Journal of Genetics and Genomics

2011, 38(3): I-II. doi: 10.1016/S1673-8527(11)00046-4

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Abstract:

The impact of next-generation sequencing on genomics

Jun Zhang, Rod Chiodini, Ahmed Badr, Genfa Zhang

2011, 38(3): 95-109. doi: 10.1016/j.jgg.2011.02.003

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Abstract:
This article reviews basic concepts, general applications, and the potential impact of next-generation sequencing (NGS) technologies on genomics, with particular reference to currently available and possible future platforms and bioinformatics. NGS technologies have demonstrated the capacity to sequence DNA at unprecedented speed, thereby enabling previously unimaginable scientific achievements and novel biological applications. But, the massive data produced by NGS also presents a significant challenge for data storage, analyses, and management solutions. Advanced bioinformatic tools are essential for the successful application of NGS technology. As evidenced throughout this review, NGS technologies will have a striking impact on genomic research and the entire biological field. With its ability to tackle the unsolved challenges unconquered by previous genomic technologies, NGS is likely to unravel the complexity of the human genome in terms of genetic variations, some of which may be confined to susceptible loci for some common human conditions. The impact of NGS technologies on genomics will be far reaching and likely change the field for years to come.

HSP70 decreases receptor-dependent phosphorylation of Smad2 and blocks TGF-β-induced epithelial-mesenchymal transition

Yihao Li, Xianjiang Kang, Qiang Wang

2011, 38(3): 111-116. doi: 10.1016/j.jgg.2011.02.001

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Abstract:
Smad2 and Smad3, the intracellular mediators of transforming growth factor β (TGF-β) signaling, are directly phosphorylated by the activated type I receptor kinase, and then shuttle from the cytoplasm into the nucleus to regulate target gene expression. Here, we report that the 70-kDa heat-shock protein (HSP70) interacts with Smad2 and decreases TGF-β signal transduction. Ectopic expression of HSP70 prevents receptor-dependent phosphorylation and nuclear translocation of Smad2, and blocks TGF-β-induced epithelial-mesenchymal transition (EMT) in HaCat cells. Our findings reveal an essential role of HSP70 in TGF-β-induced epithelial-mesenchymal transition (EMT) by impeding Smad2 phosphorylation.

Mitochondrial DNA evidence supports northeast Indian origin of the aboriginal Andamanese in the Late Paleolithic

Hua-Wei Wang, Bikash Mitra, Tapas Kumar Chaudhuri, Malliya gounder Palanichamy, Qing-Peng Kong, Ya-Ping Zhang

2011, 38(3): 117-122. doi: 10.1016/j.jgg.2011.02.005

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Abstract:
In view of the geographically closest location to Andaman archipelago, Myanmar was suggested to be the origin place of aboriginal Andamanese. However, for lacking any genetic information from this region, which has prevented to resolve the dispute on whether the aboriginal Andamanese were originated from mainland India or Myanmar. To solve this question and better understand the origin of the aboriginal Andamanese, we screened for haplogroups M31 (from which Andaman-specific lineage M31a1 branched off) and M32 among 846 mitochondrial DNAs (mtDNAs) sampled across Myanmar. As a result, two Myanmar individuals belonging to haplogroup M31 were identified, and completely sequencing the entire mtDNA genomes of both samples testified that the two M31 individuals observed in Myanmar were probably attributed to the recent gene flow from northeast India populations. Since no root lineages of haplogroup M31 or M32 were observed in Myanmar, it is unlikely that Myanmar may serve as the source place of the aboriginal Andamanese. To get further insight into the origin of this unique population, the detailed phylogenetic and phylogeographic analyses were performed by including additional 7 new entire mtDNA genomes and 113 M31 mtDNAs pinpointed from South Asian populations, and the results suggested that Andaman-specific M31a1 could in fact trace its origin to northeast India. Time estimation results further indicated that the Andaman archipelago was likely settled by modern humans from northeast India via the land-bridge which connected the Andaman archipelago and Myanmar around the Last Glacial Maximum (LGM), a scenario in well agreement with the evidence from linguistic and palaeoclimate studies.

A rice mutant displaying a heterochronically elongated internode carries a 100 kb deletion

Mika Hayashi-Tsugane, Masahiko Maekawa, Qian Qian, Hirokazu Kobayashi, Shigeru Iida, Kazuo Tsugane

2011, 38(3): 123-128. doi: 10.1016/j.jgg.2011.02.004

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Abstract:
We have isolated a recessive rice mutant, designated as indeterminate growth (ing), which displays creeping and apparent heterochronic phenotypes in the vegetative period with lanky and winding culms. Rough mapping and subsequent molecular characterization revealed that the ing mutant carries a large deletion, which corresponds to a 103 kb region in the Nipponbare genome, containing nine annotated genes on chromosome 3. Of these annotated genes, the SLR1 gene encoding a DELLA protein is the only one that is well characterized in its function, and its null mutation, which is caused by a single base deletion in the middle of the intronless SLR1 gene, confers a slender phenotype that bears close resemblance to the ing mutant phenotype. The primary cause of the ing mutant phenotype is the deletion of the SLR1 gene, and the ing mutant appears to be the first characterized mutant having the entire SLR1 sequence deleted. Our results also suggest that the deleted region of 103 kb does not contain an indispensable gene, whose dysfunction must result in a lethal phenotype.

Detection and identification of Vibrio parahaemolyticus by multiplex PCR and DNA–DNA hybridization on a microarray

Rongzhi Wang, Jiadong Huang, Wei Zhang, Guangmei Lin, Junwei Lian, Libin Jiang, Hongcong Lin, Songfa Wang, Shihua Wang

2011, 38(3): 129-135. doi: 10.1016/j.jgg.2011.02.002

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Abstract:
In this paper, we developed a rapid and accurate method for the detection of Vibrio parahaemolyticus strains, using multiplex PCR and DNA–DNA hybridization. Multiplex PCR was used to simultaneously amplify three diagnostic genes (tlh, tdh and fla) that serve as molecular markers of V. parahaemolyticus. Biotinylated PCR products were hybridized to primers immobilized on a microarray, and detected by chemiluminesce with avidin–conjugated alkaline phosphatase. With this method, forty-five samples were tested. Eight known virulent strains (tlh⁺/tdh⁺/fla⁺) and four known avirulent strains (tlh⁺/tdh⁻/fla⁺) of the V. parahaemolyticus were successfully detected, and no non-specific hybridization and cross-hybridization reaction were found from fifteen closely-related strains (tlh⁻/tdh⁻/fla⁺) of the Vibrio spp. In addition, all the other eighteen strains of non-Vibrio bacteria (tlh⁻/tdh⁻/fla⁻) gave negative results. The DNA microarray successfully distinguished V. parahaemolyticus from other Vibrio spp. The results demonstrated that this was an efficient and robust method for identifying virulent strains of V. parahaemolyticus.

2011 Vol. 38, No. 3