Project description:This study observes the origin of the last living sea nomad group in Indonesia using genome-wide SNP data, and tracks their dispersal in the archipelago. This study involves new samples on not only the sea nomad group, but also surrounding populations where the sea nomad settled. We revealed the scenario of their origin and unique admixture patterns during their dispersal and re-settlement.
Project description:A sea bass oligo microarray platform was used to profile gene expression in whole heads of 38 days-old sea bass affected by prognathism, a skeletal malformation that strongly affects sea bass production. Two different conditions: i) prognathous individuals, and ii) normal individuals were analyzed. For each condition, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of five (5) heads.
Project description:A sea bass oligo microarray platform was used to profile gene expression in mandibles of 58 days-old sea bass affected by prognathism, a skeletal malformation that strongly affects sea bass production. Two different conditions: i) protruding jaws, and ii) normal jaws were used for gene expression analysis. For each condition, total RNA was extracted from five (5) independent biological replicates, each consisting of pools of five (5) jaws.
Project description:We sampled the microbial community at the sea ice edge in McMurdo Sound, Ross Sea at the same location (-77.62S, 165.41E) for four weeks (as described in Wu et al 2019, Nat. Comms.). We had four sampling dates corresponding to weeks 1 to 4: December 28 2014, January 6, 15, and 22 2015. Large volumes of water (150--250 L) were filtered from 1 m depth at the sea ice edge, and passed through three filters sequentially (3.0, 0.8, and 0.1 um, each 293 mm Supor filters). Filters with collected biomass were then placed in tubes with a sucrose-based preservative buffer (20 mM EDTA, 400 mM NaCl, 0.75 M sucrose, 50 mM Tris-HCl, pH 8.0) and stored at -80 C until sample processing. We extracted proteins after buffer exchange into a 3\% SDS solution as previously described Wu et al 2019, Nat. Comms.
Project description:A sea bass oligo microarray platform was used to profile gene expression in mandibles of 58 days-old sea bass affected by prognathism, a skeletal malformation that strongly affects sea bass production. Two different conditions: i) protruding jaws, and ii) normal jaws were used for gene expression analysis. For each condition, total RNA was extracted from four (4) independent biological replicates, each consisting of pools of five (5) jaws. Statistical analysis with SAM (Significance Analysis of Microarray) identified 333 probes (corresponding to 242 unique transcripts) significantly down-regulated in deformed individuals compared to normal ones.
Project description:The intermediate filament protein Nestin serves as a biomarker for stem cells and has been used to identify subsets of cancer stem-like cells. However, the mechanistic contributions of Nestin to cancer pathogenesis are not understood. Here we report that Nestin binds the hedgehog pathway transcription factor Gli3 to mediate the development of medulloblastomas of the hedgehog subtype. In a mouse model system, Nestin levels increased progressively during medulloblastoma formation resulting in enhanced tumor growth. Conversely, loss of Nestin dramatically inhibited proliferation and promoted differentiation. Mechanistic investigations revealed that the tumor-promoting effects of Nestin were mediated by binding to Gli3, a zinc finger transcription factor that negatively regulates hedgehog signaling. Nestin binding to Gli3 blocked Gli3 phosphorylation and its subsequent proteolytic processing, thereby abrogating its ability to negatively regulate the hedgehog pathway. Our findings show how Nestin drives hedgehog pathway-driven cancers and uncover in Gli3 a therapeutic target to treat these malignancies. Nestin+ and Nestin- GNPs (granule neuron precursors) were purified from Nestin-CFP/Math1-Cre/Ptch1-loxp cerebella at postnatal day 4 by FACs, and total RNA from these two cell populations were extracted, and then labeled and hybridized to Affymetrix Mouse Genome 430 2.0 arrays.
Project description:Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution of isomers, including from ion mobility spectrometry.