构建7q32区域鼻咽癌和正常鼻咽上皮细胞部分基因的表达图谱

目的构建７ｑ３２区域鼻咽癌细胞和组织及原代培养人正常鼻咽上皮细胞的部分基因表达图谱。方法通过差异ＲＴ－ＰＣＲ和Ｎｏｒｔｈｅｒｎ杂交的方法检测定位于７ｑ３２区域的２０个ＥＳＴ在鼻咽癌细胞和鼻咽癌组织及原代培养人正常鼻咽上皮细胞ｍＲＮＡ的表达水平。结果８个ＥＳＴ在鼻咽癌细胞ＨＮＥ１和原代培养人正常鼻咽上皮细胞中表达量较一致，７个ＥＳＴ在两种细胞中均无表达，３个ＥＳＴ（Ｗ７２６８８、Ｈ１９８３０、ＡＡ１３０６３０）在鼻咽癌细胞株中表达上调，而２个ＥＳＴ（ＡＡ０７０４３７、Ｈ９０８８２）在原代培养人鼻咽上皮细胞中表达上调。在１３例鼻咽癌活检组织中３０．７％（４／１３）的ＡＡ０７０４３７表达下调，７７％（１０／１３）的Ｗ７２６８８和７７％（１０／１３）的Ｈ１９８３０表达上升。结论构建了７ｑ３２区域鼻咽癌细胞和组织及原代培养人正常鼻咽上皮细胞部分基因表达图谱，并初步认为Ａ０７０４３７的表达下调和Ｗ７２６８８、Ｈ１９８３０的过表达与鼻咽癌的发生有关。     

9株YONBAN相关TTV变异株全基因序列测定及其结构、分型的研究

目的：对9个TTV新分离株全基因序列测定，基因结构及基因分型的研究。方法：从9名TTV第4基因群感染阳性的婴儿血清中抽提取其DNA，用long inverted PCR扩增出全基因组，克隆和测定全基因组序列，并对测序结果进行计算机分析。结果：首次次测定了TTV第4基因群共9个新分离株的全基因序列，其中8个分离株代表核基因群首次报道的8个新基因型。结论：TTV基因组核酸序列具有高度异质性及基因型的高度多样性，但是，其独特的转录特性和基因组的基本结构在各自的基因群及基因型中十分保守。     

Sequence variation within the human immunodeficiency virus V3 loop at seroconversion

Analysis of the HIV-1 V3 quasispecies present in an individual at the time of seroconversion was carried out. The polymerase chain reaction (PCR) was used to amplify proviral HIV-1 DNA extracted from peripheral blood mononuclear cells from a patient who was viraemic (p24 = 15 pg/ml) and had an equivocal HIV-1 antibody status. The PCR products were cloned and the DNA sequence determined for 15 clones. These data showed that the V3 region contained only limited sequence heterogeneity with a major variant accounting for 66% of the protein quasispecies present. The protein sequence of the principal neutralising domain on all species contained the relatively rare GPGKTL motif rather than GPGRAF. The relevance of these data for early stages of HIV infection are discussed.     

Direct sequencing of SSP-PCR-amplified cDNA to identify new alleles in the DR52-associated DRB1 group: identification of DRB1*1115, DRB1*1117 and DRB1*1319

Abstract: Low and high resolution sequence specific oligonucleotide probe hybridization patterns were used to design an approach to direct sequencing of allele specific amplified cDNA. Several PCR amplifications were used to derive overlapping sequence fragments to define complete first domain sequences for a single allele. This method has been used to characterize three new DRB1 alleles in the DR52 family, DRB1*1115, DRB1* 1117, and DRB1*1319. All three alleles carry polymorphisms previously observed in other DRB alleles and underscore the importance of utilizing a directed sequencing approach for obtaining unambiguous typing results in matching for bone marrow transplantation between unrelated donor and recipient.     

鸡柔嫩艾美耳球虫cDNA文库构建与表达序列标签分析

为系统分析鸡球虫敏感虫株和抗药虫株不同发育阶段的基因表达情况,利用柔嫩艾美耳球虫敏感株和抗马杜霉素株(由敏感株诱导)的未孢子化卵囊、孢子化卵囊、子孢子和裂殖子为材料构建了一个混合cDNA文库,并用该文库获得了2806条3'端高质量的表达序列标签(ESTs)。通过生物信息学分析:EST序列拼接出1424个假定独立转录本(TUTs),冗余度为49.3%。从cDNA文库中筛选出大量的低丰度表达基因,约占TUT总数的91.5%,且功能未知基因约占TUT总数的83.6%。在功能注释基因中,编码MIC2蛋白、BT1家族蛋白和核糖体蛋白等入侵和发育相关的基因高丰度表达。     

Complete coding region of the new HLA-DQB1*0612 allele, obtained by RT-PCR

A novel HLA-DQB1 allele was detected by oligotyping in the Bubi population of Equatorial Guinea. In order to characterize the new allelic variant, a RT-PCR method which permitted the cloning of its complete coding region was designed. With this method, we have determined the nucleotide sequence of the new DQB1*0612 allele, related to *0604 and *0609 but differing from them at polymorphic codon 70. A proposal for the improvement of the sequencing strategies of HLA class II alleles is made.     

Six new DPB1 alleles identified in a study of 1,302 unrelated bone marrow donor-recipient pairs

Six new DPB1 alleles were identified by PCR-SSOP methodologies in the course of a retrospective study of the role of HLA matching in the outcome of unrelated donor bone marrow transplantation. Sequencing confirmed that five of these alleles (DPB1*5901, *6801, *7101, *7201, and *7301) represent novel combinations of previously described sequence motifs in the variable regions of DPB1; the sixth (DPB1*7001) appears to result from a novel point mutation. These data support previous observations which suggest that multiple mechanisms, including segmental exchange and mutation, appear to be responsible for generating sequence diversity at the DPB1 locus. The extremely low discrepancy rate of 0.1% between the two laboratories which typed the samples, and the ability to predict the new sequences from probe hybridization patterns, indicate that SSOP is an accurate and efficient method for studying polymorphism at DPB1.     

A bioinformatics pipeline for high-throughput microbial multilocus sequence typing (MLST) analyses

Multilocus sequence typing (MLST) analysis for semi-routine applications is hindered by the downstream, manually intensive steps of processing the raw sequence data files. This report describes the development of an MLST pipeline that automates DNA sequence editing and analysis in order to significantly reduce the time required for processing data. Validation using a pneumococcal dataset revealed complete agreement between the results generated by manual and automated workflows. The MLST pipeline was developed for both double-strand and single-strand sequencing.     

Identification of a novel HLA-DQB1*06 allele, DQB1*0618

We report here the identification of a novel DQB1*06 allele, DQB1*0618, found in a bone marrow donor. The new allele was detected during routine DNA-based HLA typing by an ambiguous pattern of probe hybridization, obtained by polymerase chain reaction using sequence-specific oligonucleotides (PCR-SSO). Molecular cloning and sequencing confirmed that the new allele is identical to DQB1*0609 at exon 2 except for 3 nucleotide substitutions at positions 353, 356 and 367, also found in other alleles. These nucleotide changes may explain its anomalous reactivity.