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54,099 results for “Expression”
Ectopic expression of BBS1 rescues male infertility, but not retinal degeneration, in a BBS1 mouse model
<p>Bardet-Biedl syndrome (BBS) is a rare ciliopathy for which there are no current effective treatments. BBS is a genetically heterogeneous disease, though the M390R mutation in <i>BBS1 </i>is involved in approximately 25% of all genetic diagnoses of BBS. The principle features of BBS include retinal degeneration, obesity, male infertility, polydactyly, intellectual disability, and renal abnormalities. Patients with mutations in BBS genes often present with night blindness within the first decade of life, which progresses to complete blindness. This is due to progressive loss of photoreceptor cells. Male infertility is caused by a lack of spermatozoa flagella, rendering them immobile. In this study, we have crossed the wild-type human <i>BBS1</i> gene, driven by the CAG promoter, onto the <i>Bbs1<sup>M390R/M390R </sup></i>mouse model to determine if ectopic expression of <i>BBS1</i> rescues male infertility and retinal degeneration. qRT-PCR indicates that the <i>BBS1 </i>transgene is expressed in multiple tissues throughout the mouse, with the highest expression seen in the testes, and much lower expression in the eye and hypothalamus. Immunohistochemistry of the transgene in the eye showed little if any expression in the photoreceptor outer nuclear layer. When male <i>Bbs1<sup>M30R/M390R</sup>;BBS1<sup>TG+</sup></i>mice are housed with WT females, they are able to sire offspring, indicating that the male infertility phenotype of BBS is rescued by the transgene. Using electroretinography (ERGs) to measure retinal function and optical coherence tomography to measure retinal thickness, we show that the transgene does not confer protection against retinal degeneration in <i>Bbs1<sup>M300R/M390R</sup>;BBS1<sup>TG+ </sup></i>mice.</p>
Source code for models of floral initiation in pea and gene expression data extracted from published sources
<p>The dataset contains the source code for computational models of a gene network controlling transition to flowering in pea (<em>Pisum sativum</em>). The models were based on ordinary differential equations (ODE) or neural networks. It also includes data on the expression dynamics of genes involved in the network, which was used for model fitting. The expression data was extracted from the following papers: </p> <p>Hecht, V., Laurie, R. E., Schoor, K. Vander, Ridge, S., Knowles, C. L., Liew, L. C., Sussmilch, F. C., et al. (2011). The Pea GIGAS Gene Is a FLOWERING LOCUS T Homolog Necessary for Graft-Transmissible Specification of Flowering but Not for Responsiveness to Photoperiod. 23, 147–161. doi:10.1105/tpc.110.081042</p> <p>Sussmilch, F. C., Berbel, A., Hecht, V., Schoor, K. Vander, Ferrándiz, C., Madueño, F., et al. (2015). Pea VEGETATIVE2 Is an FD Homolog That Is Essential for Flowering and Compound In fl orescence Development. 27, 1046–1060. doi:10.1105/tpc.115.136150</p> <p>The source code of the DEEP software used for parameter optimization in the model fitting can be found in the Gitlab repository (https://gitlab.com/mackoel/deepmethod/-/tree/master).</p> <p>The files are the supplement to the following manuscript, submitted to Frontiers in Genetics:</p> <p>"Dynamical Modeling of the Core Gene Network Controlling Transition to Flowering in <em>Pisum sativum</em>" by Polina Pavlinova, Maria G. Samsonova, and Vitaly V. Gursky.</p> <p>All possible questions can be sent to: Polina Pavlinova (polina.pavlina1004@gmail.com), Vitaly Gursky (gursky@math.ioffe.ru).</p>
Human tissue gene expression TPM values for the advanced forensic biology course
<p><strong>Gene expression per tissue</strong></p> <p>This dataset comes from the <a href="https://www.gtexportal.org/home/">Genotype-Tissue Expression (GTEx)</a> database that gathers gene expression data from various human tissues. Specifically, the <strong>GTEx Analysis v7</strong> version was used.</p> <p>The file is called "<a href="https://zenodo.org/api/files/9f872792-6c96-4226-b659-ce0807da66e8/GTEx_Analysis_2016-01-15_v7_RNASeQCv1.1.8_gene_median_tpm.tsv">GTEx_Analysis_2016-01-15_v7_RNASeQCv1.1.8_gene_tpm.tsv</a>" and contains tabulated-separated values of median TPM gene expression by tissue (TPM: transcript per million).</p> <p> </p> <p><strong>Genes with a favored sucutaneous-adipose expression profile</strong></p> <p>This file contains 195 genes that have a statistically (p < 0.01) favored expression profile in subcutaneous adipose tissue compared to other tissues. </p> <p>https://zenodo.org/api/files/7342bbfa-0e4d-49e7-b916-5eff5b638c33/genes_with_a_subcutaneous_adipose_favored_expression.tsv</p>
Data from: Ocean acidification induces subtle shifts in gene expression and DNA methylation in mantle tissue of the Eastern oyster (Crassostrea virginica)
<p><b><span>Early evidence suggests that DNA methylation can mediate phenotypic responses of marine calcifying species to ocean acidification (OA). Few studies, however, have explicitly studied DNA methylation in calcifying tissues through time. Here, we examined the phenotypic and molecular responses in the extrapallial fluid and mantle (fluid and tissue at the calcification site) in adult eastern oyster (</span><span>Crassostrea virginica</span><span>) exposed to experimental OA over 80 days. Oysters were reared under three experimental </span><span>p</span><span>CO</span><span><span>2</span></span><span> treatments ('control', 580 μatm; 'moderate OA', 1000 μatm; 'high OA', 2800 μatm) and sampled at 6 time points (24 hours - 80 days). We found that high OA initially induced an increase in the pH of the extrapallial fluid (pH</span><span><span>EPF</span></span><span>) relative to the external seawater that peaked at day 9, but then diminished over time. Calcification rates were significantly lower in the high OA treatment compared to the other treatments. To explore how oysters regulate their extrapallial fluid, gene expression and DNA methylation were examined in the mantle-edge tissue of oysters from days 9 and 80 in the control and high OA treatments. Mantle tissue mounted a significant global molecular response (both in the transcriptome and methylome) to OA that shifted through time. Although we did not find individual genes that were significantly differentially expressed under OA, the pH</span><span><span>EPF</span></span><span> was significantly correlated with the eigengene expression of several co-expressed gene clusters. A small number of OA-induced differentially methylated loci were discovered, which corresponded with a weak association between OA-induced changes in genome-wide gene body DNA methylation and gene expression.</span><span> </span><span>Gene body methylation, however, was not significantly correlated with the eigengene expression of pH</span><span><span>EPF</span></span><span>-correlated gene clusters. These results suggest that OA induces a subtle response in a large number of genes in </span><span>C. virginica</span><span>, but also indicate that plasticity at the molecular level may be limited. Our study highlights the need to reassess our understanding of tissue-specific molecular responses in marine calcifiers</span><span>, </span><span>as well as the role of DNA methylation and gene expression in mediating physiological and biomineralization responses to OA. </span></b></p>
Gene expression remodelling and immune response during adaptive divergence in an African cichlid fish
<p><span>Variation in gene expression contributes to ecological speciation by facilitating population persistence in novel environments. Likewise, immune response can be a relevant factor in speciation driven by adaptation to different environments. Previous studies examining gene expression differences between recently diverged ecotypes often relied on only one pair of populations, targeted the expression of only a subset of genes, or used wild caught-individuals. Here, we investigated the contribution of habitat-specific parasites and symbionts and the underlying immunological capabilities of ecotype hosts to adaptive divergence in lake-river population pairs of the cichlid fish <i>Astatotilapia burtoni</i>. To shed light on the role of phenotypic plasticity in adaptive divergence, we compared parasite and microbiota communities, immune response, and gene expression patterns of fish from natural habitats and a lake-like pond setup. In all investigated population pairs, lake fish were more heavily parasitized than river fish, both in terms of parasite taxa composition and infection abundance. Innate immune response in the wild was higher in lake than in river populations and elevated in a river population exposed to lake parasites in the pond setup. Environmental differences between lake and river habitat and their distinct parasite communities shaped differential gene expression, involving genes functioning in osmoregulation and immune response. Most changes in gene expression between lake and river samples in the wild and in the pond setup were based on a plastic response. Finally, gene expression and bacterial communities of wild-caught individuals and individuals acclimated to lake-like pond conditions showed shifts underlying adaptive phenotypic plasticity.</span></p>
ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs
<p>Genomic DNA is packed by histone proteins that carry a multitude of post-translational modifications that reflect cellular transcriptional state. Cell-free DNA (cfDNA) is derived from fragmented chromatin in dying cells, and as such it retains the histones markings present in the cells of origin. Here, we pioneer chromatin immunoprecipitation followed by sequencing of cell-free nucleosomes (cfChIP-seq) carrying active chromatin marks. Our results show that cfChIP-seq provides multidimensional epigenetic information that recapitulates the epigenetic and transcriptional landscape in the cells of origin. We applied cfChIP-seq to 268 samples including samples from patients with heart and liver pathologies, and 135 samples from 56 metastatic CRC patients. We show that cfChIP-seq can detect pathology-related transcriptional changes at the site of the disease, beyond the information on tissue of origin. In CRC patients we detect clinically-relevant, and patient-specific information, including transcriptionally active HER2 amplifications. cfChIP-seq provides genome-wide information and requires low sequencing depth. Altogether, we establish cell-free chromatin immunoprecipitation as an exciting modality with potential for diagnosis and interrogation of physiological and pathological processes using a simple blood test.</p>
Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species
<ul> <li>Polyploidization is pervasive in plants, but little is known about the niche divergence of wild allopolyploids (species that harbor polyploid genomes originating from different diploid species) relative to their diploid progenitor species and the gene expression patterns that may underlie such ecological divergence. We conducted a fine-scale empirical study on habitat and gene expression of an allopolyploid and its diploid progenitors.</li> <li> We quantified soil properties and light availability of habitats of an allotetraploid <i>Cardamine flexuosa</i> and its diploid progenitors <i>C. amara</i> and <i>C. hirsuta</i> in two seasons. We analyzed expression patterns of genes and homeologs (homeologous gene copies in allopolyploids) using RNA-seq.</li> <li>We detected niche divergence between the allopolyploid and its diploid progenitors along water availability gradient at a fine scale: the diploids in opposite extremes and the allopolyploid in a broader range between diploids, with limited overlap with diploids at both ends. Most of the genes whose homeolog expression ratio changed among habitats in <i>C. flexuosa</i> varied spatially and temporally. </li> <li>These findings provide empirical evidence for niche divergence between an allopolyploid and its diploid progenitor species at a fine scale and suggest that divergent expression patterns of homeologs in an allopolyploid may underlie its persistence in diverse habitats.</li> </ul>
Supplementary Materials for "The Effects of Chromosome Doubling on Morphology, Salinity Tolerance, Essential Oil Composition, and Gene Expression of Biosynthesis Pathway in Peppermint (Mentha piperita L.)"
<p>Shandong Province Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; zhaozjfrances@163.com (Z.Z.); yanli_wei@163.com (Y.W.); menshenlai@163.com (K.Y.); sdkinghills@sina.com (B.L.); liling33802400@163.com (L.L.); yanght@sdas.org (H.Y)</p>
Supplementary materials for the article on 'How to express evolution in English Pokémon names', published in Linguistics
<p>The zip-archive contains two folders, "Graphics" and "statistics". For the statistical analyses, cf. the Rdm-file in the "statistics" folder. The data is stored in csv-files. For a description of the data, cf. the publication itself.</p>
Haberlea darkness 2018 gene expression
<p>The desiccation-tolerant plant Haberlea rhodopensis can withstand months of darkness without any visible senescence. Here, we investigated the molecular mechanisms of this adaptation to prolonged (30 d) darkness and subsequent return to light. H. rhodopensis plants remained green and viable throughout the dark treatment. Transcriptomic analysis revealed that darkness regulated several transcription factor (TF) genes. Stress- and autophagy-related TFs such as ERF8, HSFA2b, RD26, TGA1, and WRKY33 were up-regulated, while chloroplast- and flowering-related TFs such as ATH1, COL2, COL4, RL1, and PTAC7 were repressed. PHYTOCHROME INTERACTING FACTOR4, a negative regulator of photomorphogenesis and promoter of senes-cence, also was down-regulated. In response to darkness, most of the photosynthesis- and photorespiratory-related genes were strongly down-regulated, while genes related to autophagy were up-regulated. This occurred concomitant with the induction of SUCROSE NON-FERMENTING1-RELATED PROTEIN KINASES (SnRK1) signaling pathway genes, which regulate responses to stress-induced starvation and autophagy. Most of the genes associated with chlorophyll catabolism, which are induced by darkness in dark-senescing species, were either unregulated (PHEOPHORBIDE A OXYGENASE, PAO; RED CHLOROPHYLL CATABOLITE REDUCTASE, RCCR) or repressed (STAY GREEN-LIKE, PHEOPHYTINASE, and NON-YELLOW COLORING1). Metabolite profiling revealed increases in the levels of many amino acids in darkness, suggesting increased protein degrada-tion. In darkness, levels of the chloroplastic lipids digalactosyldiacylglycerol, monogalactosyldiacylglycerol, phosphatidylglyc-erol, and sulfoquinovosyldiacylglycerol decreased, while those of storage triacylglycerols increased, suggesting degradation of chloroplast membrane lipids and their conversion to triacylglycerols for use as energy and carbon sources. Collectively, these data show a coordinated response to darkness, including repression of photosynthetic, photorespiratory, flowering, and chloro-phyll catabolic genes, induction of autophagy and SnRK1 pathways, and metabolic reconfigurations that enable survival under prolonged darkness.</p>
AhR Gene Expression in Immune cell subtypes
<p>Benjamin J. Schmiedel, Divya Singh, Ariel Madrigal, Alan G. Valdovino-Gonzalez, Brandie M. White, Jose Zapardiel-Gonzalo, Brendan Ha, Gokmen Altay, Jason A. Greenbaum, Graham McVicker, Grégory Seumois, Anjana Rao, Mitchell Kronenberg, Bjoern Peters, Pandurangan Vijayanand,<br> Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression,<br> Cell,<br> Volume 175, Issue 6,<br> 2018,<br> Pages 1701-1715.e16,<br> ISSN 0092-8674,<br> https://doi.org/10.1016/j.cell.2018.10.022.<br> (http://www.sciencedirect.com/science/article/pii/S009286741831331X)</p> <p><br> Abstract: Summary<br> While many genetic variants have been associated with risk for human diseases, how these variants affect gene expression in various cell types remains largely unknown. To address this gap, the DICE (database of immune cell expression, expression quantitative trait loci [eQTLs], and epigenomics) project was established. Considering all human immune cell types and conditions studied, we identified cis-eQTLs for a total of 12,254 unique genes, which represent 61% of all protein-coding genes expressed in these cell types. Strikingly, a large fraction (41%) of these genes showed a strong cis-association with genotype only in a single cell type. We also found that biological sex is associated with major differences in immune cell gene expression in a highly cell-specific manner. These datasets will help reveal the effects of disease risk-associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis (https://dice-database.org).<br> Keywords: DICE; immunology; GWAS; genetic variants; human immune cells; gene expression; eGenes; eQTLs; sex</p> <p>https://dice-database.org/genes/ahr#boxplot</p>
Wing plasticity and associated gene expression varies across the pea aphid biotype complex
Developmental phenotypic plasticity is a widespread phenomenon that allows organisms to produce different adult phenotypes in response to different environments. Investigating the molecular mechanisms underlying plasticity has the potential to reveal the precise changes that lead to the evolution of plasticity as a phenotype. Here, we study wing plasticity in multiple host-plant adapted populations of pea aphids as a model for understanding adaptation to different environments within a single species. We describe the wing plasticity response of different 'biotypes' to a crowded environment and find differences within as well as among biotypes. We then use transcriptome profiling to compare a highly plastic pea aphid genotype to one that shows no plasticity and find that the latter exhibits no gene expression differences between environments. We conclude that the loss of plasticity has been accompanied by a loss of differential gene expression and therefore that genetic assimilation has occurred. Our gene expression results generalize previous studies that have shown a correlation between plasticity in morphology and gene expression.
Data from: Context-dependent expression of the foraging gene in field colonies of ants: the interacting roles of age, environment and task
Task allocation among social insect workers is an ideal framework for studying the molecular mechanisms underlying behavioural plasticity because workers of similar genotype adopt different behavioural phenotypes. Elegant laboratory studies have pioneered this effort, but field studies involving the genetic regulation of task allocation are rare. Here, we investigate the expression of the foraging gene in harvester ant workers from five age- and task-related groups in a natural population, and we experimentally test how exposure to light affects foraging expression in brood workers and foragers. Results from our field study show that the regulation of the foraging gene in harvester ants occurs at two time scales: levels of foraging mRNA are associated with ontogenetic changes over weeks in worker age, location and task, and there are significant daily oscillations in foraging expression in foragers. The temporal dissection of foraging expression reveals that gene expression changes in foragers occur across a scale of hours and the level of expression is predicted by activity rhythms: foragers have high levels of foraging mRNA during daylight hours when they are most active outside the nests. In the experimental study, we find complex interactions in foraging expression between task behaviour and light exposure. Oscillations occur in foragers following experimental exposure to 13 L : 11 D (LD) conditions, but not in brood workers under similar conditions. No significant differences were seen in foraging expression over time in either task in 24 h dark (DD) conditions. Interestingly, the expression of foraging in both undisturbed field and experimentally treated foragers is also significantly correlated with the expression of the circadian clock gene, cycle. Our results provide evidence that the regulation of this gene is context-dependent and associated with both ontogenetic and daily behavioural plasticity in field colonies of harvester ants. Our results underscore the importance of assaying temporal patterns in behavioural gene expression and suggest that gene regulation is an integral mechanism associated with behavioural plasticity in harvester ants.
A single-parasite transcriptional atlas of Toxoplasma gondii reveals novel control of antigen expression
Toxoplasma gondii, a protozoan parasite, undergoes a complex and poorly understood developmental process that is critical for establishing a chronic infection in its intermediate hosts. Here, we applied single-cell RNA-sequencing (scRNA-seq) on >5,400 Toxoplasma in both tachyzoite and bradyzoite stages using three widely studied strains to construct a comprehensive atlas of cell-cycle and asexual development, revealing hidden states and transcriptional factors associated with each developmental stage. Analysis of SAG1-related sequence (SRS) antigenic repertoire reveals a highly heterogeneous, sporadic expression pattern unexplained by measurement noise, cell cycle, or asexual development. Furthermore, we identified AP2 IX-1 as a transcription factor that controls the switching from the ubiquitous SAG1 to rare surface antigens not previously observed in tachyzoites. In addition, comparative analysis between Toxoplasma and Plasmodium scRNA-seq results reveals concerted expression of gene sets, despite fundamental differences in cell division. Lastly, we built an interactive data-browser for visualization of our atlas resource.
Data from: Poison frog color morphs express assortative mate preferences in allopatry but not sympatry
The concurrent divergence of mating traits and preferences is necessary for the evolution of reproductive isolation via sexual selection, and such coevolution has been demonstrated in diverse lineages. However, the extent to which assortative mate preferences are sufficient to drive reproductive isolation in nature is less clear. Natural contact zones between lineages divergent in traits and preferences provide exceptional opportunities for testing the predicted evolutionary consequences of such divergence. The strawberry poison frog (Oophaga pumilio) displays extreme color polymorphism in and around the young Bocas del Toro archipelago. In a transition zone between red and blue allopatric lineages, we asked whether female preferences diverged along with coloration, and whether any divergent preferences persist in a zone of sympatry. When choosing among red, blue and phenotypically intermediate males, females from monomorphic red and monomorphic blue populations both expressed assortative preferences. However, red, blue, and intermediate females from the contact zone all preferred red males, suggesting that divergent preferences may be insufficient to effect behavioral isolation. Our results highlight the complexity of behavioral isolation, and the need for studies that can reveal the circumstances under which divergent preferences do and do not contribute to speciation.
Data for: Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems
<p>Advancements in the field of synthetic biology have been possible due to the development of genetic tools that are able to regulate gene expression. However, the current toolbox of gene regulatory tools for eukaryotic systems have been outpaced by those developed for simple, single-celled systems. Here, we engineered a set of gene regulatory tools by combining self-cleaving ribozymes with various upstream competing sequences that were designed to disrupt ribozyme self-cleavage. As a proof-of-concept, we were able to modulate GFP expression in mammalian cells, and then showed the feasibility of these tools in <i>Drosophila </i>embryos. For each system, the fold-reduction of gene expression was influenced by the location of the self-cleaving ribozyme/upstream competing sequence (i.e. 5′ vs. 3′ untranslated region) and the competing sequence used. Together, this work provides a set of genetic tools that can be used to tune gene expression across various eukaryotic systems.</p>
Data from: Carotenoid pigmentation in salmon: Variation in expression at BCO2-l locus controls a key fitness trait affecting red colouration
Carotenoids are primarily responsible for the characteristic red flesh colouration of salmon. Flesh colouration is an economically and evolutionarily significant trait that varies inter- and intra-specifically, yet the underlying genetic mechanism is unknown. Chinook salmon (Oncorhynchus tshawytscha) represent an ideal system to study carotenoid variation as, unlike other salmonids, they exhibit extreme differences in carotenoid utilization due to genetic polymorphisms. Here, we crossed populations of Chinook salmon with fixed differences in flesh colouration (red vs. white) for a genome-wide association study (GWAS) to identify loci associated with pigmentation. Here, the beta-carotene oxygenase 2-like (BCO2-l) gene was significantly associated with flesh colour, with the most significant SNP explaining 66% of the variation in colour. BCO2 gene disruption is linked to carotenoid accumulation in other taxa, therefore we hypothesize that an ancestral mutation partially disrupting BCO2-l activity (i.e., hypomorphic mutation) allowed the deposition and accumulation of carotenoids within Salmonidae. Indeed, we found elevated transcript levels of BCO2-l in white Chinook salmon relative to red. The long-standing mystery of why salmon are red, while no other fishes are, is thus likely explained by a hypomorphic mutation in the proto-salmonid at the time of divergence of red-fleshed salmonid genera (~30 MYA).
Data from: Electroacupuncture mimics exercise-induced changes in skeletal muscle gene expression in women with polycystic ovary syndrome
<p class="1stparatext">Context: Autonomic nervous system activation mediates the increase in whole-body glucose uptake in response to electroacupuncture but the mechanisms are largely unknown.</p> <p class="1stparatext">Objective: To identify the molecular mechanisms underlying electroacupuncture-induced glucose uptake in skeletal muscle in insulin-resistant overweight/obese women with and without polycystic ovary syndrome (PCOS).</p> <p class="1stparatext">Design/Participants: In a case-control study, skeletal muscle biopsies were collected from 15 women with PCOS and 14 controls before and after electroacupuncture. Gene expression and methylation was analyzed using Illumina BeadChips arrays.</p> <p class="1stparatext">Results: A single bout of electroacupuncture restores metabolic and transcriptional alterations and induces epigenetic changes in skeletal muscle. Transcriptomic analysis revealed 180 unique genes (<i>q </i>< 0.05) whose expression was changed by electroacupuncture, with 95% of the changes towards a healthier phenotype. We identified DNA methylation changes at 304 unique sites (<i>q </i>< 0.20), and these changes correlated with altered expression of 101 genes (<i>p</i> < 0.05). Among the 50 most upregulated genes in response to electroacupuncture, 38% were also upregulated in response to<b> </b>exercise. We identified a subset of genes that were selectively altered by electroacupuncture in women with PCOS. For example, <i>MSX1 </i>and <i>SRNX1 </i>were decreased in muscle tissue of women with PCOS and were increased by electroacupuncture and exercise. siRNA-mediated silencing of these two genes in cultured myotubes decreased glycogen synthesis, supporting a role for these genes in glucose homeostasis.</p> <p class="1stparatext">Conclusion: Our findings provide evidence that electroacupuncture normalizes gene expression in skeletal muscle in a manner similar to acute exercise. Electroacupuncture might therefore be a useful way of assisting those who have difficulties performing exercise.</p>
Data from Native adiponectin in serum binds to mammalian cells expressing T-cadherin, but not AdipoRs or calreticulin
<p>Adiponectin is an adipocyte-derived atypically abundant circulating factor that protects various organs and tissues through its receptors, AdipoRs, calreticulin, and T-cadherin. To identify the major binding partner of circulating native adiponectin, we expressed these receptors on the surface of HEK293 cells. Adiponectin, either that in mouse or human serum, purified from serum, or produced by mammalian cells, bound to cells expressing T-cadherin, but not to those expressing AdipoR1 or calreticulin. The stable introduction of T-cadherin and AdipoR1 into CHO cells resulted in the cell surface localization of these receptors. Native adiponectin in serum bound to cells expressing T-cadherin, not to those expressing AdipoR1. The knockdown of T-cadherin, but not AdipoRs resulted in the significant attenuation of native adiponectin binding to C2C12 myotubes. Therefore, native adiponectin binding depended on the amount of T-cadherin expressed in HEK293 cells, CHO cells, and C2C12 myotubes. Collectively, our mammalian cell-based studies suggest that T-cadherin is the major binding partner of native adiponectin in serum.</p> <p> </p>
Data from: Gene expression shifts in yellow-bellied marmots prior to natal dispersal
The causes and consequences of vertebrate natal dispersal have been studied extensively, yet little is known about the molecular mechanisms involved. We used RNA-seq to quantify transcriptomic gene expression in blood of wild yellow-bellied marmots (Marmota flaviventer) prior to dispersing from or remaining philopatric to their natal colony. We tested three predictions. First, we hypothesized dispersers and residents will differentially express genes and gene networks since dispersal is physiologically demanding. Second, we expected differentially expressed genes to be involved in metabolism, circadian processes, and immune function. Finally, in dispersing individuals, we predicted differentially expressed genes would change as a function of sampling date relative to dispersal date. We detected 150 differentially expressed genes, including genes that have critical roles in lipid metabolism and antigen defense. Gene network analysis revealed a module of 126 co-expressed genes associated with dispersal that was enriched for extra-cellular immune function. Of the dispersal-associated genes, 22 altered expression as a function of days until dispersal, suggesting that dispersal-associated genes do not initiate transcription on the same time scale. Our results provide novel insights into the fundamental molecular changes required for dispersal and suggest evolutionary conservation of functional pathways during this behavioral process.
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.