Finding finer functions for partially characterized proteins by protein-protein interaction networks

Based on high-throughput data, numerous algorithms have been designed to find functions of novel proteins. However, the effectiveness of such algorithms is currently limited by some fundamental factors, including (1) the low a-priori probability of novel proteins participating in a detailed function; (2) the huge false data present in high-throughput datasets; (3) the incomplete data coverage of functional classes; (4) the abundant but heterogeneous negative samples for training the algorithms; and (5) the lack of detailed functional knowledge for training algorithms. Here, for partially characterized proteins, we suggest an approach to finding their finer functions based on protein interaction sub-networks or gene expression patterns, defined in function-specific subspaces. The proposed approach can lessen the above-mentioned problems by properly defining the prediction range and functionally filtering the noisy data, and thus can efficiently find proteins’ novel functions. For thousands of yeast and human proteins partially characterized, it is able to reliably find their finer functions (e.g., the translational functions) with more than 90% precision. The predicted finer functions are highly valuable both for guiding the follow-up wet-lab validation and for providing the necessary data for training algorithms to learn other proteins.     

Molecular cloning and expression of interleukin Ibeta (IL-1β) from red seabream (Pagrus major)

The interleukin 1β (IL-1β) cDNA was cloned from the red seabream (Pagrus major) by homology cloning strategy. A cDNA fragment was amplified by PCR using two degenerated primers, which were designed according to the conserved regions of other known IL-1β sequences, and elongated by 3' ends and 5' ends RACE PCR to get the full length coding sequence of red seabream IL-1β (RS IL-1β). The sequence contained 1252 nucleotides that included a 5' untranslated region (UTR) of 84bp, a 3' UTR of 410 bp and an open reading frame (ORF) of 759 nucleotides which could be translated into a putative peptide of 253 amino acids with molecular weight of 28.6 kD and putative isoelectric point pI of 5.29. The deduced peptide contained two potential N-glycosylation sites and an identifiable IL1 family signature, but lacked the signal peptide and the clear ICE cut site, which were common in other nonmammalian IL-1β genes. The RS IL-1β had the highest homology with piscine IL-1β according to phylogenetic tree analysis.     

用微弹轰击法将GUS基因导入香蕉茎尖组织细胞

用在弹轰击法将外源ＤＮＡ导入香蕉（Ｍｕｓａ，ｓｐｐ）茎尖细胞，以ＧＵＳ基因作为报告基因，用Ｘ－Ｇｌｕｃ浴液对ＧＵＳ基因表达产物进行组织化学鉴定。样品材料细胞中发现有明显的蓝色斑点，而对照则没有。实验说明用微弹轰击法可以将外源基因导入香蕉茎尖组织并在其中成功表达，这为香蕉的外源基因导入工作提供了新的有效途径．     

水稻苯达松敏感致死基因的RAPD标记的克隆及测序

用3S Spin DNA Agarose Gel Purification Kit试剂盒将与水稻苯达松敏感致死基因相连锁的RAPD遗传标记S20—420和S316—600回收纯化，连接于pGEM—T载体并克隆测序，得到了S20—420和S316—600的全序列，其长度分别为423bp、606bp．将两端序列设计特异PCR扩增引物可用于检测水稻苯达松敏感致死基因和标记辅助育种．     

Cloning and expression of the vp39 gene ofBombyx mori nuclear polyhedrosis virus inE. coli

The nuclear capsid protein gene (vp39) ofBombyx mori nuclear polyhedrosis virus (BmNPV) was amplified successfully by PCR technique and inserted into pGEM 3zf(+). The 5′ and 3′ terminal area of the amplified vp39 gene were sequenced with silver-staining dideoxy method. Bmvp39 gene was sub-cloned into the expression vector pRSET-A, and transformed intoE. coli BL21. This gene was highly expressed by IPTG induction. SDS-PAGE analysis showed that the expressed protein is about 38 kd, and the expressed amount reached maxium in 4 h with IPTG induction. Supported by the National Natural science Foundation of China and the Doctoral Foundation of Edn carto Committee Liu Deli: born in 1954, Doctoral Candidate from Huazhong Normal University To whom correspondence should be addressed: (027-7882712-2938)     

Molecular cloning and nucleotide sequence of classical swine fever virus strain Shimen

According to the previously published CSFV sequences, 18 paris of partially overlapping primers which span the entire genome of CSFV strain Shimen were designed and synthesized. Each cDNA fragment of strain Shimen was amplified by RT-PCR method from the anticoagulant blood of strain Shimen infected pig. The PCR fragments were cloned into pGEM-T vector respectively and sequenced. The results show that we have obtained the nucleotide sequence of strain Shimen. The viral RNA consists of 12 297 nucleotides including noncoding regions of 373 and 227 bases at the 5′ and 3′ end, respectively, and a single large open reading frame spanning 11 697 nucleotides in the middle, which encodes an amino acid sequence of 3 989 residues with a calculated molecular weight of 437.6×10³. The precisely sequencing of 5′ and 3′ termini is undertaking. Supported by the National Pandeng Project Huang Qianhua: born in 1968. Graduate student     

籼粳交稻米品质性状的遗传相关分析

用种子性状遗传模型对籼粳交稻米８个主要品质性状的遗传相关进行了研究。结果表明,在籼粳杂种中,稻米品质性状之间的遗传相关主要涉及到种子直接遗传效应和母体遗传效应。其中,５个理化品质性状之间以直接效应相关为主,其次为母体效应相关;５个理化品质性状与３个外观品质性状之间只有直接加性、母体加性和母体显性相关;３个外观品质性状之间的遗传相关主要归因于母体效应。尤其是母体加性效应。在所有的性状对中,仅胶稠度和     

血小板反应素-1活性片段的克隆与表达

选择两段血小板反应素（TSP-1）中抑制血管再生的活性片段，设计两对引物，使用RT-PCR的方法从人血细胞中进行克隆并对获得片段进行测序验证．克隆片段大小分别为723和522bp，命名为聪P-1-1和聪P-1-2．利用原核表达载体pET-29a获得大肠杆菌重组子，重组子经过IPTG诱导以包涵体的形式表达相应的多肽片段．再对包涵体进行体外溶解、纯化，得到了目的多肽．     

人类染色体中的微切割与微克隆技术

微切割、微克隆是分子生物学的一项新技术，它对于基因的标记与分离、DNA文库的重组及遗传图谱的绘制都发挥着重要作用．笔者介绍了这项技术在人类染色体中的应用情况．     

极端嗜热厌氧纤维素分解菌基因文库的构建及其内切葡聚糖酶基因片段的克隆

以从云南邦拿掌温泉中分离、纯化的高温厌氧纤维素分解菌邦2菌(Cadicellulosiruptor)为材料,制备其总DNA,经限制性核酸内切酶EcoRⅠ部分酶切后,在T4DNA连接酶的作用下与经EcoRⅠ完全酶切、去磷酸化的质粒载体pUC18连接,然后转化E.coliJM109,建立了邦2的基因文库,经筛选鉴定得到6.3×103个重组子;重组子经刚果红平板验证:约有23.5%菌落呈现透明圈;重组子经EcoRⅠ酶切验证显示:重组质粒均含有外源DNA插入片段.结果表明已克隆到邦2菌纤维素酶系中的内切葡聚糖酶基因(ED基因)片段.