一种基于单分子纳米操纵的有序化测序策略

尽管包括人类在内的许多生物物种的基因组测序工作已经完成,但由于现有测序技术的限制,大部分复杂基因组还存在很多大大小小的缺口.缺口的填补以及对其他重复序列区域的测序迫切需要全新的思路和技术.基于在DNA单分子定位切割和拾取方面的实验进展,提出了一种基于原子力显微镜纳米操纵技术的单分子有序化测序策略.计算机模拟的结果表明,这一方法和策略是可行的,有助于解决目前测序工作中所遇到的一些棘手问题.     

复合菌剂M5对红螯螯虾(Cherax quadricarinatus)高密度养殖系统水质及其肠道微生物群落影响的初步研究

应用自制复合菌剂M5于红螯螯虾(Cherax quadricarinatus)的高密度养殖系统中,通过分析肠道菌群并监测养殖水质,研究了复合菌剂作用的效果及潜在的机理。结果显示,复合菌剂M5的使用可显著降低养殖水环境的pH值,降低污染物NH⁺₄、NO^-₂和COD的浓度,抑制弧菌属（Vibrio）中某些条件致病菌的生长。基于PICRUSt与KEGG数据库的功能预测及肠道菌群的群落分析,复合菌剂既可作为额外的营养补充物,缓解肠道群落之间对营养源的竞争,又可提高虾的消化能力、免疫力。新型复合菌剂M5可显著改善养殖水质并影响肠道菌群的组成与功能,从而提高养殖存活率。     

结合三代测序与二代测序技术揭示蜜蜂球囊菌孢子转录组的复杂性

【目的】蜜蜂球囊菌(Ascosphaera apis)是一种专性侵染蜜蜂幼虫的致死性真菌病原。本研究旨在利用PacBio单分子实时(singlemoleculereal-time,SMRT)测序技术对蜜蜂球囊菌孢子(AaS)中基因的可变剪切(alternative splicing,AS)和可变多聚腺苷酸化(alternative polyadenylation,APA)以及长链非编码RNA (long non-coding RNA,lncRNA)进行鉴定和分析,进而揭示蜜蜂球囊菌孢子中转录组的复杂性。【方法】采用Suppa软件对蜜蜂球囊菌孢子中基因的AS事件进行鉴定。通过RT-PCR对不同类型的AS事件进行验证。采用TAPIS pipeline对蜜蜂球囊菌孢子基因的APA位点进行鉴定。利用MEME软件分析孢子全长转录本的poly(A)剪接位点上游50bp的序列特征并鉴定motif。联用CPC和CNCI软件和比对Swiss-prot数据库的方法预测lncRNA,取三者的交集作为高可信度的lncRNA集合。进一步比较lncRNA和mRNA的转录本长度,外显子数量与长度,内含子长度,GC含...     

马尾松二代无性系种子园子代父本分析及花粉散布

目前国内较早建立的马尾松(Pinus massoniana)二代种子园正陆续进入正常开花结实期。研究马尾松二代种子园花粉散布和自由授粉子代的父本组成, 可为生产上指导马尾松高世代种子园的规划设计和遗传管理提供理论依据。该文利用筛选的11对SSR引物, 对马尾松二代无性系种子园内8个无性系单株的320个自由授粉子代和48个候选父本进行了扩增, 并采用最大似然法对子代进行父本分析。结果表明: 11个位点共检测到61个等位基因, 每个位点的等位基因数在2-11之间, 平均为5.55个。试验亲本和子代群体的总平均观测杂合度(H_o)、期望杂合度(H_e)及多态信息含量(PIC)分别为0.428、0.433和0.387。在80%的可信度水平下可为232 (72.50%)个子代确定其父本。平均每个采种母树与19个父本产生子代。在自由授粉状态下, 马尾松二代种子园自交率为1.72%, 自交现象很弱, 其交配方式以异交为主。绝大多数亲本无性系的雄性繁殖适合度在1.00%-4.00%之间, 候选父本平均繁殖适合度为2.17%, 平均形成5个后代。马尾松有效花粉的散布距离和固定交配距离的父本繁殖适合度均符合正态分布, 两者呈极显著负相关, 其主要散布距离集中在0-100 m, 而检测到的最大散布距离为192 m。种子园花粉污染率较低, 仅为4.06%。总体看来, 树冠南面子代亲本交配距离较北面有增加的趋势, 但树冠南、北面子代父本组成数并未表现明显的规律。     

大粉瘤菌小亚基rDNA片段的克隆测序

对大粉瘤菌Lycogalaflavofuscum的19SrDNA片段进行了克隆测序,序列长度为1443bp。同时将之与多头绒泡菌的相应序列进行了比较,其序列同源性为58.16%。     

Primary structure of apolipophorin-III from the greater wax moth,Galleria mellonella

The complete amino acid sequence of apolipophorin-III (apoLp-III), a lipid-binding hemolymph protein from the greater wax moth,Galleria mellonella, was determined by protein sequencing. The mature protein consists of 163 amino acid residues forming a protein of 18,075.5 Da. Its sequence is similar to apoLp-III from other Lepidopteran species, but remarkably different from the apoLp-IIIs of insects from other orders. As shown by mass spectrometric analysis, the protein carries no modifications. Thus, all of its known physiological functions, including its recently discovered immune response-stimulating activity, must reside in the protein itself.     

Molecular genetic characterization of H5N1 influenza virus strains isolated from poultry in the Kurgan region in 2005

In the second half of 2005, a large-scale outbreak of influenza in poultry and wild birds was caused by a highly pathogenic H5N1 influenza virus in Russia. The level of pathogenicity is a polygenic trait, and most individual genes contribute to the influenza A virus pathogenicity in birds, animals, and humans. The full-length nucleotide sequences were determined for H5N1 strains isolated in the Kurgan region (Western Siberia). The structure of viral proteins was analyzed using the deduced amino acid sequences. The receptor-binding site of hemagglutinin (HA) in strains A/chicken/Kurgan/05/2005 and A/duck/Kurgan/08/2005 was typical for avian influenza viruses and contained Glu and Gly at positions 226 and 228, respectively. The structure of the basic amino acid cluster located within the HA cleavage site was identical in all isolates: QGERRRKKR. According to the neuraminidase structure, all H5N1 isolates from the Kurgan region were assigned to the Z genotype. Amino acid residues typical for the avian influenza virus were revealed in 30 out of 32 positions of M1, M2, NP, PA, and PB2, determining the host range specificity. One of the strains contained Lys at position 627 of PB2. Isolates from the Kurgan region were shown to have a remantadine-sensitive genotype. Both strains contained Glu at position 92 of NS1, indicating that the virus is interferon-resistant. Phylogenetic analysis related the Kurgan isolates to subclade 2 of clade 2 of highly pathogenic H5N1 influenza viruses.     

Genomic architecture of autism from comprehensive whole-genome sequence annotation

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