Differential selection in HIV-1 gp120 between subtype B and East Asianvariant B’

HIV-1 evolves strongly and undergoes geographic differentiation as it spreads in diverse host populations around the world.For instance,distinct genomic backgrounds can be observed between the pandemic subtype B,prevalent in Europe and North-America,and its offspring clade B' in East Asia.Here we ask whether this differentiation affects the selection pressure experienced by the virus.To answer this question we evaluate selection pressure on the HIV-1 envelope protein gp120at the level of individual codons using a simple and fast estimation method based on the ratio k_alk_s of amino acid changes to synonymous changes.To validate the approach we compare results to those from a state-of-the-art mixed-effect method.The agreement is acceptable,but the analysis also demonstrates some limitations of the simpler approach.Further,we find similar distributions of codons under stabilizing and directional selection pressure in gp120 for subtypes B and B' with more directional selection pressure in variable loops and more stabilizing selection in the constant regions.Focusing on codons with increased k_alk_s values in B',we show that these codons are scattered over the whole of gp120,with remarkable clusters of higher density in regions flanking the variable loops.We identify a significant statistical association of glycosylation sites and codons with increased k_alk_s values.     

模拟UV-B辐射增强条件下灯盏花居群的生理差异及其遗传背景

在温室条件下,研究了模拟UV-B辐射（280～320 nm）增强对6个灯盏花居群的类黄酮、丙二醛(MDA)含量和抗氧化酶活性的影响及其种内差异,并利用ISSR分子标记技术对灯盏花居群进行遗传背景分析.结果表明：在UV-B辐射增强条件下,灯盏花D01、D53、D63和D65居群在成苗期、盛花期和成熟期的类黄酮含量均显著增加,成苗期与盛花期MDA含量显著降低;而D47和D48居群3个生育期的MDA含量和盛花期类黄酮含量均显著增加,成熟期显著降低.D01居群3个生育期的POD、APX活性,成苗期、盛花期CAT活性与盛花期SOD活性均显著升高;D47居群3个生育期的SOD、CAT和APX活性,成熟期POD活性显著下降;D48居群3个生育期的POD、APX活性,成苗期、成熟期的SOD活性均显著下降;D53居群成苗期和盛花期SOD、APX活性,盛花期CAT活性显著增加;D63居群3个生育期的SOD、POD和APX活性均显著上升;D65居群除成熟期的CAT和APX活性没有显著变化外,3个生育期的4种抗氧化酶活性均显著上升.灯盏花居群对UV B辐射增强的响应有明显的种内差异,D01、D53、D63和D65为UV耐性居群,而D47和D48居群的UV敏感性较高.灯盏花居群不同生育期对UV-B辐射的响应为盛花期>成苗期>成熟期.居群间的遗传多样性差异明显,在遗传距离为0.11的水平上,可将D01、D53、D63和D65居群归为一类,D47和D48居群为另一类,这与根据生理响应指数判断的UV耐性与敏感居群的结果基本一致.     

The effects of weak selection on neutral diversity at linked sites

The effects of selection on variability at linked sites have an important influence on levels and patterns of within-population variation across the genome. Most theoretical models of these effects have assumed that selection is sufficiently strong that allele frequency changes at the loci concerned are largely deterministic. These models have led to the conclusion that directional selection for selectively favorable mutations, or against recurrent deleterious mutations, reduces nucleotide site diversity at linked neutral sites. Recent work has shown, however, that fixations of weakly selected mutations, accompanied by significant stochastic changes in allele frequencies, can sometimes cause higher diversity at linked sites when compared with the effects of fixations of neutral mutations. This study extends this work by deriving approximate expressions for the mean conditional times to fixation and loss of mutations subject to selection, and analyzing the conditions under which selection increases rather than reduces these times. Simulations are used to examine the relations between diversity at a neutral site and the fixation and loss times of mutations at a linked site that is subject to selection. It is shown that the long-term level of neutral diversity can be increased over the purely neutral value by recurrent fixations and losses of linked, weakly selected dominant or partially dominant favorable mutations, or linked recessive or partially recessive deleterious mutations. The results are used to examine the conditions under which associative overdominance, as opposed to background selection, is likely to operate.     

夏季绿洲生态环境对荒漠背景地表能量过程的扰动

利用观测试验资料,对比分析了夏季典型晴天敦煌绿洲与周围荒漠戈壁背景地表过程的差异,揭示了绿洲生态系统对干旱区荒漠背景地表过程的扰动特征。结果表明:绿洲地表净辐射日平均要高出周围荒漠戈壁背景60 W/m2以上,约占绿洲净辐射的1/4以上。对绿洲高出的净辐射贡献最大的是绿洲相对低的地表长波辐射,其次是较高的太阳总辐射。而绿洲相对较低的大气长波辐射对高出的净辐射有较大的负贡献,特别是地表反射辐射也有很小的负贡献。绿洲高出的地表净辐射主要贡献于加强潜热和地热流量,还有一部分被绿洲地表能量不平衡差额所占,它实际上可能由一般地表热量平衡所不考虑的垂直热量平流来输送。而绿洲明显低于荒漠背景的感热通量则节省了一部分净辐射能量。     

肠杆菌科细菌耐药基因表达的遗传和环境调控

细菌耐药性是21世纪国际关注的重要问题,也是全球面临的重大挑战.肠杆菌科细菌是医院感染的重要病原菌之一.近年来,随着抗生素的大量使用,多种肠杆菌科耐药菌,尤其是多重耐药肠杆菌开始大量出现,对人类健康形成了日益严重的威胁.细菌可以通过耐药基因突变或水平转移的方式获得耐药性,通常情况下,可以通过已知的耐药机制预测相应的耐药...     

不同宿主来源的重组酿酒酵母混合糖代谢比较

【目的】研究不同工业酿酒酵母宿主背景对重组酵母木糖利用效率的影响。【方法】将木糖利用途径的木糖还原酶(XR)、木糖醇脱氢酶(XDH)和木酮糖激酶(XK)编码基因串联后分别转入3株不同的工业酿酒酵母中,得到重组酵母ZQ1、ZQ5和ZQ7。分别对3个木糖途径代谢基因的表达水平、酶活和重组菌株的木糖发酵效率进行比较。【结果】重组菌株在木糖代谢基因转录、酶活性和木糖利用性能方面有很大差异,其中ZQ5木糖代谢能力最强,ZQ7其次,ZQ1木糖利用能力最弱。ZQ7在初始木糖浓度为20 g/L时木糖利用速率快于ZQ5,表明木糖浓度对重组菌发酵性能评价具有影响。【结论】不同菌株的遗传背景和木糖浓度对重组菌木糖利用的影响很大,评价重组酵母的木糖利用需考虑宿主的遗传背景和底物浓度的影响。     

不同干扰背景下景观指数与物种多样性的多尺度效应——以巩义市为例

以黄河中下游山地丘陵区的巩义市为研究区,采用典型样地法对灌草丛、人工林和农田边缘3种不同干扰背景下的自然、半自然生境内的植物进行调查。基于景观生态学原理,在地理信息系统技术支持下,借助于Fragstatta3.3软件,以调查样地为中心,计算了150、250、500、750、1000、1250、1500m不同半径缓冲区内表征景观形状(Edge and patch shape)、边缘对照(Edge contrast)、相似度和邻近度(Proximity and similarity)、景观多样性(Diversity)、基质(Texture)、斑块大小和密度(Patch size and patch density)共6类52个指数,运用冗余分析(RDA)筛选出不同尺度下对该区农业景观中植物多样性有显著影响的景观指数。结果表明:不同尺度,景观指数对物种多样性的影响变化显著。灌草丛生境,在500—750m范围内,SHAPE_AM指数和PARA_AM指数能够很好的解释物种多样性,解释量为33.6%;人工林生境,SHAPE_AM指数、AREA_CV指数、SIMI指数和PAFRAC指数在1000—1250m范围内对物种多样性的解释量达到48.1%;农田边缘生境,GYRATE_CV指数、ENN_CV指数、PARA_MN指数和FRAC_AM指数在750—1250m范围内对物种多样性影响显著,解释量为32%。其中,辛普森多样性指数(SIDI)与灌草丛物种多样性在750—1250m范围内作用显著,ENN_CV指数仅对农田边缘物种多样性影响较大。景观指数对物种多样性的影响具有尺度依赖性,未来应全面综合探讨这些指数的尺度效应及在景观生态学中的应用。     

弱背景噪声对大鼠听皮层神经元频率调谐的影响

在自然环境中,人和动物常在一定的背景噪声下感知信号声刺激,然而,关于低强度的弱背景噪声如何影响听皮层神经元对声刺激频率的编码尚不清楚.本研究以大鼠听皮层神经元的频率反应域为研究对象,测定了阈下背景噪声对79个神经元频率反应域的影响.结果表明,弱背景噪声对大鼠初级听皮层神经元的听反应既有抑制性影响、又有易化性影响.一般来说,抑制性影响使神经元的频率调谐范围和最佳频率反应域缩小,易化性影响使神经元的频率调谐范围和最佳频率反应域增大.对于少数神经元,弱背景噪声并未显著改变其频率调谐范围,但却改变了其最佳频率反应域范围.弱背景噪声对63.64%神经元的特征频率和55.84%神经元的最低阈值无显著影响.神经元频率调谐曲线的尖部比中部更容易受到弱背景噪声的影响.该研究结果有助于我们进一步理解复杂声环境下大脑听皮层对听觉信息的编码机制.     

MicroID2: A Novel Biotin Ligase Enables Rapid Proximity-Dependent Proteomics

Identifying protein–protein and other proximal interactions is central to dissecting signaling and regulatory processes in cells. BioID is a proximity-dependent biotinylation method that uses an “abortive” biotin ligase to detect proximal interactions in cells in a highly reproducible manner. Recent advancements in proximity-dependent biotinylation tools have improved efficiency and timing of labeling, allowing for measurement of interactions on a cellular timescale. However, issues of size, stability, and background labeling of these constructs persist. Here we modified the structure of BioID2, derived from Aquifex aeolicus BirA, to create a smaller, highly active, biotin ligase that we named MicroID2. Truncation of the C terrminus of BioID2 and addition of mutations to alleviate blockage of biotin/ATP binding at the active site of BioID2 resulted in a smaller and highly active construct with lower background labeling. Several additional point mutations improved the function of our modified MicroID2 construct compared with BioID2 and other biotin ligases, including TurboID and miniTurbo. MicroID2 is the smallest biotin ligase reported so far (180 amino acids [AAs] for MicroID2 versus 257 AAs for miniTurbo and 338 AAs for TurboID), yet it demonstrates only slightly less labeling activity than TurboID and outperforms miniTurbo. MicroID2 also had lower background labeling than TurboID. For experiments where precise temporal control of labeling is essential, we in addition developed a MicroID2 mutant, termed lbMicroID2 (low background MicroID2), that has lower labeling efficiency but significantly reduced biotin scavenging compared with BioID2. Finally, we demonstrate utility of MicroID2 in mass spectrometry experiments by localizing MicroID2 constructs to subcellular organelles and measuring proximal interactions.     

遗传背景对小鼠四倍体胚胎发育的影响

不同遗传背景的小鼠2-细胞期胚胎经过电融合后,胚胎的融合效率和四倍体胚胎的发育能力存在着一定的差异。本试验采用C57(C57×C57)、ICR(ICR×ICR)、BALB/c(BALB/c×BALB/c)、B6D2F2(B6D2F1×B6D2F1)、B6C3D2F2(B6C3F1×B6D2F1)品系的二倍体2-细胞期胚胎在相同的条件下经过电融合处理,结果表明:小鼠四倍体胚胎的获得效率受小鼠遗传背景的影响,远交系小鼠胚胎B6D2F2和B6C3D2F2的融合率显著高于近交系C57,ICR和BALB/c(P<0.05);四倍体胚胎在体外的发育情况也受其遗传背景的影响,在桑椹胚发育率和囊胚发育率上B6D2F2和B6C3D2F2品系的四倍体胚胎都显著高于C57和BALB/c品系的四倍体胚胎(P<0.05);杂合和纯系遗传背景的小鼠四倍体胚胎囊胚细胞数目相比具有显著差异(P<0.05或P<0.01);不同遗传背景的小鼠四倍体胚胎着床率间不存在显著差异(P>0.05);杂合背景的小鼠四倍体胚胎得到5只发育至13.5dpc(dayspostcoitum,dpc)的胎儿,纯合背景的小鼠四倍体胚胎得到0只发育至11dpc的胎儿。