Impact of GC content on gene expression pattern in chicken

Background

GC content varies greatly between different genomic regions in many eukaryotes. In order to determine whether this organization named isochore organization influences gene expression patterns, the relationship between GC content and gene expression has been investigated in man and mouse. However, to date, this question is still a matter for debate. Among the avian species, chicken (Gallus gallus) is the best studied representative with a complete genome sequence. The distinctive features and organization of its sequence make it a good model to explore important issues in genome structure and evolution.

Methods

Only nuclear genes with complete information on protein-coding sequence with no evidence of multiple-splicing forms were included in this study. Chicken protein coding sequences, complete mRNA sequences (or full length cDNA sequences), and 5^′ untranslated region sequences (5^′ UTR) were downloaded from Ensembl and chicken expression data originated from a previous work. Three indices i.e. expression level, expression breadth and maximum expression level were used to measure the expression pattern of a given gene. CpG islands were identified using hgTables of the UCSC Genome Browser. Correlation analysis between variables was performed by SAS Proprietary Software Release 8.1.

Results

In chicken, the GC content of 5^′ UTR is significantly and positively correlated with expression level, expression breadth, and maximum expression level, whereas that of coding sequences and introns and at the third coding position are negatively correlated with expression level and expression breadth, and not correlated with maximum expression level. These significant trends are independent of recombination rate, chromosome size and gene density. Furthermore, multiple linear regression analysis indicated that GC content in genes could explain approximately 10% of the variation in gene expression.

Conclusions

GC content is significantly associated with gene expression pattern and could be one of the important regulation factors in the chicken genome.     

青藏高原长花马先蒿的细胞地理学研究

对青藏高原长花马先蒿9个居群的核型及细胞地理学进行研究,所有居群的染色体数目均为2n=16,染色体基数为x=8。现有的细胞学资料表明:分布于云南中甸的居群可能为较原始的类群,而分布于西藏日土和青海门源的居群较为进化。长花马先蒿的9个居群均为二倍体,并未出现多倍化现象,可能是由于在末次冰期青藏高原存在广泛的避难所,二倍体得到很好的保存,冰期对它们的影响不是很大; 也可能是对环境的选择压力造成的。     

盐穗木过氧化氢酶基因的克隆与功能分析

利用同源基因克隆法,从新疆荒漠盐碱地多年生灌木盐穗木(Halostachys caspica)中克隆获得盐穗木过氧化氢酶基因(HcCAT1)。序列分析表明,HcCAT1基因开放阅读框为1 479 bp,编码492个氨基酸,推测编码蛋白质的分子量为56.7 kD,等电点为6.84。基因序列比对发现,HcCAT1与多种植物过氧化氢酶基因具有较高的同源性。半定量RT-PCR结果表明,HcCAT1基因受盐胁迫而上调表达。将构建的重组质粒pET32a-HcCAT1转化大肠杆菌BL21(DE3),以IPTG诱导重组蛋白His-HcCAT1的表达;SDS-PAGE和Western印迹检测显示,重组蛋白的分子量大小为77.7 kD,其大小与推测的大小一致;在低温诱导下以可溶性形式表达,且表现出一定的过氧化氢酶活性。盐胁迫实验结果显示,在添加400 mmol/L NaCl、400 mmol/L KCl以及300 mmol/L甘露醇的LB培养基中,重组质粒转化菌的生长情况和生长速率明显优于对照,表明HcCAT1可明显提高大肠杆菌的耐盐性。该研究结果将有助于从抗氧化角度认识盐生植物盐穗木的耐盐分子机理。     

汶川地震对两栖动物栖息地的影响

2008年5月汶川地震对两栖动物栖息地造成了巨大的影响。采用卫星遥感照片评估了汶川地震后3种两栖动物栖息地震损状况,结果表明:(1)15.2%的两栖动物的适宜栖息地遭到了地震的破坏;(2)震损栖息地纬向分布于31°～32°N之间,震区的南部和中部;(3)被破坏的栖息地垂直分布于2000m以下的中低海拔区段。汶川地震及次生灾害使两栖动物的生存和发展面临着极严重风险。     

猴头菌多糖不同脱色方法的研究

为选择最适于猴头菌多糖的脱色方法,本论文先比较了活性炭吸附法、化学脱色法、大孔树脂法等三种常用的脱色方法对猴头菌多糖的脱色效果及脱色前后免疫活性的变化,发现大孔树脂法更适合于猴头菌多糖的脱色,接着对十种不同类型的大孔树脂进行了筛选,通过脱色前后脱色率、多糖保留率及体外免疫活性的比较,最后发现大孔弱碱性阴离子树脂D315最适合用于猴头菌粗多糖的脱色.     

Supplementation with branched-chain amino acids to a low-protein diet regulates intestinal expression of amino acid and peptide transporters in weanling pigs

This study determined the effects of dietary branched-chain amino acids (AA) (BCAA) on growth performance, expression of jejunal AA and peptide transporters, and the colonic microflora of weanling piglets fed a low-protein (LP) diet. One hundred and eight Large White × Landrace × Duroc piglets (weaned at 28 days of age) were fed a normal protein diet (NP, 20.9 % crude protein), an LP diet (LP, 17.1 % crude protein), or an LP diet supplemented with BCAA (LP + BCAA, 17.9 % crude protein) for 14 days. Dietary protein restriction reduced piglet growth performance and small-intestinal villous height, which were restored by BCAA supplementation to the LP diet to values for the NP diet. Serum concentrations of BCAA were reduced in piglets fed the LP diet while those in piglets fed the LP + BCAA diet were similar to values for the NP group. mRNA levels for Na⁺-neutral AA exchanger-2, cationic AA transporter-1, b^0,+ AA transporter, and 4F2 heavy chain were more abundant in piglets fed the LP + BCAA diet than the LP diet. However, mRNA and protein levels for peptide transporter-1 were lower in piglets fed the LP + BCAA diet as compared to the LP diet. The colonic microflora did not differ among the three groups of pigs. In conclusion, growth performance, intestinal development, and intestinal expression of AA transporters in weanling piglets are enhanced by BCAA supplementation to LP diets. Our findings provide a new molecular basis for further understanding of BCAA as functional AA in animal nutrition.     

Extraction of crude polysaccharides from Duchesnea indica (Andrews) Focke: optimization by response surface methodology

A full set of optimization procedure was applied to the extraction of anti-viral polysaccharides from Duchesnea indica (Andrews) Focke. By Plackett–Burman factorial design, three parameters (extraction time, extraction temperature, and ratio of water to raw material) were identified as significant to the extraction yield. However, no significant parameters had been identified for antiviral activity. A three-level-three-factor Box–Behnken factorial design was then employed to further optimize the extraction condition. The experimental data were fitted to a second-order polynomial equation using multiple regression analysis and also examined using appropriate statistical methods. This led to the construction of a response surface indicating the optimal values for each parameter and response studied. Concerning the extraction yield, an extraction at 98.51?ºC for 6.16 h with a ratio of water to raw material of 30.94 mL/g was found to be optimal. Under the optimized conditions, the experimental yield was 6.430 ± 0.078%, which was well matched with the predicted yield of 6.509%.     

Proteomic analysis of mismatch repair-mediated alkylating agent-induced DNA damage response

Background

Mediating DNA damage-induced apoptosis is an important genome-maintenance function of the mismatch repair (MMR) system. Defects in MMR not only cause carcinogenesis, but also render cancer cells highly resistant to chemotherapeutics, including alkylating agents. To understand the mechanisms of MMR-mediated apoptosis and MMR-deficiency-caused drug resistance, we analyze a model alkylating agent (N-methyl-N’-nitro-N-nitrosoguanidine, MNNG)-induced changes in protein phosphorylation and abundance in two cell lines, the MMR-proficient TK6 and its derivative MMR-deficient MT1.

Results

Under an experimental condition that MNNG-induced apoptosis was only observed in MutSα-proficient (TK6), but not in MutSα-deficient (MT1) cells, quantitative analysis of the proteomic data revealed differential expression and phosphorylation of numerous individual proteins and clusters of protein kinase substrates, as well differential activation of response pathways/networks in MNNG-treated TK6 and MT1 cells. Many alterations in TK6 cells are in favor of turning on the apoptotic machinery, while many of those in MT1 cells are to promote cell proliferation and anti-apoptosis.

Conclusions

Our work provides novel molecular insights into the mechanism of MMR-mediated DNA damage-induced apoptosis.

     

Atomic force microscopy imaging of live mammalian cells

Atomic force microscopy (AFM) was used to examine the morphology of live mammalian adherent and suspended cells. Time-lapse AFM was used to record the locomotion dynamics of MCF-7 and Neuro-2a cells. When a MCF-7 cell retracted, many small sawtooth-like filopodia formed and reorganized, and the thickness of cellular lamellipodium increased as the retraction progressed. In elongated Neuro-2a cells, the cytoskeleton reorganized from an irregular to a parallel, linear morphology. Suspended mammalian cells were immobilized by method combining polydimethylsiloxane-fabricated wells with poly-L-lysine electrostatic adsorption. In this way, the morphology of a single live lymphoma cell was imaged by AFM. The experimental results can improve our understanding of cell locomotion and may lead to improved immobilization strategies.     

Newly discovered insect RNA viruses in China

Insects are a group of arthropods and the largest group of animals on Earth,with over one million species described to date.Like other life forms,insects suffer from viruses that cause disease and death.Viruses that are pathogenic to beneficial insects cause dramatic economic losses on agriculture.In contrast,viruses that are pathogenic to insect pests can be exploited as attractive biological control agents.All of these factors have led to an explosion in the amount of research into insect viruses in recent years,generating impressive quantities of information on the molecular and cellular biology of these viruses.Due to the wide variety of insect viruses,a better understanding of these viruses will expand our overall knowledge of their virology.Here,we review studies of several newly discovered RNA insect viruses in China.