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Mungbean [Vigna radiata var. radiata (L.) Wilczek] production in Asia is detrimentally affected by transient soil waterlogging caused by unseasonal and increasingly frequent extreme precipitation events. While mungbean exhibits sensitivity to waterlogging, there has been insufficient exploration of germplasm for waterlogging tolerance, as well as limited investigation into the genetic basis for tolerance to identify valuable loci. This research investigated the diversity of transient waterlogging tolerance in a mini--core germplasm collection of mungbean and identified candidate genes for adaptive traits of interest using genome--wide association studies (GWAS) at two critical stages of growth: germination and seedling stage (i.e., once the first trifoliate leaf had fully--expanded). In a temperature--controlled glasshouse, 292 genotypes were screened for tolerance after (i) 4 days of waterlogging followed by 7 days of recovery at the germination stage and (ii) 8 days of waterlogging followed by 7 days of recovery at the seedling stage. Tolerance was measured against drained controls. GWAS was conducted using 3,522 high--quality DArTseq--derived SNPs, revealing five significant associations with five phenotypic traits indicating improved tolerance. Waterlogging tolerance was positively correlated with the formation of adventitious roots and higher dry masses. FGGY carbohydrate kinase domain--containing protein was identified as a candidate gene for adventitious rooting and mRNA-uncharacterized LOC111241851, Caffeoyl-CoA O-methyltransferase At4g26220 and MORC family CW-type zinc finger protein 3 and zinc finger protein 2B genes for shoot, root, and total dry matter production. Moderate to high broad--sense heritability was exhibited for all phenotypic traits, including seed emergence (81%), adventitious rooting (56%), shoot dry mass (81%), root dry mass (79%) and SPAD chlorophyll content (70%). The heritability estimates, marker--trait associations, and identification of sources of waterlogging tolerant germplasm from this study demonstrate high potential for marker--assisted selection of tolerance traits to accelerate breeding of climate--resilient mungbean varieties. [ABSTRACT FROM AUTHOR]

The prevalence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the microbiome is a major public health concern globally. Many habitats in the environment are under threat due to excessive use of antibiotics and evolutionary changes occurring in the resistome. ARB and ARGs from farms, cities and hospitals, wastewater treatment plants (WWTPs) or as water runoffs, may accumulate in water, soil, and air. We present a global picture of the resistome by examining ARG-related papers retrieved from PubMed and published in the last 30 years (1990–2020). Natural Language Processing (NLP) was used to retrieve 496,640 papers, out of which 9374 passed the filtering test and were further analyzed to determine the distribution and diversity of ARG subtypes. The papers revealed seven major antibiotic families together with their respective ARG subtypes in different habitats on six continents. Asia, especially China, had the highest number of ARGs related papers compared to other countries/regions/continents. ARGs belonging to multidrug, glycopeptide, and β-lactam families were the most common in reports from hospitals and sulfonamide and tetracycline families were common in reports from farms, WWTPs, water and soil. We also highlight the 'omics' tools used in resistome research, describe some factors that shape the development of resistome, and suggest future work needed to better understand the resistome. The goal was to show the global nature of ARB and ARGs in order to encourage collaborate research efforts aimed at reducing the negative impacts of antibiotic resistance on the One Health concept. [Display omitted] • Antibiotic resistant bacteria (ARB) are major public health concerns globally. • The diversity and distribution of antibiotic resistance genes (ARGs) are presented. • Factors that affect ARB and ARGs in different environments are discussed. • Different 'omics' tools used to study resistome development are also presented. [ABSTRACT FROM AUTHOR]

Acute hepatopancreatic necrosis disease (AHPND) is a lethal disease in marine shrimp that has caused large-scale mortalities in shrimp aquaculture in Asia and the Americas. The etiologic agent is a pathogenic Vibrio sp. carrying binary toxin genes, pir A and pir B in plasmid DNA. Developing AHPND tolerant shrimp lines is one of the prophylactic approaches to combat this disease. A selected genetic line of Penaeus vannamei was found to be tolerant to AHPND during screening for disease resistance. The mRNA expression of twelve immune and metabolic genes known to be involved in bacterial pathogenesis were measured by quantitative RT-PCR in two populations of shrimp, namely P1 that showed susceptibility to AHPND, and P2 that showed tolerance to AHPND. Among these genes, the mRNA expression of chymotrypsin A (ChyA) and serine protease (SP), genes that are involved in metabolism, and crustin-P (CRSTP) and prophenol oxidase activation system 2 (PPAE2), genes involved in bacterial pathogenesis in shrimp, showed differential expression between the two populations. The differential expression of these genes shed light on the mechanism of tolerance against AHPND and these genes can potentially serve as candidate markers for tolerance/susceptibility to AHPND in P. vannamei. This is the first report of a comparison of the mRNA expression profiles of AHPND tolerant and susceptible lines of P. vannamei. [ABSTRACT FROM AUTHOR]

The article discusses research on genes involved in hypoxia adaptation among indigenous residents of high-altitude plateaus of Central Asia, the Andes, and Tibet. Referenced research includes papers by Simonson et al. and Yi et al. elsewhere in the issue and a paper by C.M. Beall et al. in a 2010 issue of the "Proceedings of the National Academy of Sciences U.S.A." These papers are said to indicate that hypoxia-inducible factor (HIF) genes in the oxygen signaling pathway are strongly selected in the genetics of Tibetan highlanders. The article discusses the use of screening of genome-wide DNA sequence variations (polymorphisms) to resolve the contributions of chromosomal regions to high-altitude adaptation.

By altering gene expression and creating paralogs, genomic amplifications represent a key component of short‐term adaptive processes. In insects, the use of insecticides can select gene amplifications causing an increased expression of detoxification enzymes, supporting the usefulness of these DNA markers for monitoring the dynamics of resistance alleles in the field. In this context, the present study aims to characterize a genomic amplification event associated with resistance to organophosphate insecticides in the mosquito Aedes aegypti and to develop a molecular assay to monitor the associated resistance alleles in the field. An experimental evolution experiment using a composite population from Laos supported the association between the over‐transcription of multiple contiguous carboxylesterase genes on chromosome 2 and resistance to multiple organophosphate insecticides. Combining whole genome sequencing and qPCR on specific genes confirmed the presence of a ~100‐Kb amplification spanning at least five carboxylesterase genes at this locus with the co‐existence of multiple structural duplication haplotypes. Field data confirmed their circulation in South‐East Asia and revealed high copy number polymorphism among and within populations suggesting a trade‐off between this resistance mechanism and associated fitness costs. A dual‐color multiplex TaqMan assay allowing the rapid detection and copy number quantification of this amplification event in Ae. aegypti was developed and validated on field populations. The routine use of this novel assay will improve the tracking of resistance alleles in this major arbovirus vector. [ABSTRACT FROM AUTHOR]

Halogeton glomeratus (H. glomeratus) is one of the most important halophytes in Asia, and the research on the genes and salt-tolerant mechanisms of this species is limited because of the lack of an optimal and efficient in vitro regeneration system. Here, we developed an efficient plant regeneration protocol using H. glomeratus leaves as explants, which has not been previously reported. High-quality calli were successfully obtained from the H. glomeratus leaves at a frequency of 100% supplemented with 2.00 mg/L 2,4-dichlorophenoxyacetic acid, 0.50 g/L PVP, 5.00 g/L agar, and 30.00 g/L sucrose; the optimum callus subculture medium is 1.00 mg/L 2,4-dichlorophenoxyacetic acid, 0.50 g/L PVP, 5.00 g/L agar, and 30.00 g/L sucrose. Shoots were regenerated on shoot induction medium at a frequency of 100% added with 0.50 mg/L 6-benzylaminopurine, 2.00 mg/L kinetin, 0.20 mg/L naphthaleneacetic acid, 0.50 g/L PVP, 5.00 g/L agar, and 30.00 g/L sucrose; then, shoots grew up on shoot regeneration medium. Finally, roots were regenerated from the shoots on Murashige and Skoog medium with high efficiency. This study firstly offers a rapid and efficient system for plantlet regeneration from leaves of H. glomeratus. Whether our protocol applies well to other tissue regeneration of H. glomeratus needs further confirmation. This work will facilitate basic research and salt-tolerant mechanisms of this important halophyte species. [ABSTRACT FROM AUTHOR]

Background: Salinity, alkalinity, and drought stress are the main abiotic stress factors affecting plant growth and development. Sophora alopecuroides L., a perennial leguminous herb in the genus Sophora, is a highly salt-tolerant sand-fixing pioneer species distributed mostly in Western Asia and northwestern China. Few studies have assessed responses to abiotic stress in S. alopecuroides. The transcriptome of the genes that confer stress-tolerance in this species has not previously been sequenced. Our objective was to sequence and analyze this transcriptome. Results: Twelve cDNA libraries were constructed in triplicate from mRNA obtained from Sophora alopecuroides for the control and salt, alkali, and drought treatments. Using de novo assembly, 902,812 assembled unigenes were generated, with an average length of 294 bp. Based on similarity searches, 545,615 (60.43%) had at least one significant match in the Nr, Nt, Pfam, KOG/COG, Swiss-Prot, and GO databases. In addition, 1673 differentially expressed genes (DEGs) were obtained from the salt treatment, 8142 from the alkali treatment, and 17,479 from the drought treatment. A total of 11,936 transcription factor genes from 82 transcription factor families were functionally annotated under salt, alkali, and drought stress, these include MYB, bZIP, NAC and WRKY family members. DEGs were involved in the hormone signal transduction pathway, biosynthesis of secondary metabolites and antioxidant enzymes; this suggests that these pathways or processes may be involved in tolerance towards salt, alkali, and drought stress in S. alopecuroides. Conclusion: Our study first reported transcriptome reference sequence data in Sophora alopecuroides, a non-model plant without a reference genome. We determined digital expression profile and discovered a broad survey of unigenes associated with salt, alkali, and drought stress which provide genomic resources available for Sophora alopecuroides. [ABSTRACT FROM AUTHOR]

Objective: Acute hepatopancreatic necrosis disease is an emerging infectious disease of Penaeus species. The causative agent is Vibrio species, which dispels binary toxin similar to pirA and pirB, which causes mortality in infected shrimp. The aim of this research was to investigate the evolutionary relationship of pirA and pirB homologous genes present in this Asia and Costa Rica in silico. Materials and methods: The sequences for in silico analysis were all retrieved from the Basic Local Alignment Search Tool Nucleotide (BLASTN) tool of the National Center for Biotechnology Center. For pirA, a total of 25 sequences submitted from different Asian countries and Costa Rica were retrieved for analysis. Meanwhile, for pirB, a total of 11 sequences submitted from five Asian countries were retrieved. Sequences were aligned using the CLUSTAL W alignment tool under Molecular Evolutionary Genetics Analysis (MEGA) 7 software. The evolutionary history was then estimated using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) method, whereas the evolutionary distances were determined using the maximum composite likelihood model with 1,000 bootstrap replications. Results and Discussion: The results show that, among 27 DNA sequences analyzed for pirA gene, three groups were generated, while for pirB, 13 DNA sequences yielded only one group. The analysis revealed low genetic variation among isolates for both pirA and pirB genes. Conclusion: This result suggests that the low frequency of polymorphism and geographic location cannot be attributed to the differences in V. parahaemolyticus isolates in Asian countries relative to Costa Rican isolates in pirA and pirB genes. [ABSTRACT FROM AUTHOR]

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Background: ESBL and plasmid-mediated AmpC (pAmpC)-producing Enterobacteriaceae are frequently found on meat products in Dutch retail, especially on poultry.Objectives: We investigated whether vegetarians are at lower risk of carrying ESBL/pAmpC-producing Escherichia coli/Klebsiella pneumoniae (ESBL-E/K) compared with persons who consume meat.Methods: Vegetarians, pescatarians (vegetarians who eat fish) and non-vegetarians (persons who eat meat at least three times per week) were asked to send in a faecal sample and a questionnaire. ESBL-E/K were cultured and MLSTs were determined. ESBL/pAmpC genes were analysed using PCR and sequencing. The risk of ESBL-E/K carriage in the three study groups was analysed using multivariable logistic regression.Results: Prevalence of ESBL-E/K carriage was 8.0% in vegetarians (63/785; 95% CI 6.3-10.1), 6.9% in pescatarians (27/392; 95% CI 4.8-9.8) and 3.8% in non-vegetarians (14/365; 95% CI 2.3-6.3). Multivariable analysis showed an OR for ESBL-E/K carriage of 2.2 for vegetarians (95% CI 1.2-4.0) and 1.6 for pescatarians (95% CI 0.8-3.2) compared with non-vegetarians. The predominant MLST was E. coli ST131 and the most common ESBL genes were blaCTX-M-15, blaCTX-M-27, blaCTX-M-14 and blaCTX-M-1 in all diet groups. Independent risk factors for ESBL-E/K carriage were travel to Africa/Latin America/Asia (OR 4.6; 95% CI 2.8-7.7) in the past 6 months and rarely/never washing hands before food preparation (OR 2.5; 95% CI 1.2-5.0).Conclusions: Vegetarians and pescatarians did not have a lower risk of ESBL-E/K carriage compared with non-vegetarians, indicating that eating meat is not an important risk factor for ESBL-E/K carriage. [ABSTRACT FROM AUTHOR]

Background and objective: Direct-acting antivirals (DAA) facing resistance continue to be used in some areas worldwide. Thus, identifying hepatitis C virus (HCV) genotypes/subtypes and loci with certain prevalent resistance-associated substitutions (RASs) deserves attention. We investigated the global and regional frequencies of naturally occurring RASs among all confirmed HCV subtypes (n=86) and explored co-occurring and mutually exclusive RAS pairs within and between genes NS3, NS5A, and NS5B. Methods: A total of 213,908 HCV sequences available as of July 10, 2019 were retrieved from the NCBI nucleotide database. After curation, 17,312 NS3, 8,478 NS5A, and 25,991 NS5B sequence fragments from DAA-naïve patients were screened for RASs. MEGA 6.0 was used to translate aligned nucleotide sequences into amino acid sequences, and RAS pairs were identified by hypergeometric analysis. Results: RAS prevalence varied significantly among HCV subtypes. For example, D168E, highly resistanct to all protease inhibitors except voxilaprevir, was nearly absent in all subtypes except in 43.48% of GT5a sequences. RASs in NS3 exhibiting significantly different global distribution included Q80K in GT1a with the highest frequency in North America (54.49%), followed by in Europe (22.66%), Asia (6.98%), Oceania (6.62%), and South America (1.03%). The prevalence of NS3 S122G in GT1b was highest in Asia (26.6%) and lowest in Europe (2.64%). NS5A L28M, R30Q, and Y93H in GT1b, L31M in GT2b, and NS5B C316N in GT1b was most prevalent in Asia. A150V in GT3a, associated with sofosbuvir treatment failure, was most prevalent in Asia (44.09%), followed by Europe (31.19%), Oceania (24.29%), and North America (19.05%). Multiple mutually exclusive or co-occurring RAS pairs were identified, including Q80K+R155K and R155K+D168G in GT1a and L159F+C316N and R30Q (NS5A)+C316N (NS5B) in GT1b. Conclusion: Our data may be of special relevance for those countries where highly effective antivirals might not be available. Considering the specific RASs prevalence will help the clinicians to make optimal treatment choices. The RASs pairs would benefit anti-HCV drug development. [ABSTRACT FROM AUTHOR]

Purpose. To assess the association of genes in the high-density lipoprotein metabolic pathway (HDLMP) with polypoidal choroidal vasculopathy (PCV) and the genetic difference in the HDLMP between PCV and age-related macular degeneration (AMD). Methods. We performed a literature search in EMBASE, PubMed, and Web of Science for genetic studies on 7 single nucleotide polymorphisms (SNPs) from 5 genes in the HDLMP including cholesteryl ester transfer protein (CETP), hepatic lipase (LIPC), lipoprotein lipase (LPL), ATP-binding cassette transporter A1 (ABCA1), and ATP-binding cassette transporter G1 (ABCG1) in PCV. All studies were published before September 30, 2017, without language restriction. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) of each polymorphism were estimated. We also compared the association profiles between PCV and AMD and performed a sensitivity analysis. Results. Our result is based on 43 articles. After excluding duplicates and articles without complete information, 7 studies were applicable to meta-analysis. 7 polymorphisms were meta-analyzed: CETP rs2303790/rs3764261, LIPC rs10468017/rs493258, LPL rs12678919, ABCA1 rs1883025, and ABCG1 rs57137919. We found that in Asian population, CETP rs3764261 (T allele; OR = 1.46; 95% CI: 1.28–1.665, P<0.01), CETP rs2303790 (G allele; OR = 1.57; 95% CI: 1.258–1.96, P<0.01), and ABCG1 rs57137919 (A allele; OR = 1.168; 95% CI: 1.016–1.343, P<0.01) were significantly associated with PCV, and ABCG1 rs57137919 (A allele; OR = 1.208, 95% CI: 1.035–1.411, P<0.01) has different effects in PCV and AMD. The other 4 polymorphisms in LIPC/LPL/ABCA1 had no significant association with PCV (P>0.05). The sensitivity analysis validated the significance of our analysis. Conclusions. Our study revealed 7 polymorphisms in 5 genes. Among them, CETP (rs3764261/rs2303790) and ABCG1 (rs57137919) were the major susceptibility genes for PCV in Asian population and ABCG1 (rs57137919) showed allelic diversity between PCV and AMD. Since the size for PCV and AMD was small, we need to study these genes genotyping in larger samples. [ABSTRACT FROM AUTHOR]

Antibiotic resistance genes are biologically transmitted from microorganism to microorganism in particular micro-environments where dense microbial communities are often exposed to an intensive use of antibiotics, such as intestinal microflora, and the soil microflora of agricultural fields. However, recent studies have detected antibiotic-resistant bacteria and/or antibiotic resistance genes in the natural environment geographically isolated from such areas. Here we sought to examine the prevalence of antibiotic resistance genes in 54 snow and ice samples collected from the Arctic, Antarctic, Central Asia, North and South America and Africa, to evaluate the level of these genes in environments supposedly not affected by anthropogenic factors. We observed a widespread distribution of antibiotic resistance genes in samples from various glaciers in Central Asia, North and South America, Greenland and Africa. In contrast, Antarctic glaciers were virtually free from these genes. Antibiotic resistance genes, of both clinical (i.e. aac(3), blaIMP) and agricultural (i.e. strA and tetW) origin, were detected. Our results show regional geographical distribution of antibiotic resistance genes, with the most plausible modes of transmission through airborne bacteria and migrating birds. [ABSTRACT FROM AUTHOR]

Different scenarios attempting to describe the initial phases of the human dispersal from Asia into the New World have been proposed during the last two decades. However, some aspects concerning the population affinities among early and modern Asians and Native Americans remain controversial. Specifically, contradictory views based mainly on partial evidence such as skull morphology or molecular genetics have led to hypotheses such as the 'Two Waves/Components' and 'Single Wave' or 'Out of Beringia' model, respectively. Alternatively, an integrative scenario considering both morphological and molecular variation has been proposed and named as the 'Recurrent Gene Flow' hypothesis. This scenario considers a single origin for all the Native Americans, and local, within-continent evolution plus the persistence of contact among Circum-Arctic groups. Here we analyze 2D geometric morphometric data to evaluate the associations between observed craniometric distance matrix and different geographic design matrices reflecting distinct scenarios for the peopling of the New World using basic and partial Mantel tests. Additionally, we calculated the rate of morphological differentiation between Early and Late American samples under the different settlement scenarios and compared our findings to the predicted morphological differentiation under neutral conditions. Also, we incorporated in our analyses some variants of the classical Single Wave and Two Waves models as well as the Recurrent Gene Flow model. Our results suggest a better explanatory performance of the Recurrent Gene Flow model, and provide additional insights concerning affinities among Asian and Native American Circum-Arctic groups. Am J Phys Anthropol, 2011. © 2011 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Huntington disease (HD) results from CAG expansion in the huntingtin (HTT) gene. Although HD occurs worldwide, there are large geographic differences in its prevalence. The prevalence in populations derived from Europe is 10-100 times greater than in East Asia. The European general population chromosomes can be grouped into three major haplogroups (group of similar haplotypes): A, B and C. The majority of HD chromosomes in Europe are found on haplogroup A. However, in the East-Asian populations of China and Japan, we find the majority of HD chromosomes are associated with haplogroup C. The highest risk HD haplotypes (A1 and A2), are absent from the general and HD populations of China and Japan, and therefore provide an explanation for why HD prevalence is low in East Asia. Interestingly, both East-Asian and European populations share a similar low level of HD on haplogroup C. Our data are consistent with the hypothesis that different HTT haplotypes have different mutation rates, and geographic differences in HTT haplotypes explain the difference in HD prevalence. Further, the bias for expansion on haplogroup C in the East-Asian population cannot be explained by a higher average CAG size, as haplogroup C has a lower average CAG size in the general East-Asian population compared with other haplogroups. This finding suggests that CAG-tract size is not the only factor important for CAG instability. Instead, the expansion bias may be because of genetic cis-elements within the haplotype that influence CAG instability in HTT, possibly through different mutational mechanisms for the different haplogroups. [ABSTRACT FROM AUTHOR]

Background: The brown planthopper (BPH) Nilaparvata lugens (Stål) is one of the most serious insect pests of rice in Asia. However, little is known about the mechanisms responsible for the development, wing dimorphism and sex difference in this species. Genomic information for BPH is currently unavailable, and, therefore, transcriptome and expression profiling data for this species are needed as an important resource to better understand the biological mechanisms of BPH. Methodology/Principal Findings: In this study, we performed de novo transcriptome assembly and gene expression analysis using short-read sequencing technology (Illumina) combined with a tag-based digital gene expression (DGE) system. The transcriptome analysis assembles the gene information for different developmental stages, sexes and wing forms of BPH. In addition, we constructed six DGE libraries: eggs, second instar nymphs, fifth instar nymphs, brachypterous female adults, macropterous female adults and macropterous male adults. Illumina sequencing revealed 85,526 unigenes, including 13,102 clusters and 72,424 singletons. Transcriptome sequences larger than 350 bp were subjected to Gene Orthology (GO) and KEGG Orthology (KO) annotations. To analyze the DGE profiling, we mainly compared the gene expression variations between eggs and second instar nymphs; second and fifth instar nymphs; fifth instar nymphs and three types of adults; brachypterous and macropterous female adults as well as macropterous female and male adults. Thousands of genes showed significantly different expression levels based on the various comparisons. And we randomly selected some genes to confirm their altered expression levels by quantitative real-time PCR (qRT-PCR). Conclusions/Significance: The obtained BPH transcriptome and DGE profiling data provide comprehensive gene expression information at the transcriptional level that could facilitate our understanding of the molecular mechanisms from various physiological aspects including development, wing dimorphism and sex difference in BPH. [ABSTRACT FROM AUTHOR]

Objectives: R483 is a thiazolidinedione peroxisome proliferator-activated receptor gamma (PPARγ) agonist with anti-diabetic properties and also a cytochrome P450 2C19 (CYP2C19) substrate. The aim of the clinical studies reported here was to investigate the influence of the CYP2C19 genotype on the pharmacokinetics (PK) of R483 in healthy subjects and in type 2 diabetes mellitus (T2DM) patients. Methods: Data came from two clinical studies, one including 58 Japanese and Caucasian healthy subjects and another including 93 Asian T2DM patients. All subjects received multiple doses of R483, 20 mg once daily for the healthy subjects and 12 mg once daily for the T2DM patients. Blood samples were taken up to 24 h after the last dose to determine plasma concentrations of R483 and its major metabolites. Results: Poor metabolizers (PMs; CYP2C19*2/*2 or *2/*3 or *3/*3) had a higher plasma exposure and a lower clearance of the parent drug than extensive metabolizers (EMs; CYP2C19*1/*1 or *1/*2 or *1/*3). The homozygous PM/EM ratio for the area under the plasma concentration-time curve (AUC) [95% confidence interval] was 3.9 [2.7-5.7] for healthy subjects versus 2.0 [1.5-2.6] in T2DM patients. The heterozygous EMs were all T2DM patients, the PM/EM ratio for AUC was 1.5 [1.2-1.8]. The dose-normalized exposure to R483 was 1.2- (for PMs) and 2.4-fold (for EMs) higher in T2DM patients than in healthy subjects. R483 was well tolerated in both studies. Conclusions: The plasma exposure to R483 was significantly higher in PMs than in EMs. R483 exhibits different PK in healthy subjects and T2DM patients, and the difference in exposure between EM and PM was less pronounced in T2DM patients than in healthy subjects. Factors such as diabetes condition and age may influence the metabolism of R483. This knowledge allowed for a realistic dose recommendation for poor metabolizer T2DM patients. [ABSTRACT FROM AUTHOR]

Background: In 2005, the first disease-specific Helicobacter pylori virulence factor that induced duodenal ulcer and had a suppressive action on gastric cancer has been identified, and was named duodenal ulcer promoting gene (dupA). However, the importance of the dupA gene on clinical outcomes is conflicting in subsequent studies. The aim of this study was to estimate the magnitude of the risk for clinical outcomes associated with dupA gene. Methods: A meta-analysis of case-control studies which provided raw data on the infection rates with the dupApositive H. pylori detected by polymerase chain reaction was performed. Results: Seventeen studies with a total of 2,466 patients were identified in the search. Infection with the dupApositive H. pylori increased the risk for duodenal ulcer by 1.41-fold (95% confidence interval [CI], 1.12-1.76) overall. Subgroup analysis showed that the summary odds ratio (OR) was 1.57 (95% CI, 1.19-2.06) in Asian countries and 1.09 (95% CI, 0.73-1.62) in Western countries. There was no association between the presence of the dupA gene and gastric cancer and gastric ulcer. Publication bias did not exist. Conclusion: Our meta-analysis confirmed the importance of the presence of the dupA gene for duodenal ulcer, especially in Asian countries. [ABSTRACT FROM AUTHOR]

There have been many genetic studies of systemic lupus erythematosus (SLE) in Asia, but the status of SLE in Asia remains unclear. Genes that have been associated with SLE in Caucasians have shown both consistent and inconsistent results in Asians. This prompted us to review studies of SLE-associated genes and compare the degree of consistency according to ethnicity in Asia. We searched PubMed and the national databases in Korea and Japan for SLE genetic studies. A total of 755 articles were found and after applying various exclusion criteria, 442 studies including 17 linkage studies, 2 genome-wide association studies and 423 candidate-gene analyses were reviewed. Nine linkage loci were confirmed to be associated with SLE susceptibility in non-Asians, but the risk locus (16q12) has been identified in only one Asian study. A total of 156 candidate genes were analyzed, of which 92 were studied in Asians. Although there were allelic (HLA-DRB1 and IRF5) or genetic heterogeneity (FCGR gene family), HLA-DRB1, the FCGR gene family, IRF5, STAT4 and MECP2 showed consistent associations with SLE susceptibility across ethnicities. In conclusion, genetic associations often vary with ethnicity, requiring validation in different ethnic groups, and hence future SLE genetic studies will require strong worldwide collaborations.Genes and Immunity (2009) 10, 421–432; doi:10.1038/gene.2009.24; published online 9 April 2009 [ABSTRACT FROM AUTHOR]

A parentage and a paternity-based approach were tested for estimation of pollen-mediated gene flow in wild grapevine (Vitis vinifera L. subsp. silvestris), a wind-pollinated species occurring in Mediterranean Europe and southwestern Asia. For this purpose, 305 seedlings collected in 2 years at 2 locations in France from 4 wild female individuals and 417 wild individuals prospected from France and Italy were analyzed using 20 highly polymorphic niicrosatellite loci. Their profiles were compared with a database consisting of 3203 accessions from the Institut National de la Recherche Agronomique Vassal collection including cultivars, rootstocks, interspecific hybrids, and other wild individuals. Paternity was assigned for 202 (66.2%) of the 305 seedlings, confirming the feasibility of the method. Most of the fertilizing pollen could be assigned to wild males growing nearby. Estimates of pollen immigration from the cultivated compartment (i.e., the totality of cultivars) ranged from 4.2% to 26% from nearby vineyards and from hidden pollinators such as cultivars and rootstocks that had escaped from farms. In an open landscape, the pollen flow was correlated to the distance between individuals, the main pollinator being the closest wild male (accounting for 51.4-86.2% of the pollen flow). In a closed landscape, more complex poffination occurred. Analysis of the parentage of the 417 wild individuals also revealed relationships between nearby wild individuals, but in the case of 12 individuals (3%), analysis revealed pollen immigration from vineyards, confirming the fitness of the hybrid seedlings. These pollen fluxes may have a significant effect on the evolution of wild populations: on the one hand, the low level of pollen-mediated gene flow from cultivated to wild grapevine could contribute to a risk of extinction of the wild compartment (i.e., the totality of the wild individuals). On the other hand, pollen dispersal within the wild populations may induce inbreeding depression of wild grapevines. [ABSTRACT FROM AUTHOR]

A survey of British born Asian and English populations of children with congenital cardiac anomalies showed an increased incidence in the Muslim Asian population of complex lesions with visceral heterotaxia. There is a very high incidence of parental consanguinity among Muslim Asian children with complex congenital cardiac anomalies that is even higher than in the general Muslim Asian population of the area studied. The evidence suggests an important recessive genetic component in complex cardiac lesions with visceral heterotaxia, but segregation analysis does not support pure recessive inheritance. [ABSTRACT FROM AUTHOR]

The leafy liverwort Nowellia curvifolia is a widespread Holarctic species belonging to the family Cephaloziaceae. It is made up of a newly sequenced, assembled and annotated organellar genomes of two European specimens, which revealed the structure typical for liverworts, but also provided new insights into its microevolution. The plastome of N. curvifolia is the second smallest among photosynthetic liverworts, with the shortest known inverted repeats. Moreover, it is the smallest liverwort genome with a complete gene set, since two smaller genomes of Aneura mirabilis and Cololejeunea lanciloba are missing six and four protein-coding genes respectively. The reduction of plastome size in leafy liverworts seems to be mainly impacted by deletion within specific region between psbA and psbD genes. The comparative intraspecific analysis revealed single SNPs difference among European individuals and a low number of 35 mutations differentiating European and North American specimens. However, the genetic resources of Asian specimen enabled to identify 1335 SNPs in plastic protein-coding genes suggesting an advanced cryptic speciation within N. curvifolia or the presence of undescribed morphospecies in Asia. Newly sequenced mitogenomes from European specimens revealed identical gene content and structure to previously published and low intercontinental differentiation limited to one substitution and three indels. The RNA-seq based RNA editing analysis revealed 17 and 127 edited sites in plastome and mitogenome respectively including one non-canonical editing event in plastid chiL gene. The U to C editing is common in non-seed plants, but in liverwort plastome is reported for the first time. [ABSTRACT FROM AUTHOR]

Brown planthopper (BPH; Nilaparvata lugens Stal) is considered the main rice insect pest in Asia. Several BPH-resistant varieties of rice have been bred previously and released for large-scale production in various rice-growing regions. However, the frequent surfacing of new BPH biotypes necessitates the evolution of new rice varieties that have a wide genetic base to overcome BPH attacks. Nowadays, with the introduction of molecular approaches in varietal development, it is possible to combine multiple genes from diverse sources into a single genetic background for durable resistance. At present, above 37 BPH-resistant genes/polygenes have been detected from wild species and indica varieties, which are situated on chromosomes 1, 3, 4, 6, 7, 8, 9, 10, 11 and 12. Five BPH gene clusters have been identified from chromosomes 3, 4, 6, and 12. In addition, eight BPH-resistant genes have been successfully cloned. It is hoped that many more resistance genes will be explored through screening of additional domesticated and undomesticated species in due course. [ABSTRACT FROM AUTHOR]

Chinese fir (Cunninghamia lanceolata) is an economical important timber species widely planted in southeastern Asia. Decline in yield and productivity during successive rotation is believed to be linked with abiotic stress, such as drought stress and nitrogen (N) and phosphorus (P) starvation. Molecular breeding could be an option to develop tolerant genotypes. For gene expression studies using quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR), stable reference genes are needed for normalization of gene expression under different experimental conditions. However, there is no internal reference genes identified for Chinese fir under abiotic stresses. Thus, nine internal reference genes based on transcriptome data were selected and analyzed in the root of Chinese fir under drought stress and N and P starvation. Data were analyzed using geNorm, NormFinder, and BestKeeper, to screen and identify the best reference genes. The results showed that the UBQ and GAPDH genes were the two most stable genes under drought stress and the Actin1 and GAPDH were the two most stable genes under P starvation. Further, it was discovered that the Actin1 and UBC were the two most stable genes under N starvation among nine candidate reference genes. The gene expression of drought stress induced expression protein 14-3-3-4, the P transporter gene ClPht1;3, and the nitrate transporter gene NRT1.1 were used to verify the stability of the selected reference genes under drought stress and P and N starvation, respectively, and the results revealed that the screened reference genes were sufficient to normalize expression of the target genes. In conclusion, the results demonstrate that the stability of reference genes was closely related to the external conditions and reference genes applied to the roots of Chinese fir under different abiotic stress treatments were different. Our data will facilitate further studies on stress ecology and gene function analysis in Chinese fir. [ABSTRACT FROM AUTHOR]

Reports on the possible re-emergence of the bird flu virus in Asia in January 2005. Preparations taken by the World Health Organization for mass infections caused by the virus; Development of a screening test that would detect bird flu in humans; Efforts of researchers to identify the genes in the genome sequence of chickens which are responsible for the transmission of the virus.