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171.
Raffael AC Oliveira Ricardo VM Almeida Márcia DA Dantas Felipe N Castro Jo?o Paulo MS Lima Daniel CF Lanza 《BMC bioinformatics》2014,15(1)
Background
The PCR technique and its variations have been increasingly used in the clinical laboratory and recent advances in this field generated new higher resolution techniques based on nucleic acid denaturation dynamics. The principle of these new molecular tools is based on the comparison of melting profiles, after denaturation of a DNA double strand. Until now, the secondary structure of single-stranded nucleic acids has not been exploited to develop identification systems based on PCR. To test the potential of single-strand RNA denaturation as a new alternative to detect specific nucleic acid variations, sequences from viruses of the Totiviridae family were compared using a new in silico melting curve approach. This family comprises double-stranded RNA virus, with a genome constituted by two ORFs, ORF1 and ORF2, which encodes the capsid/RNA binding proteins and an RNA-dependent RNA polymerase (RdRp), respectively.Results
A phylogenetic tree based on RdRp amino acid sequences was constructed, and eight monophyletic groups were defined. Alignments of RdRp RNA sequences from each group were screened to identify RNA regions with conserved secondary structure. One region in the second half of ORF2 was identified and individually modeled using the RNAfold tool. Afterwards, each DNA or RNA sequence was denatured in silico using the softwares MELTSIM and RNAheat that generate melting curves considering the denaturation of a double stranded DNA and single stranded RNA, respectively. The same groups identified in the RdRp phylogenetic tree were retrieved by a clustering analysis of the melting curves data obtained from RNAheat. Moreover, the same approach was used to successfully discriminate different variants of Trichomonas vaginalis virus, which was not possible by the visual comparison of the double stranded melting curves generated by MELTSIM.Conclusion
In silico analysis indicate that ssRNA melting curves are more informative than dsDNA melting curves. Furthermore, conserved RNA structures may be determined from analysis of individuals that are phylogenetically related, and these regions may be used to support the reconstitution of their phylogenetic groups. These findings are a robust basis for the development of in vitro systems to ssRNA melting curves detection.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2105-15-243) contains supplementary material, which is available to authorized users. 相似文献172.
临床医学硕士研究生阶段是培养临床和科研思维能力的重要阶段,从某种意义上说是人生和医疗生涯的关键时期。神经内科硕士研究生不仅应该具有一定的临床工作能力,还应具有一定的科研能力。临床工作能力培养包括临床基本功的培训,基本理论的加强和基本技能的培养,临床思维能力的培养及医患沟通能力的培养等多个方面。科研能力包括文献阅读能力、科研思维能力和论文写作能力等。这样,硕士研究生毕业后不仅能够诊治神经内科常见病和多发病,会思考临床工作中的问题,更重要的是能想办法探索和解决这些问题。这也是硕士研究生和本科生的本质区别。因此,研究生阶段是医学生涯一个重要的里程碑,临床和科研能力的培养对个人未来的发展具有十分重要的意义。 相似文献
173.
174.
JOSHUA B. FISHER YADVINDER MALHI DAMIEN BONAL HUMBERTO R. DA ROCHA ALESSANDRO C. DE ARAÚJO MINORU GAMO MICHAEL L. GOULDEN TAKASHI HIRANO ALFREDO R. HUETE HIROAKI KONDO TOMO'OMI KUMAGAI HENRY W. LOESCHER SCOTT MILLER ANTONIO D. NOBRE YANN NOUVELLON STEVEN F. OBERBAUER SAMREONG PANUTHAI OLIVIER ROUPSARD SCOTT SALESKA KATSUNORI TANAKA NOBUAKI TANAKA KEVIN P. TU CELSO VON RANDOW 《Global Change Biology》2009,15(11):2694-2714
Tropical vegetation is a major source of global land surface evapotranspiration, and can thus play a major role in global hydrological cycles and global atmospheric circulation. Accurate prediction of tropical evapotranspiration is critical to our understanding of these processes under changing climate. We examined the controls on evapotranspiration in tropical vegetation at 21 pan-tropical eddy covariance sites, conducted a comprehensive and systematic evaluation of 13 evapotranspiration models at these sites, and assessed the ability to scale up model estimates of evapotranspiration for the test region of Amazonia. Net radiation was the strongest determinant of evapotranspiration (mean evaporative fraction was 0.72) and explained 87% of the variance in monthly evapotranspiration across the sites. Vapor pressure deficit was the strongest residual predictor (14%), followed by normalized difference vegetation index (9%), precipitation (6%) and wind speed (4%). The radiation-based evapotranspiration models performed best overall for three reasons: (1) the vegetation was largely decoupled from atmospheric turbulent transfer (calculated from Ω decoupling factor), especially at the wetter sites; (2) the resistance-based models were hindered by difficulty in consistently characterizing canopy (and stomatal) resistance in the highly diverse vegetation; (3) the temperature-based models inadequately captured the variability in tropical evapotranspiration. We evaluated the potential to predict regional evapotranspiration for one test region: Amazonia. We estimated an Amazonia-wide evapotranspiration of 1370 mm yr−1 , but this value is dependent on assumptions about energy balance closure for the tropical eddy covariance sites; a lower value (1096 mm yr−1 ) is considered in discussion on the use of flux data to validate and interpolate models. 相似文献
175.
YE‐QIN HU SHENG LIU HONG‐MEI YUAN JING LI DA‐WEI YAN JIAN‐FENG ZHANG YING‐TANG LU 《Plant, cell & environment》2010,33(10):1656-1670
Photorespiration‐associated production of H2O2 accounts for the majority of total H2O2 in leaves of C3 plants and is mainly eliminated by catalases. In Arabidopsis, lack of CAT2, but not CAT1 or CAT3, results in growth suppression and a marked accumulation of H2O2 in leaves. To evaluate the contribution of individual catalase genes and their promoters to catalase function, we investigated the growth suppression and H2O2 accumulation phenotypes of Arabidopsis derivatives expressing catalase genes from heterologous CAT promoters in a cat2 mutant background. The expression of CAT2 from the CAT2 promoter restored the wild‐type phenotype in a cat2‐1 mutant, while CAT1 and CAT3 promoter‐driven expression of CAT2 did not. Ectopic expression of CAT3 from the CAT2 promoter also restored the normal phenotype, unlike that of CAT1 which required replacement of the CAT1 3′‐untranslated region (UTR) with that of CAT2. These results demonstrated that the photorespiratory role of CAT2 is determined mainly by the regulation of its promoter activity. The 3′‐UTR of CAT2 was vital for controlling CAT2 protein levels under photorespiratory conditions. Identification of component of heterotetramers catalase isoforms suggested that there is some functional redundancy between CAT2 and CAT1 and CAT3. 相似文献
176.
177.
M. S. LOPES G. BELO MACIEL D. MENDONA F. SABINO GIL A. DA CMARA MACHADO 《Molecular ecology resources》2006,6(3):750-752
The identification of microsatellite loci in Rubus hochstetterorum provides an important tool for the characterization and conservation of wild populations of this species. Cross‐species amplification of markers may be of particular interest for the study of other Rubus species. In this study, 41 simple sequence repeat markers were identified in a genomic library of R. hochstetterorum. Fifteen of the identified microsatellite loci were characterized in a set of 30 samples and revealed to be polymorphic with three to 19 alleles per locus. All the identified markers allowed cross‐species amplification in at least one of the other three tested species from the Rosaceae family. 相似文献
178.
DEVONIAN TRILOBITES FROM THE FALKLAND ISLANDS 总被引:1,自引:0,他引:1
MARIA DA GLORIA PIRES DE CARVALHO 《Palaeontology》2006,49(1):21-34
Abstract: New trilobite material is described from the Fox Bay Formation (Lower Devonian; Pragian) of the Falkland Islands (South Atlantic). The fossils were collected from many localities in both East and West Falkland and represent the first significant collection of trilobites from East Falkland. The trilobites belong to three higher taxa: Proetida (the first proetid record in these islands); Homalonotidae, Burmeisteria Salter, 1865; and Calmoniidae, including Bainella Rennie, 1930 and Metacryphaeus Reed, 1907. All of the forms except proetids have now been found in both East and West Falkland. 相似文献
179.
180.
HU HAO‐YUAN NIU LI‐MING MA GUANG‐CHANG FU YUE‐GUAN PENG ZHENG‐QIANG HUANG DA‐WEI 《Ecological Entomology》2010,35(2):115-125
1. Figs and pollinating fig wasps provide a model system for studying mutualism. The permeability of the syconium changes during receptivity or between seasons, which may affect the behaviour of pollinators. Fig fruits are permeable during receptivity, and in some species, pollinators can enter and re‐emerge after oviposition/pollination. We studied the relationship between fig permeability and pollinator re‐emergence behaviour with a functional dioecious fig, Ficus hispida and the obligate pollinator Ceratosolen solmsi marchali. 2. The relationship reflects the interaction of figs and pollinators in the mutualism and also the conflicts of interests between the two partners: figs benefit from the enclosed fig fruits which have low permeability, but pollinators benefit from their re‐emergence behaviour, which requires high fig permeability. 3. The results showed that at the end of receptivity, the permeability of fig fruits lowered rapidly with changes to the ostiole structures, and re‐emergence rate was low, with more re‐emerging pollinators trapped in the ostiolar bracts. Our results also showed that in the rainy season, the length of receptivity was shorter and fig permeability was lower. The re‐emergence rates were also lower than those in the dry season. The results elucidated that figs' interests dominated in the conflicts between fig and pollinating wasp. 4. Based on a new criteria which employed the classification of pollinators found dead in the ostiolar bracts and which involved a survey of 6 monoecious and 12 dioecious fig species, we found that re‐emergence behaviour was prevalent among fig species, and was more prevalent in functional dioecious figs than monoecious ones. 相似文献