Characterisation of two toxic Gambierdiscus spp. (Gonyaulacales, Dinophyceae) from the Great Barrier Reef (Australia): G. lewisii sp. nov. and G. holmesii sp. nov.
Contributors: Kretzschmar, Anna Liza, Larsson, Michaela, Hoppenrath, Mona, Doblin, Martina, Murray, Shauna
... LSU, SSU and ITS rDNA sequence alignments for the description of two new toxic species of Gambierdiscus, G. holmesii and G. lewisii, on which phylogenetic inferences were based.
Searching for phylogenetic patterns of Symbiodiniaceae community structure among Indo-Pacific Merulinidae corals
Contributors: Leveque, Sébastien, Afiq-Rosli, Lutfi, Ip, Yin Cheong Aden, Jain, Sudhanshi S., Huang, Danwei
... Symbiodiniaceae DNA sequences and community datasets
Contributors: Rocha, Sara, Vieira, Jorge, Vázques, Noé, López-Fernández, Hugo, Fdez-Riverola, Florentino, Reboiro-Jato, Miguel, Sousa, André D., Vieira, Cristina P.
... Additional file 12 of the publication "ATXN1 N-terminal region explains the binding differences of wild-type and expanded forms". Each PDB file describes the docking of wt/expanded ATXN1 with an interactor.
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Contributors: Forrest , Lucy, Nelson, Matthew
... This archive contains generation files and homology models of human annexin A11’s C-terminal domain (residues 192-505) with or without 4 bound calcium ions, built using human annexin A4 with bound calcium. Representative models A single representative model was selected for the apo: anxa11_cterm.B99990009.pdb A single representative model was selected for the holo protein: anxa11_cterm.B999900038.pdb Methods The template coordinates of chain A were extracted from PDB ID 2ZOC. The alignment contains no gaps, as indicated by iTasser. In the holo model, distance restraints between calcium ions and nearby oxygen atoms were assigned based on the equivalent distances in the template, as computed using PyMol. The final model was selected from the attached ensemble of 100 models in the *all_100_models* folder. Models were generated by Modeller 9.20 with the input files in the *Modeller_files/* subfolder, before filtration with MolPDF, then ProQ, then PROCHECK, then MolProbity. Electrostatic surfaces were shown using the files in the *Electrostatics/* subfolder. The calcium atoms were renamed using *rename_cal.csh*, and the resultant pdb file *anxa11_cterm.B99990038_rename.pdb* was used as input to generate the correct partial charges using APBS v1.3 with the CHARMM force field. The maps of the calcium-free model were generated for the pdb file *anxa11_cterm.B99990009.pdb*. This assumes no major conformational changes occur as a result of calcium binding, which is likely to be the case, based on comparison of calcium-bound 2ZOC and calcium-free 2ZHJ. The pymol session containing the maps can be viewed with Pymol v2.3.0 This work was supported by the National Institutes of Health, National Institute of Neurological Disorders and Stroke intramural research program. For more details, see Liao Y-C, Fernandopulle M, Wang G, Choi H, Hao L, Drerup CM, Qamar S, Nixon-Abel J, Shen Y, Meadows W, Vendruscolo M, Knowles T, Nelson M, Czekalska M, Musteikyte G, Gachechiladze M, Patel R, Stephens C, Pasolli A, Forrest LR, St George-Hyslop P, Lippincott-Schwartz J, Ward ME, "RNA granules hitchhike on lysosomes for long-distance transport, using annexin A11 as a molecular tether" Cell (2019) in press.
"Hepatitis C virus (HCV) genotype 1 displays higher genetic variability of hypervariable region 1 (HVR1) than genotype 3"
Contributors: Kamila Caraballo Cortes
... Patients sequences dataset from the study "Hepatitis C virus (HCV) genotype 1 displays higher genetic variability of hypervariable region 1 (HVR1) than genotype 3" . They consist of error-corrected and reconstructed intra-host HVR1 genetic populations.
Contributors: Langhorst, Bradley W
... This is a reference containing the genomes matching the ATCC 20 Strain reference material. It includes the following organisms: Acinetobacter baumannii ATCC 17978 Bacillus cereus ATCC 10987 Bacteroides vulgatus ATCC 8482 Bifidobacterium adolescentis ATCC 15703 Clostridium beijerinckii ATCC 35702 Cutibacterium acnes subsp. defendens ATCC 11828 Deinococcus radiodurans R1 Enterococcus faecalis OG1RF Escherichia coli str. K-12 substr. MG1655 Helicobacter pylori 26695 Lactobacillus gasseri ATCC 33323 = JCM 1131 Neisseria meningitidis MC58 serogroup: B source Porphyromonas gingivalis ATCC 33277 Pseudomonas aeruginosa PAO1 Rhodobacter sphaeroides ATCC 17029 Schaalia odontolytica ATCC 17982 Staphylococcus aureus subsp. aureus USA300 FPR3757 Staphylococcus epidermidis Streptococcus agalactiae 2603V/R Streptococcus mutans UA159
NGS data produced in 'Rapid selection and identification of functional CD8+ T-cell epitopes from large peptide-coding libraries'; Nature Communications (2019)
Contributors: Sharma, Govinda, Rive, Craig Michael, Holt, Robert Andrew
... Sharma, G et al. Rapid selection and identification of functional CD8+ T-cell epitopes from large peptide-coding libraries. Nature Communications. Accepted (August 2019) Abstract: Cytotoxic CD8+ T-cells recognize and eliminate infected or malignant cells that present, at their cell surfaces, short peptide epitopes derived from intracellularly processed antigens. However, broadly searching for specific major histocompatibility complex (MHC)-bound peptide epitopes that are naturally processed and capable of eliciting a functional T-cell response has been challenging. Here, we report a method for deep and unbiased T-cell epitope profiling, which is done by using in vitro co-culture of CD8+ T-cells and target cells transduced with high-complexity epitope-encoding minigene libraries. Target cells that are subject to cytotoxic attack from T-cells in co-culture are isolated, before they are lost to apoptosis, by fluorescence-activated cell sorting and characterized by sequencing the minigenes encoded within. In the present study, we validate this highly parallelized method using known murine T-cell receptor/peptide-MHC pairs and diverse minigene-encoded epitope libraries to identify naturally processed and MHC-presented peptide epitopes unambiguously and with high sensitivity.
Bait set used in: Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol
Contributors: Gauthier, Mailys, Konecny-Dupré, Lara, N'guyen, Agnès, Elbrecht, Vasco, Datry, Thibault, Douady, Christophe J, Lefébure, Tristan
... Bait set used in the paper "Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol" This bait set were designed essentially from COI sequences of invertebrate species present in French streams. 16S, AP6, NAD1, CytB, NAD4 and NAD5 baits were also designed for few species. Order affiliation of each bait is integrated in its name. Baits were designed using BaitFisher software (Mayer et al, 2016).
Contributors: Charrier, N. P., Rispe, C.
... The two files contain respectively the concatenation of DNA sequences alignements for 27 species of ticks (SCO50 matrix, n=952 genes) and to the partition file indicating the positions of each gene in the concatenation. The data set corresponds to the article "A transcriptome-based phylogenetic study of hard ticks (Ixodidae)" to be published in Scientific Reports, by N Pierre Charrier, Axelle Hermouet, Caroline Hervet, Albert Agoulon, Stephen Barker, Dieter Heylen, Céline Toty, Karen McCoy, Olivier Plantard, Claude Rispe.
Contributors: Aaley, Uday Raj, Bodt, Timotheus Adrianus
... This data set contains 8 video files made of the last two known Kusunda speakers from Nepal, Gyani Maiya Sen Kusunda and Kamala Khatri (Sen Kusunda), in February and April 2019, in Kulmore, Dang Deokhuri, Nepal. The recordings constitute discussion between the participants, showing how to use flint, how to make a lean-to, and how to dig for tubers. This material is made freely available to everyone for informative or scientific purposes as long as the source (this DOI) / the collectors are properly credited. Please note that use of the material for commercial purposes of any kind, which includes conversion into commercial audio-visual media (documentaries etc.), (paid) public screening other than for educational purposes, storage and dissemination through sites that require registration & payment for access, or sites that rely on advertisement (including YouTube) is not permitted without specific written consent from the speakers and their community, obtained through the collectors of the material. By downloading our material, you agree to these restrictions. This data set falls under the Create Commons Attribution 4.0 International / Attribution-NonCommercial-ShareAlike (CC BY-NC-SA) license. This license lets you remix, tweak, and build upon this work non-commercially, as long as you credit us and license your new creations under the identical terms. License Deed on https://creativecommons.org/licenses/by-nc-sa/4.0/. Legal Code on https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode. We greatly value feedback, suggestions, advice, analysis etc. based on this material which will help in the description of the Kusunda language, especially any comments and suggestions that will enable the revitalisation of the language, including a standardisation of the phonology and a phonologically consistent but also practical orthography in both देवनागरी Devanāgarī and Roman script. Uday Raj Aaley: aarambhkhabar (at) gmail (dot) com Tim Bodt: bodttim (at) gmail (dot) com