天山一号冰川表面冰尘和底部沉积层中可培养酵母菌系统发育类群的分布及生态生理特征

【目的】揭示乌鲁木齐河源天山1号冰川表面冰尘(CS)和底部沉积层(DS)可培养酵母菌系统发育类群及其结构组成差异,分析低温酵母菌代表菌株之间的生态、生理生化特性。【方法】利用4种培养基分离天山1号冰川可培养酵母菌,采用ITS基因序列分析确定菌种的系统进化地位。对分离菌株的最适生长温度、耐盐性和产酶等生态、生理学特性进行分析。【结果】从冰尘和底部沉积层中共分离出152株酵母菌菌株,通过ITSrRNA基因序列的NCBI比对和Rep-PCR指纹分型,结果表明酵母菌类群包括担子菌门(Basidiomycota)和子囊菌(Ascomycota),分属于14个属26种,其中担子菌门柄锈菌亚门(Pucciniomycotina)88株、伞菌亚门(Agariomycotina)24株,子囊菌门40株,冰川广布酵母菌Vishniacozyma victoriae为优势菌株(占比21.84%)。17种酵母的最适生长温度为15°C、2种为10°C、6种为20°C。25株代表酵母菌株产酶分析显示,产脂肪酶、淀粉酶、蛋白酶菌株分别为11株、11株、5株,6株3种酶都不产。【结论】天山1号冰川冰尘及底部沉积层可培养低温酵母系统发育类群结构存在差异,产低温酶活性高、稳定性好,为今后冰川低温酵母菌的研究提供有价值的数据支持。     

Alleviation of the detrimental effect of water deficit on wheat (Triticum aestivum L.) growth by an indole acetic acid-producing endophytic fungus

Plant and Soil - Endophytic fungi colonization is an eco-friendly strategy to respond to environmental stresses and confer tolerance to the host plant. Here, the responses of wheat plant inoculated...     

Lateral Organ Boundaries Domain 19 (LBD19) negative regulate callus formation in Arabidopsis

Plant Cell, Tissue and Organ Culture (PCTOC) - Callus is a remarkable regeneration tissue. The genes correlated with root development can be involved in regulating callus development in higher...     

Analysis of long noncoding RNA expression profiles in the whole blood of neonates with hypoxic-ischemic encephalopathy

Long noncoding RNAs (lncRNAs) have been shown to participate in many biological processes. To investigate the expression profiles of lncRNAs and their potential functions in neonatal hypoxic-ischemic encephalopathy (HIE), we detected the lncRNA and messenger RNA (mRNA) expression in the peripheral blood samples from HIE patients and controls using a microarray. A total of 376 lncRNAs and 126 mRNAs were differentially expressed between the HIE and the non-HIE samples (fold change > 2). Quantitative real-time polymerase chain reaction was used to validate the microarray data. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed to determine the gene function. Furthermore, the lncRNA-mRNA coexpression network was generated to predict the potential targets of lncRNAs. In conclusion, our study first demonstrated the differential expression profiles of lncRNAs in the whole blood of infants with HIE and may provide a new view of the distinct lncRNA functions in HIE.     

High NEK2 confers to poor prognosis and contributes to cisplatin-based chemotherapy resistance in nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is a common malignant tumor in southern China and Southeast Asia, but the molecular mechanism of its pathogenesis is poorly understood. Our previous work demonstrated that NEK2 is overexpressed in multiple cancers. However, how NEK2 involves in NPC development remains to be elucidated. In this study, we firstly identified NEK2, located at +1q32-q33, a late event in NPC pathogenesis, overexpressed in the stage III-IV and paired sequential recurrent patients with NPC by immunohistochemistry. Furthermore, Kaplan-Meier analysis indicated high NEK2 conferred an inferior overall survival in NPC. In addition, cisplatin experiments with cell counting kit-8, colony formation, and a xenograft mice model of NPC demonstrated that NEK2 contributed to proliferation and cisplatin resistance in vitro and in vivo. On the contrary, downregulation of NEK2 by short hairpin RNA inhibited NPC cell growth and increased the sensitivity of cisplatin treatment in vitro. Thus, increased expression of NEK2 protein could not be predicted for poor survival but used as a novel biomarker for recurrence of NPC. Targeting NEK2 has the potential to eradicate the cisplatin-based chemotherapy resistant NPC cells.     

Scalable remote homology detection and fold recognition in massive protein networks

The global connectivities in very large protein similarity networks contain traces of evolution among the proteins for detecting protein remote evolutionary relations or structural similarities. To investigate how well a protein network captures the evolutionary information, a key limitation is the intensive computation of pairwise sequence similarities needed to construct very large protein networks. In this article, we introduce label propagation on low-rank kernel approximation (LP-LOKA) for searching massively large protein networks. LP-LOKA propagates initial protein similarities in a low-rank graph by Nyström approximation without computing all pairwise similarities. With scalable parallel implementations based on distributed-memory using message-passing interface and Apache-Hadoop/Spark on cloud, LP-LOKA can search protein networks with one million proteins or more. In the experiments on Swiss-Prot/ADDA/CASP data, LP-LOKA significantly improved protein ranking over the widely used HMM-HMM or profile-sequence alignment methods utilizing large protein networks. It was observed that the larger the protein similarity network, the better the performance, especially on relatively small protein superfamilies and folds. The results suggest that computing massively large protein network is necessary to meet the growing need of annotating proteins from newly sequenced species and LP-LOKA is both scalable and accurate for searching massively large protein networks.     

基于Bioperl实现远程自动获取抗逆基因序列

BioPerl对于现今大量的生物数据来说,具有很好的获取和处理能力,并且NCBI提供了可以直接访问它下属的Entrez数据库（包括PubMed）的编程接口,即E-Utilities。为了从NCBI中自动获取大量抗逆基因序列,使得生物抗逆基因二次数据库得以搭建,该文基于BioPerl设计了远程自动获取大量抗逆基因序列的程序。此程序灵巧、精悍,Perl语言强大的文本处理功能使程序能实现不同类型基因序列的远程获取。