Mitochondrial genome of the dimorphic zygomycete Mucor racemosus

Mitochondria were isolated from the dimorphic zygomycete Mucor racemosus by differential centrifugation. DNA from the organelles was purified by cesium chloride-ethidium bromide isopycnic centrifugation. Examination of the mitochondrial DNA by electron microscopy revealed a circular chromosome approximately 63.8 kbp in circumference. The chromosome was digested with restriction endonucleases and the resulting DNA fragments were separated by agarose-gel electrophoresis. Electrophoretic mobilities and stoichiometry of the fragments indicated a mixed population of mtDNA molecules each with a size of about 63.4 kbp. Physical maps were constructed from analyses of fragments generated in single and double restriction digests and from the hybridization of fragments to probes for the large and small mitochondrial rRNA genes from Saccharomyces cerevisiae. The Mucor mitochondrial chromosome was found to exist in the form of two flip-flop isomers with inverted repeat sequences encoding both rRNA genes.     

Transcriptome analysis of hagfish leukocytes: a framework for understanding the immune system of jawless fishes

Jawless fishes occupy a critical phylogenetic position in understanding the origin of the adaptive immune system. Here, we performed large-scale expressed sequence tag analysis of leukocytes isolated from the inshore hagfish Eptatretus burgeri. Although we found many immunity-related genes such as those involved in lymphocyte or hematopoietic cell signaling and development as well as cytokine and cytokine receptor genes, MHC molecules or antigen receptors were not identified. We characterized two hagfish cDNAs that closely resembled mammalian proteins with essential roles in adaptive immunity, one encoding a GATA3-like molecule and another encoding a Bruton's tyrosine kinase (Btk)-like molecule. The GATA3-like gene of hagfish was equidistant from GATA3 and GATA2 in jawed vertebrates. Similarly, the hagfish Btk-like molecule was not Btk itself, but qualified as a pre-duplicated form of Btk and Bmx in jawed vertebrates. In total, our work provides circumstantial evidence that adaptive immunity is unique to jawed vertebrates.     

大鼠肝再生中糖代谢相关基因的表达变化

目的了解糖类代谢相关基因在大鼠肝再生中的表达变化。方法本研究用搜集网站资料和查阅相关论文等方法获得糖类代谢相关基因,用大鼠基因组230 2.0芯片检测它们在大鼠再生肝中的表达情况,用比较手术组和假手术组中基因表达的差异性确定肝再生相关基因。结果初步证实上述基因中118个基因与肝再生相关。肝再生早期[部分肝切除(PH)后0.5~4h]、前期(PH后4~12h)、中期(PH后16~66h)和后期(PH后72~168h)等4个阶段起始表达的基因数为33、6、68和7;基因的总表达次数为68、44、210和83。表明肝再生相关基因主要在肝再生启动阶段起始表达,在不同阶段发挥作用。它们共上调205次,下调200次,分为12种表达方式,表明肝再生中糖代谢活动多样和复杂。其中,单糖和糖原代谢、糖蛋白和糖脂(主要为神经节苷脂)合成相关基因几乎在整个肝再生中表达增强,寡糖和糖胺聚糖合成及糖蛋白和糖脂分解相关基因表达下调。结论肝再生与糖代谢密切相关。     

脂类代谢和运输涉及的基因与大鼠肝再生的相关性分析

目的在基因转录水平了解脂类代谢和运输相关基因在大鼠肝再生(LR)中的表达变化和模式。方法用搜集网站资料和查阅相关论文等方法获得参与脂类代谢和运输基因,用大鼠基因组230 2.0芯片检测它们在大鼠再生肝中的表达情况,用比较手术和假手术中基因表达的差异性确定肝再生相关基因。结果初步证实上述基因中193个基因与肝再生相关。肝再生早期[部分肝切除(PH)后0.5~4h]、前期(PH后6~12h)、中期(PH后12~66h)、后期(PH后72~168h)等4个阶段起始表达的基因数为113、20、66和1;基因的总表达次数为250、205、796和293。共上调852次,下调630次,分为27种表达方式。肝再生早期和前期胆汁酸代谢相关基因转录减弱;早期和后期糖皮质激素分解相关基因转录增强;前期和中期磷脂合成相关基因转录增强,磷脂分解相关基因转录减弱;中期脂肪酸、白三烯和鞘糖脂合成相关基因转录增强,甘油三酯和磷脂酰肌醇代谢相关基因转录增强,鞘糖脂分解相关基因转录减弱;中期和后期前列腺素合成和脂肪酸分解相关基因转录增强;几乎在整个肝再生中性激素、糖皮质激素和孕酮合成相关基因转录增强,鞘磷脂代谢相关基因转录增强,脂类运输相关基因转录增强,胆固醇代谢相关基因转录减弱。结论肝再生中脂类代谢和运输变化较大,与肝再生密切相关。     

Chromatin interactions in differentiating keratinocytes reveal novel atopic dermatitis– and psoriasis-associated genes

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血清乙型肝炎病毒DNA水平对HBV全基因组克隆效率的影响

目的：通过比较血清HBV DNA水平对一片段PCR法和两片段PCR法这两种不同方法的HBV全基因组克隆效率的影响，选择出合适的HBV全基因组克隆技术，供后续的HBV的基础和临床研究。 方法：采集了慢性乙型肝炎（CHB）患者85份血清，分别用本研究建立的一片段PCR法及两片段PCR法扩增HBV全基因组，经双酶切鉴定后将PCR产物克隆入载体，进行HBV全基因组序列测定。同时用实时荧光定量PCR法检测上述85份血清的HBV DNA滴度。 结果： 本研究建立的一片段PCR法扩增成功需要的血清HBV DNA浓度高于两片段PCR法,两种方法扩增的效率比较为：一片段PCR法扩增的阳性率低于两片段PCR法（P<0.01）。一片段PCR法的保真性和灵敏度分析发现： 保真性：核苷酸的人为突变率为1.13 bp/kb；灵敏度：为102个初始模板。浓度大于103的重组质粒DNA80%可以成功扩增，浓度低于该值的扩增效率比较低。结论： 血清HBV DNA水平对两种扩增方法的阳性率有一定影响，滴度高低是选择合适PCR扩增方法的依据。HBV DNA滴度大于106copies/L的样本，可选用一片段PCR法的全基因组扩增、克隆技术，而对HBV DNA滴度小于106copies/L样本，则可选用两片段PCR法的全基因组扩增、克隆技术。本研究建立的一片段PCR法扩增HBV全基因组克隆的技术是一种值得推荐的好方法，但还需进一步优化。     

Genome analysis of dengue type-1 virus isolated between 1990 and 2001 in Brazil reveals a remarkable conservation of the structural proteins but amino acid differences in the non-structural proteins

We have investigated the genetic diversity of dengue type-1 (DEN-1) virus in Brazil. The full nucleotide sequences of three DEN-1 virus isolated from DEN fever (DF) and DEN hemorrhagic fever patients in northeastern Brazil in 1997 (BR/97) and one from a DF patient in the south of Brazil in 2001 (BR/01) were compared to that of the reference strain BR/90 obtained in the city of Rio de Janeiro in 1990. Sequence analysis showed that the structural proteins were remarkably conserved between all isolates. A total of 27 amino acid changes occurred throughout the non-structural proteins. Among them, nine amino acid substitutions were specific of BR/97 and BR/01 isolates, indicating that in situ evolution of these strains had occurred. Within the BR/97 and BR/01 samples, some amino acid substitutions have been previously identified in DEN-1 virus strains sequenced so far, suggesting that recombination events might have occurred.     

Variable abundance of a mitochondrial DNA fragment in cultured tobacco cells

Summary The relative abundance of a cloned 4.5 kilobase (kb) pair mitochondrial DNA sequence in two suspension cultures of tobacco (Nicotiana tabacum cv Turkish samsun and Nicotiana tabacum NT-1) has been examined. This sequence is 70-fold reduced in NT-1 relative to Turkish samsun; the reduction is correlated with an increase in supercoiled mitochondrial DNA. This sequence does not hybridize with mitochondrial DNA from watermelon, maize, or Saccharomyces cerevisiae, nor with several cloned mitochondrial genes and is thus probably not a gene. It may represent most of the plant mitochondria) genome thought to be non-essential for mitochondrial function. The sequence complexity of supercoiled mitochondrial DNA from NT-1 cells is about one-third that found for the entire mitochondrial genome and does not include the cytochrome oxidase subunit II gene.     

Construction and characterization of centric circular and acentric linear chromosomes in fission yeast

Summary Gene disruption and gap repair of chromosomal DNA have been frequently employed techniques in yeast genetics. To extend the possibility of using these gene manipulations for larger genomic regions, we have examined the maximal sizes of chromosomal DNA disrupted or repaired in vivo. Here we report a simple, potentially general, method for selectively deleting a 150 kb region, or gap-filling a 100 kb region, in the fission yeast genome. This enables the generation of acentric linear chromosomes by deletion, or the cloning of large functional centromeric DNAs into circular minichromosomes by gap-filling. The fidelity of the resulting gap-filling is high, judging from partial-digestion mapping of gap-repaired DNAs. By analysing a series of such circular minichromosomes, we conclude that only a part of the repetitive centromeric region, including the central domain, is essential for mitotic and meiotic chromosome segregation. Acentric linear chromosomes, although unstable, could be maintained, indicating that it may be possible to construct an acentric vector for large DNA fragments in this organism.     

2001至2005年上海部分地区腹泻住院患儿诺若病毒分子临床流行病学研究

目的通过对上海地区腹泻住院患儿进行诺若病毒检测,对其流行株进行基因序列的测定,以了解诺若病毒在上海地区的流行特征,为该病原体所致腹泻的防治提供基础数据和理论依据。方法收集2001至2005年复旦大学附属儿科医院5岁以下腹泻住院患儿的粪便标本。首先进行轮状病毒的检测,在轮状病毒抗原阴性标本中,每隔8个标本按编号顺序行机械随机抽样,建立RT-PCR方法进行诺若病毒的检测。对PCR产物进行双向测序,测序结果通过Clustal W和Mega 4.1软件进行分析。结果研究期间共收集腹泻患儿粪便标本5534份,轮状病毒抗原阴性4084份,机械随机抽得484份用于诺若病毒检测,45/484份(9.3%)检测到诺若病毒。对诺若病毒感染季节分布和患儿年龄特点的分析表明,除4月和7月份未检测到诺若病毒外,其余各月份均检测到诺若病毒,其高发的月份是8至11月。5~6月也呈一个小高峰。77.8%(35/45)的患儿<2岁,其中6~11个月的患儿所占比例最高,达35.6%(16/45),<6个月的婴儿占20%(9/45)。GⅡ-4型是这5年间尤其是2003年之后的主要流行型别,2001至2002年尚存在其他的流行型别GⅡ-3和GⅡ-7...