Showing papers in "Journal of Genetics in 2011"

The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers

Abstract: With an objective to develop a genetic map in pigeon pea (Cajanus spp.), a total of 554 diversity arrays technology (DArT) markers showed polymorphism in a pigeon pea F2 mapping population of 72 progenies derived from an interspecific cross of ICP 28 (Cajanus cajan) and ICPW 94 (Cajanus scarabaeoides). Approximately 13% of markers did not conform to expected segregation ratio. The total number of DArT marker loci segregating in Mendelian manner was 405 with 73.1% (P > 0.001) of DArT markers having unique segregation patterns. Two groups of genetic maps were generated using DArT markers. While the maternal genetic linkage map had 122 unique DArT maternal marker loci, the paternal genetic linkage map has a total of 172 unique DArT paternal marker loci. The length of these two maps covered 270.0 cM and 451.6 cM, respectively. These are the first genetic linkage maps developed for pigeon pea, and this is the first report of genetic mapping in any grain legume using diversity arrays technology.

Cytotaxonomical analysis of Momordica L. (Cucurbitaceae) species of Indian occurrence.

Abstract: Somatic chromosome number and detailed karyotype analysis were carried out in six Indian Momordica species viz. M. balsamina, M. charantia, M. cochinchinensis, M. dioica, M. sahyadrica and M. cymbalaria (syn. Luffa cymbalaria; a taxon of controversial taxonomic identity). The somatic chromosome number 2n = 22 was reconfirmed in monoecious species (M. balsamina and M. charantia). Out of four dioecious species, the chromosome number was reconfirmed in M. cochinchinensis (2n = 28), M. dioica (2n = 28) and M. subangulata subsp. renigera (2n = 56), while in M. sahyadrica (2n = 28) somatic chromosome number was reported for the first time. A new chromosome number of 2n = 18 was reported in M. cymbalaria against its previous reports of 2n = 16, 22. The karyotype analysis of all the species revealed significant numerical and structural variations of chromosomes. It was possible to distinguish chromosomes of M. cymbalaria from other Momordica species and also between monoecious and dioecious taxa of the genus. Morphology and crossability among the dioecious species was also studied. Evidence from morphology, crossability, pollen viability and chromosome synapsis suggests a segmental allopolyploid origin for M. subangulata subsp. renigera. The taxonomic status of the controversial taxon M. cymbalaria was also discussed using morphological, karyological and crossability data.

Wheat kernel dimensions: how do they contribute to kernel weight at an individual QTL level?

Abstract: Kernel dimensions (KD) contribute greatly to thousand-kernel weight (TKW) in wheat. In the present study, quantitative trait loci (QTL) for TKW, kernel length (KL), kernel width (KW) and kernel diameter ratio (KDR) were detected by both conditional and unconditional QTL mapping methods. Two related F8:9 recombinant inbred line (RIL) populations, comprising 485 and 229 lines, respectively, were used in this study, and the trait phenotypes were evaluated in four environments. Unconditional QTL mapping analysis detected 77 additive QTL for four traits in two populations. Of these, 24 QTL were verified in at least three trials, and five of them were major QTL, thus being of great value for marker assisted selection in breeding programmes. Conditional QTL mapping analysis, compared with unconditional QTL mapping analysis, resulted in reduction in the number of QTL for TKW due to the elimination of TKW variations caused by its conditional traits; based on which we first dissected genetic control system involved in the synthetic process between TKW and KD at an individual QTL level. Results indicated that, at the QTL level, KW had the strongest influence on TKW, followed by KL, and KDR had the lowest level contribution to TKW. In addition, the present study proved that it is not all-inclusive to determine genetic relationships of a pairwise QTL for two related/causal traits based on whether they were co-located. Thus, conditional QTL mapping method should be used to evaluate possible genetic relationships of two related/causal traits.

Identification of possible genetic polymorphisms involved in cancer cachexia: a systematic review

Abstract: Cancer cachexia is a polygenic and complex syndrome. Genetic variations in regulation of the inflammatory response, muscle and fat metabolic pathways, and pathways in appetite regulation are likely to contribute to the susceptibility or resistance to developing cancer cachexia. A systematic search of Medline and EmBase databases, covering 1986–2008 was performed for potential candidate genes/genetic polymorphisms relating to cancer cachexia. Related genes were then identified using pathway functional analysis software. All candidate genes were reviewed for functional polymorphisms or clinically significant polymorphisms associated with cachexia using the OMIM and GeneRIF databases. Genes with variants which had functional or clinical associations with cachexia and replicated in at least one study were entered into pathway analysis software to reveal possible network associations between genes. A total of 184 polymorphisms with functional or clinical relevance to cancer cachexia were identified in 92 candidate genes. Of these, 42 polymorphisms (in 33 genes) were replicated in more than one study with 13 polymorphisms found to influence two or more hallmarks of cachexia (i.e. inflammation, loss of fat mass and/or lean mass and reduced survival). Thirty-three genes were found to be significantly interconnected in two major networks with four genes (ADIPOQ, IL6, NFKB1 and TLR4) interlinking both networks. Selection of candidate genes and polymorphisms is a key element of multigene study design. The present study provides an initial framework to select genes/ polymorphisms for further study in cancer cachexia, and to develop their potential as susceptibility biomarkers of developing cachexia.

A quick method to calculate QTL confidence interval

Abstract: There is much interest in the nature of the genetic variation for quantitative traits, and mapping quantitative trait loci (QTL) is a method to reveal it (Mackay 2001). Once a QTL is identified, interest turns to determining the confidence interval (CI) of QTL location, which is a useful guide for further experimental design and analysis to reveal the real molecular nature of the variation of quantitative traits. The classic method to determine the CI of QTL location is nonparametric bootstrap suggested by Visscher et al. (1996). A series of bootstrap samples are formed by withdrawing observations randomly with replacement from the observed data, and then mapping to detect QTL at each putative position. These positions with largest test statistics of each bootstrap sample form the bootstrap distribution of QTL location. The 2.5 and 97.5 percentiles are lower limit and upper limit of 95% QTL confidence interval. Although bootstrap is timedemanding, especially for large complex populations, it has been used frequently. Some authors’ investigation showed that bootstrap CI provide appropriate coverage (Walling et al. 1998, 2002). However, some authors’ investigation showed that bootstrap CI behave poorly (Manichaikul et al. 2006). So the bootstrap CI is not very stable, perhaps because of the unusual character of distributions obtained in applications (Sugiyama et al. 2001). Bennewitz et al. (2002) presented three methods of permutation bootstrapping, which is a modification of traditional nonparametric bootstrap, to improve the precision of the CI and showed that CI will be short and less biased in a large number of simulated configurations, if the impact of markers was corrected. A quick method to determine the CI of a QTL location is to use 1-LOD and 2-LOD support intervals as 95% and 99% CI (Lander and Botstein 1989). Supposing the largest LOD score is y, then the largest (smallest) position on the left (right) of QTL where LOD score less than y-x is lower

Correlations between genetic variance and adiposity measures, and gene × gene interactions for obesity in postmenopausal Vietnamese women

Abstract: Although environmental factors are important, there is considerable evidence that genes also have a significant role in the pathogenesis of obesity. We conducted a population-based study to investigate the relationship between candidate genes for obesity (UCP1, UCP2, ADRA2B, ADRB3, LEPR, VDR and ESR1) and adiposity measures (body mass index, body fat percentage, weight, waist circumference and waist-hip ratio) in terms of individual gene and gene x gene interaction in models unadjusted and adjusted for covariates (age, years since menopause, educational level and total energy intake). Postmenopausal women with TC genotype of ESR1 gene had higher body fat percentage than those with TT genotype in the models unadjusted and adjusted for the covariates (P = 0.006 in adjusted model). In multiple logistic regression analysis, BsmI and ApaI SNPs of VDR genes were significantly associated with overweight and obesity. The UCP2-VDR ApaI interaction to susceptibility of overweight and obesity was first observed from logistic regression analysis, and then confirmed in the multifactor dimensionality reduction method unadjusted and adjusted for the covariates. This interaction had 69.09% prediction accuracy for overweight and obesity (P = 0.001, sign test). In conclusion, the study suggests the significant association of ESR1 and VDR genes with adiposity measures and the UCP2-VDR ApaI interaction to susceptibility to being overweight and obesity in postmenopausal Vietnamese women.

Quantitative trait loci for rice yield-related traits using recombinant inbred lines derived from two diverse cultivars.

Abstract: The thousand-grain weight and spikelets per panicle directly contribute to rice yield. Heading date and plant height also greatly influence the yield. Dissection of genetic bases of yield-related traits would provide tools for yield improvement. In this study, quantitative trait loci (QTL) mapping for spikelets per panicle, thousand-grain weight, heading date and plant height was performed using recombinant inbred lines derived from a cross between two diverse cultivars, Nanyangzhan and Chuan7. In total, 20 QTLs were identified for four traits. They were located to 11 chromosomes except on chromosome 4. Seven and five QTLs were detected for thousand-grain weight and spikelets per panicle, respectively. Four QTLs were identified for both heading date and plant height. About half the QTLs were commonly detected in both years, 2006 and 2007. Six QTLs are being reported for the first time. Two QTL clusters were identified in regions flanked by RM22065 and RM5720 on chromosome 7 and by RM502 and RM264 on chromosome 8, respectively. The parent, Nanyangzhan with heavy thousand-grain weight, carried alleles with increased effects on all seven thousand-grain weight QTL, which explained why there was no transgressive segregation for thousand-grain weight in the population. In contrast, Chuan7 with more spikelets per panicle carried positive alleles at all five spikelets per panicle QTL except qspp5. Further work on distinction between pleiotropic QTL and linked QTL is needed in two yield-related QTL clusters.

Mapping of shoot fly tolerance loci in sorghum using SSR markers

Abstract: Sorghum (Sorghum bicolor (L.) Moench) is one of the most important crops in the semiarid regions of the world. One of the important biotic constraints to sorghum production in India is the shoot fly which attacks sorghum at the seedling stage. Identification of the genomic regions containing quantitative trait loci (QTLs) for resistance to shoot fly and the linked markers can facilitate sorghum improvement programmes through marker-assisted selection. A simple sequence repeat (SSR) marker- based skeleton linkage map of two linkage groups of sorghum was constructed in a population of 135 recombinant inbred lines (RIL) derived from a cross between IS18551 (resistant to shoot fly) and 296B (susceptible to shoot fly). A total of 14 SSR markers, seven each on linkage groups A and C were mapped. Using data of different shoot fly resistance component traits, one QTL which is common for glossiness, oviposition and dead hearts was detected following composite interval mapping (CIM) on linkage group A. The phenotypic variation explained by this QTL ranged from 3.8%–6.3%. Besides the QTL detected by CIM, two more QTLs were detected following multi-trait composite interval mapping (MCIM), one each on linkage groups A and C for the combinations of traits which were correlated with each other. Results of the present study are novel as we could find out the QTLs governing more than one trait (pleiotropic QTLs). The identification of pleiotropic QTLs will help in improvement of more than one trait at a time with the help of the same linked markers. For all the QTLs, the resistant parent IS18551 contributed resistant alleles.

Comparison of quantitative trait loci for rice yield, panicle length and spikelet density across three connected populations.

Abstract: 1National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China 2College of Biosafety Science and Technology Hunan Agricultural University, Changsha 410128, People’s Republic of China 3Present address: Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, People’s Republic of China

Hypermutation and stress adaptation in bacteria

Abstract: Hypermutability is a phenotype characterized by a moderate to high elevation of spontaneous mutation rates and could result from DNA replication errors, defects in error correction mechanisms and many other causes. The elevated mutation rates are helpful to organisms to adapt to sudden and unforeseen threats to survival. At the same time hypermutability also leads to the generation of many deleterious mutations which offset its adaptive value and therefore disadvantageous. Nevertheless, it is very common in nature, especially among clinical isolates of pathogens. Hypermutability is inherited by indirect (second order) selection along with the beneficial mutations generated. At large population sizes and high mutation rates many cells in the population could concurrently acquire beneficial mutations of varying adaptive (fitness) values. These lineages compete with the ancestral cells and also among themselves for fixation. The one with the 'fittest' mutation gets fixed ultimately while the others are lost. This has been called 'clonal interference' which puts a speed limit on adaptation. The original clonal interference hypothesis has been modified recently. Nonheritable (transient) hypermtability conferring significant adaptive benefits also occur during stress response although its molecular basis remains controversial. The adaptive benefits of heritable hypermutability are discussed with emphasis on host-pathogen interactions.

QTL mapping for test weight by using F(2:3) population in maize.

Abstract: Test weight is an important trait in maize breeding Understanding the genetic mechanism of test weight is important for effective selection of maize test weight improvement In this study, quantitative trait loci (QTL) for maize test weight were identified In the years 2007 and 2008, a F(2:3) population along with the parents Chang7-2 and Zheng58 were planted in Zhengzhou, People's Republic of China Significant genotypic variation for maize test weight was observed in both years Based on the genetic map containing 180 polymorphic SSR markers with an average linkage distance of 110 cM, QTL for maize test weight were analysed by mixed-model composite interval mapping Five QTL, including four QTL with only additive effects, were identified on chromosomes 1, 2, 3, 4 and 5, and together explained 252% of the phenotypic variation Seven pairs of epistatic interactions were also detected, involving 11 loci distributed on chromosomes 1, 2, 3, 4, 5 and 7, respectively, which totally contributed 182% of the phenotypic variation However, no significant QTL x environment (QxE) interaction and epistasis x environment interaction effects were detected The results showed that besides the additive QTL, epistatic interactions also formed an important genetic basis for test weight in maize

The evolutionary landscape of antifolate resistance in Plasmodium falciparum

Abstract: Resistance to antifolates in Plasmodium falciparum is well described and has been observed in clinical settings for decades. At the molecular level, point mutations in the dhfr gene that lead to resistance have been identified, and the crystal structure of the wildtype and mutant dihydrofolate reductase enzymes have been solved in complex with native substrate and drugs. However, we are only beginning to understand the complexities of the evolutionary pressures that lead to the evolution of drug resistance in this system. Microbial systems that allow heterologous expression of malarial proteins provide a tractable way to investigate patterns of evolution that can inform our eventual understanding of the more complex factors that influence the evolution of drug resistance in clinical settings. In this paper we will review work in Escherichia coli and Saccharomyces cerevisiae expression systems that explore the fitness landscape of mutations implicated in drug resistance and show that (i) a limited number of evolutionary pathways to resistance are followed with high probability; (ii) fitness costs associated with the maintenance of high levels of resistance are modest; and (iii) different antifolates may exert opposing selective forces.

Domain combination of the vertebrate-like TLR gene family: implications for their origin and evolution.

Abstract: Domain shuffling, which is an important mechanism in the evolution of multi-domain proteins, has shaped the evolutionary development of the immune system in animals. Toll and Toll-like receptors (TLRs) are a class of proteins that play a key role in the innate and adaptive immune systems. Draft genome sequences provide the opportunity to compare the Toll/TLR gene repertoire among representative metazoans. In this study, we investigated the combination of Toll/interleukin-1 receptor (TIR) and leucine-rich repeat (LRR) domains of metazoan Toll/TLRs. Before Toll with both domains occurred in Cnidaria (sea anemone, Nematostella vectensis), through domain combinations, TIR-only and LRR-only proteins had already appeared in sponges (Amphimedon queenslandica). Although vertebrate-like TIR (V-TIR) domain already appeared in Cnidaria, the vertebrate-like TLR (V-TLR) with both domains appeared much later. The first combination between V-TIR domain and vertebrate-like LRR (V-LRR) domain for V-TLR may have occurred after the divergence of Cnidaria and bilateria. Then, another combination for V-TLR, a recombination of both domains, possibly occurred before or during the evolution of primitive vertebrates. Taken together, two rounds of domain combinations may thus have co-shaped the vertebrate TLRs.

Genetic polymorphism of serotonin transporter 5-HTTLPR: involvement in smoking behaviour.

Abstract: Data suggest that the serotonin (5-hydroxytryptamine, 5-HT) system is implicated in the pathogenesis of multiple neuropsychiatric disorders and may also be involved in smoking behaviour since nicotine increases brain serotonin secretion It is known that smoking behaviour is influenced by both genetic and environmental factors The present review examines the role of the serotonin transporter gene (5-HTT) in smoking behaviour and investigating studies that showed association of 5-HTT gene with smoking This study discusses a polymorphism which has been investigated by many researchers, as the bi-allelic insertion/deletion polymorphism in the 5 � - flanking promoter region (5-HTTLPR) This gene has received considerable attention in attempts to understand the molecular determinants of smoking Therefore, in the present study, the relationship between genetic polymorphism of serotonin transporter in smoking behaviour is reviewed considering the interactive effect of genetic factors

Tumour necrosis factor alpha and interleukin 10 gene polymorphisms and the risk of ischemic stroke in south Indian population.

Abstract: Stroke is the leading cause of adult disability and mortality and is the third largest cause of death worldwide (Bonita et al. 2004). Prevalence of stroke in India varies in different regions of the country and ranges from 40 to 270 per 100,000 population (Anand et al. 2001). Both environmental and genetic factors are involved in the causation of strokes (Bevan and Markus 2004). Cytokines play an important role in immune response and also maintain the normal homeostatic environment of the central nervous system. The key phenomenon in cytokine contribution to ischemic stroke is endothelial transformation altering hemostatic and immunological balance towards the prothrombotic and proinflammatory states (Ross 1993). The genes encoding diverse cytokines may play a vital role in the susceptibility to stroke, and the production of cytokine varies among individuals and depends on cytokine gene polymorphisms. The present study was carried out to evaluate the association of tumour necrosis alpha (TNFα) -308G/A and interleukin (IL) 10-1082G/A polymorphisms with ischemic stroke in south Indian population and the results showed that the IL-10 ‘GG’ genotype is significantly associated with stroke.

Association of ADAM33 gene polymorphisms with adult-onset asthma and its severity in an Indian adult population

Abstract: ADAM33, a member of the ADAM (a disintegrin and metalloprotease) gene family, is an asthma susceptibility gene originally identified by positional cloning. In the present study, we investigated the possible association of five single-nucleotide polymorphisms (SNPs) in the ADAM33 (rs511898, rs528557, rs44707, rs597980 and rs2787094) with adult-onset asthma in an Indian population. The study included 175 patients with mild intermittent (n = 44), mild persistent (n = 108) or moderate persistent (n = 23) subgroups of asthma, and 253 nonasthmatic control individuals. SNPs were genotyped with the help of restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR) method, and data were analysed using chi-square test and logistic regression model. Bonferroni’s correction for multiple comparisons was applied for each hypothesis. Genotypes and allele frequencies of SNPs rs511898 and rs528557 were significantly associated with adult-onset asthma (P = 0.010-<0.001). A significant association of the homozygous mutant genotype and mutant alleles of SNPs rs2787094, rs44707 and rs597980 with the asthma was also observed (P = 0.020-<0.001). A positive association between asthma and haplotypes AGCCT, GGCCT, AGACT, GCAGT, GGACT, ACCCC and AGACC were also found (P = 0.036-<0.001, OR = 2.07–8.49). Haplotypes AGCGT, GCAGC, ACAGC, ACAGT, GGAGC and GGCGT appear to protect against asthma (P = 0.013-<0.0001, OR = 0.34–0.10). Our data suggest that ADAM33 gene polymorphisms serve as genetic risk factors for asthma in Indian adult population.

Phenotypic and molecular characterization of selected tomato recombinant inbred lines derived from the cross Solanum lycopersicum × S. pimpinellifolium

Abstract: An important trait defining fresh tomato marketability is fruit shelf life. Exotic germplasm of Solanum pimpinellifolium is able to prolong shelf life. Sixteen recombinant inbred lines with differing values of shelf life and fruit weight were derived by antagonistic-divergent selection from an interspecific cross involving Solanum pimpinellifolium. The objective of this study was to evaluate these recombinant inbred lines for many fruit quality traits such as diameter, height, size, acidity, colour, firmness, shelf life and weight, and to characterize them by amplified fragment length polymorphism markers. For most traits, a wide range of genetic variability was found and a wide range of molecular variation was also detected. Both sets of data allowed the identification of recombinant inbred lines by means of cluster analysis and principal component analysis. Genetic association among some amplified fragment length polymorphism markers and fruit quality traits, suggested by the principal component analysis, could be identified by single point analysis. Potential molecular markers underlying agronomical traits were detected in these recombinant inbred lines.

Occurrence of differential meiotic associations and additional chromosomes in the embryo-sac mother cells of Allium roylei Stearn.

Abstract: A small population of complex translocation heterozygote plants of Allium roylei from the Bani region of Jammu Province was studied for meiosis in the female track. This study resulted in identification of two variants, having embryo-sac mother cells (EMCs) with more than 16 chromosomes. EMCs of the remaining plants invariably had diploid (2n = 16) chromosome complement. Female meiosis, in general, was found to be abnormal, with nearly 23% and 11% chromosomes associating as quadrivalents or trivalents at prophase I and at metaphase I, respectively. This was followed by irregular segregation of chromosomes at anaphase I. Amongst the variants; one had 38% EMCs with eight bivalents plus two small sized chromosomes. Their small size, dispensable nature and tendency to affect the pairing behaviour of normal complement are some of the features that latter chromosomes share with the B chromosomes. Seventeen to nineteen chromosomes were observed in 35% EMCs of other variant; the remaining cells had 16 chromosomes. Chromosomal behaviour in both kind of cells (euploid and aneuploid) was more or less similar. Unlike female meiocytes, male meiocytes analysed earlier of this strain always had 16 chromosomes which paired to form extremely complex associations involving 3-16 chromosomes. The most likely cause of this asynchrony with regards to number of chromosomes involved in multivalent formation seems to be interaction of genes controlling chiasma formation with the different physiological conditions of male and female meiocytes.

Positive association between NTNG1 and schizophrenia in Chinese Han population.

Abstract: 1Department of Psychiatry, First Affiliated Hospital, China Medical University, Nanjing North Street, Shenyang 110001, People’s Republic of China 2Shenyang Pharmaceutical University, Whenhua Road, Shenyang 110001, People’s Republic of China 3BenXi Mental Hospital, Digong Road, Benxi 117000, People’s Republic of China 4Dalian Seventh People’s Hospital, Lingshui Road, Dalian 116000, People’s Republic of China 5FuShun Coal-Mine Brain Hospital, Gaowan Road, FuShun 113000, People’s Republic of China

Molecular cytogenetic characterization of a new wheat Secale africanum 2R(a)(2D) substitution line for resistance to stripe rust.

Abstract: A stable, highly fertile wheat Secale africanum substitution line LF24, derived from the F7 generation of a cross between Mianyang11 (MY11) and Triticum durum, S. africanum amphiploid (YF) was identified through molecular cytogenetic analysis. Application of C-banding, in situ hybridization and molecular markers analysis showed that LF24 was a wheat S. africanum 2Ra(2D) substitution line. When inoculated with stripe rust isolates, T. durum and MY11 were highly susceptible, while S. africanum, YF and LF24 were immune. It is confirmed through molecular cytogenetic analysis that the stripe rust resistance of LF24 was derived from S. africanum chromosome 2Ra. We compared the banding patterns and disease resistance of reported chromosomes 2R from different S. cereale introduced into wheat background, and found that there was new stripe rust resistance gene(s) on S. africanum 2Ra. LF24 is a new substitution line which can be used as stripe rust resistant source in wheat improvement.

RAPD and microsatellite transferability studies in selected species of Prosopis (section Algarobia) with emphasis on Prosopis juliflora and P. pallida

Abstract: The genus Prosopis (Leguminosae, Mimosoideae), comprises 44 species widely distributed in arid and semi-arid zones. Prosopis pallida (Humb. & Bonpl. ex Willd.) Kunth and P. juliflora (Sw.) DC. are the two species that are truly tropical apart from P. africana, which is native to tropical Africa (Pasiecznik et al. 2004), and they have been introduced widely beyond their native ranges. However, taxonomic confusion within the genus has hampered exploitation and better management of the species. The present study focusses primarily on evaluating the genetic relationship between Prosopis species from the section Algarobia, containing most species of economic importance, though P. tamarugo from section Strombocarpa is also included for comparison. In total, 12 Prosopis species and a putative P. pallida × P. chilensis hybrid were assessed for their genetic relationships based on RAPD markers and microsatellite transferability. The results show that P. pallida and P. juliflora are not closely related despite some morphological similarity. Evidence also agrees with previous studies which suggest that the grouping of series in section Algarobia is artificial.

Variation in the PTEN-induced putative kinase 1 gene associated with the increase risk of type 2 diabetes in northern Chinese

Abstract: Type 2 diabetes mellitus (T2DM) is a multifactor disorder closely related to energy balance. Several susceptible genes that lead to mitochondrial dysfunction, such as mitochondrial D-loop gene, peroxisome proliferator activated receptor gamma coactivator 1 alpha (PGC1α) and uncoupling proteins, have been implicated in T2DM (Sun et al. 2006; Lee et al. 2008; Chen et al. 2009). PTEN-induced putative kinase 1 (PINK1) gene encodes a serine/threonine protein kinase that localizes to mitochondria and protects cells from stressinduced-mitochondrial dysfunction. Mutations in PINK1 can cause autosomal recessive early-onset Parkinson’s disease. Based on the products of PINK1 and its role in mitochondria and energy metabolism, we hypothesized that in addition to Parkinson’s disease, PINK1 might also be involved in metabolic disorders such as T2DM. PINK1 is mapped to human chromosome 1 (Valente et al. 2004) and functions as a mitochondrial Na+/Ca(2+) exchanger regulator. PINK1 deficiency causes mitochondrial accumulation of calcium, and the resulting calcium overload stimulates reactive oxygen species (ROS) production via NADPH oxidase, ROS production inhibits the glucose transporter, which reduces substrate delivery and impairs mitochondrial respiration, ultimately inducing cell death (Gandhi et al. 2009). Two missense mutations at considerable frequency are found in the coding region of PINK1 gene: a threonine/alanine substitution at residue 340 and an asparagine/threonine substitution at residue 521, which is located on exon 8 and indispensable for peptide substrate binding and phosphor-transfer. Results from gene mapping and genetic variation analysis have indicated the involvement of PINK1 gene in the development of Parkinson’s disease.

Beneficial genotype of swine FUT1 gene governing resistance to E. coli F18 is associated with important economic traits.

Abstract: 1Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, and 2College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, People’s Republic of China 3Suzhou Taihu Pig Breeding Centre, Jiangsu Province, Suzhou, Jiangsu 215000, People’s Republic of China 4Jiangsu Engineering Research Centre for Molecular Breeding of Pig, Changzhou, Jiangsu 213149, People’s Republic of China

Determination of genetic relationships among elite thermosensitive genic male sterile lines (TGMS) of rice ( Oryza sativa L.) employing morphological and simple sequence repeat (SSR) markers

Abstract: A set of morphological traits and SSR markers were used to determine the genetic relationship among 12 elite thermosensitive genic male sterile (TGMS) lines developed at three different research institutions of India. Agro-morphological data recorded on 20 morphological traits revealed a wide base of genetic variation and a set of four morphological traits could distinguish most of the TGMS lines. Analysis with 30 SSR markers (20 EST-SSRs and 10 genomic SSRs) revealed 27 markers to be polymorphic, amplifying a total of 83 alleles. Each SSR marker amplified 2–6 alleles with an average of 2.76 alleles per marker and a PIC value varying from 0.54 to 0.96. Cluster analysis based on SSR and morphological data clearly differentiated the lines according to their source of origin. Correlation analysis between morphological and molecular data revealed a very poor association (r = 0.06), which could be attributed to selection pressure, genetic drift, sampling error and unknown relationship among related lines. The SSR markers discriminated the genotypes distinctly and quantified the genetic diversity precisely among the TGMS lines. Data on the yield per plant indicated that the genotypes grouping under a similar cluster showed same heterotic behaviour as compared to the genotypes from different clusters when crossed to similar pollinators.

Molecular subgrouping of Wolbachia and bacteriophage WO infection among some Indian Drosophila species.

Abstract: Wolbachia are a group of obligate intracellular maternally inherited bacteria that infect arthropods and filarial nematodes worldwide (Werren et al. 2008). Wolbachia cause a variety of reproductive alterations in their arthropod hosts, including cytoplasmic incompatibility (CI), parthenogenesis, feminization and male killing (Werren et al. 2008). Wolbachia are not only speculated to have been associated with speciation in certain species of insects (Werren et al. 2008) but are also found to provide fitness benefits to their hosts (Teixeira et al. 2008). Therefore, characterization of the Wolbachia genotype, and determining its phenotypic effect in different hosts, is of significant importance in understanding their ecology and evolution. Wolbachia have been categorized into 11 different supergroups (alphabetically labelled A–K) on the basis of clades formed in gene phylogenies (Ros et al. 2009). Two of these supergroups, A and B, are found to infect only insects and comprise many subgroups that can be discriminated using the Wolbachia surface protein (wsp) gene. This gene, which has a very high rate of recombination, is extensively used for characterizing Wolbachia strains (Zhou et al. 1998). Bacteriophages are widespread viruses infecting bacteria and constitute one of the most effective vectors of foreign DNA. Bacteriophages often encode proteins involved in important functions such as antibiotic resistance or virulence. A particularity of Wolbachia is the high number of mobile elements present in its genome despite the intracellular lifestyle of this bacterium (Moran et al. 2008). The phage WO is widespread in Wolbachia genomes: 90% of Wolbachia strains are infected by it including strains that

Is APOE $\boldsymbol{\varepsilon}$ 3 a favourable factor for the longevity: an association study in Chinese population

Abstract: 1Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, People’s Republic of China 2National Institute of Geriatrics, Beijing Hospital, Ministry of Health P. R. China, Beijing 100730, People’s Republic of China 3Yongfu Committee of the Chinese People’s Political Consultative Conference, Yongfu 541800, People’s Republic of China 4Guangxi Zhuang Autonomous Women and Children Health Hospital, Nanning 530003, People’s Republic of China 5Guangxi Zhuang Autonomous JiangBin Hospital, Nanning 530012, People’s Republic of China

A novel POLH gene mutation in a xeroderma pigmentosum-V Tunisian patient: phenotype-genotype correlation.

Abstract: XP occurs at higher frequency in Tunisia (1:10,000) than in Japan (1:22,000) (Hirai et al. 2006) and the United States (1 per million) (Kleijer et al. 2008). XP-V cells are unable to synthesize intact daughter DNA strands on UV-irradiated templates resulting from an inability to carry out translesion synthesis (Lehmann et al. 1975; Masutani et al. 1999). Approximately 20% of XP patients belong to XP-V complementation group (Gratchev et al. 2003). In Tunisia, XP is classified into three clinical forms: severe, intermediate with or without neurological abnormalities, and moderate (Zghal et al. 2006). Previous molecular investigation showed homogeneity of mutational spectrum in XPA and XPC genes (Ben Rekaya et al. 2009; Messaoud et al. 2010a,b). The moderate clinical form of XP is characterized by mild dermatological manifestations, no neurological abnormalities and late onset of skin cancers. The median age of onset is 4 years. Mild skin symptoms and late onset of skin tumours have been already described in XP-V (Tanioka et al. 2007), XP-F (Matsumura et al. 1998) and XP-E patients (Rapic-Otrin et al. 2003). Post-UV cell survival in the presence or absence of caffeine (Itoh et al. 2000), unscheduled DNA synthesis (UDS) and detection of polymerase eta employing Western blot (Tanioka et al. 2007) cannot define exactly the molecular defects are in the polymerase eta. These laboratory assays are used to find out the UV sensitivities of the patients’ cells and the DNA repair status of their cells as

Major genes with additive effects for seed size in kabuli chickpea (Cicer arietinum L.).

Abstract: In the present investigation, inheritance of seed size was studied in a cross involving two small-seeded kabuli cultivars, ICCV 2 and L 550. Mean 100-seed weight (100 SW) of parents and that of their F1 generation were similar. However, transgressive segregants were obtained in F2 generation in both directions. Considering the segregation pattern, plants in F2 and backcross generations were divided into three groups, 100 SW less than F1/parents (F1P1P2). The numbers of plants in the three groups in F2 fitted well to an expected ratio of 5:6:5 (χ2 = 2.15, P = 0.34), and in backcross generations to an expected ratio 1:2:1 (χ2 = 0.94, P = 0.33 in BC1P1, and χ2 = 3.89, P = 0.14 in BC1P2), which suggested that seed size in the two parents is controlled by two genes exhibiting additive effects with each parent having one pair of alleles with increasing effect at one locus in homozygous form.

Association of CTLA4, CD28 and ICOS gene polymorphisms with clinicopathologic characteristics of childhood IgA nephropathy in Korean population.

Abstract: Primary IgA nephropathy (IgAN) is the most common glomerular disease in children and adolescents who undergo renal biopsy because of isolated microscopic haematuria or haematuria associated with proteinuria (Coppo 2008). Some evidence suggests the importance of the abnormal T-cell response in the pathogenesis of IgAN, and co-stimulatory molecules such as cytotoxic T-lymphocyte antigen 4 (CTLA4), CD28 molecule and inducible costimulator (ICOS) have been found to be vital for naive T-cells to initiate and terminate immune responses (Carreno and Collins 2002; Carreno et al. 2005). In this study, we tested single nucleotide polymorphisms (SNPs) of CTLA4/CD28/ICOS genes, and they were found to be associated with pathophisipology of paediatric IgAN in Korean population. The best-characterized T-cell co-stimulatory pathway involves receptors such as the CD28 and CTLA4 (also known as CD152). In addition, the ICOS has been also defined recently as a new pathway (Keir and Sharpe 2005). The CD28/CTLA4/ICOS genes lie within the 300-kb region on human chromosome 2q33 and their expressions are differentially regulated; although CD28 is constitutively present on naive T-cells, whereas CTLA4 and ICOS are present only after activation (Collins et al. 2005). Moreover, all of these molecules were found to be expressed by regulatory T-cells for the development and maintenance (Keir and Sharpe 2005).

MicroRNA expression profiling in neurogenesis of adipose tissue-derived stem cells

Abstract: Adipose tissue-derived stem cells (ADSCs) are one population of adult stem cells that can self renew and differentiate into multiple lineages. Because of advantages in method and quantity of acquisition, ADSCs are gaining attention as an alternative source of bone marrow mesenchymal stem cells. In this study, we performed microRNA profiling of undifferentiated and of neurally-differentiated ADSCs to identify the responsible microRNAs in neurogenesis using this type of stem cell. MicroRNAs from four different donors were analysed by microarray. Compared to the undifferentiation control, we identified 39–101 microRNAs with more than two-fold higher expression and 3–9 microRNAs with two-fold lower expression. The identified microRNAs were further analysed in terms of gene ontology (GO) in relation with neurogenesis, based on their target mRNAs predicted by computational analysis. This study revealed the specific microRNAs involved in neurogenesis via microRNA microarray, and may provide the basic information for genetic induction of adult stem cell differentiation using microRNAs.