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10 results for “coat proteins”
Coat protein (CP) and trimmed replication-associated protein (Rep) amino acid alignments, phylogenetic analyses, and associated metadata for ICTV-approved begomovirus RefSeq species exemplars
<p>DATA RETRIEVAL</p> <p>Annotated begomovirus coding sequences corresponding to each begomovirus species exemplar with a RefSeq accession number listed in the ICTV Virus Metadata Resource (VMR #18, 2021-10-19, <a href="https://ictv.global/vmr">https://ictv.global/vmr</a>) were downloaded from GenBank in protein FASTA file format. CP and Rep amino acid sequences were extracted and split into separate data sets for analysis. We confirmed the identity of misannotated ORF products by performing a BLAST search. For exemplar sequences missing ORF annotations (listed in metadata spreadsheet), ORFfinder (<a href="https://www.ncbi.nlm.nih.gov/orffinder/">https://www.ncbi.nlm.nih.gov/orffinder/</a>) was used to identify CP and Rep ORFs that were subsequently translated and added to each corresponding data set after BLAST confirmation.</p> <p>ALIGNMENTS</p> <p>Multiple sequence alignments were constructed using the MUSCLE method (Edgar, 2004) as implemented in MEGA 11 (Tamura et al., 2021) and manually corrected using AliView v1.26<strong> </strong>(Larsson, 2014). After an initial alignment inspection, exemplars with either severely truncated (i.e., length < 50% of the average length of the protein) or very divergent (i.e., causing us to doubt protein homology) CP or Rep sequences were excluded from the data set. Due to the difficulties in aligning the Rep sequences at the N- and C- terminal ends, the Rep alignment was trimmed to eliminate all residues prior to the iteron related domain (i.e., the known Rep functional region closest to the Rep start (Arguello-Astorga & Ruiz-Medrano, 2001)) in the N-terminus and after a conserved geminivirus motif found near the C-terminus, which corresponds to where other circular, Rep-encoding single-stranded DNA viruses possess an arginine finger motif (Kazlauskas et al., 2019; Krupovic et al., 2020). In total, our CP and Rep data sets contained amino acid sequences from 432 begomovirus species exemplars that met our inclusion criteria.</p> <p>PHYLOGENETIC ANALYSIS</p> <p>Maximum likelihood (ML) trees were inferred with IQ-Tree v2.0.7 (Minh et al., 2020) using the best fitting substitution model identified by the built-in ModelFinder feature (Kalyaanamoorthy et al., 2017). Tree inference was performed with 3000 ultrafast bootstrap (UFBoot) replicates, a perturbation strength of 0.2 and a stopping rule requiring an iteration interval of 500 iterations between unsuccessful improvements to the local optimum. The -bnni flag was enabled to reduce the risk of overestimating branch supports with UFBoot due to severe model violations. The provided phylogenies in NEXUS format are midpoint-rooted and branches are colored based on traditional begomovirus geographic groupings: exemplars sampled in the Americas in orange and exemplars sampled in the 'Africa, Asia, Europe and Oceania' (AAEO) region in blue. </p> <p>METADATA</p> <p>Metadata associated with each ICTV-approved species exemplar (n=445) – including country of isolation, geographic designation (i.e., AAEO/Americas), genome segmentation (i.e., monopartite/bipartite), presence/absence of V2/AV2 gene and length of genome/DNA-A segments – are included. Exemplars not incorporated into the other analyses are highlighted in red on the spreadsheet.</p> <p> </p>
Dataset for Diamond-coated quartz crystal microbalance sensors: Challenges in high yield production and enhanced detection of ethanol and sars-cov-2 proteins
<p>The data set to paper: </p> <p>Name: Diamond-coated quartz crystal microbalance challenges in mass production and enhanced detection of ethanol and sars-cov-2 proteins</p> <p>Authors: Tibor Izsák1*, Marian Varga1, Michal Kočí2,3, Ondrej Szabó2, Katarína Aubrechtová Dragounová2, Gabriel Vanko2, Miroslav Gál4, Jana Korčeková5, Michaela Hornychová 4, Alexandra Poturnayová5, Alexander Kromka2*</p> <p>Affiliations: 1 Department of Microelectronics and Sensors, Institute of Electrical Engineering, Slovak Academy of Sciences, Dúbravská Cesta 9, Bratislava, 841 04, Slovak Republic<br> 2 Department of Semiconductors, Institute of Physics of the Czech Academy of Sciences, Cukrovarnicka 10/112, Prague 6 162 00, Czech Republic<br> 3 Department of Microelectronics, Faculty of Electrical Engineering, Czech Technical University in Prague, Technická 2, Prague 6, 166 27, Czech Republic<br> 4 Faculty of Chemical and Food Technology, Slovak University of Technology, Bratislava, Slovak Republic<br> 5 Center of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Bratislava, Slovak Republic<br> *corresponding author: tibor.izsak@savba.sk</p> <p>Data manager: Kristýna Dostálová: dostalovak@fzu.cz</p> <p>Date of collection: 1. 5. 2023 - 31. 7. 2024</p> <p>Description: Figure 1: Photos of QCM substrates oriented horizontally or vertically on the substrate holder in the deposition chamber (left) and during the diamond CVD process with ignited plasma (right).<br> Figure 2: a) 3D model of the measurement setup and b) photograph of the open gas chamber with embedded QCM sample.<br> Figure 3: Photo of the a) measurement setup and b) disassembled flow cell with V-Dia-QCM. c) Side view photo of the assembled flow cell in the measurement setup.<br> Figure 4: a) SEM images revealing surface morphology and b) corresponding Raman spectra of Dia-QCM and Dia-Si substrates horizontally or vertically oriented on the substrate holder and corresponding optical photos. There is also the Raman spectrum of the bare QCM (Au-QCM) sample before the diamond deposition.<br> Figure 5: a) Raman spectra and b) SEM images depicting surface morphology of porous diamond film grown on Si (H-PorDia-Si) and QCM (H-PorDia-QCM) substrate. The inset in Fig. 5a represents the optical photo of diamond-coated QCM. Note: ‘H-’ in sample names means horizontally loaded samples.<br> Figure 6: The response delta fR of diamond-coated QCM sensors horizontally and vertically oriented, i.e., single-sided and double-sided diamond-coated QCMs, when applying periodic switching (at 3-minute intervals) of ethanol vapour (E) with various concentrations (from 10 ppm to 100 ppm) and synthetic air (Air).<br> Figure 7: a) First resonant frequency shift (delta fR) of individual QCM sensors and b) mean values of delta fR with corresponding error bars for each QCM sensor group dependent on ethanol concentration.<br> Figure 8: a) The changes of the resonant frequency, delta fR, after the addition of neutravidin (NA) dissolved in water, biotinylated 1C aptamers (1C APT) dissolved in PBS with MgCl2, and 50 pg/mL S-RBD protein in PBS. The addition of neutravidin, aptamers, proteins, and surface washings by water (H2O) or buffer (PBS) are highlighted by arrows. b) Zoom in on the highlighted area in Fig. 8a.<br> Figure 9: Decrease of the resonant frequency, fR, at various S-RBD protein concentrations. The comparison of the sensitivity of diamond and gold QCM surfaces on which S-RBD was determined is indicated in the graph legend.</p>
A Study of Dental Implants Coated With Bone Morphogenetic Protein
ClinicalTrials.gov study NCT00422279. IPD Sharing: NO. Countries: 1. Publications: 2.
Human serum-derived protein removes the need for coating in defined human pluripotent stem cell culture
GEO Series GSE82103. Homo sapiens. 14 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
RNA-Seq Profiling of a Defective Seed Coat Mutation in Glycine max Reveals Differential Expression of Proline Rich and Other Cell Wall Protein Transcripts
GEO Series GSE54903. Glycine max. 12 samples. Type: Expression profiling by high throughput sequencing.
RNA processing proteins regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA.
GEO Series GSE63444. Saccharomyces cerevisiae. 12 samples. Type: Expression profiling by high throughput sequencing.
LubriShieldTM - a permanent urinary catheter coating that prevents uropathogen biofilm formation in vitro independent of host protein conditioning
GEO Series GSE299077. Pseudomonas aeruginosa PAO1. 4 samples. Type: Expression profiling by high throughput sequencing.
Expression data from transgenic Nicotiana tabacum expressing a variant of coat protein and movement protein from Tobacco mosaic virus
GEO Series GSE37905. Solanum lycopersicum; Nicotiana tabacum. 6 samples. Type: Expression profiling by array.
Treatment of Local Gingival Recession With an Enamel Matrix Protein Coated Collagen Matrix
ClinicalTrials.gov study NCT05799859. IPD Sharing: NO. Countries: 0. Publications: 0.
Investigating the effect of HIV-1 Coat proteins on Primary Bovine Muller glia
GEO Series GSE210243. Bos taurus. 8 samples. Type: Expression profiling by array.
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