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Wen Wang

Publications and source records attributed to Wen Wang.

At least 91 records · Page 5Linked to original sources
PubMed2003

The origin of new genes: glimpses from the young and old.

Genome data have revealed great variation in the numbers of genes in different organisms, which indicates that there is a fundamental process of genome evolution: the origin of new genes. However, there has been little opportunity to explore how genes with new functions originate and evolve. The study of ancient genes has highlighted the antiquity and general importance of some mechanisms of gene origination, and recent observations of young genes at early stages in their evolution have unveiled unexpected molecular and evolutionary processes.

Animals↗
PubMed2003

Multiplex minisequencing screen for common Southeast Asian and Indian beta-thalassemia mutations.

BACKGROUND: Beta-thalassemia is endemic to many regions in Southeast Asia and India, and <20 beta-globin gene mutations account for > or =90% of beta-thalassemia alleles in these places. We describe a multiplex minisequencing assay to detect these common mutations. METHODS: Gap-PCR was used to simultaneously amplify the beta-globin gene from genomic DNA and to detect the Delta619bp deletion mutation. Multiplex minisequencing was then performed on the amplified beta-globin fragment to detect an additional 15 common Southeast Asian and Indian beta-thalassemia mutations. Site-specific primers of different lengths were subjected to multiple rounds of annealing and single-nucleotide extension in the presence of thermostable DNA polymerase and the four dideoxynucleotides, each labeled with a different fluorophore. Minisequencing products were separated and detected by capillary electrophoresis, followed by automated genotyping. The optimized assay was subjected to a double-blind validation analysis of 89 beta-thalassemia and wild-type DNA samples of known genotype. RESULTS: Homozygous wild-type or mutant DNA samples produced electropherograms containing only a single colored peak for each mutation site, whereas samples heterozygous for a specific mutation displayed two different-colored peaks for that mutation site. Samples were automatically genotyped based on color and position of primer peaks in the electropherogram. In the double-blind validation analysis, all 89 DNA samples were genotyped correctly (100% assay specificity). CONCLUSIONS: The described semiautomated multiplex minisequencing assay can detect the most common Southeast Asian and Indian beta-thalassemia mutations, is amenable to high-throughput scale up, and may bring population-based screening of beta-thalassemia in endemic regions a step closer to implementation.

Asia, Southeastern↗
PubMed2003

Origin of new genes: evidence from experimental and computational analyses.

Exon shuffling is an essential molecular mechanism for the formation of new genes. Many cases of exon shuffling have been reported in vertebrate genes. These discoveries revealed the importance of exon shuffling in the origin of new genes. However, only a few cases of exon shuffling were reported from plants and invertebrates, which gave rise to the assertion that the intron-mediated recombination mechanism originated very recently. We focused on the origin of new genes by exon shuffling and retroposition. We will first summarize our experimental work, which revealed four new genes in Drosophila, plants, and humans. These genes are 10(6) to 10(8) million years old. The recency of these genes allows us to directly examine the origin and evolution of genes in detail. These observations show firstly the importance of exon shuffling and retroposition in the rapid creation of new gene structures. They also show that the resultant chimerical structures appearing as mosaic proteins or as retroposed coding structures with novel regulatory systems, often confer novel functions. Furthermore, these newly created genes appear to have been governed by positive Darwinian selection throughout their history, with rapid changes of amino acid sequence and gene structure in very short periods of evolution. We further analyzed the distribution of intron phases in three non-vertebrate species, Drosophila melanogaster, Caenorhabditis elegans, and Arabidosis thaliana, as inferred from their genome sequences. As in the case of vertebrate genes, we found that intron phases in these species are unevenly distributed with an excess of phase zero introns and a significant excess of symmetric exons. Both findings are consistent with the requirements for the molecular process of exon shuffling. Thus, these non-vertebrate genomes may have also been strongly impacted by exon shuffling in general.

Cytochromes c1↗
PubMed2003

[Effect of AP-1 on expression of plasminogen activator inhibitor-1 in human vascular endothelial cells].

OBJECTIVE: To study the effect of nuclear transcription factor AP-1 on tumor necrosis factor alpha (TNF-alpha) or minimal modified low density lipoprotein (mmLDL)-induced expression of plasminogen activator inhibitor-1 (PAI-1) in human vascular endothelial cells. METHODS: Using gene recombination techniques, four luciferase reporter gene plasmids containing different length of human PAI-1 gene promoter were constructed. Through the transient transfection analysis, the roles of AP-1 element (from -823 bp to -553 bp) in PAI-1 promoter have been determined. In order to further verify the role of AP-1 element, the three site-directed mutants were recovered using PCR and sequencing assay. RESULTS: The induction by TNF-alpha or mmLDL were decreased markedly when the three AP-1 elements in PAI-1 promoter had been mutated respectively. CONCLUSIONS: These results indicate that the AP-1 element in PAI-1 promoter may have important role in PAI-1 gene transcriptions in endothelial cells induced by TNF-alpha or mmLDL.

Base Sequence↗
PubMed2003

[Effect of genistein on proliferation of renal cell carcinoma cell line GRC-1 and its influence to p27 expression].

BACKGROUND & OBJECTIVE: There has always been a significant morbidity difference of renal cell carcinoma between the Oriental and Occidental countries. The high soybean consumption in Oriental countries may be one of the reasons. We investigated the effect of a tyrosine protein kinase inhibitor extracted from soybean, namely genistein, on the proliferation of a renal cell carcinoma cell line, GRC-1; and analyzed the correlation between this effect and a well-known anti-oncogene, p27. METHODS: Inverted microscopy, MTT method, and flow cytometry (FCM) were used to examine the changes in proliferation of GRC-1 cells after treatment with genistein; and the intracellular p27 protein expression was determined by Western blot analysis. RESULTS: (1)After treatment with genistein, changed morphology of the GRC-1 cells was observed. Cell junctions decreased. In the presence of 20 micromol/L genistein, GRC-1 cells showed shuttle-shaped, and fewer pseudopodia, mitoses and cell junctions were observed. In the 40 micromol/L genistein group, many cells broke into debris, and became extremely irregular in shape. Meanwhile, mitoses and cell junctions were rarely seen. (2)Treated with 20 micromol/L genistein, 73.8% GRC-1 cells were in G(1) phase, 26.2% in G2 phase 72 hours after treatment; while in control group, 31.6% in G(1) phase and 3.8% in G2 phase, respectively. (3)After exposure to 20 micromol/L genistein for 72 hours, Western blot suggested that the band of p27 was 65.4+/-4.7 in gray scale value, while the control group was 52.3+/-6.3. CONCLUSION: Genistein can inhibit the proliferation of renal cell carcinoma cells, and cause cell cycle arrest at G(1)/M, G(2)/S phase. The possible underlying mechanism may involve its upregulation of p27 expression in the renal cancer cells.

Antineoplastic Agents↗
PubMed2003

Oral ingestion of Ginkgo biloba extract reduces thiobarbituric acid reacting (TBAR) substances in washed platelets of healthy subjects.

Thiobarbituric acid reacting (TBAR) substances were measured in washed platelets before and after ingesting 120 mg of standardized Gingko biloba extract daily for 3 months, in both normocholesterolemic (total cholesterol, 160 +/- 27 mg/dl; age 40 +/- 13 years; n = 18) and hypercholesterolemic subjects (total cholesterol, 229 +/- 35; age, 45 +/- 8 years, n = 12). Gingko biloba extract significantly reduced cellular content of TBAR substances; 42 +/- 21 vs. 28 +/- 16 pmol/10(7 platelets (p < 0.0025) and 50 +/- 17 vs. 29 +/- 13 pmol/10(7) platelets (P < 0.004), for the normo- and hypercholemic subjects, respectively. In conclusion, Gingko biloba extract is a potent antioxidant for both groups, reducing TBAR substances possibly by inhibiting platelet COX-1 isoform activity.

Journal Article↗
PubMed2002

Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster.

Non-protein-coding RNA genes play an important role in various biological processes. How new RNA genes originated and whether this process is controlled by similar evolutionary mechanisms for the origin of protein-coding genes remains unclear. A young chimeric RNA gene that we term sphinx (spx) provides the first insight into the early stage of evolution of RNA genes. spx originated as an insertion of a retroposed sequence of the ATP synthase chain F gene at the cytological region 60DB since the divergence of Drosophila melanogaster from its sibling species 2-3 million years ago. This retrosequence, which is located at 102F on the fourth chromosome, recruited a nearby exon and intron, thereby evolving a chimeric gene structure. This molecular process suggests that the mechanism of exon shuffling, which can generate protein-coding genes, also plays a role in the origin of RNA genes. The subsequent evolutionary process of spx has been associated with a high nucleotide substitution rate, possibly driven by a continuous positive Darwinian selection for a novel function, as is shown in its sex- and development-specific alternative splicing. To test whether spx has adapted to different environments, we investigated its population genetic structure in the unique "Evolution Canyon" in Israel, revealing a similar haplotype structure in spx, and thus similar evolutionary forces operating on spx between environments.

Animals↗
PubMed2002

Rickettsia-like organism associated with tremor disease and mortality of the Chinese mitten crab Eriocheir sinensis.

We report the discovery of a rickettsia-like organism (RLO) in cultured freshwater Chinese mitten crab Eriocheir sinensis. The RLO caused tremor disease and was apparently responsible for a mass mortality (30 to 90%) in 2 provinces in southeast China. Moribund crabs were investigated from different districts during outbreaks in 1999 and 2000. With electron microscopy, 3 different pathogens were detected in moribund crabs: a rickettsia-like organism (RLO), virus-like particles (VLP) and a microsporidian-like protozoan (MLP). Based on the high prevalence, infection intensity and cytopathological signs, the RLO was considered to be the probable cause of the high mortality. Both VLP and MLP occurred at low prevalences and were considered secondary infections. The RLO was 0.22 to 0.35 microm in diameter, granular or clavate, bounded by a cell wall and membrane, and possessed no nucleus but a nucleoid was present. When dividing, RLOs occurred in irregular shapes, such as dumbbells, awls, and crescents. The RLOs exhibited a predilection for muscle and connective tissues and were probably transported to various tissues and organs by hemocytes.

Animals↗
PubMed2002

Nucleotide variation along the Drosophila melanogaster fourth chromosome.

The Drosophila melanogaster fourth chromosome, believed to be nonrecombining and invariable, is a classic example of the effect of natural selection in eliminating genetic variation in linked loci. However, in a chromosome-wide assay of nucleotide variation in natural populations, we have observed a high level of polymorphism in a approximately 200-kilobase region and marked levels of polymorphism in several other fragments interspersed with regions of little variation, suggesting different evolutionary histories in different chromosomal domains. Statistical tests of neutral evolution showed that a few haplotypes predominate in the 200-kilobase polymorphic region. Finally, contrary to the expectation of no recombination, we identified six recombination events within the chromosome. Thus, positive Darwinian selection and recombination have affected the evolution of this chromosome.

Animals↗
PubMed2002

Seasonal variation of food consumption and selected nutrient intake in Linxian, a high risk area for esophageal cancer in China.

Linxian, China, is a region with high incidence of esophageal cancer and a history of poor nutritional status. Nutrition Intervention Trials were conducted in this area from 1985 through 1991 and found a reduction in total cancer mortality in the group receiving supplementation of beta-carotene/selenium/alpha-tocopherol. The positive results of those trials have, in part, been ascribed to the poor nutritional status of this population. To investigate more recent food patterns, nutrient intakes, and seasonal variations in the diet, dietary surveys were conducted among the residents of Linxian in 1996. Food consumption data were collected among 104 households in spring and 106 households in autumn using a method of food inventory changes. Intake of nutrients was estimated and compared to the Chinese Recommended Dietary Allowance (RDA). In both seasons, the five most common food groups consumed were cereals, fresh vegetables, yams, seasoning, and eggs. Low nutrient intakes were found for selenium (79% RDA and 66% RDA), zinc (72% RDA and 62% RDA), vitamin B2 (64% RDA and 52% RDA), and calcium (53% RDA and 39% RDA) in both spring and autumn. A large seasonal variation was seen in the consumption of leafy vegetables, root vegetables and eggs, all of which might have contributed to the lower intake of vitamin A (25% RDA), vitamin C (75% RDA), protein (76% RDA), and vitamin E (78% RDA) in autumn. These indicate that the nutrient intake in Linxian is inadequate for a number of vitamins and minerals including those shown to be associated with esophageal cancer.

Adolescent↗
PubMed2002

Populations of coupled electrochemical oscillators.

Experiments were carried out on arrays of chaotic electrochemical oscillators to which global coupling, periodic forcing, and feedback were applied. The global coupling converts a very weakly coupled set of chaotic oscillators to a synchronized state with sufficiently large values of coupling strength; at intermediate values both intermittent and stable chaotic cluster states occur. Cluster formation and synchronization were also obtained by applying feedback and forcing to a moderately coupled base state. The three cases differ, however, in other details. The feedback and forcing also produce periodic cluster states and more than two clusters. Configurations of two (chaotic) clusters and two, three, or four (periodic) clusters were observed. (c) 2002 American Institute of Physics.

Journal Article↗
PubMed2002

Increased expression of matrix metalloproteinase 1 (MMP1) in 11 patients with patellar tendinosis.

We studied the expression of procollagen type I, matrix metalloproteinase 1 (MMP1) and tissue inhibitor of metalloproteinase 1 (TIMP-1) by immunohistochemistry in human patellar tendinosis tissues and healthy patellar tendons. In situ gelatin zymography was used to detect collagenolytic activities. The productions of MMP1, TIMP1 and gelatinolytic activities were compared in cell cultures from tendinosis samples and controls. Tendinosis tissues and cultures showed an increase in the expression level of MMP1 and a decrease in that of TIMP1, a condition favoring collagen degradation. Gelatinolytic activities in tendinosis tissues and cultures were elevated. Collagenolysis is a striking feature in patellar tendinosis.

Adolescent↗
PubMed2002

Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene.

Processed genes are created by retroposition from messenger RNA of expressed genes. The estimated amount of processed copies of genes in the human genome is 10,000-14,000. Some of these might be pseudogenes with the expected pattern for nonfunctional sequences, but some others might be an important source of new genes. We have studied the evolution of a Phosphoglycerate mutase processed gene (PGAM3) described in humans and believed to be a pseudogene. We sequenced PGAM3 in chimpanzee and macaque and obtained polymorphism data for human coding region. We found evidence that PGAM3 likely produces a functional protein, as an example of addressing functionality for human processed pseudogenes. First, the open reading frame was intact despite many deletions that occurred in the 3' untranslated region. Second, it appears that the gene is expressed. Finally, interspecies and intraspecies variation for PGAM3 was not consistent with the neutral model proposed for pseudogenes, suggesting that a new functional primate gene has originated. Amino acid divergence was significantly higher than synonymous divergence in PGAM3 lineage, supporting positive selection acting in this gene. This role of selection was further supported by the excess of rare alleles in a population genetic analysis. PGAM3 is located in a region of very low recombination; therefore, it is conceivable that the rapid fixation events in this newly arising gene may have contributed to a selective sweep of variation in the region.

Amino Acid Sequence↗
PubMed2002

Increased expression of transforming growth factor-beta1 in patellar tendinosis.

Patellar tendinosis is characterized by longstanding localized and activity-related pain, swelling and tenderness on palpation, and characteristic features on magnetic resonance imaging and ultrasonography and during surgical excision. Histologic examination of tendinosis tissues shows disrupted collagen matrix, increased cellularity, and increased proteoglycan stainability, but lack of inflammatory cell infiltration despite the clinical signs resembling inflammation. Disturbances in inflammatory response may be associated with the development of tendinosis. Expression of cyclooxygenase-2 and transforming growth factor-beta1 were detected in tendinosis, and the in vitro production of prostaglandin E2 by tendinosis and healthy tendon fibroblast cultures also was observed. Eleven patients with patellar tendinosis and 12 control subjects with healthy patellar tendons, but deficient anterior cruciate ligaments, were included in the current study. The percentages of immunopositive cells in tendinosis samples for cyclooxygenase-2 and transforming growth factor-beta1 were 66.75 and 56.40, respectively, which were significantly higher than those of the control subjects (25.15 and 23.06 respectively). Tendinosis fibroblast culture also produced more prostaglandin E2 and active transforming growth factor-beta1. These findings indicate the involvement of prostaglandins and cytokines that may explain the clinical symptoms and nonhealing features of tendinosis.

Adolescent↗
PubMed2002

N-alkyl urea hydroxamic acids as a new class of peptide deformylase inhibitors with antibacterial activity.

Peptide deformylase (PDF) is a prokaryotic metalloenzyme that is essential for bacterial growth and is a new target for the development of antibacterial agents. All previously reported PDF inhibitors with sufficient antibacterial activity share the structural feature of a 2-substituted alkanoyl at the P(1)' site. Using a combination of iterative parallel synthesis and traditional medicinal chemistry, we have identified a new class of PDF inhibitors with N-alkyl urea at the P(1)' site. Compounds with MICs of 200 micro M for matrilysin and other mammalian metalloproteases. Structure-activity relationship analysis identified preferred substitutions resulting in improved potency and decreased cytotoxity. One of the compounds (VRC4307) was cocrystallized with PDF, and the enzyme-inhibitor structure was determined at a resolution of 1.7 A. This structural information indicated that the urea compounds adopt a binding position similar to that previously determined for succinate hydroxamates. Two compounds, VRC4232 and VRC4307, displayed in vivo efficacy in a mouse protection assay, with 50% protective doses of 30.8 and 17.9 mg/kg of body weight, respectively. These N-alkyl urea hydroxamic acids provide a starting point for identifying new PDF inhibitors that can serve as antimicrobial agents.

Amidohydrolases↗