High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling

Human individuals differ from one another at only ~0.1% of nucleotide positions, but these single nucleotide differences account for most heritable phenotypic variation. Large-scale efforts to discover and genotype human variation have been limited to common polymorphisms. However, these efforts overlook rare nucleotide changes that may contribute to phenotypic diversity and genetic disorders, including cancer. Thus, there is an increasing need for high-throughput methods to robustly detect rare nucleotide differences. Toward this end, we have adapted the mismatch discovery method known as Ecotilling for the discovery of human single nucleotide polymorphisms. To increase throughput and reduce costs, we developed a universal primer strategy and implemented algorithms for automated band detection. Ecotilling was validated by screening 90 human DNA samples for nucleotide changes in 5 gene targets and by comparing results to public resequencing data. To increase throughput for discovery of rare alleles, we pooled samples 8-fold and found Ecotilling to be efficient relative to resequencing, with a false negative rate of 5% and a false discovery rate of 4%. We identified 28 new rare alleles, including some that are predicted to damage protein function. The detection of rare damaging mutations has implications for models of human disease.     

Distribution and Identification of an Invasive Gracilaria Species that is Hampering Commercial Fishing Operations in Southeastern North Carolina, USA

A newly abundant Gracilaria species in the sounds of southeastern North Carolina has become a problem for commercial fishing and industries drawing water from the lower Cape Fear River. DNA sequence analyses have shown that this species is Gracilaria vermiculophylla, a taxon originally described from East Asia. Surveys for G. vermiculophylla have shown that it has a discontinuous distribution in the sounds of southeastern North Carolina, and suggest that it is spreading. Gracilaria vermiculophylla meets 6 of the 10 criteria used to help identify invasive species in that it has only recently appeared in southeastern North Carolina; is associated with human mechanisms of dispersal; has a restricted distribution; has disjunct populations in isolated oceans; no means of active dispersal, and an exotic evolutionary origin. The species may also meet two additional criteria as its local range is believed to be expanding, and it is filling a previously unoccupied seasonal niche. These factors taken together strongly suggest that G. vermiculophylla is an invasive species in southeastern North Carolina.     

转抗虫基因三倍体毛白杨植株体内农杆菌残存与逃逸

用部分改造的BtCry1Ac基因与慈菇蛋白酶抑制剂（APLA）基因构建的双抗虫基因表达载体,通过农杆菌介导法对三倍体毛白杨进行了转化,对转化后植株体内残存农杆菌在继代培养和移栽过程中进行了跟踪检测。结果表明：通过对转化再生植株的分子生物学检测,42个株系中,33个株系为阳性,阳性率达到80％;用Bt毒蛋白抗血清进行ELSA检测结果表明,7个转基因株系都有Bt杀虫蛋白表达;基因转化后,可采用附加50mg／L卡那霉素,300mg／L羧苄青霉素的筛选培养基消除细菌并进行抗性芽筛选。对28个转基因株系叶片、茎段和根段在含有卡那霉素50mg／LYEB培养基上进行细菌培养,通过在T-DNA区、质粒Vir区和农杆菌基因组设计引物,进行PCR检测,证明有3个株系（33、37、5号）检测到残存工程农杆菌,并在组培瓶中存活24个月。将带菌的3个株系组培苗移栽到花盆中,室内培养1个月后,在33号株系根际土壤中检测到了目的农杆菌。     

Was the "ABC" approach (abstinence, being faithful, using condoms) responsible for Uganda's decline in HIV?

BACKGROUND TO THE DEBATE: Uganda is one of the few African countries where rates of HIV infection have fallen, from about 15 percent in the early 1990s to about five percent in 2001. At the end of 2005, UNAIDS estimated that 6.7 percent of adults were infected with the virus. The reasons behind Uganda's success have been intensely studied in the hope that other countries can emulate the strategies that worked. Some researchers credit the success to the Ugandan government's promotion of "ABC behaviors"--particularly abstinence and fidelity. Uganda receives funds from the United States President's Emergency Plan for AIDS Relief, which promotes the ABC approach with a focus on abstinence-driven public health campaigns. Other researchers question whether the ABC approach was really responsible for the decline in HIV infection. Critics of the ABC approach also argue that by emphasizing abstinence over condom use, the approach leaves women at risk of infection, because in many parts of the world women are not empowered to insist on abstinence or fidelity.     

Quantitative analysis of s-adenosylmethionine and s-adenosylhomocysteine in neurulation-stage mouse embryos by liquid chromatography tandem mass spectrometry

The potential importance of the methylation cycle during embryonic development necessitates the establishment of methodology to detect alterations in the relative abundance of s-adenosylmethionine (SAM) and s-adenosylhomocysteine (SAH) in an embryonic experimental system. We have developed a precise and sensitive method for measurement of SAM and SAH based on liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) in single neurulation-stage mouse embryos. Use of a penta-fluorinated high-performance liquid chromatography (HPLC) stationary phase gave enhanced sensitivity due to optimal ionisation in organic mobile phase and increased retention time compared to standard reversed-phase separation. Calibration curves suitable for the analysis of neurulation-stage mouse embryos (SAM 0.02-25.0microM, SAH 0.01-10.0microM) were linear (r(2)>0.997) with limits of detection for SAM and SAH of 10 and 2.5nmol/L, respectively.     

Preliminary functional characterization, cloning and primary sequence of Fastuosain, a cysteine peptidase isolated from fruits of Bromelia fastuosa

The present work reports the characterization of Fastuosain, a novel cysteine protease of 25kDa, purified from the unripe fruits of Bromelia fastuosa, a wild South American Bromeliaceae. Proteolytic activity, measured using casein and synthetic substrates, was dependent on the presence of thiol reagents, having maximum activity at pH 7.0. The present work reports cDNA cloning of Fastuosain; cDNA was amplified by PCR using specific primers. The product was 1096pb long. Mature fastuosain has 217 residues, and with the proregion has a total length of 324 residues. Its primary sequence showed high homology with ananain(74%), stem bromelain (66%) and papain (44%).     

A novel approach to DNA damage assessments: measurement of the thymine glycol lesion

A different approach to the measurement of DNA damage has been developed based on the fact that many lesions can be excised from DNA in the form of modified dinucleoside monophosphates. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is used in conjunction with isotopically labeled internal standards to quantify the lesion. The method has several advantages, including high sensitivity for the detection of dinucleoside monophosphates. The method was applied to the measurement of the 5,6-dihydroxy-5,6-dihydrothymine (thymine glycol) lesion in the DNA of mouse fibroblast cells exposed in culture to various treatments including ionizing radiation, UVC light and buthionine sulfoximine (BSO), an inhibitor of glutathione synthesis. The application of the method to the measurement of other DNA lesions is discussed.     

多位点数目可变串联重复序列在结核分枝杆菌分子流行病学中的应用进展

结核分枝杆菌基因分型VNTR-MIRU方法是近年来结核病分子流行病学研究的热点,已广泛应用于TB流行病学研究的各个领域,包括调查爆发流行,追踪传染源,调查优势菌株以及传播机制等方面.VNTR-MIRU分型方法简单快速,是一种有效的结核分枝杆菌基因型分型方法.     

2'-羟基二氢黄酮诱导白血病HL-60细胞凋亡过程中抗氧化酶活性的变化

目的:观察2'-羟基二氢黄酮诱导白血病细胞HL-60凋亡过程中胞内抗氧化酶活性的变化,并探讨其抗肿瘤作用机制.方法:采用CASY-TT亚流式细胞术测定2′-羟基二氢黄酮对HL-60细胞存活率的影响;Annexin V/PI双染流式细胞仪检测分析细胞凋亡变化;化学比色法测定2′-羟基二氢黄酮作用后,HL-60细胞胞内抗氧化酶SOD、CAT、GSH-Px的活性变化.结果:2′-羟基二氢黄酮显著降低HL-60细胞存活率,其作用呈剂量和时间依赖性;凋亡分析结果显示,20 μM的2′-羟基二氢黄酮作用HL-60细胞后,细胞凋亡率逐渐升高,并在12 h后显著高于作用前水平;酶活性检测表明,20 μM 2′-羟基二氢黄酮作用后,HL-60细胞胞内抗氧化酶SOD、CAT、GSH-Px活性均显著降低.脂质过氧化产物MDA含量显著升高.结论:2′-羟基二氢黄酮显著降低白血病HL-60细胞存活率并诱导细胞凋亡,其中伴随着胞内抗氧化酶活性的显著降低.     

Visualizing the Disassembly of S. cerevisiae Rad51 Nucleoprotein Filaments

Rad51 is the core component of the eukaryotic homologous recombination machinery and assembles into elongated nucleoprotein filaments on DNA. We have used total internal reflection fluorescence microscopy and a DNA curtain assay to investigate the dynamics of individual Saccharomyces cerevisiae Rad51 nucleoprotein filaments. For these experiments the DNA molecules were end-labeled with single fluorescent semiconducting nanocrystals. The assembly and disassembly of the Rad51 nucleoprotein filaments were visualized by tracking the location of the labeled DNA end in real time. Using this approach, we have analyzed yeast Rad51 under a variety of different reaction conditions to assess parameters that impact the stability of the nucleoprotein filament. We show that Rad51 readily dissociates from DNA in the presence of ADP or in the absence of nucleotide cofactor, but that free ATP in solution confers a fivefold increase in the stability of the nucleoprotein filaments. We also probe how protein dissociation is coupled to ATP binding and hydrolysis by examining the effects of ATP concentration, and by the use of the nonhydrolyzable ATP analogue adenosine 5'-(beta, gamma-imido) triphosphate and ATPase active-site mutants. Finally, we demonstrate that the Rad51 gain-of-function mutant I345T dissociates from DNA with kinetics nearly identical to that of wild-type Rad51, but assembles 30% more rapidly. Together, these results provide a framework for studying the biochemical behaviors of S. cerevisiae Rad51 nucleoprotein filaments at the single-molecule level.