The cAMP responsive element-binding (CREB)-1 gene increases risk of major psychiatric disorders.

Bipolar disorder (BPD), schizophrenia (SCZ) and unipolar major depressive disorder (MDD) are primary psychiatric disorders sharing substantial genetic risk factors. We previously reported that two single-nucleotide polymorphisms (SNPs) rs2709370 and rs6785 in the cAMP responsive element-binding (CREB)-1 gene (CREB1) were associated with the risk of BPD and abnormal hippocampal function in populations of European ancestry. In the present study, we further expanded our analyses of rs2709370 and rs6785 in multiple BPD, SCZ and MDD data sets, including the published Psychiatric Genomics Consortium (PGC) genome-wide association study, the samples used in our previous CREB1 study, and six additional cohorts (three new BPD samples, two new SCZ samples and one new MDD sample). Although the associations of both CREB1 SNPs with each illness were not replicated in the new cohorts (BPD analysis in 871 cases and 1089 controls (rs2709370, P=0.0611; rs6785, P=0.0544); SCZ analysis in 1273 cases and 1072 controls (rs2709370, P=0.230; rs6785, P=0.661); and MDD analysis in 129 cases and 100 controls (rs2709370, P=0.114; rs6785, P=0.188)), an overall meta-analysis of all included samples suggested that both SNPs were significantly associated with increased risk of BPD (11 105 cases and 51 331 controls; rs2709370, P=2.33 × 10-4; rs6785, P=6.33 × 10-5), SCZ (34 913 cases and 44 528 controls; rs2709370, P=3.96 × 10-5; rs6785, P=2.44 × 10-5) and MDD (9369 cases and 9619 controls; rs2709370, P=0.0144; rs6785, P=0.0314), with the same direction of allelic effects across diagnostic categories. We then examined the impact of diagnostic status on CREB1 mRNA expression using data obtained from independent brain tissue samples, and observed that the mRNA expression of CREB1 was significantly downregulated in psychiatric patients compared with healthy controls. The protein-protein interaction analyses showed that the protein encoded by CREB1 directly interacted with several risk genes of psychiatric disorders identified by GWAS. In conclusion, the current study suggests that CREB1 might be a common risk gene for major psychiatric disorders, and further investigations are necessary.

A pleiotropic effect of the APOE gene: association of APOE polymorphisms with multibacillary leprosy in Han Chinese from Southwest China.

BACKGROUND: Patients with leprosy have a very low risk of Alzheimer disease (AD) and ß-amyloid (Aß) deposition is significantly lower in the brain tissue of elderly patients with leprosy compared with age-matched controls. Apolipoprotein E (ApoE) plays a critical role in lipid metabolic pathways and in the brain, facilitating the proteolytic clearance of Aß. We hypothesized that APOE confers risk of leprosy as lipid metabolism is involved in Mycobacterium leprae infection. OBJECTIVES: To investigate the potential genetic associations between APOE and leprosy in two independent Chinese case-control cohorts from the Yuxi and Wenshan prefectures, Yunnan Province of Southwest China. METHODS: Five APOE single-nucleotide polymorphisms (SNPs) were analysed in 1110 individuals (527 patients and 583 controls) from the Yuxi prefecture using a SNaPshot assay. Genetic variations in the entire APOE exons were screened in 1788 individuals (798 patients and 990 controls) from the Wenshan prefecture using next-generation sequencing technology. RESULTS: The AD-associated SNPs rs405509 and rs439401 increased the risk of leprosy per se and multibacillary leprosy (P < 0·005), but the APOE-ε4 allele did not. The SNPs rs405509 and rs439401 were cis expression quantitative trait loci (eQTL) for APOE expression in human skin. Differential APOE mRNA expression was observed in skin lesions of patients with type I reaction leprosy and those with multibacillary leprosy. APOE and related lipid genes are involved in an interaction network with leprosy susceptibility genes. CONCLUSIONS: The APOE gene is associated with leprosy, most likely by regulating lipid-metabolism-related genes.

Association of the LRRK2 genetic polymorphisms with leprosy in Han Chinese from Southwest China.

Leprosy is a chronic infectious and neurological disease that is caused by infection of Mycobacterium leprae (M. leprae). A recent genome-wide association study indicated a suggestive association of LRRK2 genetic variant rs1873613 with leprosy in Chinese population. To validate this association and further identify potential causal variants of LRRK2 with leprosy, we genotyped 13 LRRK2 variants in 548 leprosy patients and 1078 healthy individuals from Yunnan Province and (re-)analyzed 3225 Han Chinese across China. Variants rs1427267, rs3761863, rs1873613, rs732374 and rs7298930 were significantly associated with leprosy per se and/or paucibacillary leprosy (PB). Haplotype A-G-A-C-A was significantly associated with leprosy per se (P=0.018) and PB (P=0.020). Overexpression of the protective allele (Thr2397) of rs3761863 in HEK293 cells led to a significantly increased nuclear factor of activated T-cells' activity compared with allele Met2397 after lipopolysaccharides stimulation. Allele Thr2397 could attenuate 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine-induced autophagic activity in U251 cells. These data suggest that the protective effect of LRRK2 variant p.M2397T on leprosy might be mediated by increasing immune response and decreasing neurotoxicity after M. leprae loading. Our findings confirm that LRRK2 is a susceptible gene to leprosy in Han Chinese population.

Mapping genetic variants in the CFH gene for association with leprosy in Han Chinese.

Complement factor H (CFH) is an essential regulator in the homeostasis of the complement system that plays multiple roles in leprosy. We previously reported a preliminary association of CFH with leprosy, but potentially causal variants remain to be identified. In this study, we performed a fine-mapping association analysis in 1110 individuals (527 leprosy patients and 583 controls) followed by bioinformatic analyses. We identified no association of typical missense CFH variants with leprosy and factor H-binding protein was not detected in Mycobacterium leprae. However, robust associations (PBonferroni<0.003) of several CFH intronic tag single-nucleotide polymorphisms with leprosy were observed. Expression quantitative trait locus analysis showed that these leprosy-protective alleles were associated with higher CFH level and lower CFHR3 (complement factor H-related 3) level. Our results indicated that CFH variants may contribute to leprosy pathogenesis through altering CFH expression, leading to regulation of complement activity rather than mediating immune evasion by bacteria binding.

Chicken domestication: an updated perspective based on mitochondrial genomes.

Domestic chickens (Gallus gallus domesticus) fulfill various roles ranging from food and entertainment to religion and ornamentation. To survey its genetic diversity and trace the history of domestication, we investigated a total of 4938 mitochondrial DNA (mtDNA) fragments including 2843 previously published and 2095 de novo units from 2044 domestic chickens and 51 red junglefowl (Gallus gallus). To obtain the highest possible level of molecular resolution, 50 representative samples were further selected for total mtDNA genome sequencing. A fine-gained mtDNA phylogeny was investigated by defining haplogroups A-I and W-Z. Common haplogroups A-G were shared by domestic chickens and red junglefowl. Rare haplogroups H-I and W-Z were specific to domestic chickens and red junglefowl, respectively. We re-evaluated the global mtDNA profiles of chickens. The geographic distribution for each of major haplogroups was examined. Our results revealed new complexities of history in chicken domestication because in the phylogeny lineages from the red junglefowl were mingled with those of the domestic chickens. Several local domestication events in South Asia, Southwest China and Southeast Asia were identified. The assessment of chicken mtDNA data also facilitated our understanding about the Austronesian settlement in the Pacific.

Pseudomitochondrial genome haunts disease studies.

The accidental amplification of nuclear mitochondrial pseudogenes (NUMTs) can pose a serious problem for mitochondrial disease studies. This report shows that the mutation spectrum left by spurious amplification of a NUMT can be detected because it usually differs considerably from the authentic natural spectrum. This study examined the problem introduced by an ND5 gene NUMT that was recorded in a proband with hearing loss and reviews other disease studies erroneously reporting NUMT variation as genuine mutations in their patients. NUMTs can emerge in population genetic studies, as exemplified here by cases in this study and from published sources. Appropriate database searches and a phylogenetic approach can prevent hasty claims for novelty of mitochondrial DNA (mtDNA) variants inadvertently derived from NUMTs and help to direct investigators to the real source.

[Construction and identification of lentiviral vector mediated GATA-3 gene RNA interference in mouse].

Objective:The aim of this study was to construct and identify a lentiviral vector for RNA interference of mouse GATA-3.Method:The coding region of the GATA-3 gene sequences were analyzed for a single-stranded oligo design and synthesis.PCR was performed for splicing reaction of synthetic oligo,which was synthesized into the lentiviral vector and transformed into the competent cell DH5α.An expression vector shRNA-GATA-3 was constructed after sequencing and identifying the gene sequence of the recombinant clones.Accoding to the target gene sequence ,four pairs are as following: siRNA-685 group(LV3-GATA-3-Mus-685),siRNA-1152 group (LV3-GATA-3-Mus-1152),siRNA-1615 group(LV3-GATA-3-Mus-1615) and control group ,which were designed and syntheized and builded into the lentiviral carrier.The shRNA vectors were cotransfected with expression vectors into the 293T cell line,and the optimal interference sequence was screened by QPCR. The 293T cells were cotranfected with the constructed lentiviral interference vectors and packing plasmids,the viruses were packed,the virus stock was collected and concentrated by ultracentrifugation,and the titer of the viruses was determined. Result:Gene sequence proved that the recombinant clone gene sequence was correct,and the lentiviral vector was successfully constructed. The relative expression of GATA-3 mRNA in siRNA-1615 group(0.004) was significantly reduced after RNA interference comparing with that in the control group(0.022),siRNA-1152 group(0.009) and siRNA-685 group(0.009). The screened LV3-GATA-3-Mus-1615 ,as the most effective interference sequence,was constructed into the lentiviral vector.The titer of the concentrated virus of LV3-GATA-3-Mus-1615 was 5×108 TU/ml in the viral supernate of 293T cells collected at 48 hours after co-transfection. Conclusion:Alentiviral RNAi expression vector targeting the GATA-3 gene (LV3-GATA-3-Mus-1615) was successfully constrcted and identified.

Gene admixture in the silk road region of China: evidence from mtDNA and melanocortin 1 receptor polymorphism.

Mitochondrial DNA control region segment I sequences and melanocortin 1 receptor (MC1R) gene polymorphism were examined in ethnic populations in the silk road region of China. Both the frequencies of the MC1R variants and the results of mtDNA data in this region presented intermediate values between those of Europe and East and Southeast Asia, which suggested extensive gene admixture in this area and was in general agreement with previous studies. Phylogenetic analysis of the ethnic populations in the Silk Road region that based on mtDNA data didn't show expected cluster pattern according to their ethnogenesis. We suspect that a high migration rate in female among these closely related populations and other three demographic events might account for it.

[Phylogenetic relationships among Viperidae, Crotalinae based on mitochondrial 12S rRNA sequence variations].

This paper analyzed the phylogenetic relationships and classification of pit vipers (Viperidae, Crotalinae) based on mitochondrial 12S rRNA gene sequence variations. We have sequenced mtDNA 12S rRNA gene about 370 bp fragment from Gloydius saxatilis Emelianov, Gloydius shedaoensis Zhao, Gloydius ussurriensis (Emelianov), Trimeresurus stejnegeri Schmidt and Deinagkistrodon acutus, Gloydius brevicaudus (Stejneger) from two different localities, respectively. Combined with the sequence of Dinodon semicarinatus from GenBank, we have constructed two molecular phylogenetic trees using both Maximum-parsimony analysis and Neighbor-joining. Our results support the following conclusions: (1) Deinagkistrodon is a valid genus; (2) we also discussed the origin of Gloydius shedaoensis and showed it is a subspecies of Gloydius saxatilis; (3) Gloydius brevicaudsu and Gloydius ussurriensis are classified two species.

[Mitochondrial DNA sequence variations of Zhuang ethnic group in Guangxi].

The mtDNA hypervariable segment I sequences (515bp) were sequenced in 83 Zhuangs from Gunngxi Province, with the aim to learn more about the origin and genetic structure of the current Zhuangs. 66 haplotypes were identified in the samples, with 71 sites showing polymorphism. Phylogenetic analysis of the 66 haplotypes suggests that there are geographic differentiation in current Zhuangs, and those from the 4 geographic regions (Nanning, Hechi, Baise and Liuzhou) have different distribution frequencies in the cluster I, II and III in the tree. More than 50% individuals from Liuzhou and Hechi converge into cluster II, while those from Nanning and Baise have high frequency in cluster I. Combined with the analysis of the reported data, the Zhuang ethnic group shows remote affinity to those from North China, whereas it is close to those in South China. The frequencies of the radiation groups in Zhuangs, together with the phylogenetic relationship of the Zhuang ethnic group in the tree suggest that the Zhuang is a typical south population.

[Mitochondrial DNA sequence variations of Shui ethnic group].

The mtDNA hypervariable segment I sequences (HVS I) were sequenced in 64 Shuis from Guizhou Province. 73 sites were polymorphic in the 495 bp fragment that sequenced, identified 48 different haplotypes. Phylogenetic analysis of the haplotypes suggested that there were some ancestral haplotypes in current Shuis, and these haplotypes were also present in Eurasia populations as well as in other ethnic groups. Demographic analysis of the Shuis demonstrated a unimodal distribution that is typical for a population undergone expansion in the past and with a high Tau value, which suggested that the Shui group might be a ancestral population. Combined with the analysis of the reported data, the Shui ethnic group showed a generally similar genetic component with the Zhuang from Guangxi, but it is also different from these typical south populations as Zhuang, Cantonese.

Evolution of atomic rearrangements in deformation in metallic glasses.

Atomic rearrangements induced by shear stress are fundamental for understanding deformation mechanisms in metallic glasses (MGs). Using molecular dynamic simulation, the atomic rearrangements characterized by nonaffine displacements (NADs) and their spatial distribution and evolution with tensile stress in Cu50Zr50 MG were investigated. It was found that in the elastic regime the atomic rearrangements with the largest NADs are relatively homogeneous in space, but exhibit strong spatial correlation, become localized and inhomogeneous, and form large clusters as strain increases, which may facilitate the so-called shear transformation zones. Furthermore, initially they prefer to take place around Cu atoms which have more nonicosahedral configurations. As strain increases, the preference decays and disappears in the plastic regime. The atomic rearrangements with the smallest NADs are preferentially located around Cu atoms, too, but with more icosahedral or icosahedral-like atomic configurations. The preference is maintained in the whole deformation process. In contrast, the atomic rearrangements with moderate NADs distribute homogeneously, and do not show explicit preference or spatial correlation, acting as matrix during deformation. Among the atomic rearrangements with different NADs, those with largest and smallest NADs are nearest neighbors initially, but separating with increasing strain, while those with largest and moderate NADs always avoid to each other. The correlations in the fluctuations of the NADs confirm the long-range strain correlation and the scale-free characteristic of NADs in both elastic and plastic deformation, which suggests a universality of the scaling in the plastic flow in MGs.

Reappraising the relationship between mitochondrial DNA variant m.16189T>C and type 2 diabetes mellitus in East Asian populations.

The role of mitochondrial DNA (mtDNA) variant 16189T>C in type 2 diabetes mellitus (T2DM) remains hotly debated in the past decade. If mutation 16189T>C indeed posed a risk to T2DM, as echoed by some recent studies, correlation between this mutation and disease should be observed when carrying out a systematical study using data and samples collected in a large geographic region in China. To test this hypothesis, we first performed a linear regression analysis between the prevalence of T2DM and the allele frequency of 16189C variant in 10 East Asian populations, and further genotyped this variant in two casecontrol cohorts from west Han Chinese (Kunming and Xining). Linear regression analysis showed that no significant correlation was observed (r(2)=0.211, P=0.181), and the genotyping results indicated that the m.16189T>C frequency difference between case and control was not significant in either populations (P=0.38 and 0.89 for Kunming and Xining, respectively). Matrilineal backgrounds constitution (in terms of haplogroups) analysis generated a similar haplogroup distribution in both populations (P>0.1). All results failed to substantiate that m.16189T>C may play an active role in the development of T2DM in East Asian populations.

Genetic diversity of Chinese domestic goat based on the mitochondrial DNA sequence variation.

The aim of this study was to characterize the genetic diversity of domestic goat in China. For this purpose, we determined the sequence of the mitochondrial DNA (mtDNA) control region in 72 individuals of the Yangtze River delta white goat, and reanalysed 723 published samples from 31 breeds/populations across China. All goat haplotypes were classified into four haplogroups (A-D) previously described. The phylogenetic pattern that emerged from the mtDNA control region sequence was confirmed by the analysis of the entire cytochrome b sequence of eight goats representative of the four haplogroups. It appeared that in Chinese domestic goat, haplogroups A and B were dominant and distributed in nearly all breeds/populations, while haplogroups C and D were only found in seven breeds/populations. Four breeds/populations contained all four haplogroups. When grouping the breeds/populations into five geographic groups based on their geographic distributions and ecological conditions, the southern pasturing area had the highest diversity whereas the northern farming area had the lowest diversity. 84.29% and 11.37% of the genetic variation were distributed within breeds and among breeds within the ecologically geographical areas, respectively; only 4% of genetic variation was observed among the five geographic areas. We speculate that the traditional seasonal pastoralism, the annual long-distance migrations that occurred in the past, and the commercial trade would account for the observed pattern by having favoured gene flows.

Atomistic Origin of Rate-Dependent Serrated Plastic Flow in Metallic Glasses.

Nanoindentation simulations on a binary metallic glass were performed under various strain rates by using molecular dynamics. The rate-dependent serrated plastic flow was clearly observed, and the spatiotemporal behavior of its underlying irreversible atomic rearrangement was probed. Our findings clearly validate that the serration is a temporally inhomogeneous characteristic of such rearrangements and not directly dependent on the resultant shear-banding spatiality. The unique spatiotemporal distribution of shear banding during nanoindentation is highlighted in terms of the potential energy landscape (PEL) theory.

Mitochondrial DNA sequence diversity and origin of Chinese domestic yak.

In order to clarify the origin and genetic diversity of yak in China, we analysed mitochondrial DNA (mtDNA) control region sequences (approximately 891 bp) in 52 individuals from four domestic yak (Poephagus grunniens) breeds, as well as from a hybrid between yak and cattle (Pianniu). Twenty-five samples were further selected for partial (420 bp) cytochrome b sequencing based on control region sequence information. Two yak samples shared sequences with Chinese cattle (Bos taurus); the remaining yak mtDNAs converged into two major clades in the phylogenetic analysis. Genetic diversity varied substantially among the breeds, with the hybrid Pianniu yak demonstrating the highest diversity. Our results suggest that the Chinese yak was domesticated from two distinct matrilineal sources or from a heterogeneous pool containing both divergent lineages, with occasional gene introgression from cattle.

Evolutionary history of the mtDNA 9-bp deletion in Chinese populations and its relevance to the peopling of east and southeast Asia.

In total, 1218 Chinese from twelve ethnic groups and nine Han geographic groups were screened for the mtDNA 9-bp deletion motif. The frequency of the 9-bp deletion in all samples was 14.7% but ranged from 0% to 32% in the various ethnic groups. Three individuals had a triplication of the 9-bp segment. Phylogenetic and demographic analyses of the mtDNA hypervariable segment 1 (HVS 1) sequences suggest that the 9-bp deletion occurred more than once in China. The majority of the Chinese deletion haplotypes (about 90%) have a common origin as a mutational event following an initial expansion of modern humans in eastern Asia. Other deletion haplotypes and the three haplotypes with a 9-bp triplication may have arisen independently in the Chinese, presumably by replication error. HVS1 haplotype analysis suggests two possible migration routes of the 9-bp deletion in east and southeast Asia. Both migrations originated in China with one route leading to the Pacific Islands via Taiwan, the other to southeast Asia and possibly the Nicobar Islands. Along both routes of peopling, a decrease in HVSI diversity of the mtDNA haplotypes is observed. The "Polynesian motif (16217T/C, 16247A/G, and 16261C/T)" and the 16140T/C, 16266C/A, or C/G polymorphisms appear specific to each migration route.

[Separation of catechins and caffeine in tea polyphenol by isocratic elution high performance liquid chromatography].

The catechins, particularly in green tea, have been found to possess anti-mutagenic and anti-tumorigenic properties. As each catechin possesses distinct properties, a simple and rapid method that could be used for analysis of individual catechins in a complex mixture would be necessary. A relatively simple and rapid method for simultaneous separation of five catechins and caffeine in tea polyphenol by isocratic elution high performance liquid chromatography has been developed. The analysis could be finished within 30 min. They were measured using Resolve C18 column (at 43 degrees C) and UV detector (at 280 nm), water-85% phosphoric acid aqueous solution-acetonitrile-dimethyl formamide(DMF) (859:1:120:20, V/V) as mobile phase. There was a good linear relationship between the content of component and its peak area for catechins and caffeine, with the correlation coefficients of 0.9992-0.9999. The average recoveries (n = 5) were 83.33%-104.42%, and the relative standard deviations (n = 6) were 0.74%-1.43%. The effect of concentration of DMF in mobile phase was studied.