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At least 1,423 records · Page 79Linked to original sources
PubMed2004

Germ cell-autonomous Wunen2 is required for germline development in Drosophila embryos.

In many animals, primordial germ cells (PGCs) migrate through the embryo towards the future gonad, a process guided by attractive and repulsive cues provided from surrounding somatic cells. In Drosophila, the two related lipid phosphate phosphatases (LPPs), Wunen (Wun) and Wun2, are thought to degrade extracellular substrates and to act redundantly in somatic cells to provide a repulsive environment to steer the migration of PGCs, or pole cells. Wun and Wun2 also affect the viability of pole cells, because overexpression of either one in somatic cells causes pole cell death. However, the means by which they regulate pole cell migration and survival remains elusive. We report that Wun2 has a maternal function required for the survival of pole cells during their migration to the gonad. Maternal wun2 RNA was found to be concentrated in pole cells and pole cell-specific expression of wun2 rescued the pole cell death phenotype of the maternal wun2 mutant, suggesting that wun2 activity in pole cells is required for their survival. Furthermore, we obtained genetic evidence that pole cell survival requires a proper balance of LPP activity in pole cells and somatic cells. We propose that Wun2 in pole cells competes with somatic Wun and Wun2 for a common lipid phosphate substrate, which is required by pole cells to produce their survival signal. In somatic cells, Wun and Wun2 may provide a repulsive environment for pole cell migration by depleting this extracellular substrate.

Animals↗
PubMed1999

Acute intrahippocampal injection of human interleukin-1beta stimulates the anterior pituitary POMC transcription and increases plasma levels of ACTH and corticosterone in the male rat.

It has been well documented that interleukin-1beta (IL-1beta) is a major mediator for recruiting the hypothalamo-pituitary-adrenal (HPA) axis following infectious disease. The recent localization of IL-1beta receptors in neurons of the hippocampus provides further support for the role of IL-1beta as a neurotransmitter/neuromodulator in the central nervous system. In this study, we investigated whether an acute intrahippocampal injection of IL-1beta is able to rapidly stimulate HPA activity. Seven days after bilateral implantation of a guide cannula into the hippocampus, human IL-1beta (10 ng/0.5 microliter/side) was injected to freely moving male rats. Following this, animals were sacrificed at times 20, 45 and 90 min postinjection and a kinetic analysis of hIL-1beta action on plasma ACTH and corticosterone (CORT) concentrations and nuclear processing of the anterior pituitary (AP) proopiomelanocortin (POMC) was conducted. Intrahippocampal administration of hIL-1beta significantly increased both plasma ACTH and CORT concentrations at 45 and 90 min postinjection. This increase in ACTH concentration paralleled a rise in AP POMC gene transcription. Moreover, the increase in AP POMC primary transcript was followed by an increase in AP POMC intermediate processing RNA. However, at these times, no significant hIL-1beta effect on the level of AP nuclear POMC mRNA was observed. Almost identical results were obtained after intraperitoneal injection of hIL-1beta. In conclusion, our data demonstrates that the hippocampal IL-1beta/IL-1beta receptor is directly and rapidly implicated in HPA activation, in the same manner as that observed after intraperitoneal administration of hIL-1beta. These results show that IL-1 action in the hippocampus could be of immunoneuroendocrine significance for the HPA axis activation during inflammatory states.

Adrenocorticotropic Hormone↗
PubMed2026

Aqueous humour extracellular vesicle membrane protein profiling reveals pathological features of refractory macular edema.

BACKGROUND: Both diabetic macular edema (DME) and retinal vein occlusion-related macular edema (RVO-ME) can become refractory to anti-vascular endothelial growth factor (anti-VEGF) therapy, but the underlying mechanisms are unclear. Molecular discrimination of refractory disease could guide personalized treatment. This study examined whether aqueous humor-derived extracellular vesicle (EV) membrane proteins can characterize refractoriness and reveal etiology-specific pathways. METHODS: This prospective cohort study included 28 patients with DME or RVO-ME (14 each), further divided into treatment-naïve and refractory subgroups. Aqueous humour samples were collected before intravitreal anti-VEGF injection. EV membrane proteins were profiled using an EV Array chip targeting 435 antibodies. Differentially expressed proteins were analyzed by bioinformatics, including Gene Ontology, Kyoto encyclopaedia of genes and genomes (KEGG) pathway enrichment, Gene set enrichment analysis (GSEA), and cell-of-origin mapping using public single-cell RNA-seq data. RESULTS: VEGF/VEGFR2 were elevated in treatment-naïve DME and RVO-ME. Refractory DME showed upregulation of C5 and CD34 (complement/immune activation). Refractory RVO-ME exhibited increased CD68 and Annexin A1 with decreased PDGFR (chronic inflammation, vascular dysregulation). RANTES was commonly upregulated in refractory disease. Several EV proteins discriminated refractory cases with high accuracy (AUC 0.898-0.980). Cellular origin suggested immune cell-derived EVs in DME, retinal cell-derived EVs in RVO-ME. External validation confirmed key differences. CONCLUSION: Refractory ME involves distinct pathways: immune-inflammatory activation in DME versus chronic inflammation with vascular dysregulation in RVO-ME. EV membrane proteins from aqueous humor provide insights into therapeutic resistance and hold promise as biomarkers for personalized treatment decisions.

artificial intelligence↗
PubMed2001

Identification of a novel lipopolysaccharide-inducible gene with key features of both A kinase anchor proteins and chs1/beige proteins.

Mutations in chs1/beige result in a deficiency in intracellular transport of vesicles that leads to a generalized immunodeficiency in mice and humans. The function of NK cells, CTL, and granulocytes is impaired by these mutations, indicating that polarized trafficking of vesicles is controlled by CHS1/beige proteins. However, a molecular explanation for this defect has not been identified. Here we describe a novel gene with orthologues in mice, humans, and flies that contains key features of both chs1/beige and A kinase anchor genes. We designate this novel gene lba for LPS-responsive, beige-like anchor gene. Expression of lba is induced after LPS stimulation of B cells and macrophages. In addition, lba is expressed in many other tissues in the body and has three distinct mRNA isoforms that are differentially expressed in various tissues. Strikingly, LBA-green-fluorescent protein (GFP) fusion proteins are localized to vesicles after LPS stimulation. Confocal microscopy indicates this protein is colocalized with the trans-Golgi complex and some lysosomes. Further analysis by immunoelectron microscopy demonstrates that LBA-GFP fusion protein can localize to endoplasmic reticulum, plasma membrane, and endocytosis vesicles in addition to the trans-Golgi complex and lysosomes. We hypothesize that LBA/CHS1/BG proteins function in polarized vesicle trafficking by guiding intracellular vesicles to activated receptor complexes and thus facilitate polarized secretion and/or membrane deposition of immune effector molecules.

Adaptor Proteins, Signal Transducing↗
PubMed2004

Management of hepatitis B patients with antiviral resistance.

Drug resistance is an expected consequence of antiviral therapy for chronic hepatitis B because of the high rate of hepatitis B virus (HBV) replication, the lack of proof-reading during reverse transcription of the pregenomic RNA and the low efficacy of available therapies in eliminating covalently closed circular HBV DNA. Mutations involving the YMDD motif of the catalytic domain of HBV reverse transcriptase have been reported in patients who have received lamivudine, emtricitabine and telbivudine. Drug-resistant mutations affecting other regions of HBV polymerase have also been reported, but at much lower rates in patients who have received adefovir dipivoxil or entecavir. Antiviral resistance is initially manifested as virological breakthrough infection. In most patients, this is followed by biochemical breakthrough and, in some patients, hepatitis flares and hepatic decompensation. Monitoring drug resistance may improve the management of patients with antiviral-resistant HBV and can guide the selection of salvage therapy. The optimal management of patients with antiviral-resistant HBV continues to evolve. The ideal approach is to prevent antiviral resistance through judicious use of antiviral therapy and the use of more potent antiviral agents, possibly in combination.

Antiviral Agents↗
PubMed2005

Improved spliced alignment from an information theoretic approach.

MOTIVATION: mRNA sequences and expressed sequence tags represent some of the most abundant experimental data for identifying genes and alternatively spliced products in metazoans. These transcript sequences are frequently studied by aligning them to a genomic sequence template. For existing programs, error-prone, polymorphic and cross-species data, as well as non-canonical splice sites, still present significant barriers to producing accurate, complete alignments. RESULTS: We took a novel approach to spliced alignment that meaningfully combined information from sequence similarity with that obtained from PSSM splice site models. Scoring systems were chosen to maximize their power of discrimination, and dynamic programming (DP) was employed to guarantee optimal solutions would be found. The resultant program, EXALIN, performed better than other popular tools tested under a wide range of conditions that included detection of micro-exons and human-mouse cross-species comparisons. For improved speed with only a marginal decrease in splice site prediction accuracy, EXALIN could perform limited DP guided by a result from BLASTN. AVAILABILITY: The source code, binaries, scripts, scoring matrices and splice site models for human, mouse, rice and Caenorhabditis elegans utilized in this study are posted at http://blast.wustl.edu/exalin. The software (scripts, source code and binaries) is copyrighted but free for all to use.

Algorithms↗
PubMed2007

Clear cell sarcoma of tendons and aponeuroses: a review.

Clear cell sarcoma of tendons and aponeuroses, also referred to as malignant melanoma of soft parts, is a rare malignancy derived from neural crest cells. It usually presents in the distal lower extremities of young adults, frequently attached to tendons or aponeuroses. It behaves like a high-grade soft tissue sarcoma and is associated with poor overall survival. Magnetic resonance imaging studies of the lesion reveal T1 hypointensity, T2 hyperintensity, and gadolinium uptake. Grossly, the tumor is usually circumscribed with a histologic pattern of uniform polygonal to fusiform cells with clear to pale eosinophilic cytoplasm divided into variably sized clusters by fibrous septa. Immunohistochemical studies in most cases show that the neoplastic cells are positive with HMB-45 and react with antibody against S100 protein. Most cases show a reciprocal cytogenetic translocation t(12;22)(q13;q12) that creates a unique chimeric fusion EWSR1/ATF1 gene transcript. Metastasis occurs mainly to regional lymph nodes and lungs. Poor prognostic indicators include a tumor size equal to or more than 5 cm, presence of metastasis, and necrosis. The mainstay of treatment is wide excision of the tumor. The use of sentinel lymph node biopsy may become an important procedure in detecting occult regional metastasis and guiding the extent of surgery. The beneficial effects of adjuvant chemotherapy and radiotherapy have not been fully evaluated. This article provides a short overview of the current knowledge of clear cell sarcoma of tendons and aponeuroses.

Activating Transcription Factor 1↗
PubMed1991

Splice site selection and role of the lariat in a group II intron.

The structural elements involved in 5' and 3' splice site (SS) selection in a group II intron were analyzed. While 5' SS selection appears to be defined by only one element, the EBS1-IBS1 pairing, four distinct structural components contribute to 3' SS selection, one of which being analogous to the "internal guide sequence" described for group I introns. Moreover, some of the mutants analyzed during this study induce efficient 5' SS hydrolysis and suggest how 5' SS transesterification is selected against hydrolysis. Finally, the lariat structure was found to accelerate both steps of splicing, suggesting that it "locks" the ribozyme in an active configuration.

Base Sequence↗
PubMed2004

Non-peptidic small-molecule inhibitors of the single-chain hepatitis C virus NS3 protease/NS4A cofactor complex discovered by structure-based NMR screening.

NMR-based screening of a customized fragment library identified 16 small-molecule hits that bind weakly (K(D) approximately 100 microM to 10 mM) to substrate binding sites of the NS4A-bound NS3 protease of the hepatitis C virus (HCV). Analogues for five classes of NMR hits were evaluated by a combination of NMR and biochemical data yielding SAR and, in most cases, optimized hits with improved potencies (K(D) approximately K(I) approximately 40 microM to 1 mM). NMR chemical shift perturbation data were used to establish the binding location and orientation of the active site directed scaffolds in these five analogue series. Two of these scaffolds, which bind the enzyme at the proximal S1-S3 and S2' substrate binding sites, were linked together producing competitive inhibitors of the HCV NS3 protease with potencies in the micromolar range. This example illustrates that the low molecular weight scaffolds discovered from structure-based NMR screening can be optimized with focused structure-guided chemistry to produce potent nonpeptidic small-molecule inhibitors of the HCV NS3 protease.

Anilides↗
PubMed2004

AdoMet radical proteins--from structure to evolution--alignment of divergent protein sequences reveals strong secondary structure element conservation.

Eighteen subclasses of S-adenosyl-l-methionine (AdoMet) radical proteins have been aligned in the first bioinformatics study of the AdoMet radical superfamily to utilize crystallographic information. The recently resolved X-ray structure of biotin synthase (BioB) was used to guide the multiple sequence alignment, and the recently resolved X-ray structure of coproporphyrinogen III oxidase (HemN) was used as the control. Despite the low 9% sequence identity between BioB and HemN, the multiple sequence alignment correctly predicted all but one of the core helices in HemN, and correctly predicted the residues in the enzyme active site. This alignment further suggests that the AdoMet radical proteins may have evolved from half-barrel structures (alphabeta)4 to three-quarter-barrel structures (alphabeta)6 to full-barrel structures (alphabeta)8. It predicts that anaerobic ribonucleotide reductase (RNR) activase, an ancient enzyme that, it has been suggested, serves as a link between the RNA and DNA worlds, will have a half-barrel structure, whereas the three-quarter barrel, exemplified by HemN, will be the most common architecture for AdoMet radical enzymes, and fewer members of the superfamily will join BioB in using a complete (alphabeta)8 TIM-barrel fold to perform radical chemistry. These differences in barrel architecture also explain how AdoMet radical enzymes can act on substrates that range in size from 10 atoms to 608 residue proteins.

Amino Acid Sequence↗
PubMed1991

Cell-cycle specific cytotoxicity mediated by stizophyllin (2 alpha,3 beta,12 beta-trihydroxypregna-4,7,16-trien-20-one), a novel electrophilic pregnane isolated from Stizophyllum riparium.

A structurally-novel pregnane derivative, 2 alpha,3 beta,12 beta-trihydroxypregna-4,7,16-trien-20-one (stizophyllin), was isolated from an extract of Stizophyllum riparium (H.B.K.) Sandw. on the basis of bioactivity-guided fractionation and confirmed to mediate a potent cytotoxic response with cultured P-388 cells. We presently report a detailed isolation procedure and the results of studies designed to examine its mechanism of action. By means of a Michael-type addition, stizophyllin formed adducts with nucleophilic substances such as L-cysteine and beta-mercaptoethanol. The adduct with beta-mercaptoethanol was isolated, structurally characterized, and found to be 20-fold less cytotoxic than stizophyllin. Stizophyllin interacted with DNA, but no mutagenicity was observed with Salmonella typhimurium strain TM677 or cultured Chinese hamster ovary cells, and no in vitro reaction occurred with guanosine. Relative to control cell cultures, the total biosynthesis of DNA, RNA or protein was reduced when P-388 cells were treated with stizophyllin. However, the cell number did not increase in the presence of inhibitory stizophyllin concentrations (e.g., 4 micrograms/ml), and the DNA content (per cell) actually doubled after approximately 48 h. Consistent with this, stizophyllin blocked the cells in the G2 + M compartment of the cycle, and the block appeared to be specific for the G2 phase. Accordingly, stizophyllin did not modulate in vitro tubulin polymerization reactions nor did it affect the morphology of dibutyryl cAMP-treated astrocytoma cells in culture. These data suggest that the cytotoxic activity of stizophyllin is mediated by covalent reaction with a cellular component (such as a sulfhydryl-containing protein) by means of a Michael-type addition. Based on the cell-cycle specificity of the response, it appears that this interaction prevents the cells from progressing through mitosis.

Animals↗
PubMed2000

A concise guide to cDNA microarray analysis.

Microarray expression analysis has become one of the most widely used functional genomics tools. Efficient application of this technique requires the development of robust and reproducible protocols. We have optimized all aspects of the process, including PCR amplification of target cDNA clones, microarray printing, probe labeling and hybridization, and have developed strategies for data normalization and analysis.

DNA, Complementary↗
PubMed1999

Characterization of the Azoarcus ribozyme: tight binding to guanosine and substrate by an unusually small group I ribozyme.

We report novel chemical properties of the ribozyme derived from the smallest group I intron (subgroup IC3) that comes from the pre-tRNA(Ile) of the bacterium Azoarcus sp. BH72. Despite the small size of the Azoarcus ribozyme (195 nucleotides (nt)), it binds tightly to the guanosine nucleophile (Kd = 15 +/- 3 microM) and exhibits activity at high temperatures (approximately 60-70 degrees C). These features may be due to the two GA3 tetraloop interactions postulated in the intron and the high GC content of the secondary structure. The second order rate constant for the Azoarcus ribozyme, ((k(cat)/Km)S = 8.4 +/- 2.1 x 10(-5) M(-1) min(-1)) is close to that found for the related ribozyme derived from the pre-tRNA(Ile) of the cyanobacterium Anabaena PCC7120. pH dependence studies and kinetic analyses of deoxy-substituted substrates suggest that the chemical cleavage step is the rate-determining process in the Azoarcus ribozyme. This may be due to the short 3-nt guide sequence-substrate pairing present in the Azoarcus ribozyme. Finally, the Azoarcus ribozyme shares features conserved in other group I ribozymes including the pH profile, the stereospecificity for the Rp-phosphorothioate at the cleavage site and the 1000-fold decrease in cleavage rate with a deoxyribonucleoside leaving group.

Azoarcus↗
PubMed2005

Gene-expression profiling predicts recurrence in Dukes' C colorectal cancer.

BACKGROUND & AIMS: Although approximately 50% of Dukes' C colorectal cancer patients are surgically cured, it is currently not possible to distinguish these patients from those at high risk of recurrence. The recent advent of routine adjuvant chemotherapy for these patients has greatly complicated the identification of new markers predicting the response to surgery, which is now reliant on archived materials. Microarray analysis allows fine tumor classification but cannot be used with paraffin-embedded archival samples. METHODS: We used microarray analysis of a unique set of fresh-frozen tumor samples from Dukes' C patients who had surgery as the only form of treatment to identify molecular signatures that characterize tumors from patients with good and bad prognosis. RESULTS: Unsupervised hierarchical clustering and a K-nearest neighbors-based classifier identified groups of patients with significantly different survival (P = .019 and P = .0001). Expression profiling outperformed previously reported genetic markers of prognosis such as TP53 and K-RAS mutational status and allelic imbalance in chromosome 18q, which were of limited prognostic power in this study. Functional categories significantly enriched in gene-expression differences included protein transport and folding. The prognostic potential of the RAS homologue RHOA, one of the most differentially expressed genes, was further investigated using immunohistochemistry and a tissue microarray containing 137 independent Dukes' C tumor samples. Reduced RHOA expression was associated with significantly shorter survival (P = .01). CONCLUSIONS: This study shows that gene-expression profiling of surgical tumor samples can predict recurrence in Dukes' C patients. Therefore, this approach could be used to guide decisions concerning the clinical management of these patients.

Aged↗
PubMedDate not supplied

mRNA Metabolism and hereditary disorders: a tale of surveillance and escape.

The exploration of the molecular origin of hereditary diseases focused on genes and proteins for many years. Recently, mRNA has gained increasing attention. Most human genes contain introns and a considerable proportion of transcripts are not only alternatively spliced but also regulated posttranscriptionally in manifold ways. mRNA processing as well as a complex network of interactions between the steps of gene expression and associated quality control mechanisms are guided by a multitude of regulative mRNA sequence elements. Therefore it is not surprising that mutations of such elements can cause or modify human disease. The purpose of this review is the illustration of principles of physiological and dysregulated mRNA metabolism as well as a survey of new analytical tools and therapeutic approaches.

Base Sequence↗
PubMed2006

Characterization of the retinoic acid receptor genes raraa, rarab and rarg during zebrafish development.

Retinoic acid signaling is important for patterning the central nervous system, paired appendages, digestive tract, and other organs. To begin to investigate retinoic acid signaling in zebrafish, we determined orthologies between zebrafish and tetrapod retinoic acid receptors (Rars) and examined the expression patterns of rar genes during embryonic development. Analysis of phylogenies and conserved syntenies showed that the three cloned zebrafish rar genes include raraa and rarab, which are co-orthologs of tetrapod Rara, and rarg, which is the zebrafish ortholog of tetrapod Rarg. We did not, however, find an ortholog of Rarb. RNA in situ hybridization experiments showed that rarab and rarg, are maternally expressed. Zygotic expression of raraa occurs predominantly in the hindbrain, lateral mesoderm, and tailbud. Zygotic expression of rarab largely overlaps that of raraa, except that in later stages rarab is expressed more broadly in the brain and in the pectoral fin bud and pharyngeal arches. Zygotic expression of zebrafish rarg also overlaps the other two genes, but it is expressed more strongly in the posterior hindbrain beginning in late somitogenesis as well as in neural crest cells in the pharyngeal arches. Thus, these three genes have largely overlapping expression patterns and a few gene-specific expression domains. Knowledge of these expression patterns will guide the interpretation of the roles these genes play in development.

Animals↗
PubMed2006

Identification of candidate genes at the corticoseptal boundary during development.

Cortical midline glia are critical to the formation of the corpus callosum during development. The glial wedge is a population of midline glia that is located at the corticoseptal boundary and expresses repulsive/growth-inhibitory molecules that guide callosal axons as they cross the midline. The glial wedge are the first cells within the cortex to express GFAP and thus may express molecules specific for glial maturation. The corticoseptal boundary is a genetically defined boundary between the cingulate cortex (dorsal telencephalon) and the septum (ventral telencephalon). The correct dorso-ventral position of this boundary is vital to the formation of both the glial wedge and the corpus callosum. Our aim was to identify genes expressed specifically within the glial wedge that might be involved in either glial differentiation, formation of the corticoseptal boundary or development of the corpus callosum. To identify such genes we have performed a differential display PCR screen comparing RNA isolated from the glial wedge with RNA isolated from control tissues such as the neocortex and septum, of embryonic day 17 mouse brains. Using 200 different combinations of primers, we identified and cloned 67 distinct gene fragments. In situ hybridization analysis confirmed the differential expression of many of the genes, and showed that clones G24F3, G39F8 and transcription factor LZIP have specific expression patterns in the telencephalon of embryonic and postnatal brains. An RNase Protection Assay (RPA) revealed that the expression of G39F8, G24F3 and LZIP increase markedly in the telencephalon at E16 and continue to be expressed until at least P0, during the period when the corpus callosum is forming.

Animals↗
PubMed2003

Palaeoceanographic implications of genetic variation in living North Atlantic Neogloboquadrina pachyderma.

The shells of the planktonic foraminifer Neogloboquadrina pachyderma have become a classical tool for reconstructing glacial-interglacial climate conditions in the North Atlantic Ocean. Palaeoceanographers utilize its left- and right-coiling variants, which exhibit a distinctive reciprocal temperature and water mass related shift in faunal abundance both at present and in late Quaternary sediments. Recently discovered cryptic genetic diversity in planktonic foraminifers now poses significant questions for these studies. Here we report genetic evidence demonstrating that the apparent 'single species' shell-based records of right-coiling N. pachyderma used in palaeoceanographic reconstructions contain an alternation in species as environmental factors change. This is reflected in a species-dependent incremental shift in right-coiling N. pachyderma shell calcite delta18O between the Last Glacial Maximum and full Holocene conditions. Guided by the percentage dextral coiling ratio, our findings enhance the use of delta18O records of right-coiling N. pachyderma for future study. They also highlight the need to genetically investigate other important morphospecies to refine their accuracy and reliability as palaeoceanographic proxies.

Animals↗