Gene Regulatory Networks in the Genomics Era

<正>The precise regulation of gene expression is critical to the normal development and biological function of all organisms. Dysregulation of gene expression during early development can result in a spectrum of failures ranging from minor defects to the termination of development. In adult life, dysregulation ncan lead to     

Improving the evidence base for decision making during a pandemic: the example of 2009 influenza A/H1N1

This article synthesizes and extends discussions held during an international meeting on "Surveillance for Decision Making: The Example of 2009 Pandemic Influenza A/H1N1," held at the Center for Communicable Disease Dynamics (CCDD), Harvard School of Public Health, on June 14 and 15, 2010. The meeting involved local, national, and global health authorities and academics representing 7 countries on 4 continents. We define the needs for surveillance in terms of the key decisions that must be made in response to a pandemic: how large a response to mount and which control measures to implement, for whom, and when. In doing so, we specify the quantitative evidence required to make informed decisions. We then describe the sources of surveillance and other population-based data that can presently--or in the future--form the basis for such evidence, and the interpretive tools needed to process raw surveillance data. We describe other inputs to decision making besides epidemiologic and surveillance data, and we conclude with key lessons of the 2009 pandemic for designing and planning surveillance in the future.     

Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009

Background

In April 2009, a novel triple-reassortant swine influenza A H1N1 virus (“A/H1N1pdm”; also known as SOIV) was detected and spread globally as the first influenza pandemic of the 21^st century. Sequencing has since been conducted at an unprecedented rate globally in order to monitor the diversification of this emergent virus and to track mutations that may affect virus behavior.

Methodology/Principal Findings

By Sanger sequencing, we determined consensus whole-genome sequences for A/H1N1pdm viruses sampled nationwide in Canada over 33 weeks during the 2009 first and second pandemic waves. A total of 235 virus genomes sampled from unique subjects were analyzed, providing insight into the temporal and spatial trajectory of A/H1N1pdm lineages within Canada. Three clades (2, 3, and 7) were identifiable within the first two weeks of A/H1N1pdm appearance, with clades 5 and 6 appearing thereafter; further diversification was not apparent. Only two viral sites displayed evidence of adaptive evolution, located in hemagglutinin (HA) corresponding to D222 in the HA receptor-binding site, and to E374 at HA2-subunit position 47. Among the Canadian sampled viruses, we observed notable genetic diversity (1.47×10⁻³ amino acid substitutions per site) in the gene encoding PB1, particularly within the viral genomic RNA (vRNA)-binding domain (residues 493–757). This genome data set supports the conclusion that A/H1N1pdm is evolving but not excessively relative to other H1N1 influenza A viruses. Entropy analysis was used to investigate whether any mutated A/H1N1pdm protein residues were associated with infection severity; however no virus genotypes were observed to trend with infection severity. One virus that harboured heterozygote coding mutations, including PB2 D567D/G, was attributed to a severe and potentially mixed infection; yet the functional significance of this PB2 mutation remains unknown.

Conclusions/Significance

These findings contribute to enhanced understanding of Influenza A/H1N1pdm viral dynamics.     

Relative importance of water, energy, and heterogeneity in determining regional pteridophyte and seed plant richness in China

Environmental variables, such as ambient energy, water availability, and environmental heterogeneity have been frequently proposed to account for species diversity gradients. How taxon-specific functional traits define large-scale richness gradients is a fundamental issue in understanding spatial patterns of species diversity, but has not been well documented. Using a large dataset on the regional flora from China, we examine the contrast spatial patterns and environmental determinants between pteridophytes and seed plants which differ in dispersal capacity and environmental requirements. Pteridophyte richness shows more pronounced spatial variation and stronger environmental associations than seed plant richness. Water availability generally accounts for more spatial variance in species richness of pteridophytes and seed plants than energy and heterogeneity do, especially for pteridophytes which have high dependence on moist and shady environments. Thus, pteridophyte richness is disproportionally affected by water-related variables; this in turn results in a higher proportion of pteridophytes in regional vascular plant floras (pteridophyte proportion) in wet regions. Most of the variance in seed plant richness, pteridophyte richness, and pteridophyte proportion explained by energy is included in variation that water and heterogeneity account for, indicating the redundancy of energy in the study extent. However, heterogeneity is more important for determining seed plant distributions. Pteridophyte and seed plant richness is strongly correlated, even after the environmental effects have been removed, implying functional linkages between them. Our study highlights the importance of incorporating biological traits of different taxonomic groups into the studies of macroecology and global change biology.     

Increased T cell proliferative responses to islet antigens identify clinical responders to anti-CD20 monoclonal antibody (rituximab) therapy in type 1 diabetes

Type 1 diabetes mellitus is believed to be due to the autoimmune destruction of β-cells by T lymphocytes, but a single course of rituximab, a monoclonal anti-CD20 B lymphocyte Ab, can attenuate C-peptide loss over the first year of disease. The effects of B cell depletion on disease-associated T cell responses have not been studied. We compare changes in lymphocyte subsets, T cell proliferative responses to disease-associated target Ags, and C-peptide levels of participants who did (responders) or did not (nonresponders) show signs of β-cell preservation 1 y after rituximab therapy in a placebo-controlled TrialNet trial. Rituximab decreased B lymphocyte levels after four weekly doses of mAb. T cell proliferative responses to diabetes-associated Ags were present at baseline in 75% of anti-CD20- and 82% of placebo-treated subjects and were not different over time. However, in rituximab-treated subjects with significant C-peptide preservation at 6 mo (58%), the proliferative responses to diabetes-associated total (p = 0.032), islet-specific (p = 0.048), and neuronal autoantigens (p = 0.005) increased over the 12-mo observation period. This relationship was not seen in placebo-treated patients. We conclude that in patients with type 1 diabetes mellitus, anti-B cell mAb causes increased proliferative responses to diabetes Ags and attenuated β-cell loss. The way in which these responses affect the disease course remains unknown.     

Upregulation of FIk-1 by bFGF via the ERK pathway is essential for VEGF-mediated promotion of neural stem cell proliferation

Neural stem cells (NSCs) constitute the cellular basis for embryonic brain development and neurogenesis.The processis regulated by NSC niche including neighbor cells such as vascular and glial cells.Since both vascular and glial cellssecrete vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF),we assessed the effect ofVEGF and bFGF on NSC proliferation using nearly homogeneous NSCs that were differentiated from mouse embryonicstem cells.VEGF alone did not have any significant effect.When bFGF was added,however,VEGF stimulated NSCproliferation in a dose-dependent manner,and this stimulation was inhibited by ZM323881,a VEGF receptor (Flk-1)-specific inhibitor.Interestingly,ZM323881 also inhibited cell proliferation in the absence of exogenous VEGF,suggestingthat VEGF autocrine plays a role in the proliferation of NSCs.The stimulatory effect of VEGF on NSC proliferationdepends on bFGF,which is likely due to the fact that expression of Flk-1 was upregulated by bFGF via phosphoryla-tion of ERK1/2.Collectively,this study may provide insight into the mechanisms by which mieroenvironmental nichesignals regulate NSCs.     

HSC的活化、增殖与TGF-β1及其Ⅰ型受体在中晚期纤维化肝组织中的改变及护肝片对其的影响

目的 探讨护肝片对中、晚期纤维化大鼠肝组织肝星状细胞（HSC）的活化与增殖及转化生长因子-β1（TGF-β1）及其工型受体（TβRⅠ）表达的影响。方法 采用12．5％CCh诱导的大鼠肝纤维化模型,自造模之日起,大鼠分组灌胃给药（护肝片921mg·kg^-1）或溶媒,每日一次,直至8或13周末,分别处死动物,取左叶肝组织石蜡包埋,制作组织芯片,免疫组化S-P法检测大鼠肝组织α-平滑肌肌动蛋白（α-SMA）、TGF-β1及TβRⅠ蛋白的表达,并用Meta Morph图像分析系统计数α-SMA阳性细胞数、对TGF-β1。及TβRⅠ蛋白表达量进行定量分析。结果 1．模型复制8周和13周,模型组的肝损伤及其纤维化分级均明显高于正常组（P〈0．01）,护肝片组的肝损伤及其纤维化分级均轻于模型组。2．模型复制8周和13周,模型组活化的HSC（即α-SMA阳性细胞）数量较正常组明显增多、TGF-β1及TβRⅠ蛋白的表达较正常组明显增强（P〈0．01）;3．护肝片显著抑制8、13周纤维化肝组织HSC的活化与增殖和TGF-β1及TβRⅠ蛋白的表达（P〈0．01）。结论 抑制HSC的活化与增殖和TGF-β1及TβRⅠ的表达可能是护肝片抗肝纤维化作用的靶点之一。     

诱导茶树成熟胚培育成幼苗的研究

以茶树品种——农抗早的成熟胚为外植体离体培养,初次研究了2,4-D、6-BA等不同植物激素对茶树成熟胚诱导成幼苗的影响。结果表明,在合适的激素组合条件下,愈伤组织诱导为97%,在附加2.5mg/L 6-BA 0.5mg/L NAA的MS培养基上,愈伤组织的芽分化率为14.2%,附加1.5mg/L NAA的1/2 MS培养基,幼苗的根分化率为5%。     

西昆仑山两种针叶树种径向生长及其对气候变化的响应

利用西昆仑山的雪岭云杉和昆仑圆柏树芯样本,建立其树轮宽度年表。通过分析两种针叶树种树木径向生长特征与气候要素的相关关系,探讨了树种间的树木生长气候响应异同及响应关系的稳定性。结果表明：研究区域内的雪岭云杉和昆仑圆柏年表间存在显著正相关。两种针叶树种在1994年气温突变前树轮宽度年表指数和基部断面生长增量（BAI）呈上升趋势,在气温突变后年表和BAI则呈下降趋势,并且昆仑圆柏的树木径向生长速率高于雪岭云杉。与气候要素的相关性分析结果表明,雪岭云杉径向生长与上年生长季（5—6月和8—10月）和当年生长季（3—6月和10月）气温呈显著负相关,而昆仑圆柏径向生长与上年10月和当年生长季前期（4—6月）气温呈显著负相关;两者均与当年春季降水呈显著正相关。滑动相关分析结果显示,上年和当年生长季气温对两个树种树木径向生长的负响应在增强,特别是在当年生长季前期更为显著。此外,当年生长季前期降水对树木径向生长的促进作用也在增强。在有可能的气候突变年份（1994年）之后,两种针叶树种对气温和降水的响应敏感性均有所增强,并且雪岭云杉对气温的响应敏感性强于昆仑圆柏,而对降水响应敏感性要弱于昆仑圆柏。