辽宁碱蓬SlCMO基因盐胁迫表达分析及盐诱导启动子鉴定

胆碱单加氧酶（choline monooxygenase, CMO）是合成甜菜碱的关键酶,甜菜碱在植物抵抗渗透胁迫中起着重要的作用。本研究室前期克隆了盐生植物辽宁碱蓬CMO（Suaeda liaotungensis CMO）基因及启动子。本研究对SlCMO基因在盐胁迫下的表达及盐诱导启动子进行分析。qRT-PCR分析SlCMO基因在辽宁碱蓬不同器官及盐胁迫下的表达,结果表明,SlCMO基因在根、茎、叶中均有表达,其中茎、叶中的表达量较高,SlCMO基因在根、茎、叶中的表达均受盐胁迫诱导。5′端缺失分析SlCMO启动子的盐诱导区段,结果表明,pC5（-267~+128 bp）是SlCMO启动子的盐诱导功能区段,推测pC5调控SlCMO 基因的盐诱导表达。本研究为SlCMO 基因表达调控研究奠定基础,也为植物抗盐基因工程提供可用的启动子。     

化学除草剂对农田生态系统野生植物多样性的影响

农田生物多样性是全球生物多样性的重要组成部分, 除草剂的大量施用对其产生了严重影响。本文综述了化学除草剂对农田生态系统中野生植物多样性的影响, 并分析归纳了其影响机制。除草剂的施用会使敏感植物减少, 抗药性植物增多, 从而改变农田生态系统中的野生植物物种组成, 并使其趋同化, 降低遗传多样性和物种多样性, 以致植物功能群单一化, 群落稳定性下降。除草剂的主要影响机制是杀死植物或改变其生长代谢、抗性、繁殖等, 改变生境, 并与人为因素、环境因素等产生协同影响。不同种类的除草剂影响程度不同, 且不同物种间、不同群落间的响应也存在差异。我国化学除草剂使用量持续增长, 应加强除草剂对野生植物多样性的影响及其机制研究, 重视除草剂使用历史记录和野生植物的长期监测, 以及除草剂使用规范和相关政策法律研究, 更好地保护我国农田生态系统中的生物多样性。     

Genetic diversity and temporal dynamics of phytoplankton viruses in East Lake,China

Phytoplankton viruses are important components of aquatic ecosystems. However, their prevalence and genetic diversity in marine and freshwater systems are largely under estimated owing to the immense size of water bodies and limitations in virus discovery techniques. In this study, we conducted a 1-year survey of phytoplankton virus communities by collecting surface water monthly from an inland lake(East Lake) in China between May 2012 and April 2013. We examined four phytoplankton viruses, i.e., myoviruses, podoviruses, siphoviruses, and phycodnaviruses, and seven sets of primers were used to target conserved genes within these four species. In this year-long investigation, a total of 358 different virus-related sequences from four virus families were obtained. All virus families were detected in all months, except for cyanopodoviruses, which were only identified during eight of the 12 months surveyed. Moreover, virus abundance and diversity changed dynamically over time. Phylogenetic analysis revealed that the majority of viral sequences from East Lake, China displayed distinct clustering patterns compared with published sequences. These results supported the existence of a highly diverse and unique phytoplankton virus community in East Lake, China.     

Histone deacetylase 6 and cytoplasmic linker protein 170 function together to regulate the motility of pancreatic cancer cells

Pancreatic cancer is a devastating disease with the worst prognosis among all the major human malignancies. The propensity to rapidly metastasize contributes significantly to the highly aggressive feature of pancreatic cancer. The molecular mechanisms underlying this remain elusive, and proteins involved in the control of pancreatic cancer cell motility are not fully characterized. In this study, we find that histone deacetylase 6 (HDAC6), a member of the class II HDAC family, is highly expressed at both protein and mRNA levels in human pancreatic cancer tissues. HDAC6 does not obviously affect pancreatic cancer cell proliferation or cell cycle progression. Instead, it significantly promotes the motility of pancreatic cancer cells. Further studies reveal that HDAC6 interacts with cytoplasmic linker protein 170 (CLIP-170) and that these two proteins function together to stimulate the migration of pancreatic cancer cells. These findings provide mechanistic insight into the progression of pancreatic cancer and suggest HDAC6 as a potential target for the management of this malignancy.     

三倍体品种的选育和利用

概述了三倍体生物的两大基本特征(细胞巨大性和不育性)及其产生原因,对有很好经济和社会效益的三倍体杨树、甜菜、无籽西瓜和某些海洋生物选育利用作了简要介绍、展示了三倍体品种选育利用的美好前景。     

A step-wise approach significantly enhances protein yield of a rationally-designed agonist antibody fragment in E. coli

Fab59 is a rationally-designed antibody fragment (Fab) that mimics the activity of the cytokine thrombopoietin (TPO). Fab59 activity was initially detected directly from bacterial supernatants in a cell-based assay and was subsequently estimated to be equipotent to TPO using purified material. However, the expression of Fab59 was insufficient to support in vivo characterization of the Fab due to extremely low expression levels from its initial phage display expression vector. To boost expression, a new expression vector was designed and constructed, and Fab59 light chain codons were optimized for bacterial expression. However, from this a new challenge arose, in that the codon-optimized Fab59 was more toxic to Escherichia coli cells than parental Fab59. Co-expression of the bacterial chaperon protein Skp alleviated this toxicity. A two-step purification method was used to isolate monomeric Fab59 from the periplasm. Although Fab59 was prone to form aggregates during the purification process, buffer modification efficiently eliminated this problem. Overall, optimization of Fab59 expression and purification achieved a 100-fold increase in Fab59 production in E. coli relative to the starting yield. The yield of purified monomeric Fab59 from a shake flask reached up to 3.5mg/L, which was sufficient to support testing of the agonist activity of purified monomeric Fab59 in vivo. Even higher yields may be achieved by purification of Fab present in the culture media, as Skp most significantly increased accumulation of Fab59 in that location.     

A potential model for studying the plasticity and reprogramming of human epidermal stem cells through preimplantation blastocyst microinjection

Microinjection of adult stem cells (ASCs) into blastocysts provides a classic model for studying ASC plasticity. To explore the molecular mechanisms that govern the reprogramming of ASCs, we evaluated the experimental model through microinjection of human epidermal stem cells (hEpiSCs) into mouse blastocysts. Mouse blastocysts underwent regular embryogenesis after microinjection of allogeneic cells, confirmed by morphological observation and embryo cell counting. hEpiSCs survive and integrate into mouse embryos, by monitoring the migration of injected cells at 2, 4, 12, 16 and 24 h. In this xenogeneic system, hEpiSCs could be reprogrammed within 24 h, as evidenced by the silencing of CK15 and Integrin beta 1 gene expression, without activation of Oct4 and Nanog. Microinjection of hEpiSCs into mouse blastocysts provides an efficient model for studying the molecular mechanisms of their plasticity. Moreover, the possibility of inducing pluripotent stem cells without transgenes or viruses can be entertained.     

Structure and substrate recruitment of the human spindle checkpoint kinase Bub1

In mitosis, the spindle checkpoint detects a single unattached kinetochore, inhibits the anaphase-promoting complex or cyclosome (APC/C), and prevents premature sister chromatid separation. The checkpoint kinase Bub1 contributes to checkpoint sensitivity through phosphorylating the APC/C activator, Cdc20, and inhibiting APC/C catalytically. We report here the crystal structure of the kinase domain of Bub1, revealing the requirement of an N-terminal extension for its kinase activity. Though the activation segment of Bub1 is ordered and has structural features indicative of active kinases, the C-terminal portion of this segment sterically restricts substrate access to the active site. Bub1 uses docking motifs, so-called KEN boxes, outside its kinase domain to recruit Cdc20, one of two known KEN box receptors. The KEN boxes of Bub1 are required for the spindle checkpoint in human cells. Therefore, its unusual active-site conformation and mode of substrate recruitment suggest that Bub1 has an exquisitely tuned specificity for Cdc20.     

From pull-down data to protein interaction networks and complexes with biological relevance

Motivation: Recent improvements in high-throughput Mass Spectrometry(MS) technology have expedited genome-wide discovery of protein–proteininteractions by providing a capability of detecting proteincomplexes in a physiological setting. Computational inferenceof protein interaction networks and protein complexes from MSdata are challenging. Advances are required in developing robustand seamlessly integrated procedures for assessment of protein–proteininteraction affinities, mathematical representation of proteininteraction networks, discovery of protein complexes and evaluationof their biological relevance. Results: A multi-step but easy-to-follow framework for identifyingprotein complexes from MS pull-down data is introduced. It assessesinteraction affinity between two proteins based on similarityof their co-purification patterns derived from MS data. It constructsa protein interaction network by adopting a knowledge-guidedthreshold selection method. Based on the network, it identifiesprotein complexes and infers their core components using a graph-theoreticalapproach. It deploys a statistical evaluation procedure to assessbiological relevance of each found complex. On Saccharomycescerevisiae pull-down data, the framework outperformed othermore complicated schemes by at least 10% in F₁-measure and identified610 protein complexes with high-functional homogeneity basedon the enrichment in Gene Ontology (GO) annotation. Manual examinationof the complexes brought forward the hypotheses on cause offalse identifications. Namely, co-purification of differentprotein complexes as mediated by a common non-protein molecule,such as DNA, might be a source of false positives. Protein identificationbias in pull-down technology, such as the hydrophilic bias couldresult in false negatives. Contact: samatovan{at}ornl.gov Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Jonathan Wren Present address: Department of Biomedical Informatics, VanderbiltUniversity, Nashville, TN 37232. The authors wish it to be known that, in their opinion, thefirst two authors should be regarded as joint First Authors.     

CpG island density and its correlations with genomic features in mammalian genomes

Background  

CpG islands, which are clusters of CpG dinucleotides in GC-rich regions, are considered gene markers and represent an important feature of mammalian genomes. Previous studies of CpG islands have largely been on specific loci or within one genome. To date, there seems to be no comparative analysis of CpG islands and their density at the DNA sequence level among mammalian genomes and of their correlations with other genome features.