Bioscience

Down-regulation of KLF4 Required for Lineage Commitment of T Cells

Recently, Wen Xiaomin and his colleagues, under the supervision of Dr. Liu Xiaolong, at the Institute of Biochemistry and Cell Biology, CAS, find that Klf4 is the only reprogramming factor whose expression is down-regulated when earlythymic progenitors differentiate into T cells. Enforced expression of Klf4 in uncommitted progenitors severely impaired T cell development mainly at the DN2-to-DN3 transition when T cell lineage commitment occurs, and affected the transcription of a variety of genes with crucial functions in early T cell development, including genes involved in microenvironmental signaling (IL-7Rα), Notch target genes (Deltex1), and essential T cell lineage regulatory or inhibitory genes (Bcl11a, SpiB, and Id1). The survival of thymocytes and the rearrangement at the Tcrb locus were impaired in the presence of enforced Klf4 expression. The defects in the DN1-to-DN2 and DN2-to-DN3 transitions in Klf4 transgenic mice could not be rescued by the introduction of a TCR transgene but was partially rescued by restoring the expression of IL-7Rα. Thus, these data suggest that the down-regulation of Klf4 is a prerequisite for T cell lineage commitment, and also extend the known roles of reprogramming factors in the process of cell differentiation. This resutlt from Dr. Liu Xiaolong lab entitled “Down-regulation of the transcription factor KLF4 is required for the lineage commitment of T cells” was published online by Cell Research on Nov 22, 2011.

Research on DNA Barcoding Obtains Major Progress

DNA barcoding is becoming more and more important for rapid and accurate identification of plant species. With joint international efforts, the two-marker combination of rbcL+matK was proposed as the ‘core’ barcode for land plants in August 2009 by CBOL Plant Working Group 2009, and trnH-psbA and ITS suggested as supplementary barcodes. To evaluate the universality and effectiveness of the four candidate barcodes (i.e. rbcL, matK, trnH-psbA and ITS), a coordinated effort has been made to further evaluate the markers, as a response to the call of the Third International Barcoding of Life Conference in 2009. A large data set, involving 6,286 individuals representing 1,757 species in 141 genera of 75 families of seed plants, was pooled by the China Plant BOL Group led by Prof. Li Dezhu from the Kunming Institute of Botany, CAS. Comprehensive analysis of the dataset was made to assess the universality, sequence quality and discriminatory power of the markers. The results indicated that the three chloroplast markers showed higher level of universality, while ITS performed moderately well in angiosperms, but not so in gymnosperms. As to the discriminatory power, ITS provided the highest among the four markers, and a combination of ITS with any chloroplast DNA marker could improve species discrimination significantly with 69.9-79.1% discriminatory power, which was significant higher than that of rbcL+matK with 49.7%. In addition, the ITS2 also showed relatively high discriminatory power. Based on a comprehensive evaluation, ITS (or ITS2) together with rbcL, matK should be incorporated into the core barcode for seed plants (China Plant BOL Group 2011, PNAS, 108: 19641–19646).

Research on Novel MicroRNAs Sees Breakthrough

Recently, a research group led by Prof. Dr. Qin Qiwei from the CAS key lab of marine bio-resources sustainable utilization, South China Sea Institute of Oceanology, CAS made innovative progress on marine virus encoded microRNAs. Team member Dr. Yan Yang et al identified and characterized a series of novel functional miRNAs encoded by a marine virus, Singapore grouper iridovirus (SGIV) for the first time. These findings were published online in the PLoS ONE (Yan et al. 2011. Identification of a Novel Marine Fish Virus, Singapore Grouper Iridovirus-Encoded MicroRNAs Expressed in Grouper Cells by Solexa Sequencing. PLoS ONE. 2011. 6(4): e19148.). This is the first experimental demonstration of miRNAs encoded by aquatic animal viruses. The results take into insight of the miRNA world, and provide new information for the better understanding of iridovirus pathogenesis.

Another Sign of Global Warming

Recently, a group of researchers led by Prof. Sun Liguang from the Institute of Polar Environment, School of Earth and Space Sciences of USTC, inferred the relative krill population changes along the West Antarctic Peninsula (WAP) over the 20th century by analyzing the shift in δ15N of seal hair for the first time. Their results indicate that krill began to decline in this part of Antarctica nearly a century ago, correlates with increasing sea surface temperatures and dwindling sea ice cover. The paper entitled ‘Relative Changes in Krill bundance Inferred from Antarctic Fur Seal’ was published online in PloS ONE on Nov. 7, 2011. This novel method makes it possible to infer Holocene krill abundance from ancient tissues of predators, and opens a new road in the field of exploring the relationship between krill density and the climate changes in the Southern Oceans.

Whole H1N1 Virus Simulated by Computer

A research group at the Institute of Process Engineering of CAS is using molecular-dynamics simulations as a computational microscope to peer into the atomic structure of the H1N1 virus1. Using 1728GPUs on the Mole-8.5 GPU-accelerated supercomputer, which includes more than 2,200 NVIDIA Tesla GPUs, researchers successfully simulated the whole H1N1 influenza virus, enabling them to verify current theoretical and experimental understandings of the virus. “This research is an important step in developing more effective ways to control epidemics and create anti-viral drugs.” said Dr. Ren Ying, one of the chief researchers and assistant professor at the Institute. Dr. Ren Ying and her colleagues made the simulation breakthrough by developing a molecular dynamics simulation application that takes advantage of GPU acceleration. It was run on the Mole-8.5 GPU supercomputer, which is comprised of 360 server nodes. The system was able to simulate 770 picoseconds per day with an integration time step of 1 fem to second for 300 million atoms or radicals.

Stone Age Tools Unearthed

Archaeologists from the Institute of Vertebrate Paleontology and Paleanthropology (IVPP), CAS and the Erdos Bronzeware Museum started excavating an area in the basin of the Ulan Mulun River in April, discovering more than 4,200 stone implements, including stone flakes, saw-shaped tools and remnant stones, which dated back about 40,000 to 70,000 years in north China's Inner Mongolia Autonomous Region. The river is a seasonal river near the city of Erdos and is believed to have been a primary location for stone tool production in ancient times. The large number of relics uncovered near the river proves that the region was a main living area for people living during the Stone Age. The discovery of the tools and subsequent research will help to shed light on the study of Stone Age culture, according to Hou Yamei, leader of the excavation team.

Mechanism for H2O2-Induced Leaf Cell Death in Rice Found

Nitric oxide (NO) is a redox-active molecule that plays a key role in a broad spectrum of physiological and developmental functions throughout plant life cycle. To generate insights into the potential role of NO in the process of rice leaf cell death, scientists in Dr. Chu Chengcai's group from the Institute of Genetics and Developmental Biology, CAS carried out an extensive screening of their large rice T-DNA mutant population, and isolated a NO content increased mutant, named nitric oxide excess. Map-based cloning revealed that noe1 encoded a rice catalase. Further, noe1 resulted in an increase of hydrogen peroxide (H2O2) in the leaves, which consequently promoted NO production via activation of nitrate reductase (NR). Removal of excess NO reduced cell death in both leaves and suspension cultures derived from noe1 plants, implicating NO as an important endogenous mediator of H2O2-induced leaf cell death. Reduction of intracellular SNO (S-nitrosothiol) level, generated by over-expression of OsGSNOR, which regulates global levels of protein S-nitrosylation, alleviated leaf cell death in noe1 plants. Thus, S-nitrosylation was also involved in light-dependent leaf cell death in noe1. Utilizing the biotin-switch assay, nanoliquid chromatography, and tandem mass spectrometry (LC/MS/MS), S-nitrosylated proteins were identified in both wild type and noe1 plants. NO targets identified only in noe1 plants included glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and thioredoxin (TRX), which have been reported to be involved in S-nitrosylation regulated cell death in animals. The results have been online published on Plant Physiology (DOI:10.1104/pp.111.184531).

Genetic Database for Attention Deficit Hyperactivity Disorder

The genetic studies of psychiatry disorders attract increasing attention to the research of complex diseases. Recently a team led by Prof. Wang Jing from the Key Laboratory of Mental Health, Institute of Psychology, CAS has developed a genetic database for attention deficit hyperactivity disorder (ADHD) which was named as ADHDgene. As the first genetic database of this kind in China for psychiatric disorder and for ADHD, ADHDgene aims to provide researchers with a central genetic resource and analysis platform for ADHD, which is freely available at http://adhd.psych.ac.cn/. Prof. Wang’s team will continue the effort in genetic studies of mental disorders by applying bioinformatics methods. The result has been published in Nucleic Acids Research (doi:10.1093/nar/gkr992).