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Transcriptomic and metatranscriptomic approaches to characterizing genes coding for fiber digestion within the rumen ecosystemWang, Pan January 2013 (has links)
The rumen microbiome constitutes a unique genetic resource of plant fiber degrading microbial enzymes that could be used for agricultural and industrial purposes. Anaeromyces mucronatus is a poorly characterized anaerobic lignocellulolytic fungus in the rumen. This thesis aimed at better understanding A. mucronatus YE505 and the particle associated rumen microbiota based on transcriptomic and metatranscriptomic approaches. High quality RNA was isolated from the fiber-associated rumen sample based on an improved RNA extraction method. A transcriptomic study was performed to investigate the expression of the fiber degrading system of A. mucronatus YE505, and the functional diversity of the fiber-associated eukaryotes from the rumen of muskoxen (Ovibos moschatus) was explored by a metatranscriptomic study. Much carbohydrate degradation related protein modules were detected. This study established effective approaches to characterizing the functional contents of rumen eukaryotic microbiome as well as rumen fungi, and identified several candidate genes that merit further investigation. / xiv leaves : ill. (some col.) ; 29 cm
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An analysis of salmonid RNA sequences and implications for salmonid evolutionBrown, Gordon David 01 April 2008 (has links)
This work addresses two areas of computational biology: automation of sequence
processing and an assessment of the evidence for a hypothesized salmonid
genome based on an analysis of a set of expressed sequence tags.
Three problem areas in sequence processing are addressed in the first half of
the work. Chapter 3 describes an accurate technique for trimming of vector,
adapter and poly(A) sequence. Chapter 4 suggests methods for verifying the
accuracy of assembled mRNA transcripts despite a large number of
chimeras in the cDNA clone libraries. Chapter 5 is concerned with the problem
of estimating the number of transcripts in a tissue or cDNA library, concluding
that computational and statistical techniques are inadequate to estimate the
quantity accurately.
The hypothesized salmonid genome duplication has been widely accepted since
1984. If it occurred, it should have left evidence in the form of many
paralogous pairs of genes, all at approximately the same degree of sequence
divergence. To assess this question, several hundred thousand ESTs were
assembled into transcripts, compared to each other to find homologs, and
the evolutionary distances of the homologs represented as a histogram.
Evidence of a single evolutionary event was not seen. The same procedure
was applied to Xenopus laevis, which has a well-established recent
genome duplication, and Danio rerio, which is known not to have had
one. In those cases, the evidence for or against a genome duplication
appeared exactly as predicted. The conclusion is that if the salmonid
genome duplication occurred, some force altered its evolutionary development
subsequently to mask the duplication, but also that a genome duplication is not
necessary to explain the observed pattern of homolog distances.
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Luminescence-Based MicroRNA Detection MethodsCissell, Kyle A. 27 August 2012 (has links)
Indiana University-Purdue University Indianapolis (IUPUI) / MicroRNAs (miRNA) are short, 18-24 nucleotide long noncoding RNAs. These small RNAs, which are initially transcribed in the nucleus, are transported into the cell cytoplasm where they regulate protein translation either through direct cleavage of mRNA, or indirect inhibition through binding to mRNA and disrupting the protein translation machinery. Recently, miRNAs have gained much attention due to their implication in numerous diseases and cancers. It has been found that heightened or lowered levels of miRNA in diseased cells vs. healthy cells are linked to disease progression. It is therefore immensely important to be able to detect these small molecules. Current detection methods of Northern blotting, microarrays, and qRT-PCR suffer from drawbacks including low sensitivity, a lack of simplicity, being semi-quantitative in nature, time-consuming, and requiring expensive instruments. This work aims to develop novel miRNA technologies which will address these above problems. Bioluminescent labels are promising alternatives to current methods of miRNA detection. Bioluminescent labels are relatively small, similar in size to fluorescent proteins, and they emit very intense signals upon binding to their substrate. Bioluminescent labels are advantageous to fluorescent labels in that they do not require an external excitation source, rather, the excitation energy is supplied through a biochemical reaction. Therefore, background signal due to excitation is eliminated. They also have the advantage of being produced in large amounts through bacterial expression.
Four miRNA detection methods are presented which utilize luminescence-based methods. Three employ Renilla luciferase, a bioluminescent protein, and one is based on fluorescence. The presented methods are capable of detecting miRNA from the picomole (nanomolar) level down to the femtomole (picomolar) level. These methods are rapid, sensitive, simple, and quantitative, can be employed in complex matrices, and do not require expensive instruments. All methods are hybridization-based and do not require amplification steps.
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Influência da infusão parenteral de aminoácidos sobre a expressão gênica de fatores de crescimento de timidina quinase no remanescente hepático de ratos desnutridos / -Mazza, Rosangela Passos de Jesus 04 October 2004 (has links)
A Glutamina (Gln) melhora a regeneração hepática em ratos nutridos. Para avaliar o efeito molecular da Gln endovenosa no remanescente hepático, 52 ratos foram classificados em: 1. Nutridos com hepatectomia parcial (HP) e Gln (N-Gln=10) ou prolina (N-Pro=10); 2. Desnutridos com HP: (D-Gln=10) ou (D-Pro=10); 3. Nutridos e Desnutridos sem HP (N-Controle=6) e (D-Controle=6). Após 96 horas da HP os resultados foram: DNA = (D-Gln, D-Pro e D-Controle < N-Gln, N-Pro e N-controle), (N-Gln, N-Pro, D-Gln e D-Pro < N e D-Controle), (N-Gln > D-Gln); RNA= (N-Gln, N-Pro, D-Gln e D-Pro < N e D-Controle), (N-Gln > D-Gln e N-Pro). Não houve diferença nos genes transcritos (GT) para HGF, TGF-a e timidina kinase. Concluímos que: A desnutrição e HP reduzem DNA e RNA; A Gln não altera os GT estudados em ratos desnutridos 96 horas após HP / Glutamine dipeptide (Gln) improve hepatic regeneration of nourished rats. To evaluate molecular effect of Gln on liver remnant 52 rats was classified into: 1. Nourished with partial hepatectomy (PH) and Gln (N-Gln=10) or proline (N-Pro=10); 2. Malnourished (MN) with PH: (MN-Gln=10) or (MN-Pro=10); 3. Nourished and Malnourished rat without PH (N-Control=6) and (MN-Control=6). Results: DNA = (MN-Gln, MN-Pro and MN-Control < N-Gln, N-Pro and N-control), (N-Gln, N-Pro, MN-Gln and MN-Pro < N and MN-Control), (N-Gln > MN-Gln); RNA= (N-Gln, N-Pro, MN-Gln and MN-Pro < N and MN-Control), (N-Gln > MN-Gln and N-Pro). There was no difference on transcript genes (TG) for HGF, TGF-a and thymidine kinase. Conclusions: Malnutrition and PH decrease hepatic DNA and RNA; Gln does not modify TG studied 96 hours after PH in MN rats
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Influência da infusão parenteral de aminoácidos sobre a expressão gênica de fatores de crescimento de timidina quinase no remanescente hepático de ratos desnutridos / -Rosangela Passos de Jesus Mazza 04 October 2004 (has links)
A Glutamina (Gln) melhora a regeneração hepática em ratos nutridos. Para avaliar o efeito molecular da Gln endovenosa no remanescente hepático, 52 ratos foram classificados em: 1. Nutridos com hepatectomia parcial (HP) e Gln (N-Gln=10) ou prolina (N-Pro=10); 2. Desnutridos com HP: (D-Gln=10) ou (D-Pro=10); 3. Nutridos e Desnutridos sem HP (N-Controle=6) e (D-Controle=6). Após 96 horas da HP os resultados foram: DNA = (D-Gln, D-Pro e D-Controle < N-Gln, N-Pro e N-controle), (N-Gln, N-Pro, D-Gln e D-Pro < N e D-Controle), (N-Gln > D-Gln); RNA= (N-Gln, N-Pro, D-Gln e D-Pro < N e D-Controle), (N-Gln > D-Gln e N-Pro). Não houve diferença nos genes transcritos (GT) para HGF, TGF-a e timidina kinase. Concluímos que: A desnutrição e HP reduzem DNA e RNA; A Gln não altera os GT estudados em ratos desnutridos 96 horas após HP / Glutamine dipeptide (Gln) improve hepatic regeneration of nourished rats. To evaluate molecular effect of Gln on liver remnant 52 rats was classified into: 1. Nourished with partial hepatectomy (PH) and Gln (N-Gln=10) or proline (N-Pro=10); 2. Malnourished (MN) with PH: (MN-Gln=10) or (MN-Pro=10); 3. Nourished and Malnourished rat without PH (N-Control=6) and (MN-Control=6). Results: DNA = (MN-Gln, MN-Pro and MN-Control < N-Gln, N-Pro and N-control), (N-Gln, N-Pro, MN-Gln and MN-Pro < N and MN-Control), (N-Gln > MN-Gln); RNA= (N-Gln, N-Pro, MN-Gln and MN-Pro < N and MN-Control), (N-Gln > MN-Gln and N-Pro). There was no difference on transcript genes (TG) for HGF, TGF-a and thymidine kinase. Conclusions: Malnutrition and PH decrease hepatic DNA and RNA; Gln does not modify TG studied 96 hours after PH in MN rats
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