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5,381 results for “deficiencies”
Phosphotyrosine peptide abundance in control and Cul5-deficient MCF10A cells
<p>The Cullin 5 RING ligase complex inhibits Src activity and Src-dependent transformation of MCF10A epithelial cells, in part by targeting pY proteins such as pYCas for degradation by the ubiquitin-proteasome system (Teckchandani et al., 2014). Because overexpression of Cas alone did not phenocopy CRL5 inhibition (Teckchandani et al., 2014), we infer that CRL5 down-regulates additional pY proteins that become limiting when Cas is over-expressed. We sought to identify such pY proteins by screening for pY peptides whose abundance increases when Cul5 is inhibited. To this end, control and Cul5-deficient MCF10A cells were lysed under denaturing conditions, proteins were digested with trypsin, and peptides were labeled with isobaric TMT tags for quantitative pY proteomics (Zhang et al., 2007). In one experiment, samples were prepared from control and Cul5-deficient cells that were starved for epidermal growth factor (EGF) for 0, 24 or 72 hr. Starvation time had no systematic effect on peptide abundance, so, in a second experiment, we prepared biological triplicate samples from growing control and Cul5-deficient cells. Sixteen pY peptides increased significantly in Cul5-deficient cells in both experiments, including pY128 from Cas and pY117 and pY266 from BCAR3.</p>
Evaluation of the silkworm lemon mutant as an invertebrate animal model for human sepiapterin reductase deficiency
<p><span>Human sepiapterin reductase deficiency is an inherited disease caused by <i>SPR</i> gene mutations and is a monoamine neurotransmitter disorder. Here, we investigated whether the silkworm <i>lemon<sup> </sup></i>mutant could serve as a model of sepiapterin reductase deficiency. A point mutation in the<i> BmSPR</i> gene led to a five amino acid deletion at the carboxyl terminus in the <i>lemon</i> mutant. In addition, classical phenotypes seen in sepiapterin reductase deficient patients were observed in the <i>lemon</i> mutant, including a normal phenylalanine level, a decreased dopamine and serotonin content, and an increased neopterin level. A recovery test showed that replenishment of L-dopa significantly increased the dopamine level in the <i>lemon<sup> </sup></i>mutant. The silkworm <i>lemon</i> mutant also showed negative behavioral abilities. These results suggest that the silkworm <i>lemon</i> mutant has an appropriate genetic basis and meets the biochemical requirements to be a model of sepiapterin reductase deficiency. Thus, the silkworm <i>lemon</i> mutant can serve as a candidate animal model of sepiapterin reductase deficiency, which may be helpful in facilitating accurate diagnosis and effective treatment options of sepiapterin reductase deficiency.</span></p>
Dataset of confocal microscopy - Rhamnogalacturonan-II dimerization deficiency impairs the coordination between growth and adhesion maintenance in plants
<p>This contains additional data relative to version 1, corresponding to a new versio of the manuscript. </p> <p>This data set contains confocal images (3D stacks and 2D projections) from propidium iodide stained <em>Arabidopsis thaliana </em>dark grown hypocotyls of various wildtype and mutant plants reported in the study "Rhamnogalacturonan-II dimerization deficiency impairs the coordination between growth and adhesion maintenance in plants" (https://www.biorxiv.org/content/10.1101/2024.11.26.625362v1). Data was acquired following method described in the publication.</p> <p> </p>
PINK1 deficiency rewires early immune responses in a mouse model of Parkinson's disease triggered by intestinal infection
<p>Parkinson’s disease is characterized by a period of non-motor symptoms, including gastrointestinal dysfunction, preceding motor deficits by decades. This long prodrome is suggestive of peripheral immunity involvement in the initiation of disease. We previously developed a model system in PINK1 KO mice displaying PD-like motor symptoms at late stages following intestinal infections. Herein, we map the initiating immune events at the site of infection in this model. Using single-cell RNAseq, we demonstrate that peripheral myeloid cells are the earliest highly dysregulated immune cell type in PINK1 KO infected mice followed by an aberrant T cell response shortly after. We elucidate an increased propensity for antigen presentation mediated by myeloid-CD8+ T cell interaction. PINK1 KO activated myeloid cells acquire a proinflammatory profile inducing cytotoxic T cell responses. Together, our study provides the first evidence that PINK1 is a key regulator of immune functions in the gut underlying early PD-related disease mechanisms.</p>
Cadherin-11 deficiency-induced changes in pancreatic ductal adenocarcinoma
<p class="MsoNormal"><span>Pancreatic ductal adenocarcinoma (PDAC) is one of the top five deadliest forms of cancer with very few treatment options. The 5-year survival rate for PDAC is 10% following diagnosis. Cadherin 11 (Cdh11), a cell-to-cell adhesion molecule, has been suggested to promote tumor growth and immunosuppression in PDAC, and Cdh11 inhibition significantly extended survival in mice with PDAC. However, the mechanisms by which Cdh11 deficiency influences PDAC progression and anti-tumor immune responses have yet to be fully elucidated. To investigate <em>Cdh11</em>-deficiency induced changes in PDAC tumor microenvironment (TME), we crossed <em>p48-Cre; LSL-Kras<sup>G12D/+</sup>; LSL-Trp53<sup>R172H/+</sup></em> (KPC) mice with <em>Cdh11<sup>+/-</sup></em> mice and performed single-cell RNA sequencing (scRNA-seq) of the non-immune (CD45<sup>-</sup>) and immune (CD45<sup>+</sup>) compartment of KPC tumor-bearing <em>Cdh11</em> proficient (<em>KPC-Cdh11<sup>+/+</sup></em>) and <em>Cdh11</em> deficient (<em>KPC-Cdh11<sup>+/-</sup></em>) mice. Our analysis showed that <em>Cdh11</em> is expressed primarily in cancer-associated fibroblasts (CAFs) and at low levels in epithelial cells undergoing epithelial-to-mesenchymal transition (EMT). <em>Cdh11</em> deficiency altered the molecular profile of CAFs, leading to a decrease in the expression of myofibroblast markers such as <em>Acta2</em> and <em>Tagln</em> and cytokines such as <em>Il6</em>, <em>Il33</em> and Midkine<em> (Mdk)</em>. We also observed a significant decrease in the presence of monocytes/macrophages and neutrophils in <em>KPC-Cdh11<sup>+/-</sup></em> tumors while the proportion of T cells was increased. Additionally, myeloid lineage cells from <em>Cdh11</em>-deficient tumors had reduced expression of inflammatory cytokines that have previously been shown to play a role in immune suppression. In summary, our data suggests that <em>Cdh11</em> deficiency significantly alters</span> the fibroblast and immune microenvironments and contributes to the downregulation of inflammatory cytokines, leading to an increase in anti-tumor immunity and enhanced survival.</p>
Transcobalamin receptor antibodies in autoimmune vitamin B12 central deficiency
<p>Vitamin B12 is critical for hematopoiesis and myelination. Deficiency can cause neurologic deficits including loss of coordination and cognitive decline. However, diagnosis relies on vitamin B12 measurement in the blood which may not accurately reflect levels in the brain. Using programmable phage display, we identified an autoantibody targeting the transcobalamin receptor (CD320) in a patient with progressive tremor, ataxia, and scanning speech. Anti-CD320 impaired cellular uptake of cobalamin (B12) <em>in vitro</em>. Despite normal serum levels, B12 was nearly undetectable in her cerebrospinal fluid (CSF). Immunosuppressive treatment and high-dose systemic B12 supplementation were associated with increased CSF B12 levels and clinical improvement. Optofluidic screening enabled rapid isolation of a patient-derived monoclonal antibody that impaired B12 transport across an <em>in vitro</em> model of the blood-brain barrier. Autoantibodies targeting the same epitope of CD320 were identified in 7 other patients with neurologic deficits of unknown etiology, in 6% of healthy controls, and in 21.4% of a neuropsychiatric lupus cohort. In 132 paired serum and CSF samples, detection of anti-CD320 in the blood predicted B12 deficiency in the brain. However, these individuals did not display any hematologic signs of B12 deficiency despite systemic CD320 impairment. Using a genome-wide CRISPR screen, we discovered that the LDL receptor serves as an alternative B12 uptake pathway in hematopoietic cells. These findings dissect the tissue-specificity of B12 transport and elucidate an autoimmune neurologic condition that may be amenable to immunomodulatory treatment and nutritional supplementation.</p>
Dataset related to article "Amnion epithelial cells are an effective source of factor H and prevent kidney complement deposition in factor H deficient mice"
<p>File excel with raw data of parameters (column) for any single animal (line) of each experimental group</p>
Data for PNASnexus article Aldehyde dehydrogenase 3A1 deficiency leads to mitochondrial dysfunction and impacts salivary gland stem cell phenotype
<p>Adult salivary stem/progenitor cells (SSPC) have an intrinsic property to self-renew in order to maintain tissue architecture and homeostasis. Adult salivary glands have been documented to harbor SSPC, which have been shown to play a vital role in the regeneration of the glandular structures post radiation damage. We have previously demonstrated that activation of aldehyde dehydrogenase 3A1 (ALDH3A1) after radiation reduced aldehyde accumulation in SSPC, leading to less apoptosis and improved salivary function. We subsequently found that sustained pharmacological ALDH3A1 activation is critical to enhance regeneration of murine submandibular gland after radiation damage. Further investigation shows that ALDH3A1 function is crucial for SSPC self-renewal and survival even in the absence of radiation stress. Salivary glands from <em>Aldh3a1</em>-null mice have fewer acinar structures than wildtype mice. ALDH3A1 deletion or pharmacological inhibition in SSPC leads to a decrease in mitochondrial DNA copy number, lower expression of mitochondrial specific genes and proteins, structural abnormalities, lower membrane potential, and reduced cellular respiration. Loss or inhibition of ALDH3A1 also elevates ROS levels and accumulation of ALDH3A1 substrate 4-hydroxynonenal (4-HNE, a lipid peroxidation product), leading to decreased survival of murine SSPC that can be rescued by treatment with 4-HNE specific carbonyl scavengers. Our data indicate that ALDH3A1 activity protects mitochondrial function and is important for the regeneration activity of SSPC. This knowledge will help to guide our translational strategy of applying ALDH3A1 activators in the clinic to prevent radiation-related hyposalivation in head and neck cancer patients.</p>
Data for Human milk lactoferrin variation in relation to maternal inflammation and iron deficiency in northern Kenya
<p>This file contains the data utilized for a journal manuscript, "Human milk lactoferrin variation in relation to maternal inflammation and iron deficiency in northern Kenya" by Fujita, Wander, Paredes Ruvalcaba, and Odo, currently under review for publication. Data are found under the Data tab, and the variable coding information under the Code tab.</p> <p>Please contact Fujita (masakof@msu.edu) for questions regarding the data.</p> <p>In using the data, please cite the DOI for this file and the above-mentioned article. Also, please acknowledge the following parties for grant support:</p> <p> National Science Foundation (BCS-0622358, BCS-1638167);</p> <p> Wenner-Gren Foundation (Gr. 7460, Gr. 9278);</p> <p> African Futures Research Leadership Program of the Alliances for African Partnership, Michigan State University; and</p> <p> Provost Undergraduate Research Initiative Grant, Michigan State University </p> <p>The data originates in the 2006 fieldwork among the Ariaal people in northern Kenya under approvals by the institutional review boards of the University of Washington and Kenya Medical Research Institute. The lactoferrin concentration in milk was determined more recently using de-identified milk specimens, and as such required no further approvals.</p> <p> </p>
Deficiency of GRN, a frontotemporal dementia gene, results in gangliosidosis
<p>Haploinsufficiency of <em>GRN</em> causes frontotemporal dementia (FTD). The <em>GRN</em> locus produces progranulin (PGRN), which is cleaved to lysosomal granulin polypeptides. The function of lysosomal granulins and why their absence causes neurodegeneration are unclear. Here we discover that PGRN-deficient human cells and murine brains, as well as human frontal lobes from <em>GRN</em>-mutation FTD patients have increased levels of gangliosides, glycosphingolipids that contain sialic acid. In these cells and tissues, levels of lysosomal enzymes that catabolize gangliosides were normal, but levels of bis(monoacylglycero)phosphates (BMP), lipids required for ganglioside catabolism, were reduced with PGRN deficiency. Our findings indicate that granulins are required to maintain BMP levels to support ganglioside catabolism, and that PGRN deficiency in lysosomes leads to gangliosidosis. Lysosomal ganglioside accumulation may contribute to neuroinflammation and neurodegeneration susceptibility observed in FTD due to PGRN deficiency and other neurodegenerative diseases.</p>
Distinct mechanisms of mismatch repair deficiency delineate two modes of response to PD-1 immunotherapy in endometrial carcinoma
<p>Responses to immune checkpoint blockade (ICB) are variable even among mismatch repair deficient (MMRd) cancers. We completed a phase 2 clinical trial of the PD-1 inhibitor pembrolizumab in 24 patients with MMRd endometrial cancer (NCT02899793). Patients with mutational MMRd tumors (6 patients) had higher response rates and longer survival than those with epigenetic MMRd tumors (18 patients). Mutation burden was higher in tumors with mutational MMRd compared to epigenetic MMRd; however, within each category of MMRd, mutation burden was not associated with ICB response. Notably, JAK1 mutations did not confer resistance to pembrolizumab. Longitudinal single-cell RNA-seq of circulating immune cells revealed contrasting modes of anti-tumor immunity against mutational and epigenetic MMRd tumors. Whereas effector CD8+ T cell responses correlated with mutational MMRd, highly active CD16+ NK cells were associated with epigenetic MMRd tumors responsive to ICB. These data highlight factors beyond neoantigen burden that influence ICB response.</p>
T cell deficiency precipitates antibody evasion and emergence of neurovirulent polyomavirus
<p>JC polyomavirus (JCPyV) causes progressive multifocal leukoencephalopathy (PML), a life-threatening brain disease in immunocompromised patients. Inherited and acquired T cell deficiencies are associated with PML. The incidence of PML is increasing with the introduction of new immunomodulatory agents, several of which target T cells or B cells. PML patients often carry mutations in the JCPyV VP1 capsid protein, which confer resistance to neutralizing VP1 antibodies (Ab). Polyomaviruses (PyV) are tightly species-specific; the absence of tractable animal models has handicapped understanding of PyV pathogenesis. Using mouse polyomavirus (MuPyV), we found that T cell deficiency during persistent infection, in the setting of monospecific VP1 Ab, was required for outgrowth of VP1 Ab-escape viral variants. CD4 T cells were primarily responsible for limiting polyomavirus infection in the kidney, a major reservoir of persistent infection by both JCPyV and MuPyV, and checking emergence of these mutant viruses. T cells also provided a second line of defense by controlling the outgrowth of VP1 mutant viruses that evaded Ab neutralization. A virus with two capsid mutations, one conferring Ab-escape yet impaired infectivity and a second compensatory mutation, yielded a highly neurovirulent variant. These findings link T cell deficiency and evolution of Ab-escape polyomavirus VP1 variants with neuropathogenicity.</p>
Annotated and processed 3D confocal microscopy images of dorsal aorta in wild-type and Endoglin-deficient zebrafish embryos at 48 hpf and 72 hpf
<p>This repository contains the original 3D confocal microscopy images that were used for the analysis of vessel geometry and endothelial cell morphology in the dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos at 48 hours post fertilization (hpf) and 72 hpf in the article <a href="https://www.biorxiv.org/content/10.1101/2024.02.19.580931">Novel mathematical approach to accurately quantify 3D endothelial cell morphology and vessel geometry based on fluorescently marked endothelial cell contours: Application to the dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos</a>. In this article, we developed a novel mathematical approach that allows to consistently estimate 3D vessel geometry and endothelial cell surface morphology using only information from endothelial cell contours. For the article's analysis, endothelial cell contours were manually annotated on Pecam1-EGFP-labeled cell junctions. Furthermore, dorsal aorta cross-sections were outlined on Dextran Texas Red-perfused vessel lumens. Further details are provided in the article's Materials and methods section.</p> <p>This repository contains 14 images of 7 wild-type embryos, each imaged at 48hpf and 72hpf. Furthermore, 12 images of 6 Endoglin-deficient embryos, each imaged at 48hpf and 72hpf are included. These combined files (called "analysis data" in the article) are stored in "eng_wt_data.zip". Secondly, images of 2 wild-types at 72hpf with repeated cell contour annotation and outlined vessel lumens (called "validation data" in the article) are located in "wt_angiogram_data.zip". The provided files are stored in Imaris format and can be inspected using the free <a href="https://imaris.oxinst.com/imaris-viewer">Imaris Viewer software</a>.</p> <p>To allow inspection of the endothelial cell contours that we manually annotated for the article's analysis and compare them against the intermediate results of our novel mathematical approach, i.e., contour enrichments by neighboring cells, contour smoothing splines and their projections onto the estimated vessel surfaces, we imported these contours into the Imaris files. Note that the contours' coordinates in these files are slightly less precise than in our article's analysis and thus are intended for visual inspection. To exactly reproduce the results in our article, refer to the files in <a href="https://doi.org/10.5281/zenodo.10549101">our other Zenodo repository</a>.</p>
data set related to article A Nervous System-Specific Model of Creatine Transporter Deficiency Recapitulates the Cognitive Endophenotype of the Disease: a Longitudinal Study
<p>This record contains raw data related to article A Nervous System-Specific Model of Creatine Transporter Deficiency Recapitulates the Cognitive Endophenotype of the Disease: a Longitudinal Study</p>
Data and R code used in Baudson et al (2019) Developmental plasticity of Brachypodium distachyon in response to P deficiency: modulation by inoculation with phosphate-solubilizing bacteria
<p>This repository contains the raw data and R code used for the following paper: Baudson et al (2019) Developmental plasticity of <em>Brachypodium distachyon</em> in response to P deficiency: modulation by inoculation with phosphate-solubilizing bacteria</p>
Metabolic fingerprints for suboptimal mycorrhizal colonization in wild-type and the jasmonic acid deficient spr2 tomato mutant
<p>Raw data for metabolic fingerprinting of tomato roots by DLI-ESI-MS and GC-MS to examine the effect of mycorrhizal colonization on the global metabolic profile of WT and <em>spr2</em> mutant plants.</p>
Gene expression for suboptimal mycorrhizal colonization in wild-type and jasmonic acid deficient spr2 tomato mutants
<pre>Data were obtained from mycorrhizhal colonized roots of wild-type and and spr2 mutants tomato plants, at 32 and 45 days after mycorrhizhal inoculation. Amplifications were performed using SYBR Green detection chemistry and run in triplicate in 96-well reaction plates with the CFX96 Touch Real-Time PCR Detection System (Bio-Rad, Hercules, CA, USA). The data was analyzed by the delta delta ct method. </pre>
Ndufs4 knockout mice with isolated complex I deficiency engage a futile adaptive brain response - supplementary data
<p>This study aims to provide insight into the Leigh Syndrome pathomechanism at the sub-brain level. To this end, a comparative proteome analysis was performed on various brain regions of 6 wildtype (WT) and 6 whole body (WB) Ndufs4-/- (WB-KO) mice over two experiments. Samples were collected at six weeks after birth (i.e. ~ one week prior to WB-KO death). For the first experiment samples were collected from a brain slice (BrSl), which contained (parts of) the CC, HC, hypothalamus, thalamus, caudate putamen, and olfactory areas. For the second experiment the analysed brain regions consisted of cerebellum (CB), cerebral cortex (CC), hippocampus (HC), inferior colliculust (IC), and superior colliculus (SC).</p>
Color vision deficiency (CVD)
<p>The <strong>color vision deficiency</strong> dataset is designed to train and evaluate a deep neural network for image recoloring aimed at compensating for color vision deficiencies, specifically protanopia and deuteranopia. The dataset contains two types of images:</p> <ol> <li><strong>Natural Scene Images</strong>: These are photographs of real-world scenes, filtered to include images with colors that are confusing or difficult to distinguish for individuals with color vision deficiencies.</li> <li><strong>Artificial Images</strong>: These are generated images that feature color pairs specifically known to be confusing for those with protanopia and deuteranopia. The images are created by selecting color pairs from the RGB space and generating patterns designed to highlight these confusing colors.</li> </ol> <p>This dataset is used to train a neural network, employing the Swin transformer architecture, to enhance contrast and maintain naturalness in images for individuals with these types of color vision deficiencies</p>
QC and WGS around the breakpoints of deletions in the compound heterozygous PRKN-deficient PD iPSC line FINi006-A (FI.CS.PRKNDex2/Dex5-7.@40)
<p>BAM files from WGS on the regions of deletions in both <em>PRKN</em> gene alleles of the iPSC line (clone 18) derived using Sendai virus from PRKN 09/090 patient's fibroblasts </p>
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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.