A linguistically informed autosomal STR survey of human populations residing in the greater Himalayan region.

The greater Himalayan region demarcates two of the most prominent linguistic phyla in Asia: Tibeto-Burman and Indo-European. Previous genetic surveys, mainly using Y-chromosome polymorphisms and/or mitochondrial DNA polymorphisms suggested a substantially reduced geneflow between populations belonging to these two phyla. These studies, however, have mainly focussed on populations residing far to the north and/or south of this mountain range, and have not been able to study geneflow patterns within the greater Himalayan region itself. We now report a detailed, linguistically informed, genetic survey of Tibeto-Burman and Indo-European speakers from the Himalayan countries Nepal and Bhutan based on autosomal microsatellite markers and compare these populations with surrounding regions. The genetic differentiation between populations within the Himalayas seems to be much higher than between populations in the neighbouring countries. We also observe a remarkable genetic differentiation between the Tibeto-Burman speaking populations on the one hand and Indo-European speaking populations on the other, suggesting that language and geography have played an equally large role in defining the genetic composition of present-day populations within the Himalayas.

[Current status and implication of research on Bardet-Biedl syndrome].

OBJECTIVE: Bardet-Biedl syndrome (BBS) is a rare autosomal recessive disease initially reported by Bardet and Biedl in the 1920s. BBS is a pleiotropic and genetically heterogeneous disorder characterized by retinopathy, obesity, polydactyly, renal malformations and functional abnormalities, learning disabilities and hypogenitalism. BBS patients are also prone to diabetes mellitus, hypertension and congenital heart disease. To date, 16 BBS genes (BBS1-BBS16) have been identified. However, the molecular etiology of BBS is not yet entirely clear. In this article, we have reviewed recent research on BBS and discussed its implications for understanding of ciliopathology.

Resveratrol inhibits inflammatory responses via the mammalian target of rapamycin signaling pathway in cultured LPS-stimulated microglial cells.

BACKGROUND: Resveratrol have been known to possess many pharmacological properties including antioxidant, cardioprotective and anticancer effects. Although current studies indicate that resveratrol produces neuroprotection against neurological disorders, the precise mechanisms for its beneficial effects are still not fully understood. We investigate the effect of anti-inflammatory and mechamisms of resveratrol by using lipopolysaccharide (LPS)-stimulated murine microglial BV-2 cells. METHODOLOGY/PRINCIPAL FINDINGS: BV-2 cells were treated with resveratrol (25, 50, and 100 µM) and/or LPS (1 µg/ml). Nitric oxide (NO) and prostaglandin E2 (PGE2) were measured by Griess reagent and ELISA. The mRNA and protein levels of proinflammatory proteins and cytokines were analysed by RT-PCR and double immunofluorescence labeling, respectively. Phosphorylation levels of PTEN (phosphatase and tensin homolog deleted on chromosome 10), Akt, mammalian target of rapamycin (mTOR), mitogen-activated protein kinases (MAPKs) cascades, inhibitor κB-α (IκB-α) and cyclic AMP-responsive element-binding protein (CREB) were measured by western blot. Resveratrol significantly attenuated the LPS-induced expression of NO, PGE2, inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2), tumor necrosis factor-α (TNF-α), interleukin-1ß (IL-1ß) and nuclear factor-κB (NF-κB) in BV-2 cells. Resveratrol increased PTEN, Akt and mTOR phosphorylation in a dose-dependent manner or a time-dependent manner. Rapamycin (10 nM), a specific mTOR inhibitor, blocked the effects of resveratrol on LPS-induced microglial activation. In addition, mTOR inhibition partially abolished the inhibitory effect of resveratrol on the phosphorylation of IκB-α, CREB, extracellular signal-regulated kinase 1/2 (ERK1/2), c-Jun N-terminal protein kinase (JNK), and p38 mitogen-activated protein kinase (p38 MAPK). CONCLUSION AND IMPLICATIONS: This study indicates that resveratrol inhibited LPS-induced proinflammatory enzymes and proinflammatory cytokines via down-regulation phosphorylation of NF-κB, CREB and MAPKs family in a mTOR-dependent manner. These findings reveal, in part, the molecular basis underlying the anti-inflammatory properties of resveratrol.

[Rhesus monkey embryonic stem cells differentiation, proliferation and allotransplantation].

To investigate the characteristics of rhesus monkey embryonic stem cells and to promote their clinical application, the differentiation and proliferation of rosettes neural stem cells from GFP marked rhesus monkey embryonic stem cells were studied The results showed that: 1) A stable and high-efficient neural differentiation system was established. More than 95% of the embryonic stem cells were differentiated into neural stem cells on the 12(th) days of differentiation; 2) the rosettes neural stem cells differentiated from the rhesus monkey embryonic stem cells could maintain their rosettes-shape by proliferating with bFGF/EGF; 3) the neural stem cells could differentiate into neurons after transplanted into the rhesus monkey brain. In conclusion, the rosettes neural stem cells differentiated from rhesus monkey embryonic stem cells could maintain their characteristics after proliferation with bFGF/EGF and they could survive and differentiate into neurons after transplanted into the rhesus monkey brain, which strongly supports the clinical application of neural stem cells in the future.

Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia.

The regional distribution of an ancient Y-chromosome haplogroup C-M130 (Hg C) in Asia provides an ideal tool of dissecting prehistoric migration events. We identified 465 Hg C individuals out of 4284 males from 140 East and Southeast Asian populations. We genotyped these Hg C individuals using 12 Y-chromosome biallelic markers and 8 commonly used Y-short tandem repeats (Y-STRs), and performed phylogeographic analysis in combination with the published data. The results show that most of the Hg C subhaplogroups have distinct geographical distribution and have undergone long-time isolation, although Hg C individuals are distributed widely across Eurasia. Furthermore, a general south-to-north and east-to-west cline of Y-STR diversity is observed with the highest diversity in Southeast Asia. The phylogeographic distribution pattern of Hg C supports a single coastal 'Out-of-Africa' route by way of the Indian subcontinent, which eventually led to the early settlement of modern humans in mainland Southeast Asia. The northward expansion of Hg C in East Asia started approximately 40 thousand of years ago (KYA) along the coastline of mainland China and reached Siberia approximately 15 KYA and finally made its way to the Americas.

Y-chromosome distributions among populations in Northwest China identify significant contribution from Central Asian pastoralists and lesser influence of western Eurasians.

Northwest China is closely adjacent to Central Asia, an intermediate region of the Eurasian continent. Moreover, the Silk Road through the northwest of China once had a vital role in the east-west intercommunications. Nevertheless, little has been known about the genetic makeup of populations in this region. We collected 503 male samples from 14 ethnic groups in the northwest of China, and surveyed 29 Y-chromosomal biallelic markers and 8 short tandem repeats (STRs) loci to reconstruct the paternal architecture. Our results illustrated obvious genetic difference among these ethnic groups, and in general their genetic background is more similar with Central Asians than with East Asians. The ancestors of present northwestern populations were the admixture of early East Asians peopling northwestward and later Central Asians immigrating eastward. This population mixture was dated to occur within the past 10 000 years. The J2-M172 lineages likely entered China during the eastward migration of Central Asians. The influence from West Eurasia through gene flows on the extant ethnic groups in Northwest China was relatively weak.

The ADH1B Arg47His polymorphism in east Asian populations and expansion of rice domestication in history.

BACKGROUND: The emergence of agriculture about 10,000 years ago marks a dramatic change in human evolutionary history. The diet shift in agriculture societies might have a great impact on the genetic makeup of Neolithic human populations. The regionally restricted enrichment of the class I alcohol dehydrogenase sequence polymorphism (ADH1BArg47His) in southern China and the adjacent areas suggests Darwinian positive selection on this genetic locus during Neolithic time though the driving force is yet to be disclosed. RESULTS: We studied a total of 38 populations (2,275 individuals) including Han Chinese, Tibetan and other ethnic populations across China. The geographic distribution of the ADH1B*47His allele in these populations indicates a clear east-to-west cline, and it is dominant in south-eastern populations but rare in Tibetan populations. The molecular dating suggests that the emergence of the ADH1B*47His allele occurred about 10,000 to approximately 7,000 years ago. CONCLUSION: We present genetic evidence of selection on the ADH1BArg47His polymorphism caused by the emergence and expansion of rice domestication in East Asia. The geographic distribution of the ADH1B*47His allele in East Asia is consistent with the unearthed culture relic sites of rice domestication in China. The estimated origin time of ADH1B*47His allele in those populations coincides with the time of origin and expansion of Neolithic agriculture in southern China.

[Cyclin D1 gene G870A polymorphism and susceptibility to nasopharyngeal carcinoma].

OBJECTIVE: The aim of this study was to investigate the susceptibility and prognostic implications of the cyclin D1 gene (CCND1) G870A polymorphism to nasopharyngeal carcinomas (NPC) in Han population in Yunnan China. METHODS: Two hundred and forty one cases with NPC and 271 matched cancer-free controls were genotyped for the CCND1 G870A polymorphism by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and sequencing. The adjusted odds ratios (OR) and 95% confidence intervals (CI) were calculated by using unconditional logistic regression model. Overall survival was assessed using univariate and multivariate analyses. RESULTS: Contrast with homozygous CCND1 G870G, A allele significantly increasing risk of NPC was associated with homozygous A870A (OR = 4.79, 95% CI 2.77 - 8.28, P < 0.001) and heterozygous A870G (OR = 1.72, 95% CI 1.10 - 2.68, P = 0.017). The subjects at least having one CCND1 870A allele had OR of 2.40 (95% CI 1.59 - 3.63, P < 0.001). Furthermore, smoking may increase the risk of developing NPC interacting with CCND1 G870A polymorphism. Kaplan-Meier analysis and Cox regression analysis demonstrated that the five-year survival rate of subjects with AA, AG and GG genotype was 56.2%, 78.5% and 81.4% (AA vs GG, P = 0.003; AA vs AG, P = 0.012; AG vs GG, P = 0.132), but not independent prognostic factor in NPC (P = 0.501). CONCLUSIONS: The CCND1 870A allele is associated with the NPC in Han population in Yunnan China, meanwhile, showed a significant prognosis for those patients.

Winter temperature and UV are tightly linked to genetic changes in the p53 tumor suppressor pathway in Eastern Asia.

The tumor suppressor p53 is a master sensor of stress. Two human-specific polymorphisms, p53 codon 72 and MDM2 SNP309, influence the activities of p53. There is a tight association between cold winter temperature and p53 Arg72 and between low UV intensity and MDM2 SNP309 G/G in a cohort of 4029 individuals across Eastern Asia that suggests causative selection. Moreover, the two polymorphisms are not coselected. Haplotype-based selection analysis further suggests that this is a striking example of two functional polymorphisms being strongly selected for in human populations in response to environmental stresses.

Allele frequency distribution of 21 forensic autosomal STRs in 7 populations from Yunnan, China.

This study examines the genotypes and allele frequency distributions of 21 forensic autosomal STRs for 7 populations from Yunnan province, China: Han (two different population samples, n=48 and n=59, respectively), Nu (n=36), Tibetan (n=31), Du Long (n=24), Lisu (n=25) and Yi (n=24). Pairwise FST analysis shows (marginally) significant differences between some of the Yunnan populations, but not between the Yunnan populations and other population samples from China and surrounding countries.

Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations.

BACKGROUND: The phylogeography of the Y chromosome in Asia previously suggested that modern humans of African origin initially settled in mainland southern East Asia, and about 25,000-30,000 years ago, migrated northward, spreading throughout East Asia. However, the fragmented distribution of one East Asian specific Y chromosome lineage (D-M174), which is found at high frequencies only in Tibet, Japan and the Andaman Islands, is inconsistent with this scenario. RESULTS: In this study, we collected more than 5,000 male samples from 73 East Asian populations and reconstructed the phylogeography of the D-M174 lineage. Our results suggest that D-M174 represents an extremely ancient lineage of modern humans in East Asia, and a deep divergence was observed between northern and southern populations. CONCLUSION: We proposed that D-M174 has a southern origin and its northward expansion occurred about 60,000 years ago, predating the northward migration of other major East Asian lineages. The Neolithic expansion of Han culture and the last glacial maximum are likely the key factors leading to the current relic distribution of D-M174 in East Asia. The Tibetan and Japanese populations are the admixture of two ancient populations represented by two major East Asian specific Y chromosome lineages, the O and D haplogroups.

[Extraction and analysis of nuclear DNA from free margin of nail material].

To investigate the feasibility of DNA analysis from free margin of the nail, genomic DNA was extracted from the free margin of nail clipping of 10 volunteers using the proteinase K/SDS -based organic method, the Chelex-100 method, or a combined method. Target DNA was simultaneously amplified using a fluorescent multiplex AmpFlSTR Identifier kit. The PCR products were analyzed on the ABI PRISM 3130 Genetic Analyzer. The results showed that, compared with profiles achieved by genotyping of blood samples from each volunteer as reference, 100% concordance was achieved using the combined method. The STR genotype profiles obtained through the organic method were acceptable, despite preferential amplification at some loci. In contrast, no readable profiles could be determined when DNA was extracted by the Chelex-100 method, and there were a large number of alleles missing. Our data suggest that free margin of nail can be used for nuclear DNA analysis, but the type of DNA isolation method used is critical. The traditional organic extraction method works reasonably well for free margin nail DNA isolation, and combination of organic extraction and the Chelex-100 method works best.

[The production of gastrodin through biotransformation of p-hydroxybenzaldehyde by cell suspension culture of Datura stramonium].

AIM: To investigate the production of p-hydroxymethylphenol-beta-D-glucoside (gastrodin) through biotransformation by plant cell suspension cultures. METHODS: Using cell suspension cultures of Datura stramonium to convert the exogenous p-hydroxybenzaldehyde into gastrodin was conducted and the converted compounds were separated with a combination of multi-chromatography. Their chemical structures were determined on the basis of spectral analysis and chemical evidence. RESULTS: The conversion procedure of p-hydroxybenzaldehyde into gastrodin by Datura stramonium cell suspension cultures was established. The synthesized gastrodin (II) was isolated from the fermental liquor and identified by spectral analysis. At the same time, the p-hydroxybenzyl alcohol (I) converted through biotransformation of p-hydroxybenzaldehyde by cell suspension cultures of Datura stramonium was also isolated and identified. Two compounds were also isolated from the cell cultures and they were identified as beta-D-furanoallulose (III) and n-butyloxystyryl-beta-D-pyranoallulose (IV). CONCLUSION: Datura stramonium grown in suspension cultures can convert exogenous p-hydroxybenzaldehyde into the corresponding gastrodin.

[Production of gastrodin through biotransformation of p-hydroxybenzaldehyde by cell suspension cultures of Datura tatula L].

The conversion of exogenous p-hydroxybenzaldehyde to p-hydroxy-methyl-phenol-beta-D-glucoside (gastrodin) was studied by using cell suspension culture of Datura tatula L. The chemical structure of this synthesized gastrodin was identified based on the spectral analysis and chemical evidence. The conversion procedure of p-hydroxybenzaldehyde into gastrodin by D. tatula L. cell suspension cultures was established. The synthesized gastrodin (II) was isolated from the ferment liquor and identified by spectral analysis. At the same time, the p-hydroxybenzyl alcohol (I) converted through biotransformation of p-hydroxybenzaldehyde by cell suspension cultures of D. tatula L. was also isolated and identified. The efficiency of glucosylation of p-hydroxybenzaldehyde was remarkably enhanced by adding salicylic acid (0.1 mg/L) and keeping the lower pressure (0.001MPa) in 25L airlift loop bioreactor. The biotransformation of exogenous p-hydroxybenzaldehyde to gastrodin by cell suspension culture of D. tatula L. is a promising approach.

Y-chromosome evidence of southern origin of the East Asian-specific haplogroup O3-M122.

The prehistoric peopling of East Asia by modern humans remains controversial with respect to early population migrations. Here, we present a systematic sampling and genetic screening of an East Asian-specific Y-chromosome haplogroup (O3-M122) in 2,332 individuals from diverse East Asian populations. Our results indicate that the O3-M122 lineage is dominant in East Asian populations, with an average frequency of 44.3%. The microsatellite data show that the O3-M122 haplotypes in southern East Asia are more diverse than those in northern East Asia, suggesting a southern origin of the O3-M122 mutation. It was estimated that the early northward migration of the O3-M122 lineages in East Asia occurred approximately 25,000-30,000 years ago, consistent with the fossil records of modern humans in East Asia.

[The polymorphism of Y chromosome and mtDNA distribution among two Bai populations].

In the same ethnic group, people residing at different places may have genetic difference. The difference can be the results of migration and admixture events happened in history. To clarify the genetic relationship and micro-evolution of two Bai ethnic populations residing in Yunnan and Hunan province respectively,we investigated their genetic difference from paternal and maternal genealogy with six other ethnic groups as outgroups. Fourteen loci from mtDNA and thirteen loci from Y chromosome were selected for genotyping using PCR-RFLP methods. Result showed that H6 and H8 are the same dominant Y chromosome haplotypes in two Bai groups. However,the distribution of mtDNA haplogroups showed difference between two Bai populations. D, B, M8 are the predominant haplogroups in Hunan Bai ethnic population, whereas M, G, F are dominant in Yunnan Bai ethnic population. Principal Component (PC) analysis based on the Y chromosome haplotypes showed that two Bai ethic populations cluster together. It shows a close paternal genetic relationship between two Bai ethnic populations. From the mtDNA PC plot, it is clear that Hunan Bai is close to Hunan Han and Tujia, whereas Yunnan Bai is close to ethnic groups living in Yunnan province. The difference of mtDNA haplogroup distribution in two Bai people may reflect the maternal gene flow between ethnic groups living in Hunan province after the ancestors of Hunan Bai migrated from Yunnan province to Hunan province 800 years ago.

[Genetic polymorphism of mitochondrial DNA in coding region in 16 ethnic populations of Yunnan].

The genetic polymorphism of mitochondrial DNA in the coding region in 16 ethnic populations of Yunnan was analyzed using PCR-RFLP in a total of 654 samples. Seventeen haplogroups were found, four of which were undefined haplogroups. Haplogroup distribution and Principal Component (PC) analysis showed that the ethnic groups descended from Bai-Yue tribe have B, F and M7 as the predominant haplogroups,which indicated their origination from southern China. Haplogroup A, D and N9 were predominant in the Mongolian ethnic group, reflecting their north-originated characteristics. The groups descended from Di-Qiang tribe shared the predominant haplogroups with both the south and north originated groups,which demonstrated that they inherit the maternal characteristics from both southern and northern populations. There is genetic difference among the populations in the same ethnic group and is usually smaller than that among the ethnic groups from different ancient tribes, but not necessarily smaller than that among the groups from the same tribe.

[Principal component analysis of Y-chromosome haplotype distribution in 18 ethnic groups in Yunnan Province].

Based on the historical records, 18 of the 26 ethnic groups in Yunnan Province are the descendant populations of three ancient tribes, Bai-Yue, Bai-Pu and Di-Qiang, linguistically belonging to the Daic, Austro-Asiatic and Tibeto-Burman, respectively. In order to trace the origins of these native ethnic groups, a total of 13 East Asian specific Y-chromosome biallelic markers were used to study the genetic structure of 20 local populations covering all the 18 ethnic groups in Yunnan Province. Haplotypes were analysis by PCR-RFLP method. Our results showed that H11 and H12 were the predominant haplotypes in the descendant populations of Bai-Yue tribe. H5, H6 and H8 were the dominant haplotypes in Di-Qiang descendants, and the frequencies of H6, H8 and H11 were very high in the descendant populations of Bai-Pu. To investigate relationships among 20 populations, a three dimensional PC analysis were performed based on the distribution of the 13 haplotypes. All populations were divided into two clusters in the PC plot. The first cluster was mainly composed by the descendant populations of Bai-Yue, and the second one was mainly composed by the descendants of Di-Qiang tribe. This result indicated that Bai-Yue and Di-Qiang's paternal lineage had different origins, which was in agreement with the historical documents and linguistic classification.