Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane

Methyl coenzyme-M reductase A (mcrA) clone libraries were generated from microbial DNA extracted from the rumen of cattle fed a roughage diet with and without supplementation of the antimethanogenic compound bromochloromethane. Bromochloromethane reduced total methane emissions by c. 30%, with a resultant increase in propionate and branched chain fatty acids. The mcrA clone libraries revealed that Methanobrevibacter spp. were the dominant species identified. A decrease in the incidence of Methanobrevibacter spp. from the clone library generated from bromochloromethane treatment was observed. In addition, a more diverse methanogenic population with representatives from Methanococcales, Methanomicrobiales and Methanosacinales orders was observed for the bromochloromethane library. Sequence data generated from these libraries aided in the design of an mcrA-targeted quantitative PCR (qPCR) assay. The reduction in methane production by bromochloromethane was associated with an average decrease of 34% in the number of methanogenic Archaea when monitored with this qPCR assay. Dissociation curve analysis of mcrA amplicons showed a clear difference in melting temperatures for Methanobrevibacter spp. (80-82 degrees C) and all other methanongens (84-86 degrees C). A decrease in the intensity of the Methanobrevibacter spp. specific peak and an increase for the other peak in the bromochloromethane-treated animals corresponded with the changes within the clone libraries.  

Quantitative PCR analysis of selected Aspergillus, Penicillium and Paecilomyces species

A total of 65 quantitative PCR (QPCR) assays, incorporating fluorigenic 5' nuclease (TaqMan) chemistry and directed at the nuclear ribosomal RNA operon, internal transcribed spacer regions (ITS1 or ITS2) was developed and tested for the detection of selected Aspergillus, Penicillium and Paecilomyces species. The assays varied in specificity from species or subspecies to closely related species groups, subject to the amount of nucleotide sequence variation in the different organisms. A generic assay for all target species of Aspergillus, Penicillium and Paecilomyces was also developed and tested. Using a previously reported DNA extraction method, estimated conidia detection limits for target species ranged from less than one to several hundred per sample for the different assays. Conidia detection limits for non-target species were at least 1,000 fold higher in nearly all instances. The assays were used to analyze ten HVAC dust samples from different sources around the US. Total quantities of Aspergillus, Penicillium and Paecilomyces conidia in the samples, determined by the generic assay and the summed totals from the specific assays, were in general agreement, suggesting that all of the numerically dominant species in the samples were accounted for by the specific assays. QPCR analyses of these samples after spiking them with selected target organisms indicated that the enumeration results were within approximately a one-half log range of the expected values 95% of the time. Evidence is provided that the commonly used practices of enumerating Aspergillus and Penicillium as a single group or only by genus can be misleading in understanding the indoor populations of these organisms and their potential health risks.  

基于PCR技术的miRNA定量检测方法

microRNA(miRNA)是一类广泛存在于真核生物中,不编码蛋白质的短序列RNA,它广泛参与真核生物的生长发育、新陈代谢和应激反应等生命活动。但绝大多数miRNA的生物学功能还不清楚,通过灵敏的定量检测方法,了解miRNA在不同组织部位的时空表达,是探究其功能的重要环节。现着重介绍了2类7种基于PCR技术的miRNA定量检测方法的基本原理和实验流程,并分析了这些定量检测技术间的异同和适用范围。  

Biodegradation of naphthalene by enriched marine denitrifying bacteria

Numerous studies have been investigated on the PAHs biodegradation in aerobic and anaerobic environments; however, the biodegradation of PAHs under anoxic conditions, especially denitrifying conditions, has drawn less attention. In this study, four series of batch experiments were conducted to investigate the effect of temperature, pH, naphthalene concentration and nitrate concentration on the naphthalene degradation under denitrification condition. Our results showed that the degradation of naphthalene was most favorable at pH 7 and 25 °C. Results also indicated that 30 mg/l naphthalene inhibited the biodegradation and the removal efficiency was only 20.2%. Significant degradation (91.7% and 96.3%) of naphthalene occurred when nitrate concentrations were 1.0 and 5.0 mM. Moreover, the maximum degradation rates were 0.13 and 0.18 mg-NAP/(l h) depending on the concentration of nitrate. Based on 16S rDNA analysis, the denitrifying enriched culture was mainly composed of ??-Proteobacteria (19 clones out of a total of 23 clones) and Actinobacteria (4 clones). Using a primer set specific for naphthalene degrading functional gene nahAc, two operational taxonomy units were obtained in the clone library of nahAc. Both of them were closely related to nahAc genes of known species of Pseudomonas. Quantitative polymerase chain reaction (qPCR) was employed to quantify the change of naphthalene-degrading population during the degradation of naphthalene using nahAc gene as the biomarker. The maximum degradation rate and removal efficiency were strongly correlated with nahAc gene copy number, with R² of 0.69 and 0.79, respectively.  

Quantification of class 1 integron abundance in natural environments using real-time quantitative PCR

Integrons are bacterial genetic elements capable of capturing and expressing potentially adaptive genetic material. Class 1 integrons constitute the most intensely studied group of these elements to date, mainly due to their well-established role in the acquisition and dissemination of antibiotic resistance genes in clinical environments. However, virtually nothing is known about the distribution or abundance of class 1 integrons outside of the clinical context. Here we develop a SYBR Green-based real-time quantitative PCR assay capable of quantifying the abundance of class 1 integrons in environmental samples. It was shown that the abundance of the intI1 gene in creek sediment correlates with ecological condition, implying that class 1 integrons provide selective advantages relevant to environmental pressures other than the use of antibiotics. By comparing the quantities of intI1 and 16S rRNA gene in each sample, it was demonstrated that approximately 2.7% of cells potentially harbour a class 1 integron. These findings suggest that class 1 integrons are widespread in natural environments removed from clinical settings and occur in a broader range of host organisms than had previously been assumed on the basis of culture-dependent estimates.  

Spatial and temporal diversity of microcystins and microcystin-producing genotypes in Oneida Lake, NY

Oneida Lake is a shallow, eutrophic lake with a well-established cyanobacterial population with reported toxic blooms containing hepatotoxic microcystins (MC). Peak bloom events from the summers of 2002 and 2003 were analyzed to determine the principal cyanobacterial genera containing microcystin synthetase (mcy) genes. Sequence analysis of a partial mcyA amplicon targeting Microcystis, Anabaena and Planktothrix sp. indicated that Microcystis sp. was the dominant mcy genotype. This Microcystis clade was split into two distinct sub-clades. Bloom events contained members of both sub-clades with the higher MC concentrations found when both sub-clades were present in near equal proportions. The proportion of Microcystis containing the mcyD gene ranged from 0 to 37% of the total Microcystis population as determined by quantitative PCR (qPCR). The total concentration of Microcystis containing mcyD genes was linearly related to the concentration of MCs (r² = 0.63). The relationship between mcy genotype and physiochemical variables was examined to determine the factor(s) controlling the periodicity in MC production in Oneida Lake. Multivariate statistical analyses, used to correlate the continuous-response variables, revealed a strong relationship between chlorophyll a, MCs and total Microcystis.  

飞蝗可溶型海藻糖酶基因的序列分析及mRNA表达特性

海藻糖酶是海藻糖代谢过程中的一个关键酶,在昆虫发育和能量调节中具有重要作用,为进一步探讨海藻糖酶基因的功能,本文分析了飞蝗Locusta migratoria一可溶型海藻糖酶基因的氨基酸序列并对其mRNA表达特性进行了研究.结果表明:该海藻糖酶(TRE,GenBank登录号:FJ795020)不含有跨膜结构.系统进化树分析结果显示,该酶与大豆蚜Aphis glycines、豌豆蚜Acyrthosiphon pisum、褐飞虱Nilaparvata lugens和灰飞虱Laodelphax striatella可溶型海藻糖酶具有较近的亲缘关系,因此我们将该酶的基因命名为LmTre-1.对该基因在不同组织和发育时期表达量的荧光定量PCR分析表明:LmTre-1在卵发育前期、中期的表达量都很低,卵发育后期表达量显著提高；LmTre-1在5龄若虫和成虫被检测的组织部位中均有表达,在体壁中的表达量最高,其次是在脂肪体、肌肉、气管、精巢及卵巢中；5龄飞蝗刚蜕皮后LmTre-1在体壁中的表达量较高,随着生长发育其表达量逐渐降低；LmTre-1在成虫发育期体壁中稳定高表达.LmTre-1的mRNA表达特性与几丁质合成酶1基因非常相似,据此推测该基因可能与体壁几丁质的合成相关.本研究为深入探讨该基因的生理功能提供了重要的基础数据,并为以海藻糖酶为杀虫靶标的农药筛选奠定实验基础.