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3,584 results for “genomic analysis”
Fig. 4 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice
Fig. 4. Phylogenetic and exon-intron structure analysis of FBN family genes in rice and Arabidopsis. The phylogenetic analysis was performed using the amino acid sequences of 25 FBN family proteins in rice and Arabidopsis (Left). The unrooted phylogenetic tree was generated by the neighbor-joining method and displayed using MEGA7 software. Numbers above or below branches of the evolution tree indicated the bootstrap values; The exon-intron structures of 25 FBN family genes in rice and Arabidopsis were analyzed (Right), the exons were represented by yellow boxes, the UTR by blue, black lines connecting two exons were introns. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 6 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice
Fig. 6. The in vitro lipid binding assays of PAP-domains. A and C, schematic representations of the mutant residues in OsFBN2 and OsFBN4 proteins in the in vitro lipid binding assays. B and D, the in vitro lipid-binding activity assays were performed by a fluorescence lipid probe P-96 (1 mM), fatty acids with C12:0, C14:0, C16:0, C18:0, C20:0, C22:0, with each (0.5 mM) of wild type (Wt) and mutant fusion protein (Mut) of PAP domains in OsFBN2 and OsFBN4 proteins, respectively. Detection experiments were performed with three biological replicates. * and ** symbols indicated the significant difference levels of P <0.05 or P <0.01 between mutant and wild type, respectively.
Fig. 5 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice
Fig. 5. Subcellular localization of CTP domains-fused GFP proteins. These constructs of p35S-FBN1-11-CTP-GFP or p35S-Trxm5-GFP, separately, were transiently expressed in Nicotiana benthamiana mesophyll cells. The co-localizations of fluorescence patterns of CTP domains of ten OsFBN proteins except OsFBN8 fused GFP were observed with the autofluorescence of chlorophyll in chloroplasts in protoplasts. The Trxm5-GFP was used as a chloroplast marker.
Fig. 3 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice
Fig. 3. PKC domain analysis of FBN11 clade in plants. A, Homology analysis of PKC domain sequences in FBN11 clades; B, evolutionary tree analysis of PKC domain in five plant species (Oryza sativa (Os), Selaginella moellendorffii (Smo), Arabidopsis thaliana (At), Glycine max (Gm), and Zea mays (Zm)) and algae (Monoraphidium neglectum (Mon), Chlorella sorokiniana (Chlo), Chlamydomonas sp. UWO 241 (Chla), and Haemato coccus lacustris (Hae); C, the conserved motif analysis of PKC domain in FBN11 protein clades in higher plants.
Fig. 2 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice
Fig. 2. Box-plot graphs and motif analysis of CTP and PAP-domain in plants. The protein sequences of CTP domains and PAP domains were analyzed in six plant species: Selaginella moellendorffii (Smo), Physcomitrella patens (Ppa), Arabidopsis thaliana (At), Glycine max (Gm), Oryza sativa (Os), and Zea mays (Zm), The grand average of hydropathicity (GRAVY) and isoelectric point (pI) of CTP domains of FBN1-11 protein clades were showed in A and B, respectively; The GRAVY and pI of PAP domains in FBN1-11 protein clades were showed in C and D, respectively; The dotted line represented the average values of GRAVY and pI, respectively; The conserved motif sequence of PAP domains in these plants were showed in E.
Fig. 1 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice
Fig. 1. Phylogenetic tree analysis of 121 fibrillin family proteins from 10 representative species. The neighbor-joining tree was constructed using the sequences of 121 fibrillin family proteins in ten representative species: Synechococcus sp. PCC 7002 (Ssp), Erysimum siliculosus (Esi), Emiliania huxleyii (Ehu), Thalassiosira pseudonana (Tps), Chlamydomonas reinhardtii (Cre), Volvox carteri (Vca), Physcomitrella patens (Ppa), Selaginella moellendorffii (Smo), Arabidopsis thaliana (At) and Oryza sativa (Os). Bootstrap values were indicated on the branches. Each fibrillin protein was labeled by its name (Table S3). The green and red color meant the proteins present in algae or terrestrial plant, respectively; the blue color represents the proteins present in both algae and terrestrial plants. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Six genome assemblies of Drosophila species for: Identification and genetic analysis of a pervasive "needle-eye" sperm phenotype in Drosophila sterile hybrid males
<p>Interspecies hybrid sterility has been extensively studied, especially in the genus <em>Drosophila</em>. Hybrid sterility is more often found in the heterogametic (XX or ZW) sex, a trend called Haldane's rule. Although this phenomenon is pervasive, identification of a common genetic mechanism remains elusive, with modest support found for a range of potential theories. Here, we identify a single precise morphological phenotype, which we call "needle-eye sperm," that is associated with hybrid sterility in three separate species pairs that span the <em>Drosophila</em> genus. The nature of the phenotype indicates a common point of meiotic failure in sterile hybrid males. We used ten generations of backcross selection paired with whole-genome pooled sequencing to genetically map the regions underlying the needle-eye sperm phenotype. Surprisingly, the sterility phenotype was present in ~50% of males even after ten generations of backcrossing, yet the genetic map showed multiple regions associated with sterility, indicating multiple regions may have the capacity to be sufficient to induce sterility in the F1. Due to the common phenotype among sterile male hybrids and the strong effect of individual loci, further exploration of the genes uncovered here may identify a universal mechanism for the evolution of hybrid sterility. </p>
Comprehensive genomic analysis identifies a diverse landscape of sideroblastic and non-sideroblastic iron related anemias with novel and pathogenic variants in an iron deficient endemic setting
<p>The history for the 5 CMA cases are as follows:-</p> <p> </p> <p>1. <strong>HMA-2 </strong>:- 0.6 month male child presented with poor feeding and noted to have mild-moderate pallor. CBC showed Hemoglobin 9.0gm/dl, MCV- 58fl, MCH 17.3, MCHC 29, Iron 113 ug/dl, Ferritin 297 ug/l, TSAT-45%, TIBC-297 ug/dl, Hepcidin- 20.3ng/ml. No transfusions received and antenatal and neonatal history uneventful. HPLC (both parents), alpha sequencing normal. Targeted NGS shows a heterozygous VUS in GLRX5 gene along with a VUS in BMP6 gene. WES- Does not add anything further significant.</p> <p> </p> <p>2. <strong>HMA-3 </strong>:- 0.8 month male child with transfusion dependent microcytic hypochromic anemia and neurological developmental delay. Expired at 1 year of age due to secondary infection (acinetobacter and toxoplasmosis). Hb- 6.5, MCV-61.5, MCH-18.3, Iron 45 ug/dl, Ferritin 650. Targeted panel and WES - negative.</p> <p> </p> <p>3. <strong>HMA-4:</strong>- 5 year male child with severe microcytic hypochromic anemia and received just one transfusion outside. Has microcephaly and SNHL. Hb 5, MCV- 56, MCH- 18, MCHC- 23, Iron- 75, Ferritin - 330, TIBC- 290, TSAT- 41%. Targeted NGS and WES show a Homozygous VUS in BMP6 gene (? association?) </p> <p> </p> <p>4. <strong>HMA-6:-</strong> 2 year old male child with moderate microcytic hypochromic anemia and focal seizures. Hb -8, MCV- 58, MCH- 16, MCHC-27, Iron- 94, Ferritin -380, Transferrin levels- 10 (very low). Targeted NGS and WES show a single heterozygous VUS mutation in TF gene and another intrinsic rare variant but reported in pop. Database (could it make it compound her for atransferrinemia?) </p> <p> </p> <p>5. <strong>HMA-7:-</strong> 7 year male child with short stature, consanguinity in family, moderate macrocytic anemia with HB-7, MCV-113, Iron-55, Ferritin -209, TSAT-54%. Also Bone marrow shows coarse vacuolations in erythroid cells (12%) and 19% RS. Suspicion PMS- But MLPA for mitochondrial genome normal, no deletions. Targeted panel NGS and WES reveal a heterozygous VUS in LARS2 gene (? nature).</p> <p> </p>
Genomic Analysis to Identify a Predictive Biomarker for Immunotherapy
ClinicalTrials.gov study NCT03578185. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Multicenter Analysis of Genomic and Metabolic Data of Neonatal Genetic Diseases
ClinicalTrials.gov study NCT06183138. IPD Sharing: NO. Countries: 1. Publications: 8.
Genomic and Proteomic Analysis of Disease Progression in Idiopathic Pulmonary Fibrosis (IPF)
ClinicalTrials.gov study NCT00373841. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Real-world Clinical Effectiveness of Whole Genome and Transcriptome Analysis to Guide Advanced Cancer Care
ClinicalTrials.gov study NCT04141397. IPD Sharing: NO. Countries: 0. Publications: 1.
Comparative Genomic and Genetic Analysis of Paired Primary Breast - Metastatic Tumor Specimens Using High-throughput Platforms
ClinicalTrials.gov study NCT01227733. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Identification of GENEtic Markers of Aggressiveness and Malignancy by Array Comparative Genomic Hybrization Analysis (CGH)
ClinicalTrials.gov study NCT01903967. IPD Sharing: Not stated. Countries: 1. Publications: 2.
SAFIR02_Breast - Efficacy of Genome Analysis as a Therapeutic Decision Tool for Patients With Metastatic Breast Cancer
ClinicalTrials.gov study NCT02299999. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Real World and Genomic Data Based Asthma Insight Through Network Analysis
ClinicalTrials.gov study NCT06623435. IPD Sharing: YES. Countries: 1. Publications: 0.
Analysis of Prognostic and Predictive Genomic Signatures Using Archival Paraffin-embedded Breast Tumor - a Pilot Study
ClinicalTrials.gov study NCT01247467. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Exome and Genome Analysis to Elucidate Genetic Etiologies and Population Characteristics in the Plain Community
ClinicalTrials.gov study NCT02927158. IPD Sharing: YES. Countries: 1. Publications: 18.
Analysis of Prognostic and Predictive Genomic Signatures Using Archival Paraffin-embedded Tumor Specimens in Breast Cancer
ClinicalTrials.gov study NCT01247480. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Sweden Cancerome Analysis Network - Breast : Genomic Profiling of Breast Cancer
ClinicalTrials.gov study NCT02306096. IPD Sharing: UNDECIDED. Countries: 1. Publications: 39.
ScienceDex guides
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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.