RAPD技术在微生物生物多样鉴定中的应用

RAPD（随机放大多态性DNA）是1种新的DNA分子标记技术。与RFLp、AFLP及ARDRA相比，RAPD具有可在一次试验中同时观察到大量的DNA多态性片段，方法更具简单、敏感、花费少等优点。阐述了RAPD的原理方法，及目前在微生物分类鉴定研究中的应用，并分析了RAPD技术在共生固氮放线菌Frankia分类鉴定及系统发育研究中的应用前景。

镉胁迫对蚕豆幼苗基因组DNA多态性的影响

采用随机扩增多态性DNA(RAPD)技术检测镉(Cd)胁迫对蚕豆幼苗根尖DNA多态性的影响。结果表明,不同浓度(2·5、5和15mg·L-1)镉处理7d后,蚕豆幼苗根伸长及根系中可溶性蛋白质含量均受到了抑制。选用12条寡核苷酸引物(10bp)对蚕豆幼苗根尖细胞中基因组DNA进行RAPD扩增,其中有6个引物产生特异性PCR产物。对照组蚕豆幼苗根尖基因组DNA的RAPD图谱中可分辨出86条RAPD谱带,其分子量为200~2520bp。处理组与对照组RAPD图谱之间存在明显差异,且与镉浓度之间存在剂量-效应关系。这些结果表明,镉影响蚕豆幼苗根尖细胞中基因组模板的稳定性,故利用RAPD技术获得的DNA多态性变化可作为检测镉遗传毒性效应的生物标记物。

苔藓植物DNA提取方法研究

提取高质量的 DNA是对苔藓植物遗传多样性进行研究的基础。该文以苔藓植物为试材 ,用 5种方法 ,即快速提取法、改良 CTAB法、CTAB法、SDS法及高盐法 (第一种为自行设计 ,第二种是对原有方法的改进 )对苔藓植物 DNA提取方法进行了比较研究。结果表明 ,快速提取法和改良 CTAB法是 2种适合于苔藓植物 DNA提取的方法。这 2种方法提取的 DNA浓度和纯度均比较高 ,凝胶电泳显示无明显降解现象 ,适宜作为 PCR扩增的模板 ,并成功地进行了 RAPD扩增。

DNA分子标记技术在海带种质鉴定中的应用

本文在CTAB和SDS／K＋两种DAN提取方法基础上，综合与改进，建立了海带配子体DNA的提取和纯化方法。用此法得到了较高质量的海带配子体DNA，可有效地应用于海带分子标记的研究。采用RAPD，ISSR和AFLP三种DNA分子标记技术对海带配子体细胞系进行了种质鉴定和评价，结果表明：1）RAPD方法可以有效地应用于海带配子体细胞系的鉴定，用三个RAPD引物（OPC20，OPD20和OPD15）构建的DNA指纹图谱，不仅能将23个海带配子体细胞系区分开，而且能将每种海带的雌、雄配子体区分开。2）在没有其它海带配子体DNA分子标记背景资料的前提下，运用ISSR标记方法，辅证了RAPD方法的有效性及可靠性，排除了因原核生物的“污染”，所造成的RAPD标记方法的干扰，同时，也能辨别非海带配子体，这可以评价海带配子体保存的实际效果。3）AFLP分子标记结果表明，海带配子体细胞系具有高的多态性，这对海带具体性状进行连锁标记分析，可能是有效的方法。4）在RAPD标记的基础上，初步建立海带配子体SCAR标记，为海带分子标记辅助选种、育种打下基础。5）对3F、5F、12M三个实验材料，进一步用rDNA转录间隔区（ITS1）测序分析，与已知海带配子体ITS1的差别很大，说明不是海带配子体。综合上述，RAPD，ISSR和AFLP三种DNA分子标记技可以对海带种质资源进行鉴定、评估，为海带科学保种、选种提供依据。

High genetic diversity in field isolates of Trypanosoma theileri assessed by analysis of cathepsin L-like sequences disclosed multiple and new genotypes infecting cattle in Thailand

In this study, we describe the first survey in Thailand of Trypanosoma theileri, a widespread and prevalent parasite of cattle that is transmitted by tabanid flies. Investigation of 210 bovine blood samples of Thai cattle from six farms by hematocrit centrifuge technique (HCT) revealed 14 samples with trypanosomes morphologically compatible to T. theileri. Additional animals were positive for T. theileri by PCR based on the Cathepsin L-like sequence (TthCATL-PCR) despite negative by HCT, indicating cryptic infections. Results revealed a prevalence of 26 +/- 15% (95% CI) of T. theileri infection. Additionally, 12 samples positive for T. theileri were detected in cattle from other 11 farms. From a total of 30 blood samples positive by HCT and/or PCR from 17 farms, seven were characterized to evaluate the genetic polymorphism of T. theileri through sequence analysis of PCR-amplified CATL DNA sequences. All CATL sequences of T. theileri from Thai cattle clustered with sequences of the previously described phylogenetic lineages TthI and TthII, supporting only two major lineages of T. theileri in cattle around the world. However, 11 of the 29 CATL sequences analyzed showed to be different, disclosing an unexpectedly large polymorphic genetic repertoire, with multiple genotypes of T. theileri not previously described in other countries circulating in Thai cattle. (C) 2011 Elsevier B.V. All rights reserved.

Search for methylation-sensitive amplification polymorphisms in mutant figs

Fig (Ficus carica) breeding programs that use conventional approaches to develop new cultivars are rare, owing to limited genetic variability and the difficulty in obtaining plants via gamete fusion. Cytosine methylation in plants leads to gene repression, thereby affecting transcription without changing the DNA sequence. Previous studies using random amplification of polymorphic DNA and amplified fragment length polymorphism markers revealed no polymorphisms among select fig mutants that originated from gamma-irradiated buds. Therefore, we conducted methylation-sensitive amplified polymorphism analysis to verify the existence of variability due to epigenetic DNA methylation among these mutant selections compared to the main cultivar 'Roxo-de-Valinhos'. Samples of genomic DNA were double-digested with either HpaII (methylation sensitive) or MspI (methylation insensitive) and with EcoRI. Fourteen primer combinations were tested, and on an average, non-methylated CCGG, symmetrically methylated CmCGG, and hemimethylated hmCCGG sites accounted for 87.9, 10.1, and 2.0%, respectively. MSAP analysis was effective in detecting differentially methylated sites in the genomic DNA of fig mutants, and methylation may be responsible for the phenotypic variation between treatments. Further analyses such as polymorphic DNA sequencing are necessary to validate these differences, standardize the regions of methylation, and analyze reads using bioinformatic tools. © FUNPEC-RP.

Genetic structure of Aedes aegypti populations determined using pairwise comparisons

The biological characteristics of Aedes aegypti (Diptera, Culicidae), which is a vector of dengue and yellow fever, make this organism a good model for studying population structure and the events that may influence it under the effect of human activity. We assessed the genetic variability of five A. aegypti populations using RAPD-PCR technique and six primers. Four populations were from Brazil and one was from the USA. A total of 165 polymorphic DNA loci were generated. Considering the six primers and the five populations, the mean value of inter-population genetic diversity (Gst) was 0.277, which is considered high according to the Wright classification. However, pairwise comparisons of the populations gave variable Gst values ranging from 0.044 to 0.289. This variation followed the population's geographic distance to some extent but was also influenced by human activity. The lowest Gst values were obtained in the comparison of populations from cities with intensive commercial and medical contacts. These mosquito populations were previously classified as insecticide resistant, susceptible, or with decreased susceptibility; this parameter apparently had an effect on the Gst values obtained in the pairwise comparisons. ©FUNPEC-RP.

Tipagem molecular, perfis de sensibilidade e caracterização de transcritos diferencialmente expressos durante a infecção de Cryptococcus neoformans

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Characterization of immobilized biomass by amplified rDNA restriction analysis (ARDRA) in an anaerobic sequencing-batch biofilm reactor (ASBBR) for the treatment of industrial wastewater

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Gallus gallus domesticus are resistant to infection with Neospora caninum tachyzoites of the NC-1 strain

The aim of this study was to experimentally evaluate infection in Gallus gallus domesticus with Neospora caninum tachyzoites of the NC-1 strain. Experimental infection was conducted in 90-day-old chickens, embryonated eggs and bioassays in dogs. In the first experiment, poults were randomly divided into four groups. Groups I and II were provided feed with coccidiostat, whereas groups III and IV received feed without coccidiostat. When the poults from groups I and III reached 90 days of age, they received a subcutaneous inoculation of N. caninum. Once the hens entered their egg-laying period, during the following 30 days, the eggs were collected, identified, weighed and placed in an incubator. On the 70th day after inoculation, all animals, including the chicks, were euthanized. Tissue samples from the adult poultry and chicks were collected for histopathology, immunohistochemistry (IHC) and PCR. Brain tissue and pectoral muscle samples from infected birds were fed to two dogs. Notably, the average weight of the group III eggs was lower than that of the group IV eggs (p <0.05). No changes consistent with infection in adult poultry or chicks were detected by histopathology or IHC; moreover, no amplified parasite DNA was detected in the birds'tissues or dogs'feces. No dog eliminated oocysts. In the second experiment, the embryonated chicken eggs were inoculated with 1 x 10(2) N. caninum tachyzoites, on the 10th day of incubation, and chicks born from these eggs were housed in boxes suitable for the species and received commercial feed and distilled water ad libitum. On the 30th day after infection (DAI), the poultry were euthanized, and their organs were processed as described in experiment I. The amplification of parasite DNA was observed in the spleen and pectoral muscles of one of the birds. The ingestion of bird tissues by dogs did not result in oocyst elimination. These results indicate that the parasite may have been eliminated by the host and that the use of tachyzoites to induce chronic disease might be a poor source for hens. (C) 2014 Elsevier B.V. All rights reserved.

Development and application of DNA techniques for validating and improving pinniped diet estimates

Polymerase chain reaction techniques were developed and applied to identify DNA from .40 species of prey contained in fecal (scat) soft-part matrix collected at terrestrial sites used by Steller sea lions (Eumetopias jubatus) in British Columbia and the eastern Aleutian Islands, Alaska. Sixty percent more fish and cephalopod prey were identified by morphological analyses of hard parts compared with DNA analysis of soft parts (hard parts identified higher relative proportions of Ammodytes sp., Cottidae, and certain Gadidae). DNA identified 213 prey occurrences, of which 75 (35%) were undetected by hard parts (mainly Salmonidae, Pleuronectidae, Elasmobranchii, and Cephalopoda), and thereby increased species occurrences by 22% overall and species richness in 44% of cases (when comparing 110 scats that amplified prey DNA). Prey composition was identical within only 20% of scats. Overall, diet composition derived from both identification techniques combined did not differ significantly from hard-part identification alone, suggesting that past scat-based diet studies have not missed major dietary components. However, significant differences in relative diet contributions across scats (as identified using the two techniques separately) reflect passage rate differences between hard and soft digesta material and highlight certain hypothesized limitations in conventional morphological-based methods (e.g., differences in resistance to digestion, hard part regurgitation, partial and secondary prey consumption), as well as potential technical issues (e.g., resolution of primer efficiency and sensitivity and scat subsampling protocols). DNA analysis of salmon occurrence (from scat soft-part matrix and 238 archived salmon hard parts) provided species-level taxonomic resolution that could not be obtained by morphological identification and showed that Steller sea lions were primarily consuming pink (Oncorhynchus gorbuscha) and chum (Oncorhynchus keta) salmon. Notably, DNA from Atlantic salmon (Salmo salar) that likely originated from a distant fish farm was also detected in two scats from one site in the eastern Aleutian Islands. Overall, molecular techniques are valuable for identifying prey in the fecal remains of marine predators. Combining DNA and hard-part identification will effectively alleviate certain predicted biases and will ultimately enhance measures of diet richness, fisheries interactions (especially salmon-related ones), and the ecological role of pinnipeds and other marine predators, to the benefit of marine wildlife conservationists and fisheries managers.

Characterization of Immobilized Biomass by Amplified rDNA Restriction Analysis (ARDRA) in an Anaerobic Sequencing-Batch Biofilm Reactor (ASBBR) for the Treatment of Industrial Wastewater

The performance of an anaerobic sequencing-batch biofilm reactor (ASBBR-laboratory scale- 14L) containing biomass immobilized on coal was evaluated for the removal of elevated concentrations of sulfate (between 200 and 3,000 mg SO4-2.L-1) from industrial wastewater effluents. The ASBBR was shown to be efficient for removal of organic material (between 90% and 45%) and sulfate (between 95% and 85%). The microbiota adhering to the support medium was analyzed by amplified ribosomal DNA restriction analysis (ARDRA). The ARDRA profiles for the Bacteria and Archaea domains proved to be sensitive for the determination of microbial diversity and were consistent with the physical-chemical monitoring analysis of the reactor. At 3,000 mg SO4-2.L-1, there was a reduction in the microbial diversity of both domains and also in the removal efficiencies of organic material and sulfate.

Characterization of immobilized biomass by amplified rDNA restriction analysis (ARDRA) in an anaerobic sequencing-batch biofilm reactor (ASBBR) for the treatment of industrial wastewater

The performance of an anaerobic sequencing-batch biofilm reactor (ASBBR- laboratory scale- 14L )containing biomass immobilized on coal was evaluated for the removal of elevated concentrations of sulfate (between 200 and 3,000 mg SO4-2·L-1) from industrial wastewater effluents. The ASBBR was shown to be efficient for removal of organic material (between 90% and 45%) and sulfate (between 95% and 85%). The microbiota adhering to the support medium was analyzed by amplified ribosomal DNA restriction analysis (ARDRA). The ARDRA profiles for the Bacteria and Archaea domains proved to be sensitive for the determination of microbial diversity and were consistent with the physical-chemical monitoring analysis of the reactor. At 3,000 mg SO4-2·L-1, there was a reduction in the microbial diversity of both domains and also in the removal efficiencies of organic material and sulfate.

Questing Dermacentor reticulatus harbouring Babesia canis DNA associated with outbreaks of canine babesiosis in the Swiss Midlands

In 2011 and 2012, outbreaks of clinical canine babesiosis were observed in 2 areas of the Swiss Midlands that had no history of this disease so far. In one area, cases of canine babesiosis occurred over 2 consecutive tick seasons. The outbreaks involved 29 dogs, 4 of which died. All dogs were infected with large Babesia sp. as diagnosed in Giemsa-stained blood smears and/or PCR. These were identified as B. canis (formerly known as B. canis canis) by subsequent partial sequencing of the 18S rRNA gene of Babesia sp. Interestingly, the sequence indicated either a genotype with heterogeneity in the ssrRNA gene copies or double infection with different B. canis isolates. None of the dogs had a recent travel history, but one had frequently travelled to Hungary and had suffered twice from clinical babesiosis 18 and 24 months prior to the outbreak in autumn 2011. Retrospective sequencing of a stored blood DNA sample of this dog revealed B. canis, with an identical sequence to the Babesia involved in the outbreaks. For the first time in Switzerland, the partial 18S rRNA gene of B. canis could be amplified from DNA isolated from 19 out of 23 adult Dermacentor reticulatus ticks flagged in the same area. The sequence was identical to that found in the dogs. Furthermore, one affected dog carried a female D. reticulatus tick harbouring B. canis DNA. Our findings illustrate that, under favourable biogeographic and climatic conditions, the life-cycle of B. canis can relatively rapidly establish itself in previously non-endemic areas. Canine babesiosis should therefore always be a differential diagnosis when dogs with typical clinical signs are presented, regardless of known endemic areas.

Production of infectious bovine papillomavirus from cloned viral DNA by using an organotypic raft/xenograft technique

Bovine papillomavirus type 1 (BPV-1) induces fibropapillomas in its natural host and can transform fibroblasts in culture. The viral genome is maintained as an episome within fibroblasts, which has allowed extensive genetic analyses of the viral functions required for DNA replication, gene expression, and transformation. Much less is known about BPV-1 gene expression and replication in bovine epithelial cells because the study of the complete viral life cycle requires an experimental system capable of generating a fully differentiated stratified bovine epithelium. Using a combination of organotypic raft cultures and xenografts on nude mice, we have developed a system in which BPV-1 can replicate and produce infectious viral particles. Organotypic cultures were established with bovine keratinocytes plated on a collagen raft containing BPV-1-transformed fibroblasts. These keratinocytes were infected with virus particles isolated from a bovine wart or were transfected with cloned BPV-1 DNA. Several days after the rafts were lifted to the air interface, they were grafted on nude mice. After 6–8 weeks, large xenografts were produced that exhibited a hyperplastic and hyperkeratotic epithelium overlying a large dermal fibroma. These lesions were strikingly similar to a fibropapilloma caused by BPV-1 in the natural host. Amplified viral DNA and capsid antigens were detected in the suprabasal cells of the epithelium. Moreover, infectious virus particles could be isolated from these lesions and quantitated by a focus formation assay on mouse cells in culture. Interestingly, analysis of grafts produced with infected and uninfected fibroblasts indicated that the fibroma component was not required for productive infection or morphological changes characteristic of papillomavirus-infected epithelium. This system will be a powerful tool for the genetic analysis of the roles of the viral gene products in the complete viral life cycle.