A supporting role of Chinese National Immortalized Cell Bank in life science research.

A biorepository of human samples is essential to support the research of life science. Lymphoblastoid B cell line (LCL), which is easy to be prepared and can reproduce indefinitely, is a convenient form of sample preservation. LCLs are established from human B cells transformed by Epstein-Barr virus (EBV). Chinese National Immortalized Cell Bank has preserved human LCLs from different ethnic groups in China. As there are many studies on the nature of LCLs and public available resources with genome-wide data for LCLs, they have been widely applied in genetics, immunology, pharmacogenetics/genomics, regenerative medicine, cancer pathogenesis and immunotherapy, screening and generation of fully human neutralizing monoclonal antibodies and study on EBV pathogenesis. Here, we review the characteristics of LCLs and their contributions to scientific research, and introduce preserved samples in Chinese National Immortalized Cell Bank to the scientific community. We hope this bank can support more areas in the scientific research.

Extended Y chromosome investigation suggests postglacial migrations of modern humans into East Asia via the northern route.

Genetic diversity data, from Y chromosome and mitochondrial DNA as well as recent genome-wide autosomal single nucleotide polymorphisms, suggested that mainland Southeast Asia was the major geographic source of East Asian populations. However, these studies also detected Central-South Asia (CSA)- and/or West Eurasia (WE)-related genetic components in East Asia, implying either recent population admixture or ancient migrations via the proposed northern route. To trace the time period and geographic source of these CSA- and WE-related genetic components, we sampled 3,826 males (116 populations from China and 1 population from North Korea) and performed high-resolution genotyping according to the well-resolved Y chromosome phylogeny. Our data, in combination with the published East Asian Y-haplogroup data, show that there are four dominant haplogroups (accounting for 92.87% of the East Asian Y chromosomes), O-M175, D-M174, C-M130 (not including C5-M356), and N-M231, in both southern and northern East Asian populations, which is consistent with the proposed southern route of modern human origin in East Asia. However, there are other haplogroups (6.79% in total) (E-SRY4064, C5-M356, G-M201, H-M69, I-M170, J-P209, L-M20, Q-M242, R-M207, and T-M70) detected primarily in northern East Asian populations and were identified as Central-South Asian and/or West Eurasian origin based on the phylogeographic analysis. In particular, evidence of geographic distribution and Y chromosome short tandem repeat (Y-STR) diversity indicates that haplogroup Q-M242 (the ancestral haplogroup of the native American-specific haplogroup Q1a3a-M3) and R-M207 probably migrated into East Asia via the northern route. The age estimation of Y-STR variation within haplogroups suggests the existence of postglacial (∼18 Ka) migrations via the northern route as well as recent (∼3 Ka) population admixture. We propose that although the Paleolithic migrations via the southern route played a major role in modern human settlement in East Asia, there are ancient contributions, though limited, from WE, which partly explain the genetic divergence between current southern and northern East Asian populations.

Analysis of two sequence variants in peroxisome proliferator activated receptor gamma gene in Tajik population at high altitudes and Han population at low altitudes in China.

The Tajik people in China have resided at high altitude for thousands of years. We analyzed the Pro12Ala (C > G) polymorphism in exon B and the 161C > T polymorphism in exon 6 of peroxisome proliferator activated receptor gamma gene (PPARG) in Chinese Tajik population living at high altitude and Chinese Han population living at low attitude. Significant higher frequencies of the CG and GG genotypes and G allele of the Pro12Ala (C > G) polymorphism were observed in the Tajik population than that in the Han population (P < 0.0001), which suggested the G allele was associated with high-altitude adaptation in the dominate model. The significant differences were remained in both of the male and female groups after stratified by gender, and the differences were more pronounced in men (G versus C, OR = 7.700) than in women (OR = 5.056). No significant difference was observed for the 161C > T polymorphism in the two populations. The frequencies of haplotypes GT (P < 0.0001) and GC (P < 0.05) were significantly higher, while the frequency of CT (P < 0.0001) was significantly lower in the Tajik population than that in the Han population. Our results suggest that PPARG is a candidate gene for high-altitude adaptation in the Chinese Tajik population.

Analysis of two sequence variants in peroxisome proliferator-activated receptor gamma gene in a Tibetan population at high altitude and a Han population at low altitude in China.

BACKGROUND: The Tibetan people in China have lived at high altitude for thousands of years, raising the possibility that the Tibetans are genetically adapted to high altitude. In this study we analyzed the Pro12Ala (C>G) polymorphism in exon 2 and the 161C>T polymorphism in exon 6 of peroxisome proliferator-activated receptor gamma gene (PPARγ) in a Tibetan population and a Han population. MATERIAL/METHODS: We recruited 142 Tibetan volunteers who are permanent inhabitants in Qingzang plateau (higher elevation) and 266 Han volunteers who are permanent inhabitants in the plain (lower elevation). PCR/RFLP method was applied to examine the 2 polymorphisms in the 2 populations. RESULTS: Significantly higher Pro12Ala (C>G) CC genotype frequency and 161C>T CC genotype frequency were observed in the Tibetan population compared to the Han population (p<0.001). When the samples were stratified by sex, significant differences were only observed in females. The haplotypes constructed by Pro12Ala (C>G) and 161C>T were also analyzed. The frequency of the haplotype CC (p<0.0001) was significantly higher, while the frequency of the haplotype CT (p<0.0001) and GT (p<0.01) was significantly lower in the Tibetan population than in the Han population. CONCLUSIONS: Our results suggested that PPARγ might be a candidate gene for high-altitude adaptation; the Pro12Ala (C>G) CC genotype and/or the 161C>T CC genotype are possibly advantageous factors in the female Tibetan population. Alternatively, the difference of the Pro12Ala (C>G) genotype distribution and /or the difference of the 161C>T genotype distribution in the 2 populations may be due to the racial difference.

The youngest split in sympatric schizothoracine fish (Cyprinidae) is shaped by ecological adaptations in a Tibetan Plateau glacier lake.

Although new empirical evidence shows that sympatric speciation has occurred in some species, there are few indisputable model organisms for this process of speciation. The two subspecies (Gymnocypris eckloni eckloni and G. e. scoliostomus) of the schizothoracine Gymnocypris fish species complex from a small glacier lake in the Tibetan Plateau, Lake Sunmcuo, fit several of the key characteristics of the sympatric speciation model. We used combined mitochondrial control region sequences and the cytochrome b gene (1894 bp) to address the phylogenetics and population genetics of 232 specimens of G. e. eckloni and G. e. scoliostomus, as well as all of its closely related sister species. We found that: (i) a total of four old lineages were uncovered in the widespread G. e. eckloni, of which only one was shown to be shared with all G. e. scoliostomus individuals and (ii) the new subspecies (G. e. scoliostomus) evolved in Lake Sunmcuo from the ancestral G. e. eckloni population within approximately 0.057 Ma. These two taxa of the species complex are morphologically distinct, and reproductive isolation is further suggested. Ecological disruptive selection based on morphological traits (e.g. mouth cleft characters) and food utilization may be a mechanism of incipient speciation of two sympatric populations within Lake Sunmcuo. This study provides the first genetic evidence for sympatric speciation in the schizothoracine fish.

Origin, genetic diversity, and population structure of Chinese domestic sheep.

To characterize the origin, genetic diversity, and phylogeographic structure of Chinese domestic sheep, we here analyzed a 531-bp fragment of mtDNA control region of 449 Chinese autochthonous sheep from 19 breeds/populations from 13 geographic regions, together with previously reported 44 sequences from Chinese indigenous sheep. Phylogenetic analysis showed that all three previously defined lineages A, B, and C were found in all sampled Chinese sheep populations, except for the absence of lineage C in four populations. Network profiles revealed that the lineages B and C displayed a star-like phylogeny with the founder haplotype in the centre, and that two star-like subclades with two founder haplotypes were identified in lineage A. The pattern of genetic variation in lineage A, together with the divergence time between the two central founder haplotypes suggested that two independent domestication events have occurred in sheep lineage A. Considerable mitochondrial diversity was observed in Chinese sheep. Weak structuring was observed either among Chinese indigenous sheep populations or between Asian and European sheep and this can be attributable to long-term strong gene flow induced by historical human movements. The high levels of intra-population diversity in Chinese sheep and the weak phylogeographic structuring indicated three geographically independent domestication events have occurred and the domestication place was not only confined to the Near East, but also occurred in other regions.

[Divergence and systematical evolution of three Leuciscus species in Xinjiang based on mitochondrial DNA control region sequences].

Nucleotide sequence of fish mitochondria DNA (mtDNA) D-loop region from Leuciscus leuciscus baicalensis, L. merzbacheri, and L. idus in Xinjiang, China, were examined by sequencing 667 - 669 bp length of homological fragments in the D-loop from 24 individuals of the three fish species. DNA divergence ranged from 6.39% - 9.89% among the three fish species in the genius of Leuciscus cuvier. The sequence similarity is high and the variation is low between L. Leuciscus baicalensis and L. idus. In contract, the genetic distance is larger between L. Leuciscus baicalensis and L. merzbacheri. The average nucleotide variation within each of the two geographical populations (Sailimu lake and E' erqis river) of L. leuciscus baicalensis is 1.07% and 1.08%, respectively, and such variation is 1.07% between the two populations. These results demonstrate that the two geographic populations of L. leuciscus baicalensis do not appear to have significant genetic differentiation. Sequencing data showed the existence of sufficient genetic variations among three species of fish, as illustrated by distinct haplotypes for each species. The phylogenetic trees built with MEGA1.02 pointed out that the relationship between L. leuciscus baicalensis and L. idus is close, and L. merzbacheri is ancient among three Leuciscus.

Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia.

BACKGROUND: Previously reported evidence indicates that pigs were independently domesticated in multiple places throughout the world. However, a detailed picture of the origin and dispersal of domestic pigs in East Asia has not yet been reported. RESULTS: Population phylogenomic analysis was conducted in domestic pigs and wild boars by screening the haplogroup-specific mutation motifs inferred from a phylogenetic tree of pig complete mitochondrial DNA (mtDNA) sequences. All domestic pigs are clustered into single clade D (which contains subclades D1, D2, D3, and D4), with wild boars from East Asia being interspersed. Three haplogroups within D1 are dominant in the Mekong region (D1a2 and D1b) and the middle and downstream regions of the Yangtze River (D1a1a), and may represent independent founders of domestic pigs. None of the domestic pig samples from North East Asia, the Yellow River region, and the upstream region of the Yangtze River share the same haplogroup status with the local wild boars. The limited regional distributions of haplogroups D1 (including its subhaplogroups), D2, D3, and D4 in domestic pigs suggest at least two different in situ domestication events. CONCLUSION: The use of fine-grained mtDNA phylogenomic analysis of wild boars and domestic pigs is a powerful tool with which to discern the origin of domestic pigs. Our findings show that pig domestication in East Asia mainly occurred in the Mekong region and the middle and downstream regions of the Yangtze River.

Expression of an antitumor-analgesic peptide from the venom of Chinese scorpion Buthus martensii karsch in Escherichia coli.

The gene encoding a putative mature antitumor-analgesic peptide (AGAP) from the venom of the Chinese scorpion Buthus martensii Karsch was obtained by polymerase chain reaction (PCR) according to its cDNA sequence and expressed in Escherichia coli. While most of the recombinant AGAP was expressed in the form of insoluble inclusion body. The recombinant AGAP was purified to homogeneity by metal chelating affinity chromatography. Pharmaceutical tests showed that the recombinant AGAP has both analgesic and antitumor activities on mice.