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420 results for “novel associations”
FIGURE 2 in Novel hyphomycetous fungi associated with bamboo from Sichuan, China
FIGURE 2. RAxML tree generated from combined SSU, ITS, LSU, rpb2 and tef1α sequence data of Savoryellomycetidae. The tree is rooted with Tolypocladium capitatum (OSC 71233) and T. japonicum (OSC 110991). Ex-type strains are indicated in bold and newly generated sequences are in red. Bootstrap values for ML equal to or greater than 75% are placed above the branches. Branches with Bayesian posterior probabilities (BYPP) from MCMC analysis equal to or greater than 0.95 are in bold.
FIGURE 6 in Novel hyphomycetous fungi associated with bamboo from Sichuan, China
FIGURE 6. Rhexoacrodictys melanospora (HKAS 127155) a–j Colonies on natural substrate. a–c Colonies. d–f Conidiophores with conidia. g–j Conidia. k Germinating conidium. l, m Colony on PDA from above and below. n–q Sporulation observed on PDA. n–p Conidiophores with conidia. q Conidium. Scale bars: d–f, n = 20 μm, g–j, o–q = 10 μm, k = 5 μm.
COG and Pfam annotation results of the genome sequences of four novel Endozoicomonas strains associated with the octocoral Litophyton in a long-term aquarium facility
<p>COG and Pfam annotation files from DOE-JGI Microbial Genome Annotation Pipeline (MGAP) version 4(1), for four <em>Endozoicomonas</em> strains associated with the tropical octocoral Litophyton in a long-term aquarium facility. Data correspond to the assemblies of NE35, NE40, NE41, and NE43, available under the BioProject accession numbers <a href="https://www.ncbi.nlm.nih.gov/bioproject/1075803">PRJNA1075803</a>, <a href="https://www.ncbi.nlm.nih.gov/bioproject/1075804">PRJNA1075804</a>, <a href="https://www.ncbi.nlm.nih.gov/bioproject/1075805">PRJNA1075805</a> and <a href="https://www.ncbi.nlm.nih.gov/bioproject/1075806">PRJNA1075806</a>, respectively. Results were submitted to the Integrated Microbial Genomes and Microbiomes system v7 (IMG/M) (2) for comparative analysis. The genome annotations can be interactively accessed on IMG/M (https://img.jgi.doe.gov/cgi-bin/m/main.cgi) using the following identifiers: 8036267134 (strain NE35), 8036277142 (strain NE40), 8045494135 (strain NE41); 8036272146 (strain NE43). </p> <p>This dataset is part of the following study:</p> <p>Marques M, da Silva DMG, Santos E, Baylina N, Peixoto R, Kyrpides NC, Woyke T, Whitman WB, Keller-Costa T, Costa R. 2024. Genome sequences of four novel <em>Endozoicomonas </em>strains associated with a tropical octocoral in a long-term aquarium facility. Microbiology Resource Announcements</p> <p> </p> <p>Other reference sources:</p> <p>(1) Huntemann M, Ivanova NN, Mavromatis K, James Tripp H, Paez-Espino D, Palaniappan K, Szeto E, Pillay M, Chen IMA, Pati A, Nielsen T, Markowitz VM, Kyrpides NC. 2015. The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). Stand Genomic Sci 10:1–6.</p> <p>(2) Chen IMA, Chu K, Palaniappan K, Ratner A, Huang J, Huntemann M, Hajek P, Ritter SJ, Webb C, Wu D, Varghese NJ, Reddy TBK, Mukherjee S, Ovchinnikova G, Nolan M, Seshadri R, Roux S, Visel A, Woyke T, Eloe-Fadrosh EA, Kyrpides NC, Ivanova NN. 2023. The IMG/M data management and analysis system v.7: content updates and new features. Nucleic Acids Res 51:D723–D732.</p>
Data from: Using a comprehensive DNA barcode library to detect novel egg and larval host plant associations in a Cephaloleia Rolled-leaf Beetle (Coleoptera: Chrysomelidae)
To fully understand the ecology and evolution of plant-herbivore interactions, information regarding the life history of both immature and adult insect stages is essential. However, most knowledge of plant-herbivore associations is derived from observations of adults. One reason for this bias is that species identification of immature stages is usually challenging. DNA barcodes can be used to identify immature stages to the species-level. This technique compares short sequences of the appropriate DNA barcode loci (e.g., mitochondrial COI gene for insects) of an unidentified specimen to a known DNA barcode library. The accuracy of DNA-based identifications depends on the comprehensiveness of the DNA barcode library. We generated a comprehensive DNA barcode library for a community of Rolled-leaf Beetles (Coleoptera: Chrysomelidae) in a premontane tropical forest in Costa Rica. The DNA barcode COI accurately identified all beetle species included in this study. Using this DNA barcode library, we identified eggs and larvae of Cephaloleia histrionica Baly with 100% confidence. This new record of C. histrionica is unique in that this species completes its life cycle on a bromeliad, whereas most Cephaloleia species are associated with plants from the order Zingiberales. The life cycle, diet breadth, immature stages, and sexual dimorphism are described for C. histrionica.
Data from: Genome-wide association and genome partitioning reveal novel genomic regions underlying variation in gastrointestinal nematode burden in a wild bird
Identifying the genetic architecture underlying complex phenotypes is a notoriously difficult problem that often impedes progress in understanding adaptive eco-evolutionary processes in natural populations. Host–parasite interactions are fundamentally important drivers of evolutionary processes, but a lack of understanding of the genes involved in the host's response to chronic parasite insult makes it particularly difficult to understand the mechanisms of host life history trade-offs and the adaptive dynamics involved. Here, we examine the genetic basis of gastrointestinal nematode (Trichostrongylus tenuis) burden in 695 red grouse (Lagopus lagopus scotica) individuals genotyped at 384 genome-wide SNPs. We first use genome-wide association to identify individual SNPs associated with nematode burden. We then partition genome-wide heritability to identify chromosomes with greater heritability than expected from gene content, due to harbouring a multitude of additive SNPs with individually undetectable effects. We identified five SNPs on five chromosomes that accounted for differences of up to 556 worms per bird, but together explained at best 4.9% of the phenotypic variance. These SNPs were closely linked to genes representing a range of physiological processes including the immune system, protein degradation and energy metabolism. Genome partitioning indicated genome-wide heritability of up to 29% and three chromosomes with excess heritability of up to 4.3% (total 8.9%). These results implicate SNPs and novel genomic regions underlying nematode burden in this system and suggest that this phenotype is somewhere between being based on few large-effect genes (oligogenic) and based on a large number of genes with small individual but large combined effects (polygenic).
Associations of fully-automated CSF and novel plasma biomarkers with Alzheimer's disease neuropathology at autopsy
<p>The objective of this study was to study cerebrospinal fluid (CSF) biomarkers of Alzheimer's disease (AD) analyzed by fully automated Elecsys immunoassays in comparison to neuropathologic gold standards, and compare their accuracy to plasma phosphorylated tau (p-tau181) measured using a novel Simoa method. We studied <i>ante-mortem</i> Elecsys-derived CSF biomarkers in 45 individuals who underwent standardized <i>post-mortem</i> assessments of AD and non-AD neuropathologic changes at autopsy. In a subset of 26 participants, we also analysed <i>ante-mortem</i> levels of plasma p-tau181 and neurofilament light (NfL). Reference biomarker values were obtained from 146 amyloid-PET-negative healthy controls (HC). All CSF biomarkers clearly distinguished pathology-confirmed AD dementia (N=27) from HC (AUCs=0.86-1.00). CSF total-tau (t-tau), p-tau181, and their ratios with Aβ<sub>1-42</sub>, also accurately distinguished pathology-confirmed AD from non-AD dementia (N=8; AUCs=0.94-0.97). In pathology-specific analyses, intermediate-to-high Thal amyloid phases were best detected by CSF Aβ<sub>1-42</sub> (AUC[95% CI]=0.91[0.81-1]), while intermediate-to-high CERAD neuritic plaques and Braak tau stages were best detected by CSF p-tau181 (AUC=0.89[0.79-0.99] and 0.88[0.77-0.99], respectively). Optimal Elecsys biomarker cut-offs were derived at 1097/229/19 pg/ml for Aβ<sub>1-42</sub>, t-tau, and p-tau181. In the plasma subsample, both plasma p-tau181 (AUC=0.91[0.86-0.96]) and NfL (AUC=0.93[0.87-0.99]) accurately distinguished pathology-confirmed AD (N=14) from HC. However, only p-tau181 distinguished AD from non-AD dementia cases (N=4; AUC=0.96[0.88-1.00]), and showed a similar, though weaker, pathologic specificity for neuritic plaques (AUC=0.75[0.52-0.98]) and Braak stage (AUC=0.71[0.44-0.98]) as CSF p-tau181. Elecsys-derived CSF biomarkers detect AD neuropathologic changes with very high discriminative accuracy<i> in-vivo</i>. Preliminary findings support the use of plasma p-tau181 as an easily accessible and scalable biomarker of AD pathology. This study provides Class II evidence that fully-automated CSF t-tau and p-tau181measurements discriminate between autopsy-confirmed Alzheimer's disease and other dementias.</p>
FIGURES 1–4 Paracrias huberi 1 in Report of a novel biological association for Paracrias huberi Gumovsky (Hymenoptera: Eulophidae) with redescription of the female and description of the unknown male
FIGURES 1–4 Paracrias huberi 1. ♀ head, frontal. 2. ♀ antenna, lateral. 3. ♂ head, frontal. 4. ♂ antenna, medial.
FIGURES 8–11 Paracrias huberi 8 in Report of a novel biological association for Paracrias huberi Gumovsky (Hymenoptera: Eulophidae) with redescription of the female and description of the unknown male
FIGURES 8–11 Paracrias huberi 8. ♀ metasoma, dorsal. 9. ♀ metasoma, lateral. 10. ♂ metasoma, lateral. 11. ♀ left fore and hindwing, dorsal.
UK dogs data from: Genome-wide association studies for canine hip dysplasia in single and multiple populations – implications and potential novel risk loci
<p>Background: <span>Association mapping studies of quantitative trait loci (QTL) for canine hip dysplasia (CHD) </span><span>can contribute to the understanding of the genetic background of this common and debilitating disease and might contribute to its genetic improvement. The power of association studies for CHD is limited by relatively small sample numbers for CHD records within countries, suggesting potential benefits of joining data across countries. However, this is complicated due to the use of different scoring systems across countries. In this study, we incorporated routinely assessed CHD records and genotype data of German Shepherd dogs from </span><span><span>two</span></span><span> countries </span><span><span>(UK and Sweden)</span></span><span> to perform </span><span>genome-wide association stud</span><span>ies (GWAS) within populations using different variations of CHD phenotypes. As phenotypes, dogs were either classified into cases and controls based on the </span><i><span>Fédération Cynologique Internationale</span></i><span> (FCI) five-level grading of the worst hip or the FCI grade was treated as an ordinal trait. </span><span><span>In a subsequent meta-analysis, we added publicly available data from a Finnish population and performed the GWAS across all populations.</span></span><span> Genetic associations for the CHD phenotypes were evaluated in a linear mixed model using 62,089 SNPs.</span></p> <p>Results: <span><span>Multiple SNPs with genome-wide significant and suggestive</span></span><span><span> associations</span></span><span> </span><span><span>were detected in single-population GWAS and the meta-analysis.</span></span><span> Few of these SNPs overlapped between populations </span><span><span>or between single-population GWAS and the meta-analysis</span></span><span>, suggesting that many CHD-related QTL are population-specific. More significant or suggestive SNPs were identified when FCI grades were used as phenotypes in comparison to the case-control approach. </span><i><span>MED13</span></i><span> (Chr 9) and </span><i><span>PLEKHA7</span></i><span> (Chr 21) emerged as novel positional candidate genes associated with hip dysplasia.</span></p> <p>Conclusions: <span>Our findings confirm the complex genetic nature of hip dysplasia in dogs, with multiple loci associated with the trait, </span><span><span>most</span></span><span> of which are population-specific. Routinely assessed CHD information collected across countries provide an opportunity to increase sample sizes and statistical power for association studies. While the lack of standardisation of CHD assessment schemes across countries poses a challenge, we showed that conversion of traits can be utilised to overcome this obstacle.</span></p>
FIGURE 2 in An example of problems associated with DNA barcoding in tardigrades: a novel method for obtaining voucher specimens
FIGURE 2. Granulated cuticle and pores in a fresh (A, DIC) and an orcein stained (B, PhC) specimen of M. terminalis (C2868); C: Granulated cuticle (arrow head) and pores by SEM in M. terminalis (C2868); D: Smooth cuticle with pores in a fresh specimen of M. macrocalix (C2868, DIC); E: Granulated cuticle (arrow head) in the holotype of M. terminalis (C624- S60, DIC). Bar =10 µm (A, B, D, E); 5 µm (C)
FIGURE 1. A in An example of problems associated with DNA barcoding in tardigrades: a novel method for obtaining voucher specimens
FIGURE 1. A: Fresh specimen of M. terminalis; buccal pharyngeal apparatus with dorsal buccal armature (C2868, DIC); B: Fresh specimen of M. macrocalix; buccal pharyngeal apparatus with dorsal buccal armature (C2868, DIC). C: Claws with indented lunules on a hind leg of M. terminalis (C2868, SEM); D: Claws with indented lunules (arrow heads) on the hind legs of a fresh specimen of M. terminalis (C2868, DIC). Bar =10 µm (A, B, D); 5 µm (C)
FIGURE 5 in An example of problems associated with DNA barcoding in tardigrades: a novel method for obtaining voucher specimens
FIGURE 5. Neighbor joining dendrogram computed on Kimura 2-parameter distances. Numbers in bold indicate bootstrap values. Specimens are indicated with either GenBank accession numbers or with acronyms as in Table 1 (in bold).
FIGURE 3. A in An example of problems associated with DNA barcoding in tardigrades: a novel method for obtaining voucher specimens
FIGURE 3. A: Egg shell of M. terminalis (hologenophore C2868-N02 US2, DIC); B: Egg shell of M. terminalis by SEM (C2868); C: Egg shell of a M. terminalis paratype (C624-S44, PhC); D: Egg shell of M. cf. terminalis (C2341, PhC). Bar =10 µm (A, C, D); 1 µm (B).
Automated application to assist in detecting novel gene-disease associations following whole genome sequencing
<p>Results files, analysis scripts and original software from TierUp reanalysis performed on June 2020. These data contribute to the publication titled "Automated reanalysis application to assist in detecting novel gene-disease associations following whole genome sequencing". </p> <ul> <li> <p>tierup_v0-3-0.tar.gz - source code used in the reanalysis</p> </li> <li> <p>tierup_results_summary.tar.gz - raw data and python code for publication figures</p> </li> </ul> <p> </p>
Identification of four novel loci associated with psychotropic drug-induced weight gain in a Swiss psychiatric longitudinal study: A GWAS analysis
<p>Summary statistics for the GWAS with different outcomes presented in the <a href="https://pubmed.ncbi.nlm.nih.gov/37173452/">publication</a>.</p> <p>PSYMETAB_GWAS_FREQ_CEU.BMI_change_1mo_all.glm - BMI change between 1 month vs baseline</p> <p>PSYMETAB_GWAS_FREQ_CEU.BMI_change_3mo_all.glm - BMI change between 3 months vs baseline</p> <p>PSYMETAB_GWAS_FREQ_CEU.BMI_change_6mo_all.glm - BMI change between 6 months vs baseline</p> <p>PSYMETAB_GWAS_FREQ_CEU.BMI_change_all.glm - BMI change between last follow-up time vs baseline</p> <p>PSYMETAB_GWAS_FREQ_CEU.BMI_slope_6mo_all.glm - BMI slope fitted for the first 6 months of followup data</p> <p>PSYMETAB_GWAS_FREQ_CEU.BMI_slope_all.glm - BMI slope fitted for all available follow-up data</p> <p> </p> <p> </p>
Genome-Wide Association Studies meta-analysis uncovers NOJO and SGS3 novel genes involved in Arabidopsis thaliana primary root development and plasticity
<p>Postembryonic primary root growth relies on meristems that harbour multipotent stem cells that produce new cells that will duplicate and provide all the different root cell types. <em>Arabidopsis thaliana</em> primary root growth has become a model for evo-devo studies due to its simplicity and facility to record cell proliferation and differentiation. To identify new genetic components relevant to primary root growth, we used a Genome-Wide Association Studies (GWAS) meta-analysis approach using data published in the last decade. In this work, we performed intra and inter-studies analyses to discover new genetic components that could participate in primary root growth. We used 639 accessions from nine different studies and performed different GWAS tests ranging from single studies and pairwise analysis with high correlation associations, analyzing the same number of accessions in different studies to using the daily data of the root growth kinetic of the same research. We found that primary root growth changes were associated with 41 genomic loci, of which six (14.6%) have been previously described as inhibitors or promoters of primary root growth. The knockdown of genes associated with two of these loci: a gene that participates in Trans-acting siRNAs (tasiRNAs) processing <em>Suppressor of Gene Silencing</em> (<em>SGS3</em>) and a gene with a Sterile Alpha Motif (SAM) confirmed their participation as repressors of primary root growth. As none has been shown to participate in this developmental process before, our GWAS analysis identified new genes that participate in primary root growth. Overall, our findings provide novel insights into the genomic basis of root development and further demonstrate the usefulness of GWAS meta-analyses in non-human species.</p>
Novel M2-like tumor-associated macrophage-related biomarkers predict prognosis of Acute myeloid leukemia patients.
<p>The supplementary material for the Novel M2-like tumor-associated macrophage-related biomarkers predict prognosis of Acute myeloid leukemia patients.</p>
Genotype-phenotype associations in CRB1 bi-allelic patients: a novel mutation and a systematic review
<p><span><strong>Purpose</strong>: Searched for novel bi-allelic <em>CRB1</em> mutations, then analyzed the <em>CRB1</em> literature at the genotypic and phenotypic levels from 439 patients worldwide.</span></p> <p><span><strong>Approach</strong>: We screened various variables such as the <em>CRB1</em> mutation types, domains, exons, and genotypes and their relation with specific ocular phenotypes. An emphasis was given for the bi-allelic missense and nonsense mutations because of their high prevalence compared to other mutation types. Finally, we quantified the effect of various non-modifiable factors over the BCVA OU using multivariate linear regression models and identified genetic interactions.</span></p> <p><span><strong>Results</strong>: We first identified a novel bi-allelic missense in the exon 9 of <em>CRB1</em>; c.2936G>A; p.(Gly979Asp) associated with RCD. <em>CRB1</em> mutation type, exons, domains, and genotype distribution vary significantly according to Fundus characteristics, such as peripheral pigmentation and condition, optic disc, vessels, macular, and pigmentation (P<0.05). Of the 154 articles retrieved from PubMed, 96 studies with 439 bi-allelic <em>CRB1</em> patients were included. </span><span>Missense mutations were significantly associated with an absence of macular pigments, pale optic disc, and periphery pigmentation, resulting in a higher risk of RCD (P<0.05). In contrast, homozygous nonsense mutations were associated with macular pigments, periphery pigments, and a high risk of LCA (P<0.05) and increased BCVA OU (best-corrected visual acuity) levels.</span><span> We found that age, mutation types, and inherited retinal diseases were critical determinants of BCVA OU as they significantly increased it by 33%, 26%, and 38%, respectively (P<0.05). Loss of function alleles additively increased the risk of LCA, with nonsense having a more profound effect than indels. Finally, our analysis showed that p.(Cys948Tyr) and p.(Lys801Ter) and p.(Lys801Ter); p.(Cys896Ter) might interact to modify BCVA OU levels. </span></p> <p><span><strong>Conclusion</strong>: This meta-analysis updated the literature and identified genotype-phenotype associations in bi-allelic <em>CRB1</em> patients.</span></p>
Dataset associated to the manuscript "A novel method for characterising the inter- and intra-lake variability of CH4 emissions: validation and application across a latitudinal transect in the Alpine region"
<p>The dataset comprises data collected from nine specifically chosen lakes located across the eastern Alps during the ALCH4 project. The primary objective of this project was to assess the efficacy of a mobile Eddy Covariance platform in characterizing CH4 emissions. The field measurements were conducted throughout the ice-free periods in the years 2018 and 2019. This dataset encompasses: i) the EddyPro 7.0.6 (LI-COR Inc., Lincoln, NE, USA) output for all Eddy Covariance campaigns; ii) outcomes of the chamber measurements; iii) data obtained from surface samples. This research was funded by the Autonomous Province of Bozen/Bolzano.</p>
Renal Arterial Resistive Index Versus Novel Biomarkers for Early Prediction of Sepsis Associated-acute Kidney Injury
ClinicalTrials.gov study NCT03799159. IPD Sharing: NO. Countries: 1. Publications: 13.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.