Academic literature on the topic 'T-RFLP'
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Journal articles on the topic "T-RFLP"
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Nagashima, Koji, Takayoshi Hisada, Maremi Sato, and Jun Mochizuki. "Application of New Primer-Enzyme Combinations to Terminal Restriction Fragment Length Polymorphism Profiling of Bacterial Populations in Human Feces." Applied and Environmental Microbiology 69, no. 2 (February 2003): 1251–62. http://dx.doi.org/10.1128/aem.69.2.1251-1262.2003.
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ABSTRACT New primer-enzyme combinations for terminal restriction fragment length polymorphism (T-RFLP) targeting of the 16S rRNA gene were constructed by using the T-RFLP analysis program (designated TAP T-RFLP) located at the Ribosomal Database Project website, and their performance was examined empirically. By using the fluorescently labeled 516f primer (Escherichia coli positions 516 to 532) and 1510r primer (positions 1510 to 1492), the 16S rRNA gene was amplified from human fecal DNA. The resulting amplified product was digested with RsaI plus BfaI or with BslI. When the T-RFLP was carried out with fecal DNAs from eight individuals, eight predominant operational taxonomic units (OTUs) were detected with RsaI and BfaI digestion and 14 predominant OTUs were detected with BslI digestion. The distribution of the OTUs was consistent with the results of the computer simulations with TAP T-RFLP. The T-RFLP analyses of the fecal DNAs from individuals gave characteristic profiles, while the variability of the T-RFLP profiles between duplicate DNA preparations from the same samples were minimal. This new T-RFLP method made it easy to predict what kind of intestinal bacterial group corresponded to each OTU on the basis of the terminal restriction fragment length compared with the conventional T-RFLP and, moreover, made it possible to identify the bacterial species that an OTU represents by cloning and sequencing.
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Stępień-Słodkowska, Marta, Krzysztof Ficek, Mariusz Kaczmarczyk, Agnieszka Maciejewska-Karłowska, Marek Sawczuk, Agata Leońska-Duniec, Miłosz Stępiński, et al. "The Variants Within the COL5A1 Gene are Associated with Reduced Risk of Anterior Cruciate Ligament Injury in Skiers." Journal of Human Kinetics 45, no. 1 (March 1, 2015): 103–11. http://dx.doi.org/10.1515/hukin-2015-0011.
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Abstract The purpose of this study was to examine the association of the BstUI RFLP C/T (rs 12722) and DpnII RFLP C/T (rs 13946) COL5A1 polymorphisms, individually and as haplotypes, with anterior cruciate ligament ruptures in recreational skiers. Subjects were 138 male recreational skiers with surgically diagnosed primary anterior cruciate ligament ruptures. The control group consisted of 183 apparently healthy male recreational skiers, who were without any self-reported history of ligament or tendon injury. DNA was extracted from buccal cells donated by the subjects and genotyping was carried out using real-time PCR. The genotype distributions for both polymorphisms met Hardy- Weinberg expectations in both groups. There were no significant differences in genotype distribution of allele frequencies of COL5A1 BstUI RFLP C/T and COL5A1 DpnII RFLP C/T polymorphisms between the ACL rupture and control groups. The T-T (BstUI RFLP T, DpnII RFLP T) haplotype was the most common (55.6%). The haplotype T-C was not present in any of the subjects. There was an underrepresentation tendency of the C-T haplotype in the study group compared to controls under recessive mode of inheritance. Higher frequency of the COL5A1 BstUI RFLP C/T and COL5A1DpnII RFLP C/T polymorphisms haplotype is associated with reduced risk of anterior cruciate ligament injury in a group of apparently healthy male recreational skiers.
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ASHER, A. J., L. S. WALDRON, and M. L. POWER. "Rapid identification of Giardia duodenalis assemblages in NSW using terminal-restriction fragment length polymorphism." Parasitology 139, no. 8 (March 15, 2012): 1005–13. http://dx.doi.org/10.1017/s0031182012000388.
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SUMMARYHumans are infected by 2 genetic assemblages (A and B) of Giardia duodenalis, a protozoan parasite that causes gastro-intestinal disease. Sub-assemblages AI, AII, BIII and BIV are commonly identified in human cases. Detection requires amplification of G. duodenalis loci. Subsequent DNA sequencing or restriction fragment length polymorphism (RFLP) identifies sub-assemblages but is expensive (DNA sequencing) or insensitive (RFLP). This study investigated a fluorescence-based detection method, using terminal-restriction fragment length polymorphism (T-RFLP) of the glutamate dehydrogenase gene to characterize human infections. Clinical samples (n=73), positive for Giardia were collected in New South Wales, Australia, and were used to evaluate T-RFLP detection. The accuracy and sensitivity of T-RFLP detection was established by comparison to DNA sequencing and RFLP. Sub-assemblage assignment by T-RFLP identified BIV as the common subtype in N.S.W cases, whilst AI, AII and BIII were also detected. When compared to DNA sequencing and RFLP, analysis by T-RFLP was a reliable and reproducible method. Automated fluorescent detection enabled accurate sizing of restriction fragments and provided a sensitive alternative to RFLP. Discrimination of sub-assemblages by T-RFLP was comparable to DNA sequencing, but was efficient and inexpensive. The protocol described here provides a rapid and sensitive diagnostic tool for routine sample screenings in epidemiological research.
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Råberg, Ulrika, Nils O. S. Högberg, and Carl Johan Land. "Detection and species discrimination using rDNA T-RFLP for identification of wood decay fungi." Holzforschung 59, no. 6 (November 1, 2005): 696–702. http://dx.doi.org/10.1515/hf.2005.111.
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AbstractIn the present work PCR technology was used as a tool to detect the early stages of wood decay and was compared with microscopic evaluation. The wood decay fungiPostia placentaandConiophora puteanawere detectable in interior wood samples by terminal restriction fragment length polymorphism (T-RFLP) after 2weeks of incubation with monocultures, while microscopic detection of hyphae was not possible until after 7 weeks. A potential problem when fungal communities are studied with T-RFLPs of rDNA is that intra-specific variation complicates data analysis. In this work, we show that intra-specific sequence variation in the internal transcribed spacer of the rDNA inConiophora puteanaallows T-RFLP identification of this species. This is due to intra-specific variations in fragment length, in combination with the absence of point mutations in the selected restriction sites.
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Lueders, Tillmann, and Michael W. Friedrich. "Evaluation of PCR Amplification Bias by Terminal Restriction Fragment Length Polymorphism Analysis of Small-Subunit rRNA and mcrA Genes by Using Defined Template Mixtures of Methanogenic Pure Cultures and Soil DNA Extracts." Applied and Environmental Microbiology 69, no. 1 (January 2003): 320–26. http://dx.doi.org/10.1128/aem.69.1.320-326.2003.
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ABSTRACT Terminal restriction fragment length polymorphism (T-RFLP) analysis is a widely used method for profiling microbial community structure in different habitats by targeting small-subunit (SSU) rRNA and also functional marker genes. It is not known, however, whether relative gene frequencies of individual community members are adequately represented in post-PCR amplicon frequencies as shown by T-RFLP. In this study, precisely defined artificial template mixtures containing genomic DNA of four different methanogens in various ratios were prepared for subsequent T-RFLP analysis. PCR amplicons were generated from defined mixtures targeting not only the SSU rRNA but also the methyl-coenzyme M reductase (mcrA/mrtA) genes of methanogens. Relative amplicon frequencies of microorganisms were quantified by comparing fluorescence intensities of characteristic terminal restriction fragments. SSU ribosomal DNA (rDNA) template ratios in defined template mixtures of the four-membered community were recovered absolutely by PCR-T-RFLP analysis, which demonstrates that the T-RFLP analysis evaluated can give a quantitative view of the template pool. SSU rDNA-targeted T-RFLP analysis of a natural community was found to be highly reproducible, independent of PCR annealing temperature, and unaffected by increasing PCR cycle numbers. Ratios of mcrA-targeted T-RFLP analysis were biased, most likely by PCR selection due to the degeneracy of the primers used. Consequently, for microbial community analyses, each primer system used should be evaluated carefully for possible PCR bias. In fact, such bias can be detected by using T-RFLP analysis as a tool for the precise quantification of the PCR product pool.
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Seldin, M. F., H. C. Morse, J. P. Reeves, C. L. Scribner, R. C. LeBoeuf, and A. D. Steinberg. "Genetic analysis of autoimmune gld mice. I. Identification of a restriction fragment length polymorphism closely linked to the gld mutation within a conserved linkage group." Journal of Experimental Medicine 167, no. 2 (February 1, 1988): 688–93. http://dx.doi.org/10.1084/jem.167.2.688.
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A linkage map of distal mouse chromosome 1 was generated using restriction fragment length polymorphism (RFLP) analysis of DNA prepared from 95 [C3H-gld/gld X Mus spretus)F1 X C3H-gld/gld] backcross mice. The gene order was: (centromere) C4bp, Ren-1,2, Ly-5, [At-3/gld], Apoa-2/Ly-17, Spna-1 (telomere). All mice expressing the phenotype of gld homozygotes were homozygous for the At-3 RFLP characteristic of C3H mice and none of the mice heterozygous for At-3 RFLPs had characteristics of gld homozygotes, demonstrating close linkage between these genes. The identification of an RFLP closely linked to the gld gene provides a starting point for the identification of a genetic defect that results in abnormal T cells and autoimmune disease.
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Danovaro, R., G. M. Luna, A. Dell'Anno, and B. Pietrangeli. "Comparison of Two Fingerprinting Techniques, Terminal Restriction Fragment Length Polymorphism and Automated Ribosomal Intergenic Spacer Analysis, for Determination of Bacterial Diversity in Aquatic Environments." Applied and Environmental Microbiology 72, no. 9 (September 2006): 5982–89. http://dx.doi.org/10.1128/aem.01361-06.
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ABSTRACT We investigated bacterial diversity in different aquatic environments (including marine and lagoon sediments, coastal seawater, and groundwater), and we compared two fingerprinting techniques (terminal restriction fragment length polymorphism [T-RFLP] and automated ribosomal intergenic spacer analysis [ARISA]) which are currently utilized for estimating richness and community composition. Bacterial diversity ranged from 27 to 99 phylotypes (on average, 56) using the T-RFLP approach and from 62 to 101 genotypes (on average, 81) when the same samples were analyzed using ARISA. The total diversity encountered in all matrices analyzed was 144 phylotypes for T-RFLP and 200 genotypes for ARISA. Although the two techniques provided similar results in the analysis of community structure, bacterial richness and diversity estimates were significantly higher using ARISA. These findings suggest that ARISA is more effective than T-RFLP in detecting the presence of bacterial taxa accounting for <5% of total amplified product. ARISA enabled also distinction among aquatic bacterial isolates of Pseudomonas spp. which were indistinguishable using T-RFLP analysis. Overall, the results of this study show that ARISA is more accurate than T-RFLP analysis on the 16S rRNA gene for estimating the biodiversity of aquatic bacterial assemblages.
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Jackson, Colin J., Richard C. Barton, and E. Glyn V. Evans. "Species Identification and Strain Differentiation of Dermatophyte Fungi by Analysis of Ribosomal-DNA Intergenic Spacer Regions." Journal of Clinical Microbiology 37, no. 4 (1999): 931–36. http://dx.doi.org/10.1128/jcm.37.4.931-936.1999.
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Restriction fragment length polymorphisms (RFLPs) identified in the ribosomal-DNA (rDNA) repeat were used for molecular strain differentiation of the dermatophyte fungus Trichophyton rubrum. The polymorphisms were detected by hybridization ofEcoRI-digested T. rubrum genomic DNAs with a probe amplified from the small-subunit (18S) rDNA and adjacent internal transcribed spacer (ITS) regions. The rDNA RFLPs mapped to the nontranscribed spacer (NTS) region of the rDNA repeat and appeared similar to those caused by short repetitive sequences in the intergenic spacers of other fungi. Fourteen individual RFLP patterns (DNA types A to N) were recognized among 50 random clinical isolates ofT. rubrum. A majority of strains (19 of 50 [38%]) were characterized by one RFLP pattern (DNA type A), and four types (DNA types A to D) accounted for 78% (39 of 50) of all strains. The remaining types (DNA types E to N) were represented by one or two isolates only. A rapid and simple method was also developed for molecular species identification of dermatophyte fungi. The contiguous ITS and 5.8S rDNA regions were amplified from 17 common dermatophyte species by using the universal primers ITS 1 and ITS 4. Digestion of the amplified ITS products with the restriction endonucleaseMvaI produced unique and easily identifiable fragment patterns for a majority of species. However, some closely related taxon pairs, such as T. rubrum-T. soudanense andT. quinkeanum-T. schoenlenii could not be distinguished. We conclude that RFLP analysis of the NTS and ITS intergenic regions of the rDNA repeat is a valuable technique both for molecular strain differentiation of T. rubrum and for species identification of common dermatophyte fungi.
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Penny, Christian, Thierry Nadalig, Malek Alioua, Christelle Gruffaz, Stéphane Vuilleumier, and Françoise Bringel. "Coupling of Denaturing High-Performance Liquid Chromatography and Terminal Restriction Fragment Length Polymorphism with Precise Fragment Sizing for Microbial Community Profiling and Characterization." Applied and Environmental Microbiology 76, no. 3 (November 30, 2009): 648–51. http://dx.doi.org/10.1128/aem.01556-09.
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ABSTRACT Terminal restriction fragment length polymorphism (T-RFLP) is used to monitor the structural diversity of complex microbial communities in terms of richness, relative abundance, and distribution of the major subpopulations and individual members. However, discrepancies of several nucleotides between expected and experimentally observed lengths of terminal restriction fragments (T-RFs), together with the difficulty of obtaining DNA sequence information from T-RFLP profiling, often prevent accurate phylogenetic characterization of the microbial community of interest. In this study, T-RFLP analysis of DNA from an artificial assembly of five bacterial strains was carried out with a combination of two size markers with different fluorescent tags. Precise sizing of T-RFs in the 50- to 500-nucleotide range was achieved by using the same dye for both samples and size markers. Phylogenetic assignment of the component microbial strains was facilitated by coupling T-RFLP to denaturing high-performance liquid chromatography (D-HPLC) of 16S RNA gene fragments followed by direct sequencing. The proposed coupling of D-HPLC and T-RFLP provides unambiguous characterization of microbial communities containing less than 15 microbial strains.
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Egert, Markus, and Michael W. Friedrich. "Formation of Pseudo-Terminal Restriction Fragments, a PCR-Related Bias Affecting Terminal Restriction Fragment Length Polymorphism Analysis of Microbial Community Structure." Applied and Environmental Microbiology 69, no. 5 (May 2003): 2555–62. http://dx.doi.org/10.1128/aem.69.5.2555-2562.2003.
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ABSTRACT Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified genes is a widely used fingerprinting technique in molecular microbial ecology. In this study, we show that besides expected terminal restriction fragments (T-RFs), additional secondary T-RFs occur in T-RFLP analysis of amplicons from cloned 16S rRNA genes at high frequency. A total of 50% of 109 bacterial and 78% of 68 archaeal clones from the guts of cetoniid beetle larvae, using MspI and AluI as restriction enzymes, respectively, were affected by the presence of these additional T-RFs. These peaks were called “pseudo-T-RFs” since they can be detected as terminal fluorescently labeled fragments in T-RFLP analysis but do not represent the primary terminal restriction site as indicated by sequence data analysis. Pseudo-T-RFs were also identified in T-RFLP profiles of pure culture and environmental DNA extracts. Digestion of amplicons with the single-strand-specific mung bean nuclease prior to T-RFLP analysis completely eliminated pseudo-T-RFs. This clearly indicates that single-stranded amplicons are the reason for the formation of pseudo-T-RFs, most probably because single-stranded restriction sites cannot be cleaved by restriction enzymes. The strong dependence of pseudo-T-RF formation on the number of cycles used in PCR indicates that (partly) single-stranded amplicons can be formed during amplification of 16S rRNA genes. In a model, we explain how transiently formed secondary structures of single-stranded amplicons may render single-stranded amplicons accessible to restriction enzymes. The occurrence of pseudo-T-RFs has consequences for the interpretation of T-RFLP profiles from environmental samples, since pseudo-T-RFs may lead to an overestimation of microbial diversity. Therefore, it is advisable to establish 16S rRNA gene sequence clone libraries in parallel with T-RFLP analysis from the same sample and to check clones for their in vitro digestion T-RF pattern to facilitate the detection of pseudo-T-RFs.
Dissertations / Theses on the topic "T-RFLP"
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Rocha, Lidianne Leal. "Estudo de comunidades bacterianas de solos do Manguezal da Barra Grande, Icapuà â CE e SeleÃÃo de cepas com potencial para degradar hidrocarbonetos." Universidade Federal do CearÃ, 2008. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=2773.
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Os manguezais sÃo ecossistemas entremarÃs produtivos e biologicamente importantes que ocorrem em regiÃes tropicais e subtropicais do mundo. Ãreas de manguezais nÃo perturbados fornecem habitats para uma variedade de plantas, animais e microrganismos. Estes ecossistemas recebem materiais sedimentares do mar e continente, tornando-se uma Ãrea de transiÃÃo com elevada produtividade. Importantes processos, tais como ciclagem de nutrientes, estÃo diretamente conectados à atividade e diversidade das comunidades microbianas dos solos do manguezal. No entanto, devido a sua localizaÃÃo estratÃgica, manguezais tÃm sido amplamente impactados por todo o mundo. A compreensÃo da estrutura e das funÃÃes das comunidades microbianas e suas adaptaÃÃes Ãs alteraÃÃes ambientais resultantes de xenobiÃticos, alteraÃÃes climÃticas e a prÃtica industrial, tais como a exploraÃÃo petrolÃfera, à essencial para manter ou restabelecer funÃÃes desejÃveis do ecossistema. Dessa forma, o presente estudo investigou a estrutura de comunidades bacterianas de amostras de solos do manguezal da Barra Grande, Icapuà (37 20âW, 4 40âS), por mÃtodo independente de cultivo usando Polimorfismo do Tamanho de Fragmentos de RestriÃÃo Terminal (T-RFLP) e tambÃm avaliou o mÃtodo dependente de cultivo (enriquecimento) para isolar cepas de bactÃrias com potencial para degradar petrÃleo e n-Hexadecano. Um total de trÃs pontos foi amostrado ao longo do manguezal, com 150 metros de distÃncia entre cada um deles. Temperatura, pH, salinidade, matÃria orgÃnica e granulometria dos solos foram medidas. AnÃlises de T-RFLP foram feitas apÃs a digestÃo de DNA genÃmico com as enzimas HhaI e MspI e o nÃmero e diversidade de Unidades TaxonÃmicas Operacionais (OTU) de cada amostra foi analisado pelo programa T-Align (Applied Biosystems). A cepa selecionada para testes de diferentes concentraÃÃes de n-Hexadecano foi identificada pelo seqÃenciamento do gene do rRNA 16S. Esta cepa foi tambÃm avaliada em relaÃÃo à susceptibilidade a radiaÃÃo UV e antibiÃticos. Os resultados mostraram que as comunidades bacterianas de solos do manguezal sÃo semelhantes em nÃmero de OTUs, mas diferem em composiÃÃo. Provavelmente a peculiaridade das variÃveis fÃsico-quÃmicas e granulometria do solo sÃo responsÃveis pelas diferenÃas na composiÃÃo e estrutura das comunidades bacterianas. Dezoito cepas de bactÃrias foram isoladas de culturas de enriquecimento com petrÃleo e quatro cepas mostraram potencial particular para degradar n-Hexadecano. Uma cepa identificada como Acinetobacter sp. IC18 foi caracterizada como uma boa degradadora de hidrocarboneto, pois foi capaz de degradar 1% do n-Hexadecano em 48 horas. Esta cepa tambÃm utilizou cerca de 30% de uma concentraÃÃo total de 20% (v/v) de n-Hexadecano durante o mesmo perÃodo de incubaÃÃo. AlÃm disso, IC18 foi susceptÃvel a vÃrios antibiÃticos e resistente à radiaÃÃo UV. Em conclusÃo, a estrutura da comunidade bacteriana de solos do manguezal da Barra Grande parece nÃo ser afetada pela presenÃa da exploraÃÃo petrolÃfera em IcapuÃ. AlÃm disso, os solos deste manguezal sÃo colonizados por vÃrias cepas com potencial para degradar hidrocarbonetos, que à particularmente interessante em virtude do risco de derramamentos de petrÃleo.
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Mendes, Lucas William. "Análise molecular das estruturas e diversidade de comunidades microbianas em solo de manguezal preservado da Ilha do Cardoso-SP." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/64/64133/tde-27042010-112316/.
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Os manguezais tropicais são considerados um dos ecossistemas mais produtivos do mundo, sendo caracterizados pela alta taxa de ciclagem de matéria orgânica e nutrientes que ocorre entre os oceanos e os ambientes terrestres. Embora os manguezais sejam considerados áreas de proteção ambiental, a destruição desses ambientes é progressiva, devido a atividades industriais e portuárias nos estuários. Nos manguezais, a ciclagem de nutrientes está diretamente relacionada às atividades e a diversidade das comunidades microbianas presentes no solo. Este trabalho está inserido em um projeto mais amplo dentro do programa BIOTA/FAPESP, no que tange aos estudos da biodiversidade no Estado de São Paulo e utilização dessa biodiversidade de modo sustentável. O objetivo deste trabalho foi avaliar as estruturas e diversidade das comunidades de Bacteria, Archaea e Fungi presentes no solo de manguezal preservado da Ilha do Cardoso-SP. As amostras foram analisadas pelas técnicas de T-RFLP, ARISA, clonagem e seqüenciamento a fim de obter uma caracterização das estruturas das comunidades microbianas de uma área de manguezal preservado em comparação com os ambientes adjacentes de restinga e floresta e também a um manguezal antropizado. Os resultados permitiram concluir que o manguezal possui características exclusivas, com a presença de organismos distintos, revelando um possível potencial biotecnológico a ser explorado. Adicionalmente, os dados revelaram que a ação antrópica afetou as estruturas dessas comunidades de modo a ser notada uma sensível diminuição de diversidade no manguezal antropizado, evidenciando, dessa maneira, a importância da preservação desse ecossistemaThe tropical mangroves are considered one of the most productive ecosystems of the world, being characterized by the high tax of organic matter and recycling of nutrients, that happens between the oceans and the terrestrial habitats. Although the mangroves are considered areas of environmental protection, the destruction of those ecosystems is progressive, due to industrial and port activities in the estuaries. In mangroves, the recycling of nutrients is directly related to the activities and to the diversity of microbial communities present in the soil. This work is part of a wider project inside of the program BIOTA/FAPESP, with respect to the studies of the biodiversity in the State of São Paulo and use of that biodiversity in a maintainable way. The objective of this work was to evaluate the structures and diversity of communities of Bacteria, Archaea and Fungi present in the soil of preserved mangrove of Ilha do Cardoso-SP. The samples were analyzed by T-RFLP and ARISA techniques, cloning and sequencing in order to obtain a characterization of the microbial communities structure of preserved mangrove area in comparison with the adjacent environments of restinga (tropical moist forest) and forest and also to a degraded mangrove. The results allowed concluding that the mangroves present exclusive characteristics, with the presence of distinct organisms, revealing a possible biotechnological potential to be explored. Additionally, the data revealed that the human action affected the structures of those communities in a way to be noticed a sensitive diversity decrease in the degraded mangrove, evidencing, this way, the importance of the ecosystem preservation
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Fiore, Rebecca de Ara?jo. "Potencial de esp?cies florestais para remedia??o de substrato contaminado com atrazine e 2,4-D." UFVJM, 2014. http://acervo.ufvjm.edu.br:8080/jspui/handle/1/338.
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Funda??o de Amparo ? Pesquisa do estado de Minas Gerais (FAPEMIG)
Em se tratando da contamina??o de ecossistemas por res?duos de defensivos agr?colas, especial aten??o ? dada para a classe dos herbicidas, em fun??o do volume de aplica??o. Os que possuem mol?culas sol?veis pass?veis de contamina??o de len??is h?dricos subterr?neos se destacam pela abrang?ncia dos efeitos negativos. Nesse sentido, objetivou-se selecionar esp?cies vegetais arb?reas interessantes na remedia??o de ambientes contaminados por res?duos de atrazine e 2,4-D. Foram avaliados 36 tratamentos compostos pela combina??o de 12 esp?cies florestais [Inga marginata (ing?), Schizolobium parahyba (guapuruvu), Handroanthus serratifolius (ip? amarelo), Jacaranda puberula (carobinha), Cedrela fissilis (cedro), Calophyllum brasiliensis (landin), Psidium mirsinoides (goiabinha), Tibouchina glandulosa (quaresmeira), Caesalpinia f?rrea (pau-ferro), Caesalpinia pluviosa (sibipiruna), Terminalia arg?ntea (capit?o) e Schinopsis brasiliensis (bra?na)] e tr?s solu??es simulando o composto lixiviado (atrazine, 2,4-D e ?gua ? controle), com quatro repeti??es. Foram feitas 3 aplica??es dos herbicidas atrazine e 2,4-D com intervalos de 20 dias (aos 60, 80 e 100 dias ap?s o plantio), sendo cada aplica??o correspondente ? metade da dose comercial dos produtos. Para as avalia??es de crescimento foram mensuradas a altura da planta, o di?metro do caule, o n?mero de folhas, a ?rea foliar e o ac?mulo de biomassa seca. Na estimativa do efeito visual dos herbicidas ?s plantas avaliadas, optou-se pela atribui??o de notas em escala de intoxica??o. Para verifica??o de capacidade remediadora das esp?cies arb?reas procedeu-se a semeadura da esp?cie indicadora para indicativo do res?duo do herbicida no solo, (Cucumis sativus (L.)). Posteriormente em amostras de solo provenientes da esp?cie remediadora mais promissora procedeu-se a an?lise de polimorfismo de comprimento de fragmento de restri??o terminal (T-RFLP), com intuito de caracterizar a diversidade microbiana presente. As esp?cies florestais sobreviveram ? aplica??o dos herbicidas, sendo que umas se mostram mais sens?veis do que outras. O ing? apresentou bons resultados de remedia??o com o bioensaio, assim como o ip? amarelo, apesar da sua sensibilidade aos herbicidas. Observou-se aumento no conte?do relativo de macronutrientes para as plantas sob a??o dos herbicidas, na maioria dos tratamentos. Os resultados de T-RFLP confirmaram a diversidade microbiana diferenciada associada ? rizosfera de ing?, principalmente quando submetida ? a??o de atrazine.
Disserta??o (Mestrado) ? Programa de P?s-Gradua??o em Ci?ncia Florestal, Universidade Federal dos Vales do Jequitinhonha e Mucuri, 2014.
ABSTRACT In the case of contamination of ecosystems by residues of pesticides, special attention is given to the class of herbicides, according to the application volume. Those with likely contamination of underground water soluble molecules sheets are distinguished by breadth of negative effects. In this sense, the aim of this work was to select interesting woody plant species in the remediation of contaminated by residues of atrazine and 2,4-D environments. Were evaluated 36 treatments consisted of combinations of 12 forest species [Inga marginata (ing?), Schizolobium parahyba (guapuruvu), Handroanthus serratifolius (ip? amarelo), Jacaranda puberula (carobinha), Cedrela fissilis (cedro), Calophyllum brasiliensis (landin), Psidium mirsinoides (goiabinha), Tibouchina glandulosa (quaresmeira), Caesalpinia f?rrea (pau-ferro), Caesalpinia pluviosa (sibipiruna), Terminalia arg?ntea (capit?o) and Schinopsis brasiliensis (bra?na)] and three leachate solutions simulate the compound ( atrazine , 2,4 - D and water - control),with four replicates each. Three applications of atrazine and 2,4-D were made at intervals of 20 days (at 60, 80 and 100 days after planting), each application was corresponding to half of the recommended. Evaluations of growth were measured plant height, stem diameter, number of leaves, leaf area and dry biomass. In estimating the visual effect of herbicides on plants assessed, was opted for the grading scale of intoxication. To check remediation ability of tree species proceeded seeding indicator species for indication of herbicide residue in the soil (Cucumis sativus (L.)). Later in soil samples from the species most promising remedial proceeded to analysis of length polymorphism terminal restriction fragment (T-RFLP), in order to characterize the microbial diversity present. Forest species survived the herbicide application, and some are more sensitive than others. The ing? had good results with the remediation bioassay, as well as the ipe amarelo, despite their sensitivity to herbicides. Observed increase in the relative content of macronutrients for plants under the effect of herbicides in most treatments. The results of T-RFLP confirmed the differentiated microbial diversity associated with the rhizosphere of ing?, especially when subjected to the action of atrazine.
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Santana, Maiele Cintra. "Análise da comunidade de fungos em áreas de monoculturas e consórcio de Eucalyptus grandis e Acacia mangium." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/11/11138/tde-03052018-173930/.
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Os fungos representam cerca de 75% da biomassa microbiana em áreas florestais, desempenhando funções importantes, desde a mineralização dos resíduos orgânicos até a disponibilização de nutrientes para plantas por meio das associações micorrízicas, o que influencia a ciclagem de nutrientes e, consequentemente, o crescimento das árvores. O objetivo desse trabalho foi avaliar a comunidade de fungos do solo, da rizosfera e do sistema radicular de Eucalyptus grandis e Acacia mangium plantados em monocultivos e em consórcio, e encontrar respostas para os padrões observados por meio da correlação com os atributos físicos, químicos, biológicos e a profundidade do solo. A coleta das amostras foi realizada na Estação Experimental de Ciências Florestais de Itatinga, em 2016, quando as plantas estavam com 2 anos de idade. Foram coletadas amostras em quatro tratamentos: monoculturas de E. grandis e de A. mangium e consórcios de E. grandis e de A. mangium, nos quais foram construídas trincheiras para coleta das amostras nas camadas de 0-10, 10-20, 20-50 e 50-100 cm de profundidade. Foram caracterizados os atributos físicos e biológicos do solo e os atributos químicos do solo, da rizosfera e das raízes. Para a avaliação micorrízica, foi quantificado o número de esporos de fungos micorrízicos arbusculares (FMA) e as taxas de colonização radicular por FMA e por fungos ectomicorrízicos. Foi avaliada a morfologia das estruturas das micorrizas arbusculares e ectomicorriza (ECM). A estrutura da comunidade de fungos do solo e da rizosfera foi avaliada por meio da técnica de Terminal restriction fragment length polymorphism (T-RFLP). Para isso, o DNA foi amplificado utilizando os primers ITS1f-FAM e ITS4 e a restrição dos fragmentos foi realizada com a enzima HaeIII. A abundância de cópias do gene ITS do solo e da rizosfera foi quantificada por PCR quantitativo (qPCR), utilizando os primers ITS1f e 5.8s. Os atributos físicos, químicos e biológicos tiveram poucas variações entre os tratamentos avaliados, sendo as maiores diferenças encontradas entre as profundidades. O número de esporos (<29) e as taxas de colonização micorrízica (<48%) foram baixos em todos os tratamentos, e se reduziram com o aumento da profundidade. As plantas de A. mangium não formaram micorrizas arbusculares. Nas raízes de E. grandis, não houve a formação de arbúsculos, mas foi verificada a presença de hifas enroladas (hyphal coils), estrutura de micorriza do tipo Paris. A anatomia das ECM confirmou a colonização destes fungos nas raízes das plantas estudadas. O qPCR mostrou maior abundância de genes ITS na rizosfera em relação ao solo, assim como nas camadas superficiais (0-10 cm) em relação às mais profundas (10 cm abaixo). A Análise de Coordenadas Principais revelou diferenças na estrutura das comunidades de fungos nos tratamentos estudados, principalmente para a região da rizosfera, diferenciando o perfil de fungos do monocultivo de E. grandis dos demais tratamentos, assim como a influência da A. mangium na estruturação da comunidade. A análise de redundância mostrou a influência de alguns atributos químicos nas taxas de colonização e estruturação da comunidade. Dessa forma, conclui-se que em sistema de consórcio, uma espécie de planta parece ser mais influente do que a outra na estruturação da comunidade de fungos e essa influência é mais evidente na rizosfera. Além disso, os atributos químicos são fatores importantes na organização da comunidade fúngica.The fungi represent about 75% of the microbial biomass in forest areas, performing important functions, from the mineralization of the organic residues to the availability of nutrients to plants through mycorrhizal associations, which influences the nutrient cycling and, consequently, the growth of trees. The objective of this work was to evaluate the community of fungi of the soil, rhizosphere and root system of Eucalyptus grandis and Acacia mangium planted in monocultures and consortium, and to find explanations for the observed patterns through the correlation with physical and chemical soil attributes and soil depth. The samples were collected at the Experimental Station of Forest Sciences of Itatinga in 2016, when the plants were 2 years old. Samples were collected in four treatments: monocultures of E. grandis and A. mangium and consortia of E. grandis and A. mangium, in which trenches were constructed to collect samples in the 0-10, 10-20, 20 -50 and 50-100 cm deep. The physical and biological attributes of the soil and the chemical attributes of soil, rhizosphere and roots were characterized. For the mycorrhizal evaluation, the number of spores of arbuscular mycorrhizal fungi (AMF) and the rates of root colonization by AMF and ectomycorrhizal fungi were quantified. The morphology of arbuscular mycorrhizal and ectomycorrhizal (ECM) structures was evaluated. The structure of the soil and rhizosphere fungi community by was evaluated by the technique of Terminal restriction fragment length polymorphism (T-RFLP). For this, the DNA was amplified using primers ITS1f-FAM and ITS4 and restriction of the fragments was performed with the enzyme HaeIII. The abundance of ITS gene copies of soil and rhizosphere was quantified by quantitative PCR (qPCR), using primers ITS1f and 5.8s. The physical, chemical and biological attributes had few variations among the evaluated treatments, being the greatest differences found between the depths. The number of spores (<29) and mycorrhizal colonization rates (<48%) were low in all treatments, and reduced with increasing depth. A. mangium plants did not form FMA. In the roots of E. grandis, there was no formation of arbuscules, but we found the presence of hyphal coils, mycorrhizal structures of the Paris type. The anatomy of the ECM confirmed the colonization of these fungi in the roots of the studied plants. The qPCR showed higher abundance of ITS genes in the rhizosphere in relation to the soil, as well as in the superficial layers (0-10 cm) in relation to the deeper ones (10 cm below). The Principal Coordinates Analysis revealed differences in the structure of the fungal communities in the treatments studied, especially for the rhizosphere region, differentiating the fungal profile of the E. grandis monoculture from the other treatments, as well as the influence of A. mangium on the structure of the community. The redundancy analysis showed the influence of some chemical soil attributes on the rates of colonization and community structuring. Thus, it is concluded that in a consortium system, one plant species seems to be more influential than the other in structuring the fungal community, and this influence is more evident in the rhizosphere. In addition, chemical attributes are important factors in the organization of the fungal community.
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Miao, Yu. "Development and use of T-RFLP for studies of take-all infection of wheat." Thesis, University of Nottingham, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.490991.
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Take-all of wheat is caused by the soil-borne fungus Gaeumannomyces graminis var. tritici (Ggt), and is a widespread and destructive disease in temperate climates around the world where losses may be as high as 50%. Several practices are used to limit the disease on susceptible crops, including tillage, rotation, choice of variety, N fertilizer, and chemical and biological seed treatments. In relation to biological control, it is necessary to better understand the effects of different treatments on microbial dynamics in the rhizosphere and on roots.
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Fornazari, Anna Cristina Zari. "Determinação da comunidade microbiana pelo método molecular T-RFLP em carnes refrigeradas embaladas a vácuo." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/11/11141/tde-22112011-085341/.
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O estufamento de embalagens a vácuo de carnes refrigeradas, também conhecido como blown pack, é atribuído a bactérias psicrófilas e psicrotróficas, dentre as quais fazem parte algumas espécies de clostrídios, enterobactérias e bactérias lácticas. A capacidade desses microrganismos crescer em temperaturas de refrigeração adequadas torna um desafio o seu controle pela indústria. O Brasil é um dos grandes produtores de carne bovina no mundo e apesar da importância que a indústria de carne representa para o país, existem poucos estudos sobre as possíveis causas da deterioração do tipo blown pack. A importância deste trabalho fundamenta-se na escassez de pesquisas sobre esse problema que afeta a indústria de carne. O objetivo dessa pesquisa foi avaliar a presença dos principais microrganismos envolvidos na deterioração tipo blown pack, com ênfase em clostrídios, enterobactérias e bactérias láticas. Assim, o método Terminal- Restriction Fragment Length Polymorphism, disponível no laboratório de Biologia Molecular do CENA-USP, foi empregado por permitir um diagnóstico rápido e preciso para detecção de microrganismos. Foram analisadas 15 amostras de carne bovinas refrigeradas, embaladas a vácuo e estufadas, provenientes de frigoríficos dos estados de São Paulo, Mato Grosso do Sul e Goiás. Os cortes utilizados para as análises foram contrafilé, músculo, alcatra, cupim, picanha e filé de costela. As amostras apresentavam características de deterioração tipo blown pack dentro da data de validade, com períodos armazenamento variando de 30 a 120 dias. Foram identificadas as espécies Clostridium algidicarnis, Clostridium gasigenes, Clostridium putrefaciens, Clostridium frigidicarnis, Lactobacillus sakei, Hafnia alvei e Serratia liquefaciens pela técnica T-RFLP, que se mostrou uma excelente ferramenta de identificação microbiana nas amostras de carne. Devido à alta prevalência de enterobactérias nas amostras de carnes detectadas pela técnica de T-RFLP, foram realizadas análises convencionais com isolamento e identificação de enterobactérias, a fim de confirmar a presença destes microrganismos viáveis e cultiváveis nas amostras. As espécies de enterobactérias cultivadas e identificadas foram H. alvei, Ser. liquefaciens, Citrobacter braakii, Pantoea sp e Yersinia enterocolitica, sendo esta última potencialmente patogênica e de interesse em saúde pública. Observou-se que a H. alvei foi a espécie predominante nas amostras avaliadas, tanto pela técnica de T-RFLP como pelas análises microbiológicas convencionais. Com o objetivo de complementar os resultados, foram realizadas análises convencionais de cultivo visando o isolamento de Clostridium estertheticum e Clostridium gasigenes nas amostras de carne. A técnica de PCR foi empregada com a finalidade de identificação dos isolados obtidos.The distension of the packaging of vacuum packed chilled meat, also know as blown pack, is assigned to psichrophilic and psychrotrophic bacteria, among which are part some clostridium, enterobacteria and lactic bacteria.The ability of these microorganisms to grow at refrigeration temperatures makes it an appropriate challenge its control by the industry. Brazil is a major producer of beef in the world and despite the importance of the beef industry represents for the country, there are few studies on the possible causes of deterioration of blown pack type. The importance of this work is based on the dearth of research on this problem that affects the meat industry. The aim of this study was to evaluate the presence of the main microorganisms involved in the deterioration blown pack type, with emphasis on clostridia, enterobacteria and lactic bacteria. Thus, the method-Terminal Restriction Fragment Length Polymorphism, available at Molecular biology laboratory of CENA-USP, was used to allow a rapid and accurate diagnosis for the detection of microorganisms. We analyzed 15 samples of beef chilled, vacuum packed wich abundant gas production, refrigerators from the states of São Paulo, Mato Grosso do Sul and Goiás cuts used for the analysis were striploin, shin, rump, hump, cop of rump and cube roll. The samples showing signs of deterioration such blown pack within the shelf life, with storage periods ranging from 30 to 120 days. Were identified Clostridium algidicarnis, Clostridium gasigenes, Clostridium putrefaciens, Clostridium frigidicarnis, Lactobacillus sakei, Hafnia alvei and Serratia liquefaciens by TRFLP technique, which proved an excellent tool for microbial identification in meat samples. The high prevalence of enterobacteria in samples of meat detected by the technique of TRFLP analysis was performed with conventional isolation and identification of enterobacteria, in order to confirm the presence of viable and culturable microorganisms in the samples. The species of enterobacteria were identified and cultivated H. alvei, Ser. liquefaciens, Citrobacter braakii, Pantoea sp. and Yersinia enterocolitica, the latter being potentially pathogenic and interest in public health. It was observed that H. alvei was the predominant species in the samples evaluated by both the T-RFLP technique and by conventional microbiological tests. In order to complement the results were analyzed conventional cultivation and isolation of Clostridium estertheticum and Clostridium gasigenes in meat samples. The PCR technique was employed for the purpose of identification of isolates.
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Paes, Fernanda Araujo. "AnÃlise de comunidades microbianas de solo de manguezal por T-RFLP e microarranjos de DNA." Universidade Federal do CearÃ, 2008. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=2712.
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FundaÃÃo de Amparo à Pesquisa do Estado do CearÃThe mangroves are essistemas important and productive, found along the coastline of tropical and subtropical regions. Important processes such as nutrient cycling, are directly connected to the activity of soil microbial communities. Given its strategic position the mangroves are very impacted the world. In Brazil, important areas such as the Bay of All Saints (BA) are severely affected by the presence of oil. Understanding the adaptation of the microbiota and its local dynamics, before the environmental change is essential to be able to maintain or restore these ecosystems. This thesis investigated the structure and function of microbial communities in a mangrove area of the Bay of All Saints polluted by the oil industry. Two sites were sampled - one located in the refinement of the industry and another, distant location and used as the control. Besides the measured abiotic data, two independent methods of cultivation were used: T-RFLP and DNA microarranjos. The results of both sites in the experiments of T-RFLP showed that the two bacterial communities differ in their structure. For the site sampled in the refinery, a greater number of Otus suggests an environmental stimulus, the bacterial community, a fact associÃvel the high organic matter content of the site. For microarranjos DNA, similar categories of genes were detected in both places, but the specificity of their sequences were distinct. The genes that encode for the remediation organic, were more representative, more than 40% in total in the two sites. Even detecting similar categories, only 4% of the gene sequences were common to the sites. These data show that different bodies are responsible for similar functions at each point. The difference between the sites observed in the experiments can be related with the fact that Site 1 is located in a region heavily affected by oil. Using the ecological data rates of T-RFLP indicated the site 1 as the most diverse, while the results with the DNA microarranjos show the opposite. In conclusion, the structure and function of the local microbiota are affected by the presence of the oil industry. Additional studies may help understand the dynamics of microbial communities, facing the future exposure to the oil and / or derivatives.
Os manguezais sÃo essistemas importantes e produtivos, encontrados ao longo da linha da costa de regiÃes tropicias e subtropicais. Processos importantes como a ciclagem de nutrientes, estÃo diretamente conectados à atividade das comunidades microbianas desses solos. Dada sua posiÃÃo estratÃgica os manguezais sÃo bastante impactados no mundo todo. No Brasil, Ãreas importantes como a da BaÃa de todos os Santos (BA) sÃo severamente afetadas pela presenÃa do petrÃleo. Compreender as adaptaÃÃes da microbiota local e sua dinÃmica, frente Ãs alteraÃÃes ambientais, à essencial para que se consiga manter ou restaurar esses ecossistemas. A presente dissertaÃÃo investigou a estrutura e a funÃÃo de comunidades microbianas em uma Ãrea de manguezal da baÃa de Todos os Santos poluÃda pela indÃstria do petrÃleo. Dois locais foram amostrados - um, situado na Ãrea de refinamento dessa indÃstria e o outro, distante desse local e usado como controle. AlÃm dos dados abiÃticos medidos, dois mÃtodos independentes de cultivo foram utilizados: T-RFLP e microarranjos de DNA. Os resultados de ambos os sÃtios nos experimentos de T-RFLP mostraram que as duas comunidades bacterianas diferem quanto à sua estrutura. Para o sÃtio amostrado na refinaria, um nÃmero maior de OTUs sugere um estÃmulo ambiental, na comunidade bacteriana, fato associÃvel ao alto teor de matÃria orgÃnica desse local. Para os microarranjos de DNA, categorias similares de genes foram detectados, em ambos os locais, mas a especificidade de suas sequÃncias foi distinta. Os genes que codificam para a remediaÃÃo orgÃnica, foram os mais representativos, mais de 40% no total nos dois sÃtios. Mesmo detectando categorias semelhantes, apenas 4% das sequÃncias genÃticas foram comuns aos sÃtios. Estes dados mostram que organismos diferentes sÃo responsÃveis por funÃÃes similares em cada ponto. A diferenÃa entre os locais observadas nos experimentos pode ser relacionada, com o fato do sÃtio 1 situar-se numa regiÃo fortemente afetada por hidrocarbonetos. Utilizando-se Ãndices ecolÃgicos os dados de T-RFLP indicaram o sÃtio 1 como o mais diverso, enquantoo os resultados com os microarranjos de DNA mostram o oposto. Concluindo, a estrutura e funÃÃo da microbiota local sÃo afetadas pela presenÃa da indÃstria do petrÃleo. Estudos adicionais poderÃo ajudar a compreender a dinÃmica dessas comunidades microbianas, frente Ãs futuras exposiÃÃes ao Ãleo e/ou derivados.
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Paes, Fernanda Araújo. "Análise de comunidades microbianas de solo de manguezal por T-RFLP e microarranjos de DNA." reponame:Repositório Institucional da UFC, 2008. http://www.repositorio.ufc.br/handle/riufc/4926.
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PAES, F. A. Análise de comunidades microbianas de solo de manguezal por T-RFLP e microarranjos de DNA. 2008. XVI; 128 f. Dissertação (Mestrado em Ciências Marinhas Tropicais) - Instituto de Ciências do Mar, Universidade Federal do Ceará, Fortaleza, 2008.Submitted by Solange Gomes (solagom@yahoo.com.br) on 2013-02-06T18:56:41Z No. of bitstreams: 1 Fernanda Araujo Paes.pdf: 880237 bytes, checksum: 6153306cc4bd44febecb7ee196c60094 (MD5)
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Os manguezais são ecossistemas importantes e produtivos, encontrados ao longo da linha da costa de regiões tropicais e subtropicias. Processos importantes, como a ciclagem de nutrientes, estão diretamente conectados à atividade das comunidades microbianas desses solos. Dada sua posição estratégica, os manguezais são bastante impactados no mundo todo. No Brasil, áreas importantes como a da Baía de todos os Santos (BA) são severamente afetadas pela presença do petróleo. Compreender as adaptações da microbiota local e sua dinâmica, frente às alterações ambientais, é essencial para que se consiga manter ou restaurar esses ecossistemas. A presente dissertação investigou a estrutura e a função de comunidades microbianas em uma área do manguezal da baía de Todos os Santos, poluída pela indústria do petróleo. Dois locais foram amostrados – um, situado na área de refinamento dessa indústria e o outro, distante desse local e usado como controle. Além dos dados abióticos medidos, dois métodos independentes de cultivo foram utilizados: T-RFLP e microarranjos de DNA. Os resultados de ambos os sítios, nos experimentos de T-RFLP, mostraram que as duas comunidades bacterianas diferem quanto à sua estrutura. Para o sítio amostrado na área da refinaria, um número maior de OTUs sugere um estímulo ambiental, na comunidade bacteriana, fato associável ao alto teor de matéria orgânica desse local. Para os microarranjos de DNA, categorias similares de genes foram detectadas, em ambos os locais, mas a especificidade de suas sequências foi distinta. Os genes que codificam para a remediação orgânica foram os mais representativos, mais de 40% do total nos dois sítios. Mesmo detectando categorias semelhantes, apenas 4% das sequências genéticas foram comuns aos sítios. Estes dados mostram que organismos diferentes são responsáveis por funções similares em cada ponto. A diferença entre os locais, observada nos experimentos, pode ser relacionada com o fato do sítio 1 situar-se numa região fortemente afetada por hidrocarbonetos. Utilizando-se índices ecológicos, os dados de T-RFLP indicaram o sítio 1 como mais diverso, enquanto os resultados dos microarranjos de DNA mostraram o oposto. Concluindo, a estrutura e função da microbiota local são afetadas pela presença da indústria do petróleo. Estudos adicionais poderão ajudar a compreender a dinâmica dessas comunidades microbianas, frente às futuras exposições ao óleo e/ou derivados.
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Andrade, Pedro Avelino Maia de. "A composição da comunidade bacteriana do solo como fator determinante na micorrização de cana-de-açúcar por Glomus clarum." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/11/11140/tde-26062013-143930/.
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A cana-de-açúcar é uma das principais culturas do sistema agrícola brasileiro, e apresenta-se atualmente em plena expansão. Porém o uso do solo e a implementação de diferentes tecnologias de manejo têm originado alterações no equilíbrio ambiental, onde importantes interações microbianas ocorrem de forma essencial para o desenvolvimento vegetal. Dentre a vasta diversidade de microrganismos do solo, destacam-se os fungos micorrízicos, organismos intimamente associados as raízes das plantas, auxiliando a mesma, dentre outras formas, na obtenção de água e nutrientes. Estes fungos, no entanto, interagem também com outros organismos do solo, como por exemplo, com a comunidade bacteriana presente neste ambiente. Desta forma, o presente trabalho buscou estudar a dinâmica de interação entre cana-de-açúcar e o fungo micorrízico arbuscular (FMA) G.clarum em solos com diferentes composições da comunidade bacteriana. A metodologia utilizada foi a \'diluição para extinção\', onde diluições seriadas (10-1; 10-3; 10-6 e 10-9) de um solo natural foram usadas para inocular o solo estéril. Sobre esta base, foi monitorada pelo período de 60 dias, a colonização da planta pelo FMA e a estruturação das comunidades bacterianas. Como resultado, foi observada uma maior colonização das raízes de cana-de-açúcar para os tratamentos inoculada com menores diluições da comunidade original (solo natural e diluições 10-1 e 10-3), sendo da mesma forma observada uma distinção entre as comunidades bacterianas destes tratamentos para os demais. Estabelecendo correlações entre os grupos microbianos e as taxas de colonização micorrízica, foi possível nomear, com base no sequenciamento massivo da região V6 do gene ribossomal 16S DNAr, a alteração conjunta da micorrização com mudanças nos grupos de Actinobacteria,Bacteriodetes,Firmicutes,Proteobacteria,Verrucomicrobiae Acidobacteria. Concluindo, este trabalho demonstra a dependência que um processo importante, como a micorrização, possui da comunidade bacteriana do solo, e indica que em áreas degradadas, com menores níveis de diversidade bacteriana, tal processo pode ocorrer com menor eficiência.Sugarcane is an important Brazilian agricultural system crop and presents currently booming. Nevertheless, land use, and implementation of different management technologies have originated changes in environmental balance, where important microbial interactions occur as essential for plant development. Among the wide diversity of soil microorganisms, the mycorrhizal fungi is highilighted as organisms closely associated with plant roots, helping plants, in any way, to obtain water and nutrients. These fungi however, also interact with other soil organisms, such as for example, bacterial community in these environments. Thus, the present work aimed to study the dynamics of interaction between sugarcane and arbuscularmycorrhizal fungi (AMF) Glomusclarum in soils with different compositions of the bacterial community. The methodology used was \"dilution to extinction\", where serial dilutions (10-1, 10-3, 10-6 and 10-9) of a natural soil were used to inoculate a sterile soil. On this basis, were monitored along a period of 60 days, plant colonization by AMF, and structure of bacterial communities. As a result, we observed a higher colonization of roots of cane sugar for treatments inoculated with lower dilutions of the original community (natural soil and dilutions 10-1 and 10-3), and likewise observed a distinction between these bacterial communities treatments to others. Establishing correlations between microbial groups with observed rates of colonization, it was possible to name, based on the massive sequencing of the region V6 ribosomal gene 16S rDNA, the joint amendment of mycorrhiza with changes in groups of Actinobacteria; Bacteriodetes; Firmicutes, Proteobacteria; Verrucomicrobia and Acidobacteria. In conclusion, this work demonstrates the dependence of an important process, as the AMF, has tosoil bacterial community, and indicates that degraded areas, with lower levels of bacterial diversity, such a process can occur with lower efficiency.
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Campana, Felippe Buck. "Monitoramento temporal e espacial de contaminações bacterianas na produção de bioetanol: caracterização molecular por T-RFLP e detecção quantitativa por qPCRde comunidades formadoras de biofilmes." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/64/64133/tde-25102012-164236/.
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A contaminação bacteriana por espécies dos gêneros Lactobacillus, Bacillus e Leuconostoc entre outras bactérias lácticas é um dos principais fatores que afetam o rendimento da fermentação alcoólica. A formação de biofilmes acaba protegendo as bactérias e é uma fonte permanente de contaminação. Objetivando caracterizar tais contaminações em (1) biofilmes de centrífuga, dorna, trocador de calor e tubulação de água e (2) melaço, mosto, levedo, levedo tratado (com H2SO4) e vinho, amostras foram coletadas em diferentes períodos de um sistema fermentativo de alto teor alcoólico (16%). As enzimas de restrição AluI, BstUI, HaeIII, HinfI, MseI e MspI utilizadas nas análises de T-RFLP foram definidas por análises in silico com sequências do gene 16S rRNA de contaminantes freqüentes. Essas enzimas geram uma maior quantidade de T-RFs únicos entre 30 e 650 pb. Os DNAs extraídos das amostras foram submetidos às análises de T-RFLP para obtenção do perfil molecular das comunidades microbianas dos pontos de coleta. Os índices de diversidade de Shannon foram calculados com base no número dos T-RFs. Foram realizadas as análises dos componentes principais (PCA) e a inferência filogenética dos contaminantes com base nos perfis dos T-RFs. A quantificação dos principais táxons contaminantes foi feita por qPCR utilizando primers específicos delineados neste estudo e considerando a média de cópias do gene 16S rRNA presentes no genoma de cada táxon bacteriano. Na primeira coleta o biofilme de água apresentou maior índice de diversidade microbiana e na segunda, melaço e mosto. PCA sugere que os biofilmes (e não as fontes externas) são os principais contaminantes desse processo fermentativo devido as suas semelhanças com a composição das outras comunidades analisadas. Espécies de Lactobacillus e Bacillus predominaram entre as amostras da primeira coleta. Halomonas, Streptococcus, Lactococcus e Pseudomonas foram detectados em amostras de biofilme e em amostras líquidas, sendo os principais contaminantes provindos de biofilme no momento da primeira coleta. Na segunda coleta Bacillus foi o principal contaminante e novamente gêneros produtores de ácido lático como Streptococcus, Lactobacillus e Staphylococcus foram os mais freqüentes. Os resultados concordam com o reportado na literatura sobre sistemas fermentativos convencionais. Apenas os primers desenhados para amplificação do gene 16S rRNA de Burkholderia, Pseudomonas e Weissella apresentaram especificidade em testes com isolados. Halomonas sp. foi encontrada em biofilme de dorna através do sequenciamento utilizando primers para esse gênero. Halomonas pode produzir levânio podendo haver o consumo da sacarose disponível para fermentação. Biofilme da centrífuga teve a maior quantidade de micro-organismos nos dois momentos de coleta (1,93E+06 UFC.mg-1 e 2,14E+07 UFC.mg-1, respectivamente) assim como as amostra de levedo entre as amostras líquidas (1,03E+08 UFC.ml-1 e 2,96E+06 UFC.ml-1, na primeira e segunda coleta, respectivamente), indicando níveis consideráveis de contaminantes. Burkholderia e Pseudomonas foram os mais abundantes entre as amostras de biofilmes da primeira e segunda coleta. Nas amostras líquidas Burkholderia apresentou-se em maior quantidade na maioria das amostras da primeira coleta; enquanto Pseudomonas e Weissella em geral predominaram equivalentemente entre as amostras da segunda coletaBacterial contamination by Lactobacillus, Bacillus and Leuconostoc and other lactic acid bacteria is one of the main factors that affects the yield in alcoholic fermentation process. Biofilm formation protects the bacteria community and it is a permanent source of contamination. For characterization of these contaminations in (1) biofilms from centrifuge, tank fermentation, heat exchanger and water pipe and (2) molasses, must, yeast, yeast treated (with H2SO4) and wine, samples were taken at two different periods from fermentation system characterized by high alcohol yields (16%). Restriction enzymes AluI, BstUI, HaeIII, HinfI, MseI and MspI used in T-RFLP analysis were defined by 16S rRNA gene sequences analysis in silico from common contaminants. These enzymes generate high number of unique T-RFs between 30 and 650 bp. DNA from samples were used as template in T-RFLP reactions in order to obtain molecular profiles of microbial communities present at each sample. Shannon diversity index was calculated based on T-RFs numbers. Principal component analysis (PCA) and phylogenetic inference of contaminants were performed based on T-RFs profiles. The main contaminant bacterial taxa were quantified by qPCR using specific primers designed in this study and considering the average of 16S rRNA gene copies previously counted into the genome of each bacterial taxon. Water pipe biofilm showed the highest rate of bacterial diversity in the samples collected in the first sampling period. For the samples collected in the second sampling, the highest rate of bacterial diversity was revealed for molasses and must. PCA suggested that biofilms (but not external sources) are the main contaminants in the studied fermentation process. It is probably due their similarities with the composition of other analyzed communities. Lactobacillus and Bacillus species predominated in first sampling period. Halomonas, Streptococcus, Lactococcus and Pseudomonas were detected in biofilm and liquid samples. They were the main contaminants from biofilm at this time of sampling. In the second sampling period, Bacillus was the most common genera and other lactic acid bacteria such Streptococcus, Staphylococcus and Lactobacillus were also the most frequent contaminants. These results agree with other reported in the literature about conventional fermentation systems. Only the primers designed in this study to amplify the 16S rRNA gene of Burkholderia, Pseudomonas and Weissella showed specificity in tests with bacterial strains. Halomonas sp. was revealed in biofilms from tank fermentation by DNA sequencing using designed primers for genera. Halomonas can produce levan and may consume sucrose available for generation of alcohol. Centrifugal biofilm had the highest amount of bacteria in both sampling periods (1.93E+06 CFU.mg-1 and 2.14E+07 CFU.mg-1, respectively). In liquid samples, yeast had the highest amount of bacteria in both sampling periods (1.03E+08 CFU.ml-1 and 2.96E+06 CFU.ml-1, respectively); it shows significant levels of contaminants. Burkholderia and Pseudomonas were more abundant among biofilm samples of all samplings. Burkholderia was present in high quantities in the majority of liquid samples taken during the first sampling period; Pseudomonas and Weissella equivalently predominated among samples taken during the second sampling period
Book chapters on the topic "T-RFLP"
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Tebbe, Christoph C., Anja B. Dohrmann, Michael Hemkemeyer, and Astrid Näther. "Microbial Community Profiling: SSCP and T-RFLP Techniques." In Springer Protocols Handbooks, 101–26. Berlin, Heidelberg: Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/8623_2015_158.
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Hodgetts, Jennifer, and Matt Dickinson. "T-RFLP for Detection and Identification of Phytoplasmas in Plants." In Methods in Molecular Biology, 233–44. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-089-2_20.
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Park, Min Sik, Aida Barbetti, Toshinao Takenouchi, and Paul I. Terasaki. "Analysis of Class II RFLP Patterns and T-Cell Clone Reactions." In Immunobiology of HLA, 921–42. New York, NY: Springer New York, 1989. http://dx.doi.org/10.1007/978-1-4612-3552-1_267.
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Osborne, Catherine A. "Terminal Restriction Fragment Length Polymorphism (T-RFLP) Profiling of Bacterial 16S rRNA Genes." In Methods in Molecular Biology, 57–69. Totowa, NJ: Humana Press, 2014. http://dx.doi.org/10.1007/978-1-62703-712-9_5.
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Païssé, S., M. S. Goñi-Urriza, A. Fahy, and R. Duran. "Molecular Profiling of Bacterial Communities via 16S rRNA Gene Based Approaches – Focus T-RFLP." In Handbook of Hydrocarbon and Lipid Microbiology, 4113–25. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-540-77587-4_321.
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Kim, Sang-Hoon, and Terence Marsh. "Section 3 update: The Analysis of Microbial Communities with Terminal Restriction Fragment Length Polymorphism (T-RFLP)." In Molecular Microbial Ecology Manual, 2691–710. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-2177-0_315.
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Siqueira, José F., Mitsuo Sakamoto, and Alexandre S. Rosado. "Microbial Community Profiling Using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and Denaturing Gradient Gel Electrophoresis (DGGE)." In Methods in Molecular Biology, 71–85. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-820-1_6.
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Tiquia, Sonia M. "Using Terminal Restriction Fragment Length Polymorphism (T-RFLP) Analysis to Assess Microbial Community Structure in Compost Systems." In Methods in Molecular Biology, 89–102. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60761-439-5_6.
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Siqueira, José F., Mitsuo Sakamoto, and Alexandre S. Rosado. "Microbial Community Profiling Using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and Denaturing Gradient Gel Electrophoresis (DGGE)." In Methods in Molecular Biology, 91–104. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2780-8_7.
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Siqueira, José F., Mitsuo Sakamoto, and Alexandre S. Rosado. "Microbial Community Profiling Using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and Denaturing Gradient Gel Electrophoresis (DGGE)." In Methods in Molecular Biology, 139–52. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6685-1_8.
Full textConference papers on the topic "T-RFLP"
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Mounce, Stephen R., Henriette S. Jensen, Catherine A. Biggs, and Joby B. Boxall. "Data mining T-RFLP profiles from urban water system sampling using self-organizing maps." In 2012 8th International Conference on Natural Computation (ICNC). IEEE, 2012. http://dx.doi.org/10.1109/icnc.2012.6234528.
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Dong, Ping, Yujiao Sun, Hongqi Wang, Liding Chen, and Hui Zhang. "Notice of Retraction: Study on Riparian Zone Microbial Community Structure of the Wenyu River by T-RFLP Analysis." In 2011 5th International Conference on Bioinformatics and Biomedical Engineering. IEEE, 2011. http://dx.doi.org/10.1109/icbbe.2011.5780057.
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Sharma, Vineeta, Pallavi Singhal, Anoop Kumar, V. G. Ramachandran, Shukla Das, and Mausumi Bharadwaj. "Association of TNF-α–rs 281865419 polymorphism with reproductive tract infections in Indian population." In 16th Annual International Conference RGCON. Thieme Medical and Scientific Publishers Private Ltd., 2016. http://dx.doi.org/10.1055/s-0039-1685357.
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Aim: To investigate the presence of reproductive tract infections (RTIs) in symptomatic and asymptomatic women in North India and association of SNPs in TNF? gene (rs-281865419 C/T) with susceptibility to these RTIs. Methods: We collected 100 symptomatic (cases) and 100 asymptomatic women (controls) samples and screened them for RTIs. Then genotyping of TNF-? gene was performed by PCR-RFLP. Results: Among cases the frequencies of RTIs infection is higher than control. The prevalence of HPV, C. trachomatis, T. vaginalis, Bacterial vaginosis and N. gonorrhoeae are 28% and 6%; 11%, 32% respectively while in controls it was 5%, 2%, 1% and 8% and 1%. In the present study we found that the frequency of wild homozygous genotype (TT) was lower in cases 30% (6/20) as compared to controls 60% (12/20). The frequency of the heterozygous polymorphic genotype (CT) was higher in cases 65% (65/100) as compared to controls 32% (32/100). It was interesting to note that the frequency of the polymorphic homozygous genotype (CC) was higher in cases 15% (15/100) than controls 2% (2/100). While the frequency of the carrier genotype (CT + TT) was found to be more in cases 70% (70/100) than in controls 40/100 (40%). This study shows that T allele may be risk factor for reproductive tract infections as its percentage is higher in cases as compare to normal controls. Conclusion: TNF-? rs-281865419 locus may serve as an important biomarker for RTIs predisposition in Indian population though larger sample size is needed to validate the findings.
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Sharma, Vineeta, Pallavi Singhal, Anoop Kumar, V. G. Ramachandran, Shukla Das, and Mausumi Bharadwaj. "Association of TNF-α rs-281865419 polymorphism with reproductive tract infections in Indian population." In 16th Annual International Conference RGCON. Thieme Medical and Scientific Publishers Private Ltd., 2016. http://dx.doi.org/10.1055/s-0039-1685270.
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Aim: To investigate the presence of reproductive tract infections (RTIs) in symptomatic and asymptomatic women in North India and association of SNPs in TNFα gene (rs-281865419 C/T) with susceptibility to these RTIs. Methods: We collected 100 symptomatic (cases) and 100 asymptomatic women (controls) samples and screened them for RTIs. Then genotyping of TNF-α gene was performed by PCR-RFLP. Results: Among cases the frequencies of RTIs infection is higher than control. The prevalence of HPV, C. trachomatis, T. vaginalis, Bacterial vaginosis and N. gonorrhoeae are 28% & 6%; 11%, 32% respectively while in controls it was 5%, 2%, 1% and 8% & 1%. In the present study we found that the frequency of wild homozygous genotype (TT) was lower in cases 30% (6/20) as compared to controls 60% (12/20). The frequency of the heterozygous polymorphic genotype (CT) was higher in cases 65% (65/100) as compared to controls 32% (32/100). It was interesting to note that the frequency of the polymorphic homozygous genotype (CC) was higher in cases 15% (15/100) than controls 2% (2/100). While the frequency of the carrier genotype (CT + TT) was found to be more in cases 70% (70/100) than in controls 40/100 (40%). This study shows that T allele may be risk factor for Reproductive tract infections as its percentage is higher in cases as compare to normal controls. Conclusion: TNF-? rs-281865419 locus may serve as an important biomarker for RTIs predisposition in Indian population though larger sample size is needed to validate the findings.
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Táncsics, András, István Szabó, Sándor Szoboszlay, Erzsébet Baka, Károly Márialigeti, and Sára Révész. "The role of Beta-Proteobacteria in aromatic hydrocarbon degradation: fingerprinting of 16S rRNA gene and catechol 2,3-dioxygenase gene by T-RFLP in BTEX degradative bacterial communities." In Proceedings of the II International Conference on Environmental, Industrial and Applied Microbiology (BioMicroWorld2007). WORLD SCIENTIFIC, 2009. http://dx.doi.org/10.1142/9789812837554_0138.
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Sakaguchi, Alberto Yoich, Marla Karine Amarante, Carlos Eduardo Coral Oliveira, Fausto Celso Trigo, and Maria Angelica Ehara Watanabe. "INFLUÊNCIA DO POLIMORFISMO GENÉTICO DO RECEPTOR II DO TGF BETA NA APRESENTAÇÃO CLÍNICA DE PACIENTES COM LEUCEMIA LINFOIDE AGUDA INFANTOJUVENIL NA POPULAÇÃO BRASILEIRA." In I Congresso Brasileiro de Hematologia Clínico-laboratorial On-line. Revista Multidisciplinar em Saúde, 2021. http://dx.doi.org/10.51161/rems/625.
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Introdução: A leucemia linfoide aguda (LLA) é uma neoplasia hematológica que acomete a diferenciação celular e a proliferação exacerbada de células precursoras das linhagens B, T e Natural Killer, apresentando maior incidência na faixa pediátrica. O receptor para o fator de crescimento transformador beta (TGFβR) parece estar envolvido em doenças hematológicas, e um polimorfismo de nucleotídeo único foi identificado em sua região promotora (G-875A) parecendo modificar a expressão de TGFβRII nas células. Objetivo: Avaliar o envolvimento do TGFβRII G-875A na LLA infantil brasileira, com foco na suscetibilidade, parâmetros clínico-patológicos e estratificação de risco. Material e métodos: Estudo de associação caso-controle, envolvendo 127 pacientes com LLA e 161 crianças livres de neoplasia. A avaliação foi realizada através da reação em cadeia da polimerase (PCR) seguida da análise do polimorfismo do comprimento do fragmento de restrição (RFLP). Resultados: Em relação à distribuição dos genótipos, não houve diferença estatisticamente significativa entre os subgrupos de LLA e as crianças controle. Verificou-se que o G-875A foi estatisticamente associado ao aumento da suscetibilidade para LLA-B no modelo recessivo (OR = 2,16; IC = 1,02–4,57; p <0,05), também foi observada associação significativamente aumentada para alto risco (AR) para recidiva no mesmo modelo (OR = 5,14; IC = 1,05–25,12; p <0,05). Além disso, foi observada correlação positiva entre o grupo de risco e o polimorfismo G-875A no modelo recessivo na LLA-B (p = 0,02). Em relação à LLA-T, foi observada correlação positiva entre recidiva e G-875A nos modelos aditivo e dominante (p=0,05 e p=0,028, respectivamente). Conclusão: Verificou-se que o G-875A foi associado ao aumento da suscetibilidade para LLA-B e AR para recidiva em modelo recessivo. Também houve correlação positiva entre a recidiva de LLA e G-875A nos modelos aditivo e dominante, podendo este polimorfismo ser um forte candidato a um possível marcador prognóstico na LLA.
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Bernaedi, F., V. Bertagnolo, S. Bartolai, L. Rossi, F. Panicucci, and F. Conconi. "A POINT MUTATION AND A GENE DELETION OF FVIII GENE IN SEVERE HAEMOPHILIA." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644047.
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The presence of Factor VIII (FVIII) gene lesions has been investigated in 100 haemophilia A patients using cDNA probes for the 3'part of FVIII gene (exons 14-26 ).In two related severe patients without inhibitor a deletion removesthe exon 26; the gene lesion has been confirmed with several restriction enzymes and has been shown by densitometry of the autoradiographic pattern in a woman of the same family. The complete deletionof the exon 26 has been described by Gitschier et al. in a patient with inhibitor. Thus the comparison of the end points of the two deletions could help to define the mechanism originating these gene lesions and the relation between gene lesions and the presence of antibody.In a patient with severe Haemophilia and without inhibitor a mutation removing the TaqI site in the exon 24 and originating an abnormal band of 4.2 Kb has been found. A C→T transition in this TaqI site, originating a nonsense codon and a new Hindlll site, has been reported by Gitschier et al in a patient presenting inhibitor. The DNA from our patient tested with Hindlll shows a normal pattern thus indicating a C→T transition in the antisense strand. This mutation should causean aminoacid change (CGA→CAA, Arg→Gln) possiblyresponsible for the FVIII inactivation but that does not remove theantigenic determinants present in the COOH terminal part of FVIII.In addition the same mutation has been observed in an unrelated (asdemonstrated by RFLPs analysis) Italian haemophilic patient confirming the observation of Youssoufian et al that TaqI sites are mutational hot spots in FVIII gene.
Reports on the topic "T-RFLP"
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Michel Jr., Frederick C., Harry A. J. Hoitink, Yitzhak Hadar, and Dror Minz. Microbial Communities Active in Soil-Induced Systemic Plant Disease Resistance. United States Department of Agriculture, January 2005. http://dx.doi.org/10.32747/2005.7586476.bard.
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Induced Systemic Resistance (ISR) is a highly variable property that can be induced by compost amendment of potting media and soils. For example, previous studies showed that only 1 of 79 potting mixes prepared with different batches of mature composts produced from several different types of solid wastes were able to suppress the severity of bacterial leaf spot of radish caused by Xanthomonas campestris pv. armoraciae compared with disease on plants produced in a nonamended sphagnum peat mix. In this project, microbial consortia in the rhizosphere of plants grown in ISR-active compost-amended substrates were characterized. The plants used included primarily cucumber but also tomato and radish. Rhizosphere microbial consortia were characterized using multiple molecular tools including DGGE (Israel) and T -RFLP (Ohio) in both ISR-active field plots and potting media. Universal as well as population-specific bacterial and fungal PCR primers were utilized. T -RFLP analyses using universal bacterial primers showed few significant differences in overall bacterial community composition in ISR-active and inactive substrates (Ohio). In addition, the community members which were significantly different varied when different ISR-activecomposts were used (Ohio). To better characterize the shifts in microbial community structure during the development of ISR, population specific molecular tools were developed (Israel, Ohio).-PCR primers were designed to detect and quantify bacterial groups including Pyrenomycetes, Bacillus, Pan toea, Pseudomonas, Xanthomonas and Streptomyces as well as Trichoderma and Fusarium; two groups of fungi that harbor isolates which are ISR active (Isreal and Ohio). Bacterial consortia associated with cucumber plants grown in compost-amended potting mixtures were shown to be dominated by the phylogenetic taxon Bacteroidetes, including members of the genus Chryseobacterium, which in some cases have been shown to be involved in biocontrol (Israel). Nested-PCR-DGGE analyses coupled with long l6S rDNA sequencing, demonstrated that the Chryseobacteriumspp. detected on seed and the root in compost-amended treatments were derived from the compost itself. The most effective ISR inducing rhizobacterial strains were identified as Bacillus sp. based on partial sequencing of l6S rDNA. However, these strains were significantly less effective in reducing the severity of disease than Trichoderma hamatum382 (T382). A procedure was developed for inoculation of a compost-amended substrate with T -382 which consistently induced ISR in cucumber against Phytophthora blight caused by Phytophthora capsiciand in radish against bacterial spot (Ohio). Inoculation of compost-amended potting mixes with biocontrol agents such as T -382 and other microbes that induce systemic resistance in plants significantly increased the frequency of systemic disease control obtained with natural compost amendments.
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Dubcovsky, Jorge, Tzion Fahima, and Ann Blechl. Positional cloning of a gene responsible for high grain protein content in tetraploid wheat. United States Department of Agriculture, September 2003. http://dx.doi.org/10.32747/2003.7695875.bard.
Full textAbstract:
High Grain Protein Content (GPC) is a desirable trait in breadmaking and pasta wheat varieties because of its positive effects on quality and nutritional value. However, selection for GPC is limited by our poor understanding of the genes involved in the accumulation of protein in the grain. The long-term goal of this project is to provide a better understanding of the genes controlling GPC in wheat. The specific objectives of this project were: a) to develop a high-density genetic map of the GPC gene in tetraploid wheat, b) to construct a T. turgidum Bacterial Artificial Chromosome (BAC) library, c) to construct a physical map of the GPC gene and identify a candidate for the GPC gene. A gene with a large effect on GPC was detected in Triticum turgidum var. dicoccoides and was previously mapped in the short arm of chromosome 6B. To define better the position of the Gpc-B1 locus we developed homozygous recombinant lines with recombination events within the QTL region. Except for the 30-cM region of the QTL these RSLs were isogenic for the rest of the genome minimizing the genetic variability. To minimize the environmental variability the RSLs were characterized using 10 replications in field experiments organized in a Randomized Complete Block Design, which were repeated three times. Using this strategy, we were able to map this QTL as a single Mendelian locus (Gpc-B1) on a 2.6-cM region flanked by RFLP markers Xcdo365 and Xucw67. All three experiments showed that the lines carrying the DIC allele had an average absolute increase in GPC of 14 g/kg. Using the RFLP flanking markers, we established the microcolinearity between a 2.l-cM region including the Gpc-B1 gene in wheat chromosome 6BS and a 350-kb region on rice chromosome 2. Rice genes from this region were used to screen the Triticeae EST collection, and these ESTs were used to saturate the Gpc-B1 region with molecular markers. With these new markers we were able to map the Gpc-B1 locus within a 0.3-cM region flanked by PCR markers Xucw83 and Xucw71. These flanking markers defined a 36-kb colinear region with rice, including one gene that is a potential candidate for the Gpc-B1 gene. To develop a physical map of the Gpc-B1 region in wheat we first constructed a BAC library of tetraploid wheat, from RSL#65 including the high Gpc-B1 allele. We generated half- million clones with an average size of l3l-kb (5.1 X genome equivalents for each of the two genomes). This coverage provides a 99.4% probability of recovering any gene from durum wheat. We used the Gpc-BI flanking markers to screen this BAC library and then completed the physical map by chromosome walking. The physical map included two overlapping BACs covering a region of approximately 250-kb, including two flanking markers and the Gpc-B1 gene. Efforts are underway to sequence these two BACs to determine if additional wheat genes are present in this region. Weare also developing new RSLs to further dissect this region. We developed PCR markers for flanking loci Xucw79andXucw71 to facilitate the introgression of this gene in commercial varieties by marker assisted selection (httQ://maswheat.ucdavis.edu/ orotocols/HGPC/index.hlm). Using these markers we introgressed the Gpc-B1 gene in numerous pasta and common wheat breeding lines.