Biomedical subjects

Daru Lu

Publications and source records attributed to Daru Lu.

31 records · Page 2Linked to original sources

PubMed2005

Genetic polymorphisms in XRCC1, APE1, ADPRT, XRCC2, and XRCC3 and risk of chronic benzene poisoning in a Chinese occupational population.

DNA damage induced by benzene is an important mechanism of its genotoxicity that leads to chronic benzene poisoning (CBP). Therefore, genetic variation in DNA repair genes may contribute to susceptibility to CBP in the exposed population. Because benzene-induced DNA damage includes single- and double-strand breaks, we hypothesized that single-nucleotide polymorphisms in X-ray repair cross-complementing group 1 (XRCC1), apurinic/apyrimidinic endonuclease (APE1), ADP ribosyltransferase (ADPRT), X-ray repair cross-complementing group 2 (XRCC2), and X-ray repair cross-complementing group 3 (XRCC3) are associated with risk of CBP. We genotyped single-nucleotide polymorphisms at codons 194, 280, and 399 of XRCC1, codon 148 of APE1, codon 762 of ADPRT, codon 188 of XRCC2, and codon 241 of XRCC3 in 152 CBP patients and 152 healthy workers frequency matched on age and sex among those who were occupationally exposed to benzene. The genotypes were determined by PCR-RFLP technique with genomic DNA. We found that no individuals had the XRCC2 codon 188 variant alleles or Met/Met genotype of XRCC3 codon 241 in this study population. However, individuals carrying the XRCC1 194Trp allele (i.e., Arg/Trp+Trp/Trp genotypes) had a decreased risk of CBP [adjusted odds ratio (OR(adj)), 0.60; 95% confidence interval (95% CI), 0.37-0.98; P = 0.041] compared with subjects with the Arg/Arg genotype whereas individuals carrying the XRCC1 280His allele (i.e., Arg/His+His/His genotypes) had an increased risk of CBP compared with those with the Arg/Arg genotype (OR(adj), 1.91; 95% CI, 1.17-3.10; P = 0.009). The analysis of haplotypes of polymorphisms in XRCC1 showed that there was a 2.96-fold (OR, 2.96; 95% CI, 1.60-5.49; chi(2) = 12.39, P = 0.001) increased risk of CBP for subjects with alleles of XRCC1 194Arg, XRCC1 280His, and XRCC1 399Arg compared with those carrying alleles of XRCC1 194Arg, XRCC1 280Arg, and XRCC1 399Arg. Therefore, our results suggest that polymorphisms at codons 194 and 280 of XRCC1 may contribute to CBP in a Chinese occupational population.

Adult↗

PubMed2005

[Alignment-free biomolecular sequence comparison method].

Biosequence analysis is the primary research field of bioinformatics. In this field, useful information can be extracted by comparison analysis methods. Among them, sequence alignment is the most common comparison method. However the sequence comparison by alignment, which assumes conservation of contiguity between homologous segments, is at odds with genetic recombination. Especially for the multisequence alignment, there exists the difficulty in the complexity of calculation. Therefore, alignment-free sequence comparison methods are required. In this paper, two main categories of alignment-free sequence comparison methods are reviewed. The first one is based on the word (oligomer) frequency and its distribution. The sequences are compared using the distances defined in a Cartesian space by the frequency vectors. In the second category, sequences are compared using Kolmogorov complexity and chaos theory.

Algorithms↗

PubMed2004

Genetic structure of Hmong-Mien speaking populations in East Asia as revealed by mtDNA lineages.

Hmong-Mien (H-M) is a major language family in East Asia, and its speakers distribute primarily in southern China and Southeast Asia. To date, genetic studies on H-M speaking populations are virtually absent in the literature. In this report, we present the results of an analysis of genetic variations in the mitochondrial DNA (mtDNA) hypervariable segment 1 (HVS1) region and diagnostic variants in the coding regions in 537 individuals sampled from 17 H-M populations across East Asia. The analysis showed that the haplogroups that are predominant in southern East Asia, including B, R9, N9a, and M7, account for 63% (ranging from 45% to 90%) of mtDNAs in H-M populations. Furthermore, analysis of molecular variance (AMOVA), phylogenetic tree analysis, and principal component (PC) analysis demonstrate closer relatedness between H-M and other southern East Asians, suggesting a general southern origin of maternal lineages in the H-M populations. The estimated ages of the mtDNA lineages that are specific to H-M coincide with those based on archeological cultures that have been associated with H-M. Analysis of genetic distance and phylogenetic tree indicated some extent of difference between the Hmong and the Mien populations. Together with the higher frequency of north-dominating lineages observed in the Hmong people, our results indicate that the Hmong populations had experienced more contact with the northern East Asians, a finding consistent with historical evidence. Moreover, our data defined some new (sub-)haplogroups (A6, B4e, B4f, C5, F1a1, F1a1a, and R9c), which will direct further efforts to improve the phylogeny of East Asian mtDNAs.

Asia, Southeastern↗

PubMed2004

Genetic evidence supports demic diffusion of Han culture.

The spread of culture and language in human populations is explained by two alternative models: the demic diffusion model, which involves mass movement of people; and the cultural diffusion model, which refers to cultural impact between populations and involves limited genetic exchange between them. The mechanism of the peopling of Europe has long been debated, a key issue being whether the diffusion of agriculture and language from the Near East was concomitant with a large movement of farmers. Here we show, by systematically analysing Y-chromosome and mitochondrial DNA variation in Han populations, that the pattern of the southward expansion of Han culture is consistent with the demic diffusion model, and that males played a larger role than females in this expansion. The Han people, who all share the same culture and language, exceed 1.16 billion (2000 census), and are by far the largest ethnic group in the world. The expansion process of Han culture is thus of great interest to researchers in many fields.

Agriculture↗

PubMed2004

Analyses of genetic structure of Tibeto-Burman populations reveals sex-biased admixture in southern Tibeto-Burmans.

An unequal contribution of male and female lineages from parental populations to admixed ones is not uncommon in the American continents, as a consequence of directional gene flow from European men into African and Hispanic Americans in the past several centuries. However, little is known about sex-biased admixture in East Asia, where substantial migrations are recorded. Tibeto-Burman (TB) populations were historically derived from ancient tribes of northwestern China and subsequently moved to the south, where they admixed with the southern natives during the past 2600 years. They are currently extensively distributed in China and Southeast Asia. In this study, we analyze the variations of 965 Y chromosomes and 754 mtDNAs in >20 TB populations from China. By examining the haplotype group distributions of Y-chromosome and mtDNA markers and their principal components, we show that the genetic structure of the extant southern Tibeto-Burman (STB) populations were primarily formed by two parental groups: northern immigrants and native southerners. Furthermore, the admixture has a bias between male and female lineages, with a stronger influence of northern immigrants on the male lineages (approximately 62%) and with the southern natives contributing more extensively to the female lineages (approximately 56%) in the extant STBs. This is the first genetic evidence revealing sex-biased admixture in STB populations, which has genetic, historical, and anthropological implications.

Chromosomes, Human, Y↗

PubMed2004

Molecular cloning and expression of two closely related GTP-binding proteins from zebrafish.

Developmentally regulated GTP-binding proteins (DRGs) are a subclass of GTP-binding proteins that have been discovered recently. Here we report two zebrafish DRG cDNA clones closely related to human and mouse DRG genes. The two DRG sequences showed a high degree of similarity (55% identity, 72% similarity) at the amino acids level. Whole mount in situ hybridization revealed expression of zebrafish DRGs maternally, following the onset of zygotic transcription at the mid-blastula transition (MBT) and throughout embryonic. The expression of these two genes in different tissues follows a similar pattern, suggesting that they may serve a similar function.

Amino Acid Sequence↗

PubMed2003

GSTP1 A1578G (Ile105Val) polymorphism in benzidine-exposed workers: an association with cytological grading of exfoliated urothelial cells.

A polymorphism at codon 105 (Ile/Val) in the GSTP1 gene has been associated with a higher risk for different cancer types. To assess the role of GSTP1 polymorphisms in the development of benzidine-related bladder cancer, GSTP1 AA, AG and GG genotypes were determined in occupationally benzidine-exposed Chinese workers without known disease and benzidine-exposed bladder cancer patients from the same cohort of the Shanghai area. An increased but not significant frequency of GSTP1 AG or GG carriers was observed in the occupationally exposed bladder cancer patient group [odds ratio (OR)=1.95, 95% confidence interval (CI) 0.70-5.46]. The odds ratios for the most important non-genetically determined risk factors for bladder cancer in male individuals were as follows: age (increase per year): OR 1.05, 95% CI 0.99-1.11; ever smoker: OR 1.31, 95% CI 0.47-3.69; duration of exposure (increase per year): OR 1.19, 95% CI 1.10-1.29; and high exposure: OR 4.50, 95% CI 0.70-5.46. Significant differences were found between all benzidine-exposed workers without known disease with modified exfoliated urothelial cells (grade II and higher) and all workers without known disease with at most minor changes (less than grade II) according to Papanicolaou (OR 1.90, 95% CI 1.13-3.20). These findings show for the first time an association between the GSTP1 AG or GG genotype and higher cytological gradings of exfoliated urothelial cells from formerly benzidine-exposed workers.

Aged↗

PubMed2002

Improvement of combination chemotherapy tolerance by introduction of polycistronic retroviral vector drug resistance genes MGMT and MDR1 into human umbilical cord blood CD34+ cells.

We obtained a full-length cDNA fragment encoding human O(6)-methylguanine-DNA-methyltransferase (MGMT) from the liver tissue of a patient with cholelithiasis by RT-PCR and confirmed by DNA sequencing. The polycistronic retrovirus vector G1Na-MGMT-Neo(r)-IRES-MDR1 was constructed and verified by restriction endonuclease analysis and DNA sequencing. The vector was transfected into packaging cells GP+E86 and PA317 by the LipofectAMINE method. Cord blood CD34+ cells were transfected with the supernatant of retrovirus containing human MGMT and MDR1cDNA under stimulation of hematopoietic growth factors. PCR, RT-PCR, Southern Blot, Western Blot, FACS and MTT analyses showed that dual drug resistance genes have been integrated into the genomic DNA of cord blood CD34+ cells and expressed efficiently. The transgene cord blood CD34+ cells conferred 5.8-6.3-fold stronger resistance to P-glycoprotein effluxed drugs and 5-fold to BCNU than untransduced cells. The polycistronic retrovirus vector mediated transfer of two different types of drug resistance genes into human cord blood CD34+ cells and co-expression provided an experimental foundation for improving combination chemotherapy tolerance in clinical practice.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2002

[Two single nucleotide polymorphisms of beta 2-adrenoceptor gene in elderly patients with hypertension].

OBJECTIVE: To investigate the association of two single nucleotide polymorphisms (SNPs) of beta 2-adrenoceptor (beta 2-AR) gene with hypertension in elderly patients. METHODS: The study samples were collected from unrelated Chinese Han population of Dabie Mountain in Anhui province. Eighty-six elderly patients with hypertension and 43 controls were selected. Genotypes of +1053 and +1239 SNPs were typed by polymerase chain reaction-restriction fragment length polymorphism. RESULTS: The frequencies of the two SNPs complied well with the Hardy-Weinberg equilibrium in normal group. The distribution of genotypes AA, GA,GG of the SNP at locus +1239 in moderate and severe hypertension group was significantly different from that in normal group (chi square=8.67, P<0.05). There were evident differences in the frequencies of alleles of the two groups (chi square=4.02, P<0.05). No significant difference was observed in the distribution of genotypes of the SNP at locus +1053 between the two groups. CONCLUSION: These data indicate that the SNP at locus +1239 of beta 2-AR gene is associated with hypertension in elderly patients.

Aged↗

PubMed2002

[Analysis of three Y-STR loci polymorphism in isolated populations].

OBJECTIVE: To figure out the polymorphism of three Y-STR loci in isolated populations and explore the consanguinity of the populations with the use of Y-STR. METHODS: Male samples were selected from two isolated populations(80 and 60 males) in Zhejiang province and one open population (36 males), genescan was performed with males' DNA by genescan technology with ABI PRISM 377 sequencer at Y chromosome loci DYS388, DYS390 and DYS395. RESULTS: DYS388, DYS390, DYS395 allele counts in Yushan island population, Taohua island population and open population were 8, 9, 7, 5, 6, 7 and 6, 6, 5 respectively. Gene diversity was between 0.70-0.80 in the three populations. There was no difference in distribution of allele frequency and shared genotypes between the isolated populations and the open population by statistical test. Genetic distance is long between Taohua island population and open population, short between Yushan island population and open population, and moderate between Yushan island population and Taohua island population. CONCLUSION: The main allele is 129 at DYS388; 215 at DYS390; and 119 at DYS395. The distribution of allele frequency and gene diversity at DYS388, DYS390, DYS395 loci, and the shared genotypes between populations as well as the genetic distance are unable to explain the blood relationship between the isolated and open populations, suggesting the additional studies in large sample size will be necessary to use Y-STR for exploring the blood relationship between populations.

Alleles↗

PubMed2002

[Analysis of mutation sites of BRCA1 gene in Chinese patients with breast cancer].

OBJECTIVE: To detect the mutation sites of exons 2, 20, 11A and 11B in Chinese patients with breast cancer. METHODS: A total of 86 patients with breast cancer without blood relationship were randomly selected. Polymerase chain reaction (PCR) and double-strand DNA direct sequencing were applied. RESULTS: No mutations, especially deletions were found in exons 2, 20 and 11 with carefully checking the sequencing results, although they were reported frequently in Europe populations with breast cancer. We found one polymorphism in exon 11, with high frequency, and in the test of chi-square, the frequencies of two alleles had no significant difference between the patients and controls. CONCLUSION: The above results suggest this SNP may not be associated with the breast cancer in Chinese population, and indicates that the gene sequence of what we have studied doesn't account much for occurrence of the breast cancer in the population of China.

Asian People↗

PubMed2000

[Construction and Expression of Retroviral Vector Encoding Enhanced Green Fluorescent Protein]

Retroviral vectors are wildly used as vehicles for gene transfer into hematopoietic cells based on its potency for efficient gene delivery and integration of transgene in host genome. The development of better transduction protocols depends on gene markers that allow a rapid detection and effective selection of genetically transduced cells. In this study, the enhanced green fluorescent protein (EGFP), a gene that is optimized for detection and expression in mammalian cells, was firstly amplified and cloned by high-fidelity PCR. The vector LGSN carrying EGFP gene was then constructed and the retroviral producer cell lines that yield high titers of LGSN vector in supernatants were developed by liposome-mediated transfection in combination with cross infection. Both GP + envAm12 murine fibroblasts and K562 leukemic cells transduced with EGFP virus demonstrated a stable green fluorescence signal readily detectable by flow cytometry or fluorescence microscopy in up to 97% and 86% of examined cells, respectively. The integration of LGSN provirus in transduced cells was confirmed by PCR analysis. These results indicate EGFP is a suitable reporter molecule for gene transfer and expression in hematopoietic cells. Therefore, the bright and long-term expression of EGFP in living cells will advance the study of gene therapy in vitro and in vivo, particularly for human applications.

Journal Article↗

PubMedDate not supplied

Association study of six activity SNPS in adrenal steroid hormone metabolism and IBM related genes with precocious puberty in Chinese girls.

OBJECTIVES: In order to investigate whether the variances in the candidate genes (Insulin receptor substrate IRS-1, beta3-adrenergic receptor ADRB3, 3 beta-hydro-xysteroid dehydrogenase HSD3B2, glucocorticoid receptor GRL and 21-hydroxylase CYP21) which affect the metabolism of adrenal steroids hormone and body composition, are associated with precocious puberty in Chinese girls. METHODS: PCR-RFLP analysis method was applied in the typing of six activity SNPs in five genes in two groups: 176 precocious puberty girls as case and 192 healthy girls as control. RESULTS: The typing results showed that the frequencies of the allele CYP21 L282 polymorphism were 32.7% and 32.6% in case and control groups (P=0.518), respectively. For IRS-1 R972, they were 0.6% in cases and 2.3% in controls (P=0.043), for ADRB3 R64, 13.6% in cases and 12% in controls (P=0. 378), and for GRL S363, 7.4% in cases and 5.73% in controls (P=0.335). No sample in the two groups carries the variation of CYP21 I172N and HSD3B2 L236S. CONCLUSION: Among these six activity SNPs in five candidate genes, IRS-1 972R was statistically associated with the onset time of puberty in Chinese girls. In order to confirm whether the candidate genes have any other activity SNPs that are associated with the onset time of puberty in Chinese girls, resequencing of these candidate genes is needed in following time.

3-Hydroxysteroid Dehydrogenases↗