 264 publications

(202 citation statements)

References 5 publications

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“…Various reports suggest that some secretable enzyme families such as pectin lyase, pectin methylesterase and polygalacturonase are found in Gram‐negative bacteria (Abbott and Boraston ). Also, as a result of bioinformatic analyses using the UniProt database according to Pundir et al () we confirmed the presence of polygalacturonic enzymes in Pseudomonas genus such as PglA (polygalacturonase), PehA (glycoside hydrolase), PehB (exo‐poly‐galacturonase signal peptide protein), PehC (polygalacturonase transmembrane protein) and PehX (exo‐poly‐alpha‐ d ‐galacturonosidase) (González and Allen ). Furthermore, some sequences were found related to polygalacturonase enzymes such as polygalacturonase (PglA), endopolygalacturonase (PehX) and glycoside hydrolase family 28 (AdhA) in the Enterobacter and Citrobacter genus.…”

Section: Discussionsupporting

confidence: 67%

Evaluation of process involved in the production of aromatic compounds in Gram‐negative bacteria isolated from vanilla ( Vanilla planifolia ex. Andrews) beans

et al. 2019

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Aim The present investigation was aimed at isolating and identifying bacterial strains from cured vanilla beans. Additionally, the study focused on evaluating bacterial processes pertaining to the aromatic compounds production (ACP). Methods and Results Three bacteria were isolated from Vanilla planifolia beans, previously subjected to the curing process. According to morphological, biochemical and 16S rRNA analysis, the strains were identified as Citrobacter sp., Enterobacter sp. and Pseudomonas sp. The polygalacturonase activity (PGA) was determined using the drop, cup‐plate and DNS methods. Aromatic compounds production was analysed by cup‐plate method using FA as substrate and quantified by high performance liquid chromatography (ppm), the functional groups of vanillic acid (VA) were identified by FT‐IR and the aromatic compounds (AC) resistance was determined and reported as minimum inhibitory concentration. Citrobacter sp., Enterobacter sp. and Pseudomonas showed PGA (70·31 ± 364, 76·07 ± 12·47 and 51 ± 10·92 U ml−1 respectively), were producers of VA (3·23 ± 0·49, 324 ± 41 and 265·99 ± 11·61 ppm respectively) and were resistant to AC. Conclusions The Gram‐negative bacteria isolated from V. planifolia beans were responsible for ACP. Significance and Impact of the Study This is the first evidence for the role of Gram‐negative bacterial isolates from cured Mexican V. planifolia beans in the process related to ACP.

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Section: Discussionsupporting

confidence: 67%

Evaluation of process involved in the production of aromatic compounds in Gram‐negative bacteria isolated from vanilla ( Vanilla planifolia ex. Andrews) beans

et al. 2019

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“…The remaining transcripts were used in a blastx 72 search using default parameters against the UniProt/SwissProt database 73 . Any transcripts that shared >30% sequence identity with known proteins with an e-value >1E-2 were eliminated.…”

Section: Rna-seq Analysismentioning

confidence: 99%

A genome-wide assessment of the ancestral neural crest gene regulatory network

Hockman

Chong

Gavriouchkina

et al. 2018

Preprint

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The neural crest is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the transcriptional profiles and chromatin accessibility of neural crest cells in the basal sea lamprey, in order to gain insight into the ancestral state of the neural crest gene regulatory network (GRN) at the dawn of vertebrates. Transcriptome analyses reveal clusters of co-regulated genes during neural crest specification and migration that show high conservation across vertebrates for dynamic programmes like Wnt modulation during the epithelial to mesenchymal transition, but also reveal novel transcription factors and cell-adhesion molecules not previously implicated in neural crest migration. ATAC-seq analysis refines the location of known cis-regulatory elements at the Hox-α2 locus and uncovers novel cis-regulatory elements for Tfap2B and SoxE1. Moreover, cross-species deployment of lamprey elements in zebrafish reveals that the lamprey SoxE1 enhancer activity is deeply conserved, mediating homologous expression in jawed vertebrates. Together, our data provide new insight into the core elements of the GRN that are conserved to the base of the vertebrates, as well as expose elements that are unique to lampreys.

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“…Figures A and B show extracted ion chromatograms for the Na v 1.6‐overexpressed HEK239 cells and mouse brain hippocampus tissues tryptic digests using the selected targeted MRM transitions listed in Table corresponding to eight unique peptides to Na v 1.6. The uniqueness of these peptides to Na v 1.6 was verified by aligning protein sequences of Na v 1.6 with those of other sodium channels (Na v 1.1, 1.2, 1.3, 1.5, 1.7 and 1.8) as well as with other major brain proteins using Uniprot . With the exception of the peptide INQDCELPR all peptides showed three targeted transitions, providing partial evidence of their identity.…”

Section: Resultsmentioning

confidence: 90%

On the feasibility of quantifying sodium channel Na_v1.6 protein in mouse brain using targeted ultra‐high‐performance/electrospray ionization multiple reaction monitoring mass spectrometry

Sojo

Kwan

Dang

et al. 2019

Rapid Comm Mass Spectrometry

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Rationale Nav1.6 is a transmembrane voltage gated sodium channel implicated in various forms of epilepsy. Modulation of its activity in epilepsy animal models can be accomplished using inhibitors which may result in changes in its expression. There is a need to generate reliable quantitative measurements of Nav1.6 expression in animal models. This research explores the feasibility of quantifying Nav1.6 expression in mouse brains using targeted multiple reaction monitoring (MRM) mass spectrometry. Methods A combination of in silico tryptic Nav1.6 peptides and MRM transitions were used to select target peptides. This was followed by a simple proteomic work‐up including plasma membrane isolation, trypsin‐based proteolysis and ultra‐high‐performance/electrospray ionization tandem mass spectrometry (UHPLC/ESI‐MS/MS) to detect the presence of Nav1.6 in induced HEK293 cells. The unique Nav1.6 peptide, DSLFIPR, was selected as probe for quantifying Nav1.6 levels in brains from C57BL/6J wild‐type mice as well as two kinds of mutants including Scn8aN1768D/+ and heterozygous null Scn8a+/− mice using isotope dilution targeted mass spectrometry. Results The feasibility of using targeted MRM for quantifying Nav1.6 expression in mice brains was demonstrated. Expression of Nav1.6 in brains (hippocampi) from wild‐type and mutant Scn8aN1768D/+ mice were found to be around 0.40 fmol/μg. Mutant null Scn8a+/− heterozygous mice, on the other hand, showed levels of 0.22 fmol/μg as expected based on this particular mutation which only generates 50% of the expression in wild‐type mice. Nav1.6‐overexpressed HEK293 cells showed 3.7 fmol/μg of Nav1.6 expression, suitable for screening new compounds for Nav1.6 blocking activity. Conclusions The results of the present feasibility study support the use of DSLFIPIR for quantification of Nav1.6 in brain tissues using UHPL/ESI‐MS/MS.

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UniProt Protein Knowledgebase

Cited by 264 publications

References 5 publications

Evaluation of process involved in the production of aromatic compounds in Gram‐negative bacteria isolated from vanilla ( Vanilla planifolia ex. Andrews) beans

Evaluation of process involved in the production of aromatic compounds in Gram‐negative bacteria isolated from vanilla ( Vanilla planifolia ex. Andrews) beans

A genome-wide assessment of the ancestral neural crest gene regulatory network

On the feasibility of quantifying sodium channel Na_v1.6 protein in mouse brain using targeted ultra‐high‐performance/electrospray ionization multiple reaction monitoring mass spectrometry

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UniProt Protein Knowledgebase

Cited by 264 publications

References 5 publications

Evaluation of process involved in the production of aromatic compounds in Gram‐negative bacteria isolated from vanilla ( Vanilla planifolia ex. Andrews) beans

Evaluation of process involved in the production of aromatic compounds in Gram‐negative bacteria isolated from vanilla ( Vanilla planifolia ex. Andrews) beans

A genome-wide assessment of the ancestral neural crest gene regulatory network

On the feasibility of quantifying sodium channel Nav1.6 protein in mouse brain using targeted ultra‐high‐performance/electrospray ionization multiple reaction monitoring mass spectrometry

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Product

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On the feasibility of quantifying sodium channel Na_v1.6 protein in mouse brain using targeted ultra‐high‐performance/electrospray ionization multiple reaction monitoring mass spectrometry