Spectrum structures and biological functions of 8-mers in the human genome

The spectra of k-mer frequencies can reveal the structures and evolution of genome sequences. We confirmed that the trimodal spectrum of 8-mers in human genome sequences is distinguished only by CG2, CG1 and CG0 8-mer sets, containing 2,1 or 0 CpG, respectively. This phenomenon is called independent selection law. The three types of CG 8-mers were considered as different functional elements. We conjectured that (1) nucleosome binding motifs are mainly characterized by CG1 8-mers and (2) the core structural units of CpG island sequences are predominantly characterized by CG2 8-mers. To validate our conjectures, nucleosome occupied sequences and CGI sequences were extracted, then the sequence parameters were constructed through the information of the three CG 8-mer sets respectively. ROC analysis showed that CG1 8-mers are more preference in nucleosome occupied segments (AUC > 0.7) and CG2 8-mers are more preference in CGI sequences (AUC > 0.99). This validates our conjecture in principle.     

Impacts of benzophenone-type UV filters on cladoceran Daphnia carinata

Limnology - The impacts of three commonly used benzophenone-type UV filters including benzophenone (BP), 2-hydroxy-4-methoxy-benzophenone (BP3), and 2-hydroxy-4-methoxy-benzophenone-5-sulfonicacid...     

Systematic analysis of multigene predictors in gastric cancer exploiting gene expression signature

Gastric cancer (GC) is the second most common cause of cancer death worldwide but could be more curable if diagnosed at an earlier stage. At present, the capability to predict the efficaciousness of molecular diagnosis for GC for each patient remains elusive. The purpose of this study was to identify tumor biomarkers through systems analysis of multigene predictors exploiting the available data resource. In this study, we investigated the top 10% overexpressed genes in GC from five data sets of the Oncomine platform, with 265 GC samples versus 174 normal gastric mucosa samples. Sixteen candidate genes were identified as predictors of GC, of which 14 genes were verified through the comparison of expression levels in specimens from normal (chronic gastritis, 21 samples) and GC groups (38 samples). In addition, unique molecular portraits of diffuse adenocarcinoma (DA), intestinal adenocarcinoma (IA), and mixed adenocarcinoma (MA) were studied through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, where DA showed higher extracellular matrix alteration while IA and MA showed higher cell-cycle alteration than other types. We also found that the elevated expressions of genes during GC progression were independent of gene mutations, and high core-binding factor subunit β expression is correlated with a high overall survival rate in GC patients. Our research may provide an efficient clinical diagnosis of GC at an early stage with high accuracy and thus help improve the overall survival rate through early therapeutic interventions.     

Phylogeography of Lagochilus ilicifolius (Lamiaceae) in relation to Quaternary climatic oscillation and aridification in northern China

Using two chloroplast DNA intergenic spacers, a phylogeographical study of Lagochilus ilicifolius with 168 individuals from 14 populations was performed to assess geographical patterns and genetic variation in relation to past climate change. Population structure and history were inferred by nested clade analysis, neutrality tests, divergence time estimates, and mismatch distribution analysis. Twelve haplotypes were identified. Genetic differentiation among populations within groups was also elevated (F_SC = 0.772), suggesting restricted gene flow among populations within groups. Divergence time was at approximately 0.71 Ma, consistent with aridification and desert expansion during the middle Pleistocene. The Helan Mountains contained a large proportion of the haplotypes, which implies that the region may be the center of diversification for the species, whereas the Loess Plateau as a dispersal corridor for postglacial re-colonization northward. Climatic oscillation, aridification, and desert expansion within these regions have molded current distribution and biodiversity of L. ilicifolius.     

A modified cornish pasty method for ex ovo culture of the chick embryo development

Chick embryos grown in ex ovo culture by the modified Cornish pasty method reported in Nagai, Lin and Sheng in this issue.     

幽门螺杆菌致病岛CagL重组抗原的可溶性表达及其多克隆抗体的制备和分析*

目的:利用原核表达和蛋白质纯化技术获得高纯度的幽门螺杆菌致病岛CagL重组抗原(rCagL),利用其制备anti-CagL多克隆抗体,并分析抗体的特异性。方法:通过生物信息学软件分析rCagL的抗原结构;利用PCR长片段DNA合成技术合成不含有信号肽序列的幽门螺杆菌致病岛CagL基因,将其插入表达质粒pCzn1中,构建重组质粒pCzn1-rCagL。然后,将pCzn1-rCagL转入大肠杆菌Arctic Express中,经IPTG诱导表达后,通过Ni-IDA镍离子亲和层析纯化重组抗原rCagL,利用Western blot鉴定rCagL与His标签抗体和Anti-H. pylori抗体的免疫反应性;最后,通过rCagL辅以弗氏佐剂免疫BALB/c小鼠,制备anti-CagL多克隆抗血清,通过ELISA方法分析抗血清的特异性。结果:生物信息学软件表明重组抗原rCagL具有较好的抗原性质;重组质粒pCzn1-rCagL经双酶切和基因测序等技术鉴定,证实rCagL核苷酸序列与理论序列完全一致;基因工程菌株pCzn1-rCagL/Arctic Express在低温11℃条件经IPTG诱导表达。 SDS-PAGE实验结果证实:rCagL可实现相对高效地可溶性蛋白表达,可溶性蛋白约占包涵体的62.07%。经Ni-IDA亲和层析柱纯化,可获得高纯度rCagL,纯度约为96.6%。Western blot结果证实:重组抗原rCagL可特异性与His标签抗体和Anti-H. pylori抗体结合。ELISA结果证实:经rCagL免疫小鼠制备的多克隆抗体anti-CagL可特异性识别rCagL和H. pylori裂解物,具有较高的抗体特异性。结论:重组抗原rCagL在低温条件下可实现可溶性表达,经纯化可获得高纯度抗原蛋白;rCagL具有较好的抗原性,制备的多克隆抗体具有较好的免疫特异性,为发展H. pylori相关诊断试剂奠定了实验基础。     

从国际非专利名称纵观全球生物药发展

生物药(bio-therapeutics)是指采用生物技术制备的、临床上用于疾病治疗的大分子生物制品,具有结构复杂、异质性高等特点,科学严谨的生物药通用名命名,是区分生物药物质基础的主要依据,也是药品生命周期管理的重要基础。世界卫生组织(World Health Organization,WHO)协调建立的国际非专利名称(International Nonproprietary Names,INN)是全球药物命名的标准化体系。从INN的起源,以及生物药INN的类别、发生与发展为主线,以较为详实的数据统计和分析,呈现了全球生物药的衍化进程,从不同的角度纵览生物药技术发展历程,对生物药的研发设计、技术标准及监管策略的考量均具有一定的参考意义。