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  1. Fulltext A comparison of assays for accurate copy number measurement of the low-affinity Fc gamma receptor genes FCGR3A and FCGR3B
    Haridan US, Mokhtar U, Machado LR, Abdul Aziz AT, Shueb RH, Zaid M, et al.
    PLoS One, 2015;10(1):e0116791.
    PMID: 25594501 DOI: 10.1371/journal.pone.0116791
    The FCGR3 locus encoding the low affinity activating receptor FcγRIII, plays a vital role in immunity triggered by cellular effector and regulatory functions. Copy number of the genes FCGR3A and FCGR3B has previously been reported to affect susceptibility to several autoimmune diseases and chronic inflammatory conditions. However, such genetic association studies often yield inconsistent results; hence require assays that are robust with low error rate. We investigated the accuracy and efficiency in estimating FCGR3 CNV by comparing Sequenom MassARRAY and paralogue ratio test-restriction enzyme digest variant ratio (PRT-REDVR). In addition, since many genetic association studies of FCGR3B CNV were carried out using real-time quantitative PCR, we have also included the evaluation of that method's performance in estimating the multi-allelic CNV of FCGR3B. The qPCR assay exhibited a considerably broader distribution of signal intensity, potentially introducing error in estimation of copy number and higher false positive rates. Both Sequenom and PRT-REDVR showed lesser systematic bias, but Sequenom skewed towards copy number normal (CN = 2). The discrepancy between Sequenom and PRT-REDVR might be attributed either to batch effects noise in individual measurements. Our study suggests that PRT-REDVR is more robust and accurate in genotyping the CNV of FCGR3, but highlights the needs of multiple independent assays for extensive validation when performing a genetic association study with multi-allelic CNVs.
    Matched MeSH terms: Dengue/genetics; Receptors, IgG/genetics*; Genetic Predisposition to Disease/genetics; DNA Copy Number Variations/genetics; GPI-Linked Proteins/genetics
  2. Patterns of linkage disequilibrium at PARK16 may explain variances in genetic association studies
    Li H, Teo YY, Tan EK
    Mov Disord, 2015 Sep;30(10):1335-42.
    PMID: 25758099 DOI: 10.1002/mds.26176
    Reproducing genomewide association studies findings in different populations is challenging, because the reproducibility fundamentally relies on the similar patterns of linkage disequilibrium between the unknown causal variants and the genotyped single-nucleotide polymorphisms (SNPs).
    Matched MeSH terms: Parkinson Disease/genetics*; Linkage Disequilibrium/genetics*; Polymorphism, Single Nucleotide/genetics*; European Continental Ancestry Group/genetics*; Asian Continental Ancestry Group/genetics*
  3. Fulltext Novel population specific autosomal copy number variation and its functional analysis amongst Negritos from Peninsular Malaysia
    Mokhtar SS, Marshall CR, Phipps ME, Thiruvahindrapuram B, Lionel AC, Scherer SW, et al.
    PLoS One, 2014;9(6):e100371.
    PMID: 24956385 DOI: 10.1371/journal.pone.0100371
    Copy number variation (CNV) has been recognized as a major contributor to human genome diversity. It plays an important role in determining phenotypes and has been associated with a number of common and complex diseases. However CNV data from diverse populations is still limited. Here we report the first investigation of CNV in the indigenous populations from Peninsular Malaysia. We genotyped 34 Negrito genomes from Peninsular Malaysia using the Affymetrix SNP 6.0 microarray and identified 48 putative novel CNVs, consisting of 24 gains and 24 losses, of which 5 were identified in at least 2 unrelated samples. These CNVs appear unique to the Negrito population and were absent in the DGV, HapMap3 and Singapore Genome Variation Project (SGVP) datasets. Analysis of gene ontology revealed that genes within these CNVs were enriched in the immune system (GO:0002376), response to stimulus mechanisms (GO:0050896), the metabolic pathways (GO:0001852), as well as regulation of transcription (GO:0006355). Copy number gains in CNV regions (CNVRs) enriched with genes were significantly higher than the losses (P value <0.001). In view of the small population size, relative isolation and semi-nomadic lifestyles of this community, we speculate that these CNVs may be attributed to recent local adaptation of Negritos from Peninsular Malaysia.
    Matched MeSH terms: Genetics, Population*; Genome, Human/genetics*; Chromosome Disorders/genetics*; DNA Copy Number Variations/genetics*
  4. The complete mitogenome of the Macquarie perch, Macquaria australasica Cuvier, 1830 (Teleostei: Percichthyidae)
    Gan HM, Tan MH, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(1):383-4.
    PMID: 24617484 DOI: 10.3109/19401736.2014.895996
    The complete mitochondrial genome of the conservationally significant Macquarie perch (Macquaria australasica) was obtained from low-coverage shotgun sequencing using the MiSeq sequencer. The M. australasica mitogenome has 16,496 base pairs (55% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 819 bp non-coding AT-rich region. This is the first mitogenome sequence for the genus Macquaria, and the third to be reported for the family Percichthyidae.
    Matched MeSH terms: Perches/genetics*; Perciformes/genetics; RNA, Ribosomal/genetics; RNA, Transfer/genetics; Fish Proteins/genetics
  5. Phenotypic screening and molecular analysis of blast resistance in fragrant rice for marker assisted selection
    Khan MA, Sen PP, Bhuiyan R, Kabir E, Chowdhury AK, Fukuta Y, et al.
    C. R. Biol., 2014 May;337(5):318-24.
    PMID: 24841958 DOI: 10.1016/j.crvi.2014.02.007
    Experiments were conducted to identify blast-resistant fragrant genotypes for the development of a durable blast-resistant rice variety during years 2012-2013. The results indicate that out of 140 test materials including 114 fragrant germplasms, 25 differential varieties (DVs) harbouring 23 blast-resistant genes, only 16 fragrant rice germplasms showed comparatively better performance against a virulent isolate of blast disease. The reaction pattern of single-spore isolate of Magnaporthe oryzae to differential varieties showed that Pish, Pi9, Pita-2 and Pita are the effective blast-resistant genes against the tested blast isolates in Bangladesh. The DNA markers profiles of selected 16 rice germplasms indicated that genotype Chinigura contained Pish, Pi9 and Pita genes; on the other hand, both BRRI dhan50 and Bawaibhog contained Pish and Pita genes in their genetic background. Genotypes Jirakatari, BR5, and Gopalbhog possessed Pish gene, while Uknimodhu, Deshikatari, Radhunipagol, Kalijira (3), Chinikanai each contained the Pita gene only. There are some materials that did not contain any target gene(s) in their genetic background, but proved resistant in pathogenicity tests. This information provided valuable genetic information for breeders to develop durable blast-resistant fragrant or aromatic rice varieties in Bangladesh.
    Matched MeSH terms: Plant Diseases/genetics*; Oryza/genetics*; Genes, Plant/genetics; DNA, Plant/genetics; Disease Resistance/genetics*
  6. Association of leptin/receptor and TNF-α gene variants with adolescent obesity in Malaysia
    Ng ZY, Veerapen MK, Hon WM, Lim RL
    Pediatr Int, 2014 Oct;56(5):689-97.
    PMID: 24628746 DOI: 10.1111/ped.12336
    BACKGROUND: Leptin (LEP) G-2548A (rs7799039), leptin receptor (LEPR) Q223R (rs1137101) and tumor necrosis factor (TNF)-α G-308A (rs1800629) gene variants have been reported to be associated with obesity, although results for subjects from different countries have been controversial. The aim of this study was to determine the prevalence of overweight and obesity in Malaysian adolescents and the association of these polymorphisms with overweight and obese or over-fat adolescents.
    METHODS: A total of 613 adolescents (241 Malay, 219 Chinese, 153 Indian) were enrolled. Anthropometric measurements of body mass index (BMI) and body fat percentage were used to classify subjects as controls (non-overweight/obese or normal fat) or as cases (overweight/obese or over-fat). Genomic DNA was extracted from oral buccal mucosa cells for genotyping using polymerase chain reaction-restriction fragment length polymorphism and data obtained were statistically analyzed.
    RESULTS: A total of 23.3% of subjects were overweight/obese whereas 11.4% were over-fat; there were significantly more overweight/obese and over-fat Indian and Malay adolescents compared to Chinese (P < 0.001). A allele was the minor one for LEPR Q223R and TNF-α G-308A in all ethnic groups, whereas G allele was minor for LEP G-2548A in Chinese and Malay adolescents, except for Indian adolescents. Indian male adolescents with AA genotype for LEP G-2548A were associated with overweight/obesity (P = 0.025; odds ratio, 3.64; 95% confidence interval: 1.15-11.54). Despite the lack of association observed for LEPR Q223R and TNF-α G-308A, Indian and Chinese subjects with AA risk genotype for LEPR Q223R/LEP G-2548A and TNF-α G-308A/LEP G-2548A, respectively, had increased mean BMI (P = 0.049, P = 0.016).
    CONCLUSIONS: Genotype distribution and association of these polymorphisms with overweight/obesity vary between ethnic groups and genders. Nevertheless, the LEP G-2548A risk allele may be associated with overweight/obese Indian male adolescents in Malaysia.
    KEYWORDS: adolescents; body fat percentage; body mass index; leptin; leptin receptor; single nucleotide polymorphism; tumor necrosis factor-α
    Matched MeSH terms: Tumor Necrosis Factor-alpha/genetics*; Leptin/genetics*; Overweight/genetics; Receptors, Leptin/genetics*; Pediatric Obesity/genetics*
  7. Fulltext A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance
    Miah G, Rafii MY, Ismail MR, Puteh AB, Rahim HA, Islam KhN, et al.
    Int J Mol Sci, 2013;14(11):22499-528.
    PMID: 24240810 DOI: 10.3390/ijms141122499
    Over the last few decades, the use of molecular markers has played an increasing role in rice breeding and genetics. Of the different types of molecular markers, microsatellites have been utilized most extensively, because they can be readily amplified by PCR and the large amount of allelic variation at each locus. Microsatellites are also known as simple sequence repeats (SSR), and they are typically composed of 1-6 nucleotide repeats. These markers are abundant, distributed throughout the genome and are highly polymorphic compared with other genetic markers, as well as being species-specific and co-dominant. For these reasons, they have become increasingly important genetic markers in rice breeding programs. The evolution of new biotypes of pests and diseases as well as the pressures of climate change pose serious challenges to rice breeders, who would like to increase rice production by introducing resistance to multiple biotic and abiotic stresses. Recent advances in rice genomics have now made it possible to identify and map a number of genes through linkage to existing DNA markers. Among the more noteworthy examples of genes that have been tightly linked to molecular markers in rice are those that confer resistance or tolerance to blast. Therefore, in combination with conventional breeding approaches, marker-assisted selection (MAS) can be used to monitor the presence or lack of these genes in breeding populations. For example, marker-assisted backcross breeding has been used to integrate important genes with significant biological effects into a number of commonly grown rice varieties. The use of cost-effective, finely mapped microsatellite markers and MAS strategies should provide opportunities for breeders to develop high-yield, blast resistance rice cultivars. The aim of this review is to summarize the current knowledge concerning the linkage of microsatellite markers to rice blast resistance genes, as well as to explore the use of MAS in rice breeding programs aimed at improving blast resistance in this species. We also discuss the various advantages, disadvantages and uses of microsatellite markers relative to other molecular marker types.
    Matched MeSH terms: Plant Diseases/genetics*; Oryza/genetics*; Microsatellite Repeats/genetics*; Chromosomes, Plant/genetics; Disease Resistance/genetics*
  8. Fulltext Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds
    Singh R, Ong-Abdullah M, Low ET, Manaf MA, Rosli R, Nookiah R, et al.
    Nature, 2013 Aug 15;500(7462):335-9.
    PMID: 23883927 DOI: 10.1038/nature12309
    Oil palm is the most productive oil-bearing crop. Although it is planted on only 5% of the total world vegetable oil acreage, palm oil accounts for 33% of vegetable oil and 45% of edible oil worldwide, but increased cultivation competes with dwindling rainforest reserves. We report the 1.8-gigabase (Gb) genome sequence of the African oil palm Elaeis guineensis, the predominant source of worldwide oil production. A total of 1.535 Gb of assembled sequence and transcriptome data from 30 tissue types were used to predict at least 34,802 genes, including oil biosynthesis genes and homologues of WRINKLED1 (WRI1), and other transcriptional regulators, which are highly expressed in the kernel. We also report the draft sequence of the South American oil palm Elaeis oleifera, which has the same number of chromosomes (2n = 32) and produces fertile interspecific hybrids with E. guineensis but seems to have diverged in the New World. Segmental duplications of chromosome arms define the palaeotetraploid origin of palm trees. The oil palm sequence enables the discovery of genes for important traits as well as somaclonal epigenetic alterations that restrict the use of clones in commercial plantings, and should therefore help to achieve sustainability for biofuels and edible oils, reducing the rainforest footprint of this tropical plantation crop.
    Matched MeSH terms: Genome, Plant/genetics*; Arecaceae/genetics*; Chromosomes, Plant/genetics; Carbohydrate Metabolism/genetics; Lipid Metabolism/genetics
  9. Fulltext Isolation and characterization of microsatellite markers for an important tropical tree, Aquilaria malaccensis (Thymelaeaceae)
    Tnah LH, Lee CT, Lee SL, Ng KK, Ng CH, Nurul-Farhanah Z, et al.
    Am J Bot, 2012 Nov;99(11):e431-3.
    PMID: 23108468 DOI: 10.3732/ajb.1200165
    Aggressive collections and trade activities in recent decades have resulted in heavy pressure on the natural stands of Aquilaria malaccensis and concerns over its long-term survival potential. To aid DNA profiling and assessment of its genetic diversity, microsatellite markers were developed for the species.
    Matched MeSH terms: Trees/genetics*; DNA Primers/genetics; DNA, Plant/genetics; Microsatellite Repeats/genetics*; Thymelaeaceae/genetics*
  10. Fulltext Elaeis oleifera genomic-SSR markers: exploitation in oil palm germplasm diversity and cross-amplification in arecaceae
    Zaki NM, Singh R, Rosli R, Ismail I
    Int J Mol Sci, 2012;13(4):4069-88.
    PMID: 22605966 DOI: 10.3390/ijms13044069
    Species-specific simple sequence repeat (SSR) markers are favored for genetic studies and marker-assisted selection (MAS) breeding for oil palm genetic improvement. This report characterizes 20 SSR markers from an Elaeis oleifera genomic library (gSSR). Characterization of the repeat type in 2000 sequences revealed a high percentage of di-nucleotides (63.6%), followed by tri-nucleotides (24.2%). Primer pairs were successfully designed for 394 of the E. oleifera gSSRs. Subsequent analysis showed the ability of the 20 selected E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The average Polymorphism Information Content (PIC) value for the SSRs was 0.402, with the tri-repeats showing the highest average PIC (0.626). Low values of observed heterozygosity (H(o)) (0.164) and highly positive fixation indices (F(is)) in the E. oleifera germplasm collection, compared to the E. guineensis, indicated an excess of homozygosity in E. oleifera. The transferability of the markers to closely related palms, Elaeis guineensis, Cocos nucifera and ornamental palms is also reported. Sequencing the amplicons of three selected E. oleifera gSSRs across both species and palm taxa revealed variations in the repeat-units. The study showed the potential of E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The markers are also a valuable genetic resource for studying E. oleifera and other genus in the Arecaceae family.
    Matched MeSH terms: Genetic Markers/genetics; DNA Primers/genetics; DNA, Plant/genetics*; Microsatellite Repeats/genetics*; Arecaceae/genetics*
  11. Development of a multiplex PCR assay for rapid identification of Burkholderia pseudomallei, Burkholderia thailandensis, Burkholderia mallei and Burkholderia cepacia complex
    Koh SF, Tay ST, Sermswan R, Wongratanacheewin S, Chua KH, Puthucheary SD
    J Microbiol Methods, 2012 Sep;90(3):305-8.
    PMID: 22705921 DOI: 10.1016/j.mimet.2012.06.002
    We have developed a multiplex PCR assay for rapid identification and differentiation of cultures for Burkholderia pseudomallei, Burkholderia thailandensis, Burkholderia mallei and Burkholderia cepacia complex. The assay is valuable for use in clinical and veterinary laboratories, and in a deployable laboratory during outbreaks.
    Matched MeSH terms: RNA, Bacterial/genetics; RNA, Ribosomal, 16S/genetics; Burkholderia pseudomallei/genetics*; Burkholderia cepacia complex/genetics*; Burkholderia mallei/genetics*
  12. Fulltext PanSNPdb: the Pan-Asian SNP genotyping database
    Ngamphiw C, Assawamakin A, Xu S, Shaw PJ, Yang JO, Ghang H, et al.
    PLoS One, 2011;6(6):e21451.
    PMID: 21731755 DOI: 10.1371/journal.pone.0021451
    The HUGO Pan-Asian SNP consortium conducted the largest survey to date of human genetic diversity among Asians by sampling 1,719 unrelated individuals among 71 populations from China, India, Indonesia, Japan, Malaysia, the Philippines, Singapore, South Korea, Taiwan, and Thailand. We have constructed a database (PanSNPdb), which contains these data and various new analyses of them. PanSNPdb is a research resource in the analysis of the population structure of Asian peoples, including linkage disequilibrium patterns, haplotype distributions, and copy number variations. Furthermore, PanSNPdb provides an interactive comparison with other SNP and CNV databases, including HapMap3, JSNP, dbSNP and DGV and thus provides a comprehensive resource of human genetic diversity. The information is accessible via a widely accepted graphical interface used in many genetic variation databases. Unrestricted access to PanSNPdb and any associated files is available at: http://www4a.biotec.or.th/PASNP.
    Matched MeSH terms: Gene Frequency/genetics; Haplotypes/genetics*; Polymorphism, Single Nucleotide/genetics*; Asian Continental Ancestry Group/genetics*; DNA Copy Number Variations/genetics
  13. KCNQ1 variants associate with type 2 diabetes in Malaysian Malay subjects
    Saif-Ali R, Muniandy S, Al-Hamodi Z, Lee CS, Ahmed KA, Al-Mekhlafi AM, et al.
    Ann Acad Med Singap, 2011 Nov;40(11):488-92.
    PMID: 22206064
    INTRODUCTION: Type 2 diabetes (T2D) candidate gene: potassium voltage-gated channel, KQT-like subfamily, member 1 (KCNQ1) was suggested by conducting a genome wide association study (GWAS) in Japanese population. Association studies have been replicated among East Asian populations; however, the association between this gene and T2D in Southeast Asian populations still needs to be studied. This study aimed to investigate the association of KCNQ1 common variants with type 2 diabetes in Malaysian Malay subjects.

    MATERIALS AND METHODS: The KCNQ1 single nucleotide polymorphisms (SNPs): rs2237892, rs2283228, and rs2237895 were genotyped in 234 T2D and 177 normal Malay subjects.

    RESULTS: The risk allele of the rs2283228 (A) was strongly associated with T2D (OR = 1.7, P = 0.0006) while the rs2237892 (C) was moderately associated with T2D (OR = 1.45, P = 0.017). The recessive genetic models showed that rs2283228 was strongly associated with T2D (OR = 2.35, P = 0.00005) whereas rs2237892 showed a moderate association with T2D (OR = 1.69, P = 0.01). The haplotype block (TCA), which contained the protective allele, correlated with a protection from T2D (OR = 0.5, P = 0.003). Furthermore, the diplotype (CAA-TCA) that contained the protective haplotype was protected against T2D (OR = 0.46, P = 0.006).

    CONCLUSION: The KCNQ1 SNPs, haplotypes and diplotypes are associated with T2D in the Malaysian Malay subjects.

    Matched MeSH terms: Diabetes Mellitus, Type 2/genetics*; Genetics, Population; Haplotypes/genetics; Polymorphism, Single Nucleotide/genetics; KCNQ1 Potassium Channel/genetics*
  14. Fulltext Optimization of PCR conditions to amplify Cyt b, COI and 12S rRNA gene fragments of Malayan gaur (Bos gaurus hubbacki) mtDNA
    Rosli MK, Zamzuriada AS, Syed-Shabthar SM, Mahani MC, Abas-Mazni O, Md-Zain BM
    Genet. Mol. Res., 2011;10(4):2554-68.
    PMID: 22033937 DOI: 10.4238/2011.October.19.2
    PCR has been extensively used for amplification of DNA sequences. We conducted a study to obtain the best amplification conditions for cytochrome b (Cyt b), cytochrome c oxidase I (COI) and 12S rRNA (12S) gene fragments of Malayan gaur mtDNA. DNA from seven Malayan gaur samples were extracted for PCR amplification. Various trials and combinations were tested to determine the best conditions of PCR mixture and profile to obtain the best PCR products for sequencing purposes. Four selected target factors for enhancing PCR, annealing temperature, concentration of primer pairs, amount of Taq polymerase, and PCR cycle duration, were optimized by keeping the amount of DNA template (50 ng/μL) and concentration of PCR buffer (1X), MgCl(2) (2.5 mM) and dNTP mixture (200 μM each) constant. All genes were successfully amplified, giving the correct fragment lengths, as assigned for both forward and reverse primers. The optimal conditions were determined to be: 0.1 μM primers for Cyt b and COI, 0.3 μM primers for 12S, 1 U Taq polymerase for all genes, 30 s of both denaturation and annealing cycles for Cyt b, 1 min of both stages for 12S and COI and annealing temperature of 58.4 ° C for Cyt b, 56.1 ° C for 12S and 51.3 ° C for COI. PCR products obtained under these conditions produced excellent DNA sequences.
    Matched MeSH terms: Electron Transport Complex IV/genetics*; DNA, Mitochondrial/genetics*; RNA, Ribosomal/genetics*; Ruminants/genetics*; Cytochromes b/genetics*
  15. Development of single-locus DNA microsatellite markers using 5'anchored ISSR-PCR method for the mangrove horseshoe crab, Carcinoscorpius rotundicauda (Latreille, 1802) in Peninsular Malaysia
    Adibah AB, Ling LP, Tan SG, Faridah QZ, Christianus A
    Mol Biol Rep, 2012 Apr;39(4):3815-20.
    PMID: 21744263 DOI: 10.1007/s11033-011-1159-6
    Horseshoe crabs are said to be declining worldwide. However, there is still no published report on the status of horseshoe crabs in Malaysia. Thus, we report here eight informative microsatellite markers that were developed using the 5'-anchored ISSR-PCR enrichment procedure to diagnose the population genetic structure of the mangrove horseshoe crab, Carcinoscorpius rotundicauda from Peninsular Malaysia. This set of markers was tested on 127 samples and showed polymorphism in this species. Hence they should be useful in future essential population genetic studies of these living fossils in the Southeast Asian region.
    Matched MeSH terms: DNA/genetics*; Genetic Markers/genetics; Horseshoe Crabs/genetics*; Microsatellite Repeats/genetics*; Genetic Loci/genetics*
  16. Metal inducible activity of the oil palm metallothionein-like gene promoter (MT3-A) in prokaryotes
    Kamaladini H, Abdullah SN, Aziz MA
    J Biosci Bioeng, 2011 Feb;111(2):217-25.
    PMID: 21044862 DOI: 10.1016/j.jbiosc.2010.09.010
    Reporter gene activity under the regulation of the oil palm metallothionein-like gene, MT3-A promoter was assessed in prokaryotes. Vector constructs containing MT3-A promoter with (W1MT3-A) and without (W2MT3-A) five prime untranslated region (5'-UTR) fused to ß-glucuronidase (GUS) gene in pCAMBIA 1304 vector were produced. 5'-rapid amplification of cDNA ends (RACE) using mRNA isolated from Escherichia coli and Agrobacterium tumefaciens harboring W1MT3-A confirmed that fusion transcripts of MT3-A 5'-UTR-GUS were successfully produced in both bacteria. Competitive PCR and GUS fluorometric assay showed changes in the level of GUS gene transcripts and enzyme activity in response to increasing concentrations of Cu²+ and Zn²+. The application of Cu²+ increased GUS activity and GUS mRNA level in both bacteria. In E. coli, a high level of GUS activity driven by W1MT3-A and W2MT3-A was observed in treatment with 25 μM Cu²+ resulting in an increase in the GUS mRNA level to 7.2 and 7.5 x 10⁻⁴ pmol/μl respectively, compared to the control (5.1 x 10⁻⁴ pmol/μl). The lowest GUS activity and GUS mRNA level were obtained for W1MT3-A and W2MT3-A in the presence of 100 μM Cu²+ in both bacteria compared to the control (without Cu²+). The application of different Zn²+ concentrations resulted in a strong decrease in the GUS activity and GUS mRNA level in E. coli and A. tumefaciens. These findings showed that the oil palm MT3-A promoter is functional in prokaryotes and produced detectable GUS transcripts and enzyme activities. This promoter may potentially be used in prokaryotic systems which require metal inducible gene expression.
    Matched MeSH terms: Escherichia coli/genetics; Glucuronidase/genetics; Metallothionein/genetics*; Agrobacterium tumefaciens/genetics; Arecaceae/genetics*
  17. Fulltext Roles of Sema4D and Plexin-B1 in tumor progression
    Ch'ng ES, Kumanogoh A
    Mol. Cancer, 2010;9:251.
    PMID: 20858260 DOI: 10.1186/1476-4598-9-251
    Sema4D, also known as CD100, is a protein belonging to class IV semaphorin. Its physiologic roles in the immune and nervous systems have been extensively explored. However, the roles of Sema4D have extended beyond these traditionally studied territories. Via interaction with its high affinity receptor Plexin-B1, Sema4D-Plexin-B1 involvement in tumor progression is strongly implied. Here, we critically review and delineate the Sema4D-Plexin-B1 interaction in many facets of tumor progression: tumor angiogenesis, regulation of tumor-associated macrophages and control of invasive growth. We correlate the in vitro and in vivo experimental data with the clinical study outcomes, and present a molecular mechanistic basis accounting for the intriguingly contradicting results from these recent studies.
    Matched MeSH terms: Neoplasms/genetics; Nerve Tissue Proteins/genetics; Receptors, Cell Surface/genetics; Antigens, CD/genetics; Semaphorins/genetics
  18. Maternal uniparental heterodisomy of chromosome 6 in a boy with an isolated cleft lip and palate
    Salahshourifar I, Halim AS, Sulaiman WA, Zilfalil BA
    Am J Med Genet A, 2010 Jul;152A(7):1818-21.
    PMID: 20583164 DOI: 10.1002/ajmg.a.33526
    We describe a chromosome 6 uniparental disomy (UPD6) in a boy, discovered during a screening for the genetic cause of cleft lip and palate. In the medical literature, almost all documented cases of UPD6 are paternal in origin, and only four were maternal. We present here a report of complete maternal chromosome 6 uniparental heterodisomy. Haplotype analysis was performed using highly polymorphic short tandem repeat (STR) markers that span both arms of chromosome 6. Analysis of these markers revealed the presence of two maternal alleles but no paternal allele, indicating an instance of maternal uniparental heterodisomy. Chromosome analysis of peripheral blood lymphocytes confirmed a normal male karyotype. Advanced maternal age at the time of the infant's birth and heterodisomy of markers around the centromere favors a meiosis-I error. No specific phenotype has been reported for maternal UPD6. Therefore, the cleft lip and palate in the present case probably occurred due to other risk factors. This report provides further evidence that maternal UPD6 has no specific clinical consequences and adds to the collective knowledge of this rare chromosomal finding.
    Matched MeSH terms: Chromosomes, Human, Pair 6/genetics*; Cleft Lip/genetics*; Cleft Palate/genetics*; Microsatellite Repeats/genetics; Uniparental Disomy/genetics*
  19. Fulltext Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation
    Fornarino S, Pala M, Battaglia V, Maranta R, Achilli A, Modiano G, et al.
    BMC Evol. Biol., 2009;9:154.
    PMID: 19573232 DOI: 10.1186/1471-2148-9-154
    Central Asia and the Indian subcontinent represent an area considered as a source and a reservoir for human genetic diversity, with many markers taking root here, most of which are the ancestral state of eastern and western haplogroups, while others are local. Between these two regions, Terai (Nepal) is a pivotal passageway allowing, in different times, multiple population interactions, although because of its highly malarial environment, it was scarcely inhabited until a few decades ago, when malaria was eradicated. One of the oldest and the largest indigenous people of Terai is represented by the malaria resistant Tharus, whose gene pool could still retain traces of ancient complex interactions. Until now, however, investigations on their genetic structure have been scarce mainly identifying East Asian signatures.
    Matched MeSH terms: DNA, Mitochondrial/genetics*; Genetics, Population*; Chromosomes, Human, Y/genetics*; Asian Continental Ancestry Group/genetics
  20. Fulltext Simultaneous differential detection of human pathogenic and nonpathogenic Vibrio species using a multiplex PCR based on gyrB and pntA genes
    Teh CS, Chua KH, Thong KL
    J Appl Microbiol, 2010 Jun;108(6):1940-5.
    PMID: 19891709 DOI: 10.1111/j.1365-2672.2009.04599.x
    To develop a multiplex PCR targeting the gyrB and pntA genes for Vibrio species differentiation.
    Matched MeSH terms: Bacterial Proteins/genetics; DNA, Bacterial/genetics; NADP Transhydrogenases/genetics*; Vibrio/genetics; DNA Gyrase/genetics*
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