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Biomedical subjects

Z Lai

Publications and source records attributed to Z Lai.

At least 19 recordsLinked to original sources
PubMed2006

Identification and chromosomal location of major genes for resistance to Pyrenophora teres in a doubled-haploid barley population.

Net blotch, caused by Pyrenophora teres, is one of the most economically important diseases of barley worldwide. Here, we used a barley doubled-haploid population derived from the lines SM89010 and Q21861 to identify major quantitative trait loci (QTLs) associated with seedling resistance to P. teres f. teres (net-type net blotch (NTNB)) and P. teres f. maculata (spot-type net blotch (STNB)). A map consisting of simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers was used to identify chromosome locations of resistance loci. Major QTLs for NTNB and STNB resistance were located on chromosomes 6H and 4H, respectively. The 6H locus (NTNB) accounted for as much as 89% of the disease variation, whereas the 4H locus (STNB resistance) accounted for 64%. The markers closely linked to the resistance gene loci will be useful for marker-assisted selection.

Ascomycota↗
PubMed2005

Identification and mapping of SNPs from ESTs in sunflower.

More than 67,000 expressed sequence tags (ESTs) have recently been generated for sunflower (Helianthus), including 44,000 from cultivated confectionery (RHA280) and oilseed (RHA801) lines of Helianthus annuus and 23,000 from drought- and salt-tolerant wild sunflowers, H. argophyllus and H. paradoxus, respectively. To create a transcript map for sunflower, we identified 605 ESTs that displayed small insertion-deletion polymorphism (SNP) variation in silico, had apparent tissue-specific expression patterns, and/or were ESTs with candidate functions in traits such as development, cell transport, metabolism, plant defense, and tolerance to abiotic stress. Primer pairs for 535 of the loci were designed from the ESTs and screened for polymorphism in recombinant inbred lines derived from a cross between the same cultivars (RHA280 x RHA801) employed for sequencing. In total, 273 of the loci amplified polymorphic products, of which 243 mapped to the 17 linkage groups previously identified for sunflower. Comparisons with previously mapped QTL revealed some cases where ESTs with putatively related functions mapped near QTLs identified in other crosses for salt tolerance and for domestication traits such as stem diameter, shattering, flowering time, and achene size.

Chromosome Mapping↗
PubMed2001

[Helicobacter pylori associated gastric mucosal inflammation and histopathological assessment].

OBJECTIVE: To investigate the pathological features of Helicobacter pylori associated gastric mucosal inflammation and to establish relevant histopathological assessment standards. METHODS: Biopsy specimens from the gastric antrum, body of stomach, and gastric angle were taken from 2 134 cases of H. pylori associated gastric mucosal inflammation. H. pylori was identified by means of rapid urase test and toluidine blue staining or immunohistological staining. The severity of mucosal inflammation was evaluated with HE staining. Ultrastucture evaluation was conducted for part of the specimens. RESULTS: In H. pylori positive cases lymphocytic infiltration could be observed in glandulous epithelium. which was not found in normal gastric mucosa. Scoring of severity of mucosal inflammation reflected the status of H. pylori infection and was not influenced by the biopsy site, size of specimen, and direction of sectioning. Severe active inflammation could be seen in 39.6% of the H. pylori positive cases, and 0.4% of the H. pylori negative cases. The severity score of inflammation was significantly correlated with the amount of H. pylori colonization. CONCLUSION: Reflecting the real status of H. pylori associated mucosal inflammation. The grading method reported here is simple, reliable, and easy to master.

Adolescent↗
PubMed2001

Human mdm2 mediates multiple mono-ubiquitination of p53 by a mechanism requiring enzyme isomerization.

The mdm2 gene product is an important regulator of p53 function and stability. mdm2 is an E3 ubiquitin ligase for p53 and the RING finger domain of mdm2 is critical for ligase activity. Ubiquitin (Ub) conjugation is a general targeting modification and poly-ubiquitin chains specifically target proteins to the proteasome for degradation. In this report, we show that the multistep cascade of mdm2-mediated p53 ubiquitination can be reduced to three purified recombinant proteins: ubiquitin-conjugated E2, mdm2, and p53. This simplification allows enzymatic analysis of the isolated ligase reaction. The simplified reaction recapitulates the ubiquitination of p53 observed with individual components and the p53-Ub((n)) is qualitatively similar to p53-Ub((n)) detected in lactacystin-treated cells. Surprisingly, we find that p53 is modified with multiple mono-ubiquitin moieties as opposed to a poly-ubiquitin chain. Finally, kinetic analysis indicates the transfer reaction proceeds either through a modified Ping Pong mechanism involving requisite enzyme isomerization steps, or through a Rapid Equilibrium Random Bi Bi mechanism involving very large anti-cooperative interactions between the two substrate binding pockets on the enzyme, mediated through allosteric changes in enzyme structure.

Ethylmaleimide↗
PubMed2001

The sequence of the human genome.

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Algorithms↗
PubMed2001

Design of a compartmentalized shotgun assembler for the human genome.

Two different strategies for determining the human genome are currently being pursued: one is the "clone-by-clone" approach, employed by the publicly funded project, and the other is the "whole genome shotgun assembler" approach, favored by researchers at Celera Genomics. An interim strategy employed at Celera, called compartmentalized shotgun assembly, makes use of preliminary data produced by both approaches. In this paper we describe the design, implementation and operation of the "compartmentalized shotgun assembler".

Chromosomes, Artificial, Bacterial↗
PubMed2001

[Effects of vascular endothelial growth factor on adhesion molecular expression of hepatocellular carcinoma HepG].

OBJECTIVE: To study the effect of vascular endothelial growth factor (VEGF) on homotypic adhesion and E-cadherin of hepatocellular carcinoma cells. METHODS: We measured the function of homotypic adhesion with (3)H-TdR infiltration and the expression of E-cadherin with laser scanning confocal microscope. RESULTS: After 60, 90, 120min, the values (dpm/min) of (3)H-TdR infiltration in HepG(2) cells induced by 1ng/ml, 5ng/ml VEGF were 1758.67+/-289.46, 1380.03+/-328.55, 2657.43 +/- 310.31 and 3124.30+/-262.14, 2245.60+/-273.24, 2091.52+/-213.84. The values by 10ng/ml VEGF were 1232.32+/-201.04, 2337.50+/-333.04, 2236.99 +/- 237.07, which were significantly lower than those in control group (P<0.05 or 0.01). The expression of E-cadherin in hepatocellular carcinoma cells induced by 5ng/ml VEGF was 352+/-56 and much lower than that in control group (757+/-103, P<0.01). CONCLUSIONS: VEGF can decrease homotopic adhesion of hepatocellular carcinoma HepG(2) cell, which is connected with the less expression of E-cadherin in hepatocellular carcinoma HepG(2) cell.

Cadherins↗
PubMed2001

[The mutation of anti-CD3 antibody (HIT3a) gene and its expression].

OBJECTIVE: To improve the expression of anti-CD(3) single chain Fv (scFv) by site mutation and identify its biological activity. METHODS: Anti-CD(3) scFv gene was mutated by PCR, the target clones were screened by both the fingerprints of DNA restriction endonuclease digestion and Western blot, the antigen-binding activity of scFv was examined by FACS, competitive inhibition was performed with (125)I-labeled HIT3a and the cytotoxic effect mediated by the anti-CD(3) scFv-activated T lymphocytes was analyzed by (51)Cr-released assays. RESULTS: The DNA sequencing showed that the 6th amino acid of the anti-CD(3) antibody (HIT3a) heavy chain gene was mutated from E (GAG) to Q (CAG). The expression of mutated anti-CD(3) scFv (m2) was increased by 100 times higher than that of the parent scFv, and there was no difference in the Jurkat cell (CD(3)(+))-binding activity between the (m2) and parent scFv. The preliminary results of competitive assays showed that m2 could partially block the sites of CD(3)(+) Jurkat cells where the parent antibody bound to. Cytotoxicity assays demonstrated that CD(3)AK cells induced by IL-2 and m2 showed stronger cytotoxic effect than that of LAK cells induced by IL-2 alone in vitro. CONCLUSION: By site mutation, a high expression fragment m2 of anti-CD(3) scFv antibody was obtained. The results of some experiments indicated that m2 could bind to CD(3)(+) Jurkat cells, furthermore, by co-stimulated with IL-2, it could activate peripheral T lymphocytes and induce CD(3)AK cytotoxic effect.

CD3 Complex↗
PubMed2000

Intercellular delivery of a herpes simplex virus VP22 fusion protein from cells infected with lentiviral vectors.

Effective gene therapy depends on the efficient transfer of therapeutic genes and their protein products to target cells. Lentiviral vectors appear promising for virus-mediated gene delivery and long-term expression in nondividing cells. The herpes simplex virus type 1 tegument protein VP22 has recently been shown to mediate intercellular transport of proteins, raising the possibility that it may be helpful in a setting where the global delivery of therapeutic proteins is desired. To investigate the effectiveness of lentiviral vectors to deliver genes encoding proteins fused to VP22, and to test whether the system is sufficiently potent to allow protein delivery from transduced cells in vitro and in vivo, fusion constructs of VP22 and the enhanced green fluorescent protein (EGFP) were prepared and delivered into target cells by using HIV-1-based lentiviral vectors. To follow the spread of VP22-EGFP to other cells, transduced COS-7 cells were coplated with a number of different cell types, including brain choroid plexus cells, human endothelial cells, H9 cells, and HeLa cells. We found that VP22-EGFP fusion proteins were transported from transduced cells to recipient cells and that such fusion proteins accumulated in the nucleus and in the cytoplasm of such cells. To determine the ability to deliver fusion proteins in vivo, we injected transduced H9 cells as well as the viral vector directly into the brain of mice. We present evidence that VP22-EGFP fusion proteins were transported effectively from lentivirus transduced cells in vivo. We also show that the VP22-EGFP fusion protein encoded by the lentivirus is transported between cells. Our data indicate that such fusion proteins are present in the nucleus and in the cytoplasm of neighboring cells. Therefore, lentiviral vectors may provide a potent biological system for delivering genes encoding therapeutic proteins fused to VP22.

Animals↗
PubMed2000

Thermodynamics of p53 binding to hdm2(1-126): effects of phosphorylation and p53 peptide length.

Upon exposure to DNA-damaging agents, the p53 tumor suppressor protein is stabilized and activated, leading to cell cycle arrest, DNA repair, or apoptosis. One of the major factors that regulates the level and the transcriptional activity of p53 is the hdm2 oncoprotein. hdm2 binds to the N-terminal transactivation domain of p53 to block the transcriptional activity of p53 directly. hdm2 also functions as the E3 ligase that ubiquitinates p53 for proteasome degradation. Fluorescence anisotropy was employed to measure directly the binding of hdm2(1-126) to a p53 N-terminal peptide labeled with Oregon Green (an analogue of fluorescein). Phosphorylation of Ser15 and Ser2O did not affect the binding of the p53 peptide to hdm2. Thrl8 phosphorylation, on the other hand, reduced the binding by at least 20-fold. This suggests that phosphorylation of Thr18 could be a regulatory mechanism that disrupts the hdm2-p53 complex, thus activating p53 in response to DNA damage. The effect of p53 peptide length on binding to hdm2 was also measured quantitatively. Interestingly, p53(18-26) exhibits 10-fold higher affinity to hdm2 than do longer peptides (20- or 35-mer). This result may reflect a strong entropic barrier to binding for the longer peptides.

Crystallography, X-Ray↗
PubMed2000

A whole-genome assembly of Drosophila.

We report on the quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it. Three independent external data sources essentially agree with and support the assembly's sequence and ordering of contigs across the euchromatic portion of the genome. In addition, there are isolated contigs that we believe represent nonrepetitive pockets within the heterochromatin of the centromeres. Comparison with a previously sequenced 2.9- megabase region indicates that sequencing accuracy within nonrepetitive segments is greater than 99. 99% without manual curation. As such, this initial reconstruction of the Drosophila sequence should be of substantial value to the scientific community.

Algorithms↗
PubMed2000

The Drosophila homolog of Onecut homeodomain proteins is a neural-specific transcriptional activator with a potential role in regulating neural differentiation.

We report here the characterization of the Drosophila homolog of the onecut homeobox gene, which encodes a protein product with one cut domain and one homeodomain. We present evidence that D-Onecut can bind to similar DNA sequences with high specificity and affinity as other Onecut proteins through the highly conserved cut domain and homeodomain. Interestingly, the cut domain alone can mediate DNA-binding, but the homeodomain cannot. However, depending upon the promoter context, we observed cooperative interactions between the two domains to confer high DNA-binding affinity and specificity. D-Onecut appears to be a moderate transcriptional activator and functions as a nuclear protein in neuronal tissues of both the CNS and PNS during development and in the adult. In the eye, D-Onecut expression is independent of glass, a transcriptional regulator of R cell differentiation. Taken together, our results suggest a role for D-Onecut in the regulation of some aspects of neural differentiation or maintenance. In support of this notion, overexpression of a putative dominant negative form of D-Onecut during eye development does not affect early cell fate specification, but severely affects photoreceptor differentiation.

Amino Acid Sequence↗
PubMed2000

Steady-state kinetic analysis of human ubiquitin-activating enzyme (E1) using a fluorescently labeled ubiquitin substrate.

We report the synthesis of fluorescently labeled ubiquitin (Ub) and its use for following ubiquitin transfer to various proteins. Using Oregon green (Og) succinimidyl ester, we prepared a population of Ub mainly labeled by a single Og molecule; greater than 95% of the Og label is associated with Lys 6 of Ub. We demonstrate that Og-Ub is efficiently accepted by Ub-utilizing enzymes, such as the human ubiquitin-activating enzyme (E1). We used this fluorescent substrate to follow the steady-state kinetics of human E1-catalyzed Ub-transfer to the ubiquitin-carrier enzyme Ubc4. In this reaction, E1 uses three substrates: ATP, Ubc4, and Ub. The steady-state kinetics of Og-Ub utilization by E1 is presented. We have also used analytical ultracentrifugation methods to establish that E1 is monomeric under our assay condition (low salt) as well as under physiological condition (150 mM NaCl).

Binding, Competitive↗
PubMed2000

Generation of alphabeta T-cell receptor+ CD4- CD8+ cells in major histocompatibility complex class I-deficient mice upon activation of the aryl hydrocarbon receptor by 2,3,7,8-tetrachlorodibenzo-p-dioxin.

Gene-targeted mice lacking the beta2 microglobulin gene (beta2m-/- mice), and hence functional major histocompatibility complex (MHC) class I molecules, do not develop CD4- CD8+ cells. We show here that both in vitro and in vivo treatment with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a trans-activating ligand of the endogenous aryl hydrocarbon receptor (Ah-R), bypasses the need for MHC class I molecules for selection into the CD4- CD8+ cell pool. When beta2m-/- dams were given a single dose of 50 microg of TCDD, approximately 13% of CD4- CD8+ thymocytes could be detected in their newborn pups. In TCDD-exposed fetal thymus organ cultures of beta2m-/- mice, approximately 35% CD4- CD8+ thymocytes were detectable. About 16% of these CD4- CD8+ cells bore the alpha beta T-cell receptor (TCR) and approximately 33% bore CD3. Only a minority of the CD8+ cells were heat-shock antigen positive. The cells possessed killing activity as shown using the 51Cr-release assay comprising gamma delta TCR- CD4- CD8+ thymocytes from 3 to 4-day-old b2m-/- mice. Thus, TCDD leads to a significant increase of mature CD4- CD8+ thymocytes in relative and absolute numbers. High numbers of CD4- CD8+ thymocytes developed also in organ cultures from thymi, lacking both MHC class I and class II molecules, exposed to TCDD. A 10-fold transient increase of Notch1 mRNA in thymocytes from fetal thymus organ culture, exposed for 4 days to TCDD, was detected in CD4+ CD8+ cells compared with controls. We suggest that TCDD affects thymic selection and directs the lineage commitment of CD4+ CD8+ thymocytes towards CD4- CD8+ cells, possibly via up-regulation of the Notch1 gene.

Animals↗
PubMed2000

Differential expression of the G protein beta(5) gene: analysis of mouse brain, peripheral tissues, and cultured cell lines.

A neurally expressed heterotrimeric G protein beta subunit, Gbeta(5), has been found to exhibit functional specialization with respect to its interactions with effector targets and Galpha subunits. A splice variant of Gbeta(5) that contains an N-terminal 42-residue extension, Gbeta(5)-long, has been described in the retina. To define better the potential range of its specialized interactions, analysis of Gbeta(5) gene transcript and protein expression in mouse brain and other tissues and cell lines was performed. Quantification by ribonuclease protection assay of Gbeta(5) transcript expression in the developing brain demonstrates a fivefold increase that occurs postnatally. Analysis of transcript expression by in situ hybridization and ribonuclease protection assay indicates that the Gbeta(5) gene is differentially expressed among multiple adult mouse brain regions, including the motor and occipital cortex, the olfactory bulb and associated rhinencephalic structures, hypothalamus, pontine cochlear nuclei, and Purkinje cells in the cerebellum. Gbeta(5) is also expressed in several cultured cell lines of neuroendocrine origin, including murine alphaT3-1 pituitary gonadotrophs and GT1-7 hypothalamic cells, and rat PC12 pheochromocytoma cells. Immunoblotting of tissue homogenates with antibodies to two peptides common to Gbeta(5) and Gbeta(5)-long confirmed expression of Gbeta(5) in multiple brain regions and in spinal cord and expression of Gbeta(5)-long in retina. Taken together, these results suggest that the specialized molecular properties of Gbeta(5) have been adapted to diverse neural functions in the adult brain.

Aging↗
PubMed2000

Optical mapping of BAC clones from the human Y chromosome DAZ locus.

The accurate mapping of clones derived from genomic regions containing complex arrangements of repeated elements presents special problems for DNA sequencers. Recent advances in the automation of optical mapping have enabled us to map a set of 16 BAC clones derived from the DAZ locus of the human Y chromosome long arm, a locus in which the entire DAZ gene as well as subsections within the gene copies have been duplicated. High-resolution optical mapping employing seven enzymes places these clones into two contigs representing four distinct copies of the DAZ gene and highlights a number of differences between individual copies of DAZ.

Chromosome Mapping↗
PubMed2000

Development of multigene and regulated lentivirus vectors.

Previously we described safe and efficient three-component human immunodeficiency virus type 1 (HIV-1)-based gene transfer systems for delivery of genes into nondividing cells (H. Mochizuki, J. P. Schwartz, K. Tanaka, R. O. Brady, and J. Reiser, J. Virol. 72:8873-8883, 1998). To apply such vectors in anti-HIV gene therapy strategies and to express multiple proteins in single target cells, we have engineered HIV-1 vectors for the concurrent expression of multiple transgenes. Single-gene vectors, bicistronic vectors, and multigene vectors expressing up to three exogenous genes under the control of two or three different transcriptional units, placed within the viral gag-pol coding region and/or the viral nef and env genes, were designed. The genes encoding the enhanced version of green fluorescent protein (EGFP), mouse heat-stable antigen (HSA), and bacterial neomycin phosphotransferase were used as models whose expression was detected by fluorescence-activated cell sorting, fluorescence microscopy, and G418 selection. Coexpression of these reporter genes in contact-inhibited primary human skin fibroblasts (HSFs) persisted for at least 6 weeks in culture. Coexpression of the HSA and EGFP reporter genes was also achieved following cotransduction of target cells using two separate lentivirus vectors encoding HSA and EGFP, respectively. For the regulated expression of transgenes, tetracycline (Tet)-regulatable lentivirus vectors encoding the reverse Tet transactivator (rtTA) and EGFP controlled by a Tet-responsive element (TRE) were constructed. A binary HIV-1-based vector system consisting of a lentivirus encoding rtTA and a second lentivirus harboring a TRE driving the EGFP reporter gene was also designed. Doxycycline-modulated expression of the EGFP transgene was confirmed in transduced primary HSFs. These versatile vectors can potentially be used in a wide range of gene therapy applications.

Animals↗