Detection of Verotoxigenic Escherichia coli by Magnetic Capture-Hybridization PCR

Magnetic capture-hybridization PCR (MCH-PCR) was used for the detection of 36 verotoxigenic (verotoxin [VT]-producing) Escherichia coli (VTEC), 5 VTEC reference, and 13 non-VTEC control cultures. The detection system employs biotin-labeled probes to capture the DNA segments that contain specific regions of the genes for VT1 and VT2 by DNA-DNA hybridization. The hybrids formed were isolated by streptavidin-coated magnetic beads which were collected by a magnetic particle separator and, subsequently, amplified directly by conventional PCR. The detection system was found to be specific for VTEC: no amplification was obtained from non-VTEC controls, whereas VTEC isolates tested positive for one or two specific PCR products. With 5, 7, or 10 h of enrichment, the limits of detection were 10³, 10², and 10⁰ CFU/ml, respectively, by agarose gel electrophoresis. Southern hybridization did not seem to improve the limit of the detection. When applied to food, MCH-PCR was capable of detecting 10⁰ CFU of VTEC per g of ground beef with 15 h of nonselective enrichment. The results of MCH-PCR for pure cultures of VT1- and/or VT2-producing E. coli cells were in total agreement with toxin production as measured by a VT enzyme-linked immunosorbent assay.     

Polyamidoamine dendrimers inhibit binding of Tat peptide to TAR RNA

The binding of polyamidoamine (PAMAM) dendrimer or Tat peptide to trans-acting responsive element (TAR) RNA has been studied using microgravimetric quartz crystal microbalance (QCM). Experimental results showed that PAMAM dendrimer could form complexes with TAR RNA. Especially, PAMAM dendrimer could disrupt the interaction of Tat peptide with TAR RNA, which is essential for HIV-1 virus replication, suggesting that QCM is a powerful tool for studying the binding processes of Tat peptide-TAR RNA and drug-TAR RNA and has great significance for the design of new drugs. An equation to measure the binding ability between TAR RNA and other species has been proposed.     

粪便宏基因组来源低分子量碱性β-半乳糖苷酶的异源表达及酶学性质

【背景】β-半乳糖苷酶在食品加工、临床医疗及基因工程等领域有重要的应用价值,开发酶活性高、热稳定性强的β-半乳糖苷酶已成为研究热点。【目的】从西黑冠长臂猿（Nomascus concolor）粪便微生物宏基因组中挖掘新型β-半乳糖苷酶并进行酶学性质研究。【方法】以西黑冠长臂猿粪便微生物宏基因组DNA为模板扩增β-半乳糖苷酶基因GalNC1-8,构建重组表达质粒pEASY-E2/GalNC1-8,转化至大肠杆菌（Escherichia coli） BL21（DE3）异源表达,研究其酶学性质。【结果】获得GH35家族碱性β-半乳糖苷酶GalNC1-8,其分子量为28.18 kDa,最适温度为50°C,最适pH为8.0。将该酶在30-50°C下处理1 h,剩余酶活仍保持在80%以上;pH 7.0-9.0下处理1 h,剩余酶活大于54%。在含乙醇的反应体系中,其酶活性几乎不受影响;β-巯基乙醇、丙三醇、甲醇、Na⁺、K⁺和Li⁺对其酶活性有促进作用。在0.5-3.5 mol/L NaCl下处理1 h后,仍保留50%以上的酶活性。...     

A Germline Variant on Chromosome 4q31.1 Associates with Susceptibility to Developing Colon Cancer Metastasis

We tested for germline variants showing association to colon cancer metastasis using a genome-wide association study that compared Ashkenazi Jewish individuals with stage IV metastatic colon cancers versus those with stage I or II non-metastatic colon cancers. In a two-stage study design, we demonstrated significant association to developing metastatic disease for rs60745952, that in Ashkenazi discovery and validation cohorts, respectively, showed an odds ratio (OR) = 2.3 (P = 2.73E-06) and OR = 1.89 (P = 8.05E-04) (exceeding validation threshold of 0.0044). Significant association to metastatic colon cancer was further confirmed by a meta-analysis of rs60745952 in these datasets plus an additional Ashkenazi validation cohort (OR = 1.92; 95% CI: 1.28–2.87), and by a permutation test that demonstrated a significantly longer haplotype surrounding rs60745952 in the stage IV samples. rs60745952, located in an intergenic region on chromosome 4q31.1, and not previously associated with cancer, is, thus, a germline genetic marker for susceptibility to developing colon cancer metastases among Ashkenazi Jews.     

The H1 and H2 polypeptides associate to form the asialoglycoprotein receptor in human hepatoma cells

Antibody-induced degradation and chemical cross-linking experiments have been carried out to assess the nature of the interaction between the two asialoglycoprotein-receptor polypeptides, H1 and H2, synthesized in HepG2 cells. Incubation of HepG2 cell monolayers with anti-H1 antibody caused a specific and equal loss of both H1 and H2 polypeptides. The same result was obtained with anti-H2 antibody. Control serum did not affect the level of H1 or H2 not did anti-H1 or anti-H2 antibodies affect the level of the transferrin receptor. The chemical cross-linking reagent, difluorodinitrobenzene, has been used to demonstrate that H1 can be cross-linked to H2 in HepG2 cell microsomal membranes. Dimer and trimer species with apparent molecular masses of 93 and 148 kD, respectively, were readily observed upon chemical cross-linking and some dimers and trimers were immunoreactive with both anti-H1 and anti-H2 antibodies. The putative trimer, possibly two H1 and one H2 molecules, is a minimum estimate of the true size of the asialoglycoprotein receptor in intact HepG2 cell, and it is possible that larger hetero-oligomeric forms of the receptor exist. The results of both types of experiments indicate that H1 and H2 form an oligomeric complex in HepG2 cells and thus, both polypeptides constitute the human asialoglycoprotein receptor.     

Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions

Background

Colorectal cancer is the second leading cause of cancer death in the United States, with over 50,000 deaths estimated in 2014. Molecular profiling for somatic mutations that predict absence of response to anti-EGFR therapy has become standard practice in the treatment of metastatic colorectal cancer; however, the quantity and type of tissue available for testing is frequently limited. Further, the degree to which the primary tumor is a faithful representation of metastatic disease has been questioned. As next-generation sequencing technology becomes more widely available for clinical use and additional molecularly targeted agents are considered as treatment options in colorectal cancer, it is important to characterize the extent of tumor heterogeneity between primary and metastatic tumors.

Results

We performed deep coverage, targeted next-generation sequencing of 230 key cancer-associated genes for 69 matched primary and metastatic tumors and normal tissue. Mutation profiles were 100% concordant for KRAS, NRAS, and BRAF, and were highly concordant for recurrent alterations in colorectal cancer. Additionally, whole genome sequencing of four patient trios did not reveal any additional site-specific targetable alterations.

Conclusions

Colorectal cancer primary tumors and metastases exhibit high genomic concordance. As current clinical practices in colorectal cancer revolve around KRAS, NRAS, and BRAF mutation status, diagnostic sequencing of either primary or metastatic tissue as available is acceptable for most patients. Additionally, consistency between targeted sequencing and whole genome sequencing results suggests that targeted sequencing may be a suitable strategy for clinical diagnostic applications.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0454-7) contains supplementary material, which is available to authorized users.     

Fine Particulate Matter and Incident Cognitive Impairment in the REasons for Geographic and Racial Differences in Stroke (REGARDS) Cohort

Studies of the effect of air pollution on cognitive health are often limited to populations living near cities that have air monitoring stations. Little is known about whether the estimates from such studies can be generalized to the U.S. population, or whether the relationship differs between urban and rural areas. To address these questions, we used a satellite-derived estimate of fine particulate matter (PM_2.5) concentration to determine whether PM_2.5 was associated with incident cognitive impairment in a geographically diverse, biracial US cohort of men and women (n = 20,150). A 1-year mean baseline PM_2.5 concentration was estimated for each participant, and cognitive status at the most recent follow-up was assessed over the telephone using the Six-Item Screener (SIS) in a subsample that was cognitively intact at baseline. Logistic regression was used to determine whether PM_2.5 was related to the odds of incident cognitive impairment. A 10 µg/m³ increase in PM_2.5 concentration was not reliably associated with an increased odds of incident impairment, after adjusting for temperature, season, incident stroke, and length of follow-up [OR (95% CI): 1.26 (0.97, 1.64)]. The odds ratio was attenuated towards 1 after adding demographic covariates, behavioral factors, and known comorbidities of cognitive impairment. A 10 µg/m³ increase in PM_2.5 concentration was slightly associated with incident impairment in urban areas (1.40 [1.06–1.85]), but this relationship was also attenuated after including additional covariates in the model. Evidence is lacking that the effect of PM_2.5 on incident cognitive impairment is robust in a heterogeneous US cohort, even in urban areas.     

浙江省红楠生境地群落数量分类和环境解析

为探讨群落结构与环境因子对红楠Machilus thunbergii在浙江省分布及发展的影响,采用双向指示种分类(TWINSPAN)、典范对应分析(CCA)并结合种间联结分析,对浙江省172个红楠生境地群落进行数量分类排序与环境解析。结果表明:(1)TWINSPAN将172个样地群落分成8个群落类型,红楠在群落中为优势种或主要伴生种。群落类型的不同是影响红楠生长及更新的重要原因。(2)海拔高度及坡度是决定红楠分布及发展的主导环境因子。红楠作为优势种的生境地主要特征为海拔900m以下、坡度35°以下。(3)甜槠(Castanopsis eyrei)、青冈(Cyclobalanopsis glauca)、木荷(Schima superba)为群落中的稳定优势种,种间联结结果显示与红楠均为显著正关联。     

西黑冠长臂猿粪便微生物宏基因组来源的高比活α-l-阿拉伯呋喃糖苷酶的重组表达及酶学性质

【背景】α-l-阿拉伯呋喃糖苷酶是一类重要的半纤维素酶,能协同其他半纤维素酶降解木聚糖,在食品、医药、生物质能转化中具有应用价值。【目的】挖掘新型α-l-阿拉伯呋喃糖苷酶基因,对其进行异源表达、纯化并研究其酶学性质。【方法】从西黑冠长臂猿粪便微生物宏基因组中扩增α-l-阿拉伯呋喃糖苷酶基因,在大肠杆菌BL21(DE3)中进行异源表达,并进行酶学性质研究。【结果】从粪便微生物宏基因组中扩增得到α-l-阿拉伯呋喃糖苷酶基因AbfNC2b_38,并获得重组α-l-阿拉伯呋喃糖苷酶AbfNC2b_38,其分子量为57.04 kDa。AbfNC2b_38的最适作用条件为55 ℃、pH 6.0,K_m和V_max分别为(6.48±0.73) mmol/L和(1 248.0±114.6) U/mg,与其他宏基因组来源的α-l-阿拉伯呋喃糖苷酶相比具有最高比活300.81 U/mg。AbfNC2b_38具有较好的乙醇和NaCl耐受性,30%乙醇下耐受1 h保持68%的活性;25% NaCl中耐受1 h,相对酶活仍保持在约70%。与木聚糖酶协同降解山毛榉木聚糖时,协同率最高为1.21。【结论】从西黑冠长臂猿粪便微生物宏基因组中获得新型α-l-阿拉伯呋喃糖苷酶基因AbfNC2b_38并成功异源表达。AbfNC2b_38具有较好的乙醇和NaCl耐受性,能与木聚糖酶协同作用提高木聚糖的降解效率,在饲料、食品加工等领域具有潜在的应用价值。