Biomedical subjects

Y Xu

Publications and source records attributed to Y Xu.

At least 793 records · Page 44Linked to original sources

PubMed1997

Automated gene identification in large-scale genomic sequences.

Computational methods for gene identification in genomic sequences typically have two phases: coding region recognition and gene parsing. While there are a number of effective methods for recognizing coding regions (exons), parsing the recognized exons into proper gene structures, to a large extent, remains an unsolved problem. We have developed a computer program which can automatically parse the recognized exons into gene models that are most consistent with the available Expressed Sequence Tags (ESTs) and a set of biological heuristics, derived empirically. The gene modeling algorithm used in this program provides a general framework for applying EST information so the modeling accuracy improves as the amount of available EST information increases. Based on preliminary tests on a number of large DNA sequences, using the dbEST database, we have observed that the algorithm can (1) accurately model complicated multiple gene structures, including embedded genes, (2) identify falsely-recognized exons and locate missed exons by the initial exon recognition phase, and (3) make more accurate exon boundary predictions, if the necessary EST information is available. We have extended this EST-based gene modeling algorithm to model genes on unfinished DNA contigs at the end of the shotgun sequencing. This extended version can automatically determine the orientations and the relative order of the DNA contigs (with gaps between them) using the available ESTs as reference models, before the gene modeling phase.

Algorithms↗

PubMed1997

Cloning, expression, and chromosomal localization to 11p12-13 of a human LIM/HOMEOBOX gene, hLim-1.

We have identified a putative transcription factor, designated hLim-1, from human fetal brain using degenerate polymerase chain reaction (PCR) and cDNA library screening. The deduced open reading frame, derived from sequencing a 3.0-kb hLim-1 cDNA, encodes a protein of 384 amino acids with two cysteine-rich LIM domains and one homeobox (HOX) DNA-binding domain. The nucleotide sequence of hLim-1 cDNA is 87% identical to mouse Lim-1 and the predicted amino acid sequence is greater than 97% conserved. Expression patterns of hLim-1 were evaluated by Northern analysis and reverse transcription (RT)-PCR coupled with Southern blotting. HLim-1 expression was observed in human brain, thymus, and tonsillar tissue. Expression of hLim-1 was also observed in 58% of acute myelogenous leukemia (AML) cell lines and in four of five primary samples from patients with chronic myeloid leukemia (CML) in myeloid blast transformation. The gene encoding hLim-1 was mapped using fluorescence in situ hybridization (FISH) to human chromosome 11p12-13. The expression pattern and structural characteristics of the hLim-1 gene suggest that it encodes a transcriptional regulatory protein involved in the control of differentiation and development of neural and lymphoid cells. Its expression in CML in blast crisis suggests that it may be involved with progression in this disease; a prospective study is required to confirm this.

Amino Acid Sequence↗

PubMed1997

Effect of topical aclacinomycin on glaucoma filtration surgery in rabbits.

A prospective, randomized, double-masked and placebo-controlled study was performed to compare the effects of a single 5-minute intraoperative exposure to aclacinomycin (AMC) 0.4 mg/ml or 0.8 mg/ml with control eyes treated with saline solution on the success of glaucoma filtration surgery in 26 rabbits. Intraocular pressure (IOP), bleb survival, fistula patency and complications were evaluated. The results showed that IOP in the eyes treated with AMC was significantly lower than that in the control eyes from days 5-40 in the 0.4 mg/ml group and from days 5-20 in the 0.8 mg/ml group. The bleb survival lasted significantly longer in the two treated groups than in the control group and in the AMC 0.4 mg/ml group than in the AMC 0.8 mg/ml group. At 40 days, the rate of sclera fistula occlusion was 0% in the AMC 0.4 mg/ml eyes, 43.8% in the AMC 0.8 mg/ml eyes, and 100% in the control eyes. Significant complications, such as anterior chamber inflammation, hyphema, moderate and severe corneal haze, dense corneal neovascularization and mild cataract occurred only in the eyes treated with AMC 0.8 mg/ml. The results indicated that intraocular treatment with AMC at a dose of 0.4 mg/ml had a markedly beneficial effect on IOP, bleb appearance and fistula patency after experimental filtration surgery in rabbits.

Aclarubicin↗

PubMed1997

Homozygous alpha6 integrin mutation in junctional epidermolysis bullosa with congenital duodenal atresia.

Junctional epidermolysis bullosa with congenital pyloric or duodenal atresia is a distinct variant within this group of autosomal recessive blistering skin diseases. In this study we demonstrate, for the first time, a homozygous mutation in the alpha6 integrin gene (ITGA6) in a family with three affected individuals. For this purpose, we first determined the genomic organization of ITGA6, and placed the gene on chromosome 2q by high resolution radiation hybrid mapping. Heteroduplex analysis of PCR products containing the individual exons of ITGA6, followed by direct nucleotide sequencing, revealed that the proband was homozygous for a G-to-T transversion in the +1 position of intron 12. This mutation, 1856+1G-->T, affects an invariant base of the 5' donor splice site predicting aberrant splicing involving exon 12. The mutation was verified in the proband's DNA by restriction enzyme digestion which also confirmed that the parents were heterozygous carriers of this mutation. Altered expression of alpha6 integrin, which forms a heterodimer with the beta4 subunit at the dermal-epidermal junction, would explain fragility and blistering as a result of minor trauma to the skin.

Antigens, CD↗

PubMed1997

Antagonistic but complementary actions of phytochromes A and B allow seedling de-etiolation.

Using dichromatic radiation, we show that the actions of phytochromes A and B (phyA and phyB) in Arabidopsis thaliana are antagonistic in mediating red and far-red radiation effects on seedling de-etiolation and yet act in a complementary manner to regulate de-etiolation, irrespective of spectral composition. At low phytochrome photoequilibria inhibition of hypocotyl extension was strong, because of the action of a far-red high-irradiance response mediated by phyA. At high phytochrome photoequilibria inhibition of hypocotyl extension was also strong, because of the action of phyB. At intermediate photoequilibria hypocotyl inhibition was less strong. In their natural environment, this dual action will strongly retard hypocotyl growth and promote cotyledon opening and expansion both in open daylight and under dense vegetation. Overlapping action by phyA and phyB will substantially promote de-etiolation in sparse vegetation. The antagonistic and complementary actions of phyA and phyB, therefore, allow the optimum regulation of seedling growth after emergence from the soil.

Arabidopsis↗

PubMed1997

Predominance of the recurrent mutation R635X in the LAMB3 gene in European patients with Herlitz junctional epidermolysis bullosa has implications for mutation detection strategy.

Junctional forms of epidermolysis bullosa (JEB) are characterized by tissue separation at the level of the lamina lucida. We have recently disclosed specific mutations in the LAMA3, LAMB3, and LAMC2 genes encoding the subunit polypeptides of the anchoring filament protein laminin 5 in 66 families with different variants of JEB. Examination of the JEB mutation database revealed recurrence of a particular C-->T substitution at nucleotide position 1903 (exon 14) of LAMB3, resulting in the mutation R635X. The inheritance of this nonsense mutation was noted on different genetic backgrounds, suggesting that R635X is a hotspot mutation. In this study, we have performed mutation evaluation in a European cohort of 14 families with the lethal, Herlitz type of JEB (H-JEB). The families were first screened for the presence of the R635X mutation by restriction enzyme digestion of the PCR product corresponding to exon 14. Four of the probands were found to be homozygous and six were heterozygous for R635X. The remaining alleles were subjected to mutation screening by PCR amplification of individual exons of LAMB3 and LAMC2, followed by heteroduplex analysis and nucleotide sequencing. In three families (six alleles), mutations in LAMC2 were disclosed. In the remaining eight alleles, additional pathogenetic LAMB3 mutations were found. None of the patients had LAMA3 mutation. Thus, LAMB3 mutations accounted for 22 of 28 JEB alleles (79%), and a total of 14 of 22 LAMB3 alleles (64%) harbored the R635X mutation, signifying its prevalence as a predominant genetic lesion underlying H-JEB in this European cohort of patients. This recurrent mutation will facilitate screening of additional JEB patients for the purpose of prenatal testing of fetuses at risk for recurrence.

Antigens↗

PubMed1997

Sorting and secretion of a melanosome membrane protein, gp75/TRP1.

The melanosome is an organelle specialized for melanin synthesis that is derived from the endocytic pathway. Several melanosome membrane proteins have been identified, forming a family of proteins known as tyrosinase-related proteins. Two members of this family, tyrosinase and gp75, are well-characterized melanocyte differentiation antigens. Our previous studies have shown that gp75, the mouse brown locus protein, is sorted to melanosomes along the endocytic pathway, directed by a hexapeptide sorting signal located in the cytoplasmic tail. In this study, we report the unexpected finding that a portion of gp75 is secreted. Substantial levels of secretory gp75 were detected in melanocytic cells. Cell surface expression of gp75 was also detected, representing 2% of cellular gp75. Characterization of secretory gp75 cells showed that it is: (i) a truncated form that lacks the transmembrane region, the cytoplasmic tail where the endosomal sorting signal is located, and a small portion of the lumenal domain; (ii) more extensively glycosylated than endocytic/melanosomal gp75, containing trans-Golgi processed sugar residues; and (iii) generated post-translationally in an acid sensitive compartment after processing in the trans-Golgi, and secreted rapidly after generation. Thus, these endocytic/melanosomal membrane proteins can be processed to abundant secretory forms, probably in an endocytic compartment through a potentially novel secretory pathway.

Animals↗

PubMed1997

Triazine dyes inhibit HIV-1 entry by binding to envelope glycoproteins.

We have attempted to purify envelope (Env) glycoproteins of human immunodeficiency virus (HIV) from the culture supernatants of CHO-Sec cells that secreted truncated 140-kDa precursor and mature 120-kDa Env glycoproteins. The concentrated culture supernatants were applied to a column coupled with cibacron blue 3GA (CB3GA) to separate albumin from the Env proteins because CB3GA, a triazine dye, has been known to have a high affinity to albumin. Unexpectedly, Env proteins as well as albumin bound to the column, and the bound Env proteins were eluted by increasing the ionic strength using KCl. Gp120 was eluted at 0.5-0.9 M of KCl, while a higher concentration (0.9-1.5 M) was necessary for the elution of gp140. The agarose gel coupled with reactive red 120 (RR120), another triazine dye with similar characteristics, also retained both Env proteins, and the bound Env proteins could be eluted in a similar manner. In addition, these agents inhibited syncytium formation caused by HTLV-IIIB and HTLV-IIIMN. Inhibition was also seen when a virus-free fusion assay between Env protein expressed in CHO cells and fluorescent labeled SupT1 cells were used. These findings indicate that triazine dyes bind to the functional regions of Env proteins of HIV-1 that play important role(s) for HIV infection.

Albumins↗

PubMed1997

Enterococcus faecalis antigens in human infections.

Genomic libraries of two Enterococcus faecalis strains, OG1RF and TX52 (an isolate from an endocarditis patient), were constructed in cosmid vectors pBeloBAC11 and pLAFRx, and screened with a serum from a rabbit immunized with surface proteins of an E. faecalis endocarditis isolate and sera from four patients with enterococcal endocarditis. Seventy-five cosmid clones reacted with at least two of the sera. Thirty-eight of the 75 immunopositive clones were considered to contain distinct inserts based on their DNA restriction patterns and were chosen for further subcloning into a pBluescript vector. Each sublibrary was screened with one of the five sera, and the DNA sequence of the immunopositive subclones was determined. Analysis of these sequences revealed similarities to a range of proteins, including bacterial virulence factors, transporters, two-component regulators, metabolic enzymes, and membrane or cell surface proteins. Fourteen subclones did not show significant similarity to any sequence in the databases and may contain novel genes. Thirteen of the immunopositive cosmid clones did not yield immunopositive subclones, and one such cosmid clone produced a nonprotein antigen in Escherichia coli.

Antibodies, Bacterial↗

PubMed1997

The transcriptional regulator SoxS is required for resistance of Salmonella typhimurium to paraquat but not for virulence in mice.

In Escherichia coli, the SoxRS regulon is required for resistance to redox-cycling agents which elevate cytosolic superoxide levels, as well as for resistance to nitric oxide-dependent macrophage killing. In Salmonella typhimurium, SoxS is also required for enhanced expression of Mn-superoxide dismutase and resistance to paraquat, but not for resistance to nitric oxide donor compounds in vitro, resistance to macrophage killing, or virulence in mice. Differences in other antioxidant defense systems or compensation by homologous regulons may account for species-specific differences in the role of SoxS.

Animals↗

PubMed1997

Propanediol utilization genes (pdu) of Salmonella typhimurium: three genes for the propanediol dehydratase.

The propanediol utilization (pdu) operon of Salmonella typhimurium encodes proteins required for the catabolism of propanediol, including a coenzyme B12-dependent propanediol dehydratase. A clone that expresses propanediol dehydratase activity was isolated from a Salmonella genomic library. DNA sequence analysis showed that the clone included part of the pduF gene, the pduABCDE genes, and a long partial open reading frame (ORF1). The clone included 3.9 kbp of pdu DNA which had not been previously sequenced. Complementation and expression studies with subclones constructed via PCR showed that three genes (pduCDE) are necessary and sufficient for propanediol dehydratase activity. The function of ORF1 was not determined. Analyses showed that the S. typhimurium propanediol dehydratase was related to coenzyme B12-dependent glycerol dehydratases from Citrobacter freundii and Klebsiella pneumoniae. Unexpectedly, the S. typhimurium propanediol dehydratase was found to be 98% identical in amino acid sequence to the Klebsiella oxytoca propanediol dehydratase; this is a much higher identity than expected, given the relationship between these organisms. DNA sequence analyses also supported previous studies indicating that the pdu operon was inherited along with the adjacent cobalamin biosynthesis operon by a single horizontal gene transfer.

Cobamides↗

PubMed1997

Cloning, sequencing, and analysis of a gene cluster from Chelatobacter heintzii ATCC 29600 encoding nitrilotriacetate monooxygenase and NADH:flavin mononucleotide oxidoreductase.

Nitrilotriacetate (NTA) is an important chelating agent in detergents and has also been used extensively in processing radionuclides. In Chelatobacter heintzii ATCC 29600, biodegradation of NTA is initiated by NTA monooxygenase that oxidizes NTA to iminodiacetate and glyoxylate. The NTA monooxygenase activity requires two component proteins, component A and component B, but the function of each component is unclear. We have cloned and sequenced a gene cluster encoding components A and B (nmoA and nmoB) and two additional open reading frames, nmoR and nmoT, downstream of nmoA. Based on sequence similarities, nmoR and nmoT probably encode a regulatory protein and a transposase, respectively. The NmoA sequence was similar to a monooxygenase that uses reduced flavin mononucleotide (FMNH2) as reductant; NmoB was similar to an NADH:flavin mononucleotide (FMN) oxidoreductase. On the basis of this information, we tested the function of each component. Purified component B was shown to be an NADH:FMN oxidoreductase, and its activity could be separated from that of component A. When the Photobacterium fischeri NADH:FMN oxidoreductase was substituted for component B in the complete reaction, NTA was oxidized, showing that the substrate specificity of the reaction resides in component A. Component A is therefore an NTA monooxygenase that uses FMNH2 and O2 to oxidize NTA, and component B is an NADH:FMN oxidoreductase that provides FMNH2 for NTA oxidation.

Amino Acid Sequence↗

PubMed1997

p53 gene mutations, and CYP1A1 and GSTM1 genotypes in pulmonary squamous cell carcinomas.

To investigate mechanisms causing p53 mutations in lung cancer cases, relations between p53 gene mutations and aetiological factors such as smoking history or family history of cancers cases. The contribution of genotypes related to carcinogen metabolism (CYP1A1 and GSTM1) was also analysed. p53 mutations were observed in 13 cases (37.5%). Seven (53.8%) of the 13 patients with p53 mutation compared with five (22.7%) of 22 patients without had a family history of cancer. However, there was no significant relation between p53 mutation or family history of cancer and CYP1A1 or GSTM1 genotypes. In conclusion, p53 mutation might be associated with the inherited characteristics that result in familial aggregation of lung cancer; however, this association was not explained by genotypes of enzymes related to carcinogen metabolisms.

Adult↗

PubMed1997

Work environment and low back pain: the influence of occupational activities.

OBJECTIVES: To find associations between the prevalence of low back pain and occupational activities. METHODS: Interviews of a random sample of 5185 19-59 year old Danish employees analysed by logistic regression. RESULTS: Increased risks of low back pain were found for "vibration affecting the whole body" (odds ratio (OR) = 1.28), "physically hard work" (OR = 1.28), "frequently twisting or bending" (OR = 1.71), "standing up" (OR = 1.20), and "concentration demands" (OR = 1.28). In the analysis of dose-response relations between low back pain and the risk factors, the one year period prevalence increased with increasing exposure time during a working day to each of the risk factors. The prevalence proportion ratio for those reporting to be exposed for most of the working time were 1.30 for vibrations affecting the whole body, 1.54 for physically hard work, 1.48 for frequently twisting or bending, 1.29 for standing up, and 1.13 for concentration demands. These associations seemed to be stronger in the subset of subjects who worked for 37 hours or more per week. The population attributable fractions were 15.1% for frequently twisting or bending, 15.0% for standing up, 7.6% for concentration demands, and 4.4% for physically hard work. CONCLUSION: Vibrations affecting the whole body, physically hard work, frequently twisting or bending, standing up, and concentration demands proved to be risk factors for the occurrence of low back pain, even after controlling for age, sex, educational level, and duration of employment in a specific occupation.

Adult↗

PubMed1997

Comparative evaluation of within-cultivar variation of rice (Oryza sativa L.) using microsatellite and RFLP markers.

The objective of this study was to determine an efficient way of detecting within-cultivar variation in rice varieties obtained from national and international germplasm collections. Seventy-one rice cultivars were evaluated for within-cultivar variation using a combination of phenotypic, RFLP, and microsatellite or simple sequence length polymorphism (SSLP). Variation between individuals within and accession and between duplicate accessions within a cultivar was detected even in cultivars that had been purified by phenotypic evaluation. Landrace cultivars were more heterogeneous and displayed a larger number of both RFLP and SSLP alleles than did modern cultivars. Microsatellite markers detected a greater number of alleles and were able to discriminate between even closely related individuals more efficiently than RFLPs. Some microsatellite markers were more informative than others for assessing genetic diversity. Single markers revealed 5.6-61.1% of the total variation detected by the 10 SSLP markers. Some marker combinations were complementary, providing more information than others. Several combinations of 4 SSLP markers detected as much as 94% of the total within-cultivar variation detected by the 10 SSLP markers. These results suggest that the use of four well-chosen microsatellites would be an efficient method for evaluating the heterogeneity of rice accessions.

Gene Frequency↗

PubMed1997

Hydrogen peroxide-induced liver cell necrosis is dependent on AP-1 activation.

To determine whether intracellular signaling events involved in apoptosis may also mediate necrosis, the role of the transcription factor AP-1 was investigated in a hepatoma cell model of cellular necrosis induced by oxidant stress. Treatment of the human hepatoma cell line HuH-7 with H2O2 caused dose-dependent necrosis as determined by light microscopy, fluorescent staining, and an absence of DNA fragmentation. H2O2 treatment led to increases in c-fos and c-jun mRNA levels, Jun nuclear kinase activity, and AP-1 DNA binding. AP-1 transcriptional activity measured with an AP-1-driven luciferase reporter gene was also increased. To determine whether this AP-1 activation contributed to H2O2-induced cell necrosis, HuH-7 cells were stably transfected with an antisense c-jun expression vector. Cells expressing antisense c-jun had decreased levels of AP-1 activation and significantly increased survival after H2O2 exposure. These data indicate that AP-1 activation occurs during oxidant-induced cell necrosis and contributes to cell death. Necrosis is therefore not always a passive process but may involve the activation of intracellular signaling pathways similar to those that mediate apoptosis.

Carcinoma, Hepatocellular↗

PubMed1997

Pulmonary artery smooth muscle cells from chronically hypoxic neonatal calves retain fetal-like and acquire new growth properties.

Growth properties retained and acquired by immature pulmonary artery (PA) smooth muscle cells (SMC) in vivo after chronic exposure to hypoxia and the mechanisms that regulate hypoxia-induced change in proliferative phenotype are not known. We tested the hypothesis that PA SMC from neonatal calves exposed to hypoxia after birth would both retain fetal-like and acquire new growth characteristics and that these changes would be at least partially dependent on protein kinase C (PKC), a key proproliferative signal transduction pathway. Like fetal cells, PA SMC from hypoxic calves grew faster in the presence and absence of serum and were more responsive to insulin-like growth factor I and platelet-derived growth factor-BB than control neonatal and adult cells. PA SMC from hypoxic calves also acquired other growth properties (i.e., including increased hypoxic growth after PKC activation) that were new compared with those observed for fetal cells. The proliferative response to hypoxia was first detectable in the neonatal period and was further increased in cells from hypoxic calves. SMC from fetuses and hypoxic calves were more susceptible to the growth-inhibiting effects of PKC antagonists (dihydrosphingosine and calphostin C) than control neonatal and adult cells. To test if the Ca(2+)-dependent isozymes of PKC were uniquely important in the developmental and acquired growth changes observed, the antagonistic effect of the specific, but isozyme nonselective, PKC inhibitor Ro-81-8220 was then compared with GF-109203X, a structural analog with relative specificity for the Ca(2+)-dependent isozymes of PKC (alpha and beta in PA SMC). The faster growing PA SMC from bovine fetuses and hypoxia-exposed calves again demonstrated greater growth inhibition in response to both inhibitors. GF-109203X was equipotent to Ro-31-8220, and its antiproliferative effects were shown to not be due to an increase in apoptosis. Phorbol ester-induced PKC downregulation, another inhibitor strategy that selectively depletes bovine PA SMC of PKC-alpha, but not -beta, mimicked the antiproliferative effects of GF-109203X. Whole cellular PKC catalytic activity paralleled the pattern of peptide-induced growth and susceptibility to PKC inhibition. These results suggest that PA SMC from hypoxia-exposed neonatal calves retain enhanced fetal-like proliferative capacity and acquire new growth properties that are at least partially dependent on the Ca(2+)-regulated isozymes of PKC and in particular PKC-alpha.

Aging↗

PubMed1997

Lhx2, a LIM homeobox gene, is required for eye, forebrain, and definitive erythrocyte development.

We investigated the function of Lhx2, a LIM homeobox gene expressed in developing B-cells, forebrain and neural retina, by analyzing embryos deficient in functional Lhx2 protein. Lhx2 mutant embryos are anophthalmic, have malformations of the cerebral cortex, and die in utero due to severe anemia. In Lhx2-/- embryos specification of the optic vesicle occurs; however, development of the eye arrests prior to formation of an optic cup. Deficient cellular proliferation in the forebrain results in hypoplasia of the neocortex and aplasia of the hippocampal anlagen. In addition to the central nervous system malformations, a cell non-autonomous defect of definitive erythropoiesis causes severe anemia in Lhx2-/- embryos. Thus Lhx2 is necessary for normal development of the eye, cerebral cortex, and efficient definitive erythropoiesis.

Anemia↗