Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Sequence Count Data”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 577 records · Page 32Linked to original sources
PubMed2001

Retinal ganglion cell genesis requires lakritz, a Zebrafish atonal Homolog.

Mutation of the zebrafish lakritz (lak) locus completely eliminates the earliest-born retinal cells, the ganglion cells (RGCs). Instead, excess amacrine, bipolar, and Müller glial cells are generated in the mutant. The extra amacrines are found at ectopic locations in the ganglion cell layer. Cone photoreceptors appear unaffected by the mutation. Molecular analysis reveals that lak encodes Ath5, the zebrafish eye-specific ortholog of the Drosophila basic helix-loop-helix transcription factor Atonal. A combined birth-dating and cell marker analysis demonstrates that lak/ath5 is essential for RGC determination during the first wave of neurogenesis in the retina. Our results suggest that this wave is skipped in the mutant, leading to an accumulation of progenitors for inner nuclear layer cells.

Amino Acid Sequence↗
PubMed1999

The human homologue of Caenorhabditis elegans CED-6 specifically promotes phagocytosis of apoptotic cells.

A key feature of the process of programmed cell death (apoptosis) is the efficiency with which the dying cells are recognized and engulfed by phagocytes [1]. Apoptotic cells are rapidly cleared either by neighbouring cells acting as semi-professional phagocytes or by experts of the macrophage line, so that an inflammatory response is avoided [2]. The Caenorhabditis elegans gene ced-6 is required for efficient engulfment of apoptotic cells [3] and is one of a group of genes that define two partially redundant parallel pathways for the engulfment process [4] [5]. These pathways may be conserved across evolution, as two other engulfment genes have human homologues. A CED-5 homologue is part of a human CrkII-DOCK180-Rac signaling pathway proposed to mediate cytoskeletal reorganization [6] [7] [8] and a CED-7 homologue is similar to the ABC transporters [9] [10]. Here, we report the cloning and characterization of human CED-6, a human homologue of C. elegans CED-6. The 34 kDa hCED-6 protein is expressed in most tissues, some human cancer cells, and in primary human macrophages. We developed an assay that quantitates the phagocytic activity of mammalian macrophages: the number of apoptotic cells that have been internalized is measured by the uptake of lacZ-positive apoptotic cells by adherent transgenic macrophages. The results of this assay demonstrate that overexpression of hCED-6 promotes phagocytosis only of apoptotic cells and suggest that hCED-6 is the mammalian orthologue of C. elegans CED-6 and is a part of a highly conserved pathway that specifically mediates the phagocytosis of apoptotic cells.

Animals↗
PubMed2000

DAP12-deficient mice fail to develop autoimmunity due to impaired antigen priming.

DAP12 is an ITAM-bearing membrane adaptor molecule implicated in the activation of NK and myeloid cells. In mice rendered DAP12 deficient by targeted gene disruption, lymphoid and myeloid development was apparently normal, although the activating Ly49 receptors on NK cells were downregulated and nonfunctional. To analyze the consequences of DAP12 deficiency in vivo, we examined the susceptibility of DAP12-/- mice to experimental autoimmune encephalomyelitis (EAE). DAP12-/- mice were resistant to EAE induced by immunization with myelin oligodendrocyte glycoprotein (MOG) peptide. Resistance was associated with a strongly diminished production of IFNgamma by myelin-reactive CD4+ T cells due to inadequate T cell priming in vivo. These data suggest that DAP12 signaling may be required for optimal antigen-presenting cell (APC) function or inflammation.

Adaptor Proteins, Signal Transducing↗
PubMed1997

Thiobacillus sp. W5, the dominant autotroph oxidizing sulfide to sulfur in a reactor for aerobic treatment of sulfidic wastes.

The floating filter technique was successfully adapted for the isolation of the dominant, chemolithoautotrophic, sulfide-oxidizing bacterium from a sulfur-producing reactor after conventional isolation techniques had failed. The inoculated polycarbonate filters, floating on mineral medium, were incubated under gaseous hydrogen sulfide at non-toxic levels. This technique gave 200-fold higher recoveries than conventional isolation techniques. Viable counts on the filters, making up 15% of the total count, appeared to be all of the same species. Chemostat cultures of the new isolate had a very high sulfur-forming capacity, converting almost all hydrogen sulfide in the medium to elemental sulfur under high sulfide loads (27.5 mmol l-1 h-1) and fully aerobic conditions. This behaviour closely resembled that of the microbial community in the sulfur-producing reactor. Moreover, similar protein patterns were obtained by electrophoresis of cell-free extracts from the isolate and the mixed culture. It has therefore been concluded that this isolate represents the dominant sulfide-oxidizing population in the reactor. The isolate has been shown to be a new Thiobacillus species, related to Thiobacillus neapolitanus. In view of the general confusion currently surrounding the taxonomy of the thiobacilli, a new species has not been formally created. Instead, the isolate has been given the working name Thiobacillus sp. W5.

Aerobiosis↗
PubMed2004

Activation of the complement system generates antibacterial peptides.

The complement system represents an evolutionary old and significant part of the innate immune system involved in protection against invading microorganisms. Here, we show that the anaphylatoxin C3a and its inactivated derivative C3a-desArg are antibacterial, demonstrating a previously unknown direct antimicrobial effect of complement activation. The C3a peptide, as well as functional epitopes in the sequence, efficiently killed the Gram-negative bacteria Escherichia coli, Pseudomonas aeruginosa, and the Gram-positive Enterococcus faecalis. In mice, a C3a-derived peptide suppressed infection by Gram-positive Streptococcus pyogenes bacteria. Fluorescence and electron microscopy demonstrated that C3a binds to and induces breaks in bacterial membranes. C3a was also found to induce membrane leakage of liposomes. These findings provide an interesting link between the complement system and antimicrobial peptides, which are two important branches of innate immunity.

Amino Acid Sequence↗
PubMed1995

T cells with gamma/delta T cell receptors (TCR) of intestinal type are preferentially expanded in TCR-alpha-deficient lpr mice.

Fas-mediated apoptosis is essential for activation-induced cell death of alpha/beta T cells, but it is not clear what role, if any, it plays in regulating other components of the immune system. To study the role of Fas in gamma/delta T cell development, Fas-deficient lpr mice were bred with T cell receptor alpha gene-ablated (TCR-alpha-/-) mice to generate mice deficient in one or both genes. The TCR-alpha-/-, lpr/lpr mice had a nearly 10-fold increase in total lymph node cell (LNC) number compared with Fas-intact TCR-alpha-/- mice, because of expansion of TCR-gamma/delta+ and TCR-beta+ cells. In Fas-intact TCR-alpha-/- mice, approximately one third of the LNCs expressed TCR-gamma/delta. These were evenly divided between the CD4-, CD8-alpha+ and the CD4-, CD8- subsets, and rarely expressed the B220 epitope of CD45. In contrast, in TCR-alpha-/-, lpr/lpr mice, TCR-gamma/delta+ cells comprised half of the LNCs and were primarily CD4-, CD8-, and B220+. Moreover, Fas deficiency in TCR-alpha-/- mice caused a preferential expansion of gamma/delta T cells expressing variable region genes characteristic of intestinal intraepithelial lymphocytes. These results demonstrate a role for Fas in regulating the gamma/delta T cell contribution to peripheral lymph nodes. This mechanism may be most important in limiting the access of activated intestinal intraepithelial lymphocytes to the peripheral lymphoid system.

Animals↗
PubMed2000

Wild-type huntingtin reduces the cellular toxicity of mutant huntingtin in vivo.

We have developed yeast artificial chromosome (YAC) transgenic mice expressing normal (YAC18) and mutant (YAC46 or YAC72) human huntingtin (htt), in a developmental- and tissue-specific manner, that is identical to endogenous htt. YAC72 mice develop selective degeneration of medium spiny projection neurons in the lateral striatum, similar to what is observed in Huntington disease. Mutant human htt expressed by YAC transgenes can compensate for the absence of endogenous htt and can rescue the embryonic lethality that characterizes mice homozygous for targeted disruption of the endogenous Hdh gene (-/-). YAC72 mice lacking endogenous htt (YAC72 -/-) manifest a novel phenotype characterized by infertility, testicular atrophy, aspermia, and massive apoptotic cell death in the testes. The testicular cell death in YAC72 -/- mice can be markedly reduced by increasing endogenous htt levels. YAC72 mice with equivalent levels of both wild-type and mutant htt (YAC72 +/+) breed normally and have no evidence of increased testicular cell death. Similar findings are seen in YAC46 -/- mice compared with YAC46 +/+ mice, in which wild-type htt can completely counteract the proapoptotic effects of mutant htt. YAC18 -/- mice display no evidence of increased cellular apoptosis, even in the complete absence of endogenous htt, demonstrating that the massive cellular apoptosis observed in YAC46 -/- mice and YAC72 -/- mice is polyglutamine-mediated toxicity from the mutant transgene. These data provide the first direct in vivo evidence of a role for wild-type htt in decreasing the cellular toxicity of mutant htt.

Animals↗
PubMed2003

Characterization of gag gene of plasma HIV type 1 in combination therapy-treated AIDS patients with high viral load and stable CD4+ T cell counts.

Many AIDS patients retain a high CD4+ T cell count despite a significant increase in polymerase chain reaction (PCR)-determined viral load after various periods of treatment by combination therapy. Our study involved 10 such AIDS patients who showed this discordance. In this study, we characterized changes in the gag gene of HIV-1 isolated from the plasma of such patients. Viral RNA was extracted from plasma samples and the gag gene was amplified by reverse transcription-PCR. The PCR product was cloned and three clones from each patient were sequenced. All the sequences were aligned and compared with similar HIV-1 isolated from nontreated AIDS patients. Several kinds of changes were observed in the sequences including substitutions, frameshifts, and deletions. One patient showed a frameshift due to a missing G residue in the capsid-encoding region of the gene whereas another patient had virus with two different deletions. Such changes are probably due to combination therapy.

Amino Acid Sequence↗
PubMed2005

Heterosexual transmission of novel CRF01_AE and subtype B recombinant forms of HIV type 1 in northern Thailand.

The increased proportion of CRFO1_AE/subtype B recombinant infections among injecting drug users raised a concern that such recombinant forms may also spread in a heterosexual population in Thailand. Using the BootScan method, we reanalyzed pol gene sequences among 114 heterosexually infected individuals in northern Thailand, who were tested for a drug-resistance genotype between July 2000 and July 2001. Two individuals were suspected of carrying a recombinant HIV-1. Thus we analyzed a nearly full-length HIV genome in the two individuals and their spouses. An identical recombinant form of CRF01_AE and subtype B was found in one couple, indicating that this recombinant virus was heterosexually transmitted. Interestingly, this recombinant form had multiple breakpoints in the core protein of Gag and both infected individuals had a high CD4+ cell count without antiretroviral therapy. CRFO1/subtype B recombinant forms exist in a heterosexual population in northern Thailand. Some recombinant virus may be associated with a slow rate of HIV disease progression.

Acquired Immunodeficiency Syndrome↗
PubMed2003

Hypoxia regulates assembly of cilia in suppressors of Tetrahymena lacking an intraflagellar transport subunit gene.

We cloned a Tetrahymena thermophila gene, IFT52, encoding a homolog of the Chlamydomonas intraflagellar transport protein, IFT52. Disruption of IFT52 led to loss of cilia and incomplete cytokinesis, a phenotype indistinguishable from that of mutants lacking kinesin-II, a known ciliary assembly transporter. The cytokinesis failures seem to result from lack of cell movement rather than from direct involvement of ciliary assembly pathway components in cytokinesis. Spontaneous partial suppressors of the IFT52 null mutants occurred, which assembled cilia at high cell density and resorbed cilia at low cell density. The stimulating effect of high cell density on cilia formation is based on the creation of pericellular hypoxia. Thus, at least under certain conditions, ciliary assembly is affected by an extracellular signal and the Ift52p function may be integrated into signaling pathways that regulate ciliogenesis.

Algal Proteins↗
PubMed2026

shinyDeepGxP: a user-friendly R shiny app for predicting surface protein abundance from scRNA-seq expression using deep learning in blood cells.

MOTIVATION: Understanding accurate immune cell heterogeneity and function in single-cell datasets requires access to protein-level information, which is often unavailable due to experimental limitations. RESULTS: We present shinyDeepGxP, an interactive web application featuring our deep learning model, DeepGxP, for predicting surface protein abundance from single-cell RNA-sequencing (scRNA-seq) data. This platform makes DeepGxP accessible to researchers without programming skills. Users can upload scRNA-seq count matrices and use "Predict Protein" to predict the abundance of 224 biologically relevant surface proteins. shinyDeepGxP provides visualizations to help identify distinct cell populations based on predicted protein profiles. Moreover, users can choose "Explore Model" to reveal key RNA predictors and their associated biological pathways for each protein. Overall, shinyDeepGxP is a user-friendly, freely available web tool that provides protein-level detail for RNA-only single-cell datasets, enabling multimodal discovery without additional experiments. AVAILABILITY AND IMPLEMENTATION: shinyDeepGxP can be launched on https://shiny.crc.pitt.edu/deepgxp/.

Journal Article↗
PubMed1999

Apolipoprotein E peptide stimulation of rat ovarian theca cell androgen synthesis is mediated by members of the low density lipoprotein receptor superfamily.

Ovarian androgen production is rate limiting for follicular maturation and can induce follicular atresia. Thus, it is important to define the actions of the intraovarian agents, such as apolipoprotein (apo) E, that modulate theca cell androgen production. Theca cell androgen production is stimulated at low concentrations and inhibited at higher concentrations of native apo E. The apo E peptide, acetyl-Y(LRKLRKRLLRDADDL)(2)C or acetyl-Y(141-155)(2)C, has low density lipoprotein (LDL) receptor and LDL receptor-related protein-binding activity, and it mimics the activity of native apo E in the theca-interstitial cell system. To define the role of members of the LDL receptor superfamily in the apo E peptide-mediated responses, we found that receptor-associated protein prevented the stimulation without altering the inhibition of androstenedione production. The apo E peptide (129-162), which has no LDL receptor-binding activity, did not stimulate androstenedione production. The apo E peptide acetyl-Y(141-155)(2)C did not stimulate androstenedione production when cell surface heparan sulfate proteoglycans were degraded with heparinase. The apo E peptide acetyl-Y(141-155)(2)C bound to heparin, a property of LDL receptor ligands, and in this complex the peptide had no effect on androstenedione production. These observations support the conclusion that apo E-mediated stimulation, but not inhibition, of ovarian theca cell androstenedione production was mediated by members of the LDL receptor superfamily.

Amino Acid Sequence↗
PubMed2002

Co-expression of interleukin-5 influences replication of simian/human immunodeficiency viruses in vivo.

The positive effect of the co-expression of T helper (Th) cell type 2 cytokine interleukin-5 (IL-5) on nef-deleted simian/human immunodeficiency virus (SHIV) replication in vitro has been observed previously. To analyse whether the growth advantage of IL-5-containing SHIV (NI-IL5) in vitro would be relevant in vivo, the virus was inoculated into monkeys. Three rhesus macaques were inoculated intravenously with 10(4) TCID(50) of NI-IL5. Results were compared with those obtained previously from SHIV NM-3rN (intact) and SHIV-dn (nef-deleted)-infected monkeys. Cytokine production, analysed by IL-5 ELISA, showed a twofold increase in IL-5 concentration in the plasma soon after the peak of virus replication. Virus replication and antibody production were greater in monkeys inoculated with IL-5-expressing SHIV than in monkeys inoculated with nef-deleted SHIV without IL-5. These findings show a stimulation of SHIV replication by co-expression of IL-5 and suggest the important role of Th2-type cytokines in human immunodeficiency virus type 1 infection.

Animals↗
PubMed1992

Translational activation of the non-AUG-initiated c-myc 1 protein at high cell densities due to methionine deprivation.

c-myc belongs to a small, yet growing, group of eukaryotic mRNAs that initiate translation inefficiently from a non-AUG codon upstream from a more efficient AUG codon. We have examined the translational regulation of non-AUG-initiated c-myc 1 and AUG-initiated c-myc 2 protein synthesis in avian and mouse cells during proliferation. As lymphoid, erythroid, and embryo fibroblast cells approached high densities in culture, there was a sustained 5- to 10-fold induction in the synthesis of c-myc 1 protein to levels greater than or equal to c-myc 2 protein synthesis. Treatment with conditioned/depleted media from high-density cells was able to reproduce this activation in low-density cells within 5 hr. Additional studies with the conditioned/depleted media revealed that amino acid availability, specifically methionine deprivation, was responsible for this unique translational control. Our results describe a specific and dramatic regulation of dual translational initiation. Furthermore, these results represent a novel translational activation of a specific gene in higher eukaryotes in response to nutrient deprivation.

Amino Acid Sequence↗
PubMed2006

Quantification of mcrA by quantitative fluorescent PCR in sediments from methane seep of the Nankai Trough.

A quantitative fluorogenic PCR method for group-specific methyl coenzyme M reductase subunit A genes (mcrA) from methanotrophic archaea was established and applied to the characterization of microbial communities in anoxic methane seep sediments at the accretionary prism of the Nankai Trough. All of the previously identified subgroups of anaerobic methanotroph (ANME) mcrA genes were detected in the cores up to 25 cm below the seafloor, but distributional patterns of mcrA genes were found to differ according to depth. These findings suggest a distinct distribution of phylogenetically and physiologically diverse methanotrophic archaea that mediate methane oxidation in the anoxic sediments. This quantification method will contribute to future investigations of methanotrophic microbial ecosystems in anoxic marine sediments.

Anaerobiosis↗
PubMed2006

Differences in structure and dynamics of Polynucleobacter communities in a temperate and a subtropical lake, revealed at three phylogenetic levels.

The results of ecological studies investigating bacteria by cultivation-independent methods are expected to be influenced by the phylogenetic resolution of the applied molecular tools. This potential influence was investigated in a comparative community study on Polynucleobacter cluster bacteria (Betaproteobacteria) inhabiting the pelagic of the large, shallow, partially hypertrophic Taihu Lake located in subtropical East Asia, and the deep oligo-mesotrophic Lake Mondsee located in temperate Central Europe. The two contrasting habitats were sampled over the same period of 12 months. The community dynamics were investigated at three phylogenetic levels by fluorescent in situ hybridizations with a set of nested probes specific for the beta II clade (including the Polynucleobacter cluster), the genus-like monophyletic Polynucleobacter cluster, and four species-like subclusters. Subcluster B was the numerically dominating subcluster in both lakes over the investigation periods, but demonstrated different population dynamics in the two habitats. Interhabitat comparisons of the Polynucleobacter community structure in the two lakes in the study, and a previously investigated acidic pond indicated ecological diversification within the phylogenetically narrow Polynucleobacter cluster. These results could be obtained by help of the subcluster-specific probes, but would have been missed with probes of a lower phylogenetic resolution.

Austria↗
PubMed1996

Simultaneous pharmacodynamic analysis of the lag and bactericidal phases exhibited by beta-lactams against Escherichia coli.

Antibiotic-bacterium interactions are complex in nature. In many cases, bacterial killing does not commence immediately after the addition of an antibiotic, and a lag period is observed. Antibiotic permeation and/or the intermediate steps that exist between antibiotic-receptor binding and expression of cell death are two major possible causes for such lag period. This study was primarily designed to determine the relationship, if any, between antibiotic concentrations and the lag periods by a modeling approach. Short-term time-kill studies were conducted for amoxicillin, ampicillin, penicillin-G, oxacillin, and dicloxacillin against Escherichia coli. In conjunction with the use of a saturable rate model to describe the concentration-dependent killing process, a first-order induction (initiation) rate constant was used to characterize the delay in bacterial killing during the lag period. For all of the beta-lactams tested, parameters describing the bactericidal effect suggest that amoxicillin and ampicillin were much more potent than oxacillin and dicloxacillin. The induction rate constant estimates for both ampicillin and amoxicillin were found to relate linearly to concentrations. Nevertheless, these induction rate constant estimates were lower for penicillin-G, oxacillin, and dicloxacillin and increased nonlinearly with concentrations until an apparent plateau was observed. These findings support the hypothesis that the permeation process is potentially a rate-limiting step for the rapid bactericidal beta-lactams such as ampicillin and amoxicillin. However, as suggested by previous observations of the various morphological changes induced by beta-lactams, the contribution of the steps following antibiotic-receptor complex formation to the lag period might be significant for the less bactericidal antibiotics such as oxacillin and dicloxacillin. Findings from the present modeling approach can potentially be used to guide future bench experimentation.

Anti-Bacterial Agents↗