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Valdman, Alexander. "Molecular genetic markers of prostate cancer development /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-618-9/.
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Hoerder, Anna. "Mouse cortical subplate neurones : molecular markers, connectivity and development." Thesis, University of Oxford, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.442449.
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Tar'an, Bunyamin. "Development and application of molecular markers in common bean breeding." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0015/NQ47413.pdf.
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Song, Youqiang. "Development of polymorphic molecular markers for bovine gene mapping and selection." Thesis, University of Reading, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.262235.
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Liu, Shaolin 1968. "Oligonucleotides applied in genomics, bioinformatics and development of molecular markers for rice and barley." Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=85569.
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A genome sequence can be conceptualized as a 'book' written with four nucleotide 'letters' in oligonucleotide (oligo) 'words'. These words can be used in genomics, bioinformatics and the development of molecular markers. The whole-genome sequence for rice (Oryza sativa L.) is almost finished and has been assembled into pseudomolecules. For barley ( Hordeum vulgare L.) expressed sequence tags (ESTs) have been assembled into 21,981 tentative consensus sequences (TCs). The availability of such sequence information provides opportunities to investigate oligo usage within and between genomes. For the first of three studies reported in this thesis, a C++ program was written to automatically design oligos that are conserved between two sets of sequence information. In silico mapping between rice coding sequences (CDS) and barley TCs indicated that oligos between 18 and 24 bp provide good specificity and sensitivity (83% and 86%, respectively, for 20mers). Conserved oligos used as PCR primers had a high (91%) success rate on barley lines. Sequencing of PCR products revealed conservation in exon sequence, size and order between barley and rice. Introns were not conserved in sequence but were relatively stable in size. Map locations of eight new markers in barley revealed both genome colinearity and rearrangements between barley and rice. The second study reported in this thesis examined word frequency within the rice genome. A non-random landscape composed of high-frequency and low-frequency zones was observed. Interestingly, high-frequency words seemed to be rice specific while single-copy words were gene specific and conserved across species. As in the first study, oligos of 12 bp or less were not specific, and 18 bp seemed to be a critical length for the specificity of oligos. The third study reported in this thesis involved the development of molecular markers for known genes using public sequence information. Six new polymorphic markers were d
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Fazaeli, Asghar. "Development of molecular markers for the typing and genetic analysis of Toxoplasma gondii." Thesis, University of Aberdeen, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.367484.
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To develop robust and reproducible methods for molecular typing of Toxoplasma strains, the DNA regions of 5S rDNA, 28S-18S rDNA IGS SAG2, and GRA6 loci were examined. The 5S sequences were identical among 24 different strains; sequencing of the IGS region showed a few polymorphisms (0.66%) distinguishing virulence types. The IGS PCR-RFLP methods were developed and used to examine 29 strains of different virulence types. Sequence analysis of the IGS 5'-end showed great diversity between Neospora caninum and T. gondii. The IGS-RFLPs also clearly distinguished between those two closely related species. Nucleotide sequencing of the SAG2 locus (a surface antigen coding gene) showed 1.37% polymorphisms among 24 strains. Apart from a single nucleotide change at the 5'-flanking region, the type III and type I strains were identical. However, three new alleles of this locus were identified in minor variants of the strains. Analysis of the coding region of the GRA6 locus (a dense granule antigen coding gene) revealed a great degree of polymorphisms (3.24%) among 33 strains. Nine different alleles, representing the three current types and the minor variants of strains were characterised at this locus. A PCR-RFLP based on GRA6 polymorphisms was developed which could distinguish the three major types of T. gondii. This marker proved to be a suitable tool for a population study of the Toxoplasma parasite. The predominance of non-synonymous nucleotide substitutions in SAG2 and GRA6 genes confirmed positive selection in these loci, suggesting they play an important role in the parasite virulence. Phylogenetic analysis based on the multi-locus sequence alignment showed the existence of more than three lineages in Toxoplasma populations.
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Bickley, Jane. "Development of molecular markers for studying the ecology and epidemiology of Helicobacter pylori." Thesis, Open University, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.386793.
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Pharmawati, Made. "DNA-based approaches for development of markers to assist Grevillea and Leucadendron breeding." University of Western Australia. School of Plant Biology, 2006. http://theses.library.uwa.edu.au/adt-WU2006.0110.
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[Truncated abstract] Grevillea and Leucadendron belong to Proteaceae and both have economic importance to the floriculture industry. Grevillea is a highly diverse genus endemic to Australia and very attractive for landscaping. Leucadendron is a South African Proteaceae but is cultivated in Australia and is well known as a cut flower. This thesis focuses on the application of DNA-based molecular markers to these genera. Several groupings within Grevillea were suggested by previous researchers based on morphological characteristics. In this thesis the monophyly of the groupings among 12 Grevillea species from New South Wales was tested using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) analyses. To test the robustness of the data, UPGMA using Jaccard similarity, Neighbor Joining using total character difference and Wagner parsimony analyses were undertaken. The relationship trees generated supported monophyly of the groupings. Chloroplast DNA (cpDNA) was used to develop phylogenetic relationships among Leucadendron species. Inheritance and variation of cpDNA were evaluated using PCR-RFLP. The study demonstrated that cpDNA was inherited maternally and a phylogenetic tree of Leucadendron species using parsimony analysis was constructed. ... A fingerprinting study conducted using ISSR, produced a dendrogram showing the relationships among 30 cultivars. From the results, i a fingerprinting key was developed. Three examples of synonymous cultivar pairs were identified. In Leucadendron the male and female flowers develop on separate plants, and sex identification is only possible at time of flowering. ISSR, suppression subtractive hybridisation (SSH), and SSH combined with mirror orientation selection (MOS) were used in attempts of identifying sex-dependent DNA fragments at earlier stages of plant development. Neither of these techniques was able to identify sex-specific markers in Leucadendron. Nevertheless, the results did indicate that cpDNA copy number may differentiate male and female plants. Also, it was demonstrated that the genomes of male and female plants are quite homologous, which increases the difficulty in identifying sex-specific sequences. This thesis highlights the potential of DNA-based markers to determine species relationships in Grevillea and Leucadendron, as well as to identify Leucadendron cultivars. The information produced during the research for this thesis provides a basis for Grevillea and Leucadendron variety development and may be used to assist the design of interspecific crosses, to identify cultivars and the parents of hybrids. In addition, the results offer insights into the likelihood, problems and strategies of finding sex-specific markers for genes controlling sex in Leucadendron. ii
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Rosales, Rivera Luis Carlos. "Development of an electrochemical sensor for coeliac disease serological markers." Doctoral thesis, Universitat Rovira i Virgili, 2012. http://hdl.handle.net/10803/96661.
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La celiaquía, intolerancia al gluten, es una enfermedad autoinmune que afecta principalmente a la parte próxima del intestino delgado y que está presente en el 1% de la población mundial. La ingestión de gluten (proteína presente en el trigo, la cebada, el centeno) desencadena la producción de anticuerpos anti-gliadina (AGA) y anti-transglutaminasa tisular (anti-tTG) que pueden provocar inflamación y daños en el intestino delgado. La detección de estos anticuerpos mediante el uso de pruebas serológicas representa una alternativa rápida, confiable y no invasiva.
El objetivo principal de esta Tesis es el desarrollo de inmunosensores usando monocapas de tioles autoensambladas en superficies de oro que sean rápidos, sensibles y de bajo coste, pero eficientes para su uso en muestras reales. Dos estrategias para inmovilizar los antígenos fueron exploradas: i) Usando monocapas autoensambladas de un alcanotiol bípedo, que posee grupos carboxílicos, ii) Introduciendo grupos disulfuro a través de los distintos grupos presentes en los antígenos: carboxílicos, aminos e hidroxilos. Ambas estrategias para construir los inmunosensores fueron optimizadas y usadas para la detección amperométrica de los marcadores serológicos de la celiaquía en muestras humanas de suero.Coeliac disease (CD), a gluten-sensitive enteropathy, is an autoimmune disorder of the upper small intestine triggered from the gluten ingestion (cereal protein found in wheat, rye and barley) and affects 1% of the population around the globe. The ingestion of gluten, triggers the production of a series of autoantibodies against gliadin (AGA) and tissue transglutaminase (anti-tTG) which can provoke inflammation and damage some parts of the intestine. The detection of those antibodies through serological testing represent a non-invasive, fast and reliable approach. The main objective of this Thesis is the development of a sensitive, rapid and cost-efficient real-sample-oriented immunosensor using thiol-self assembled monolayers on gold surfaces. Two strategies for the antigen immobilisation have been investigated: i) The use of monolayers of a carboxylic acid-ended bipodal alkanethiol, ii) The introduction of disulfide groups through three different moieties of the antigens: amine, carboxylic and hydroxyl. Both immunosensor approaches were optimized and used for the amperometric detection of CD serological markers from human serum samples.
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Chadwick, Martin. "Development of molecular markers linked to quantitative and qualitative assessment of bitterness in lettuce." Thesis, University of Reading, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.628530.
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Taste is an important factor in foods, particularly minimally processed foods such as salad. The sensory profile of lettuce was assessed using members of an F9 recombinant inbred line (RIL) mapping population derived from the iceberg cultivar Lactuca sativa cv. Salinas and Lactuca serrio/a UC96US23, its wild progenitor. Customers were able to discern differences in bitterness in samples as the result of bitter sesquiterpene lactones (SLs), and sweetness from sugars, with high correlation between scores for these taste parameters and concentration of the metabolites. Customers preferred sweeter varieties over more bitter varieties. Subsequent analysis of 104 RILs and the parents of the mapping population by 'H NMR for a range of metabolites identified 285 NMR peaks representing 39 known compounds. NMR analysis was done in three environments, representing controlled environment, a restricted nitrogen field environment, and a high nitrogen field environment. The change in metabolome was assessed for each of the parents, showing variation in a range of compounds such as sugars, phenolics, fatty acids and amino acids. This was compared to other analysis methods to confirm that NMR was robust enough to quantify traits for quantitative trait loci (QTL) analysis
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Hooi, Wei Yeng. "Search for early molecular markers of the mantled floral variation of oil palm." Thesis, Montpellier, 2015. http://www.theses.fr/2015MONTS244.
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Titre du projet: Recherche de marqueurs moléculaires précoces de l’anomalie florale mantled du palmier à huile Objectifs : - identifier des marqueurs d’expression de la variation somaclonale mantled par comparaison entre les transcriptomes conformes et variants.- valider la capacité de discrimination des marqueurs sélectionnés lors des stades précoces du processus in vitro. Stratégie et Méthode: Analyse transcriptomique de l’inflorescence normale de palmier à huile et construction d’un transcriptome de référence. Technique : RNAseq, séquençage Illumina.Identification des séquences et voies de régulation d’intérêt. Technique: analyse bioinformatique des données de séquençage.Comparaison entre les trancriptomes issus d’inflorescences normales vs. mantled par re-séquençage de banques obtenues ) partir de différents génotypes clonaux. Technique : Illumina.Identification des séquences présentant de manière cohérente des profils d’expression dépendant du phénotype. Technique : analyse bioinformatique des données de séquençage, analyse statistique des profils d’expression. Validation des marqueurs candidats sur des paires de régénérants normal/mantled issus de lignées clonales variées, ainsi que sur des cultures in vitro à différents stades du processus de régénération. Technique : PCR quantitative (q-PCR)Project title : Search for early molecular markers of the mantled floral variation of oil palmObjectives : - identifying expression markers of the mantled somaclonal variation through the comparison between the true-to-type and the variant transcriptome. - assessing the discriminating power of the selected markers at early stages of the in vitro process.Strategy and Methods : Transcriptomic analysis of the normal oil palm inflorescence, construction of a reference transcriptome. Technique : RNAseq, Illumina sequencing.Identification of sequences and pathways of interest. Technique : bioinformatic analysis of sequencing data.Comparison between the normal and the mantled inflorescence transcriptome through the re-sequencing of libraries generated from several different clonal lines. Technique : Illumina. Identification of sequences displaying consistently a phenotype-dependent differential expression pattern. Technique : bioinformatic analysis of sequencing data, statistical analysis of expression patterns. Validation of candidate markers on normal/mantled regenerant palm pairs from different clonal lines and on normal-/mantled-derived in vitro cultures at various stages of the industrial regeneration process. Technique : quantitative PCR (q-PCR)
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Paltridge, Nicholas G. "The development of molecular markers for barley Yd2, the barley yellow dwarf virus resistance gene /." Title page, contents and summary only, 1998. http://web4.library.adelaide.edu.au/theses/09APSP/09apspp183.pdf.
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Douglas, Stephanie. "The development of molecular markers for use across all plant species using expressed sequence tags." FIU Digital Commons, 2006. http://digitalcommons.fiu.edu/etd/3234.
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There are over a half a million plant species on earth, and we use them in virtually every aspect of our lives. Little or no genomic information exists about the vast majority of these plants. This study investigated the use of Expressed Sequence Tags (ESTs) to locate highly conserved sequences from which to design a set of universal molecular markers for all plant species. Plant species for this study were chosen to representative of the plant kingdom. This was done by sampling several individuals of at least one species from all of the major terrestrial plant groups.
Conserved sequences are generally found in a wide range of plants species and often in all plant species. A set of eight degenerate primers was designed specifically to detect Single Nucleotide Polymorphisms (SNPs) using capillary array electrophoresis-single stranded conformational polymorphism (CAE-SSCP). The results of this research confirmed that homologous regions of the genome could be used to design universal molecular markers for all plant species.
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Dufresne, Philippe J. "Development and validation of molecular markers for the detection of disease resistance alleles in Lactuca sativa." Thesis, McGill University, 2002. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=78352.
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In this study, RAPD (Randomly Amplified Polymorphic DNA) and SCAR (Sequence Amplified Characterized Region) markers found within 5 centiMorgans of known disease resistance loci in L. sativa were tested for their potential use in MAS. Out of thirty RAPD and SCAR markers evaluated, ten were found to be reliable predictors of disease resistance or susceptibility across a wide range of commercial and reference cultivars. Direct sequencing of seven selected markers did not reveal any significant similarity with known sequences. Three SNPs (Single Nucleotide Polymorphism) associated with two markers found in close proximity to corky root (cor) and Lettuce mosaic virus resistance (mo12) genes were identified. This information was used in the development of a non-electrophoresis PCR-based assay called FRET (Fluorescence Resonance Energy Transfer) hybridization probes assay.
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Liang, Wei <1982>. "Molecular strategies for genetic diversity analysis and development of markers linked to resistance traits in apple." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2013. http://amsdottorato.unibo.it/5910/.
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The goal of many plant scientists’ research is to explain natural phenotypic variation in term of simple changes in DNA sequence. DNA-based molecular markers are extensively used for the construction of genome-wide molecular maps and to perform genetic analysis for simple and complex traits. The PhD thesis was divided into two main research lines according to the different approaches adopted. The first research line is to analyze the genetic diversity in an Italian apple germplasm collection for the identification of markers tightly linked to targeted genes by an association genetic method. This made it possible to identify synomym and homonym accessions and triploids. The fruit red skin color trait has been used to test the reliability of the genetic approaches in this species. The second line is related to the development of molecular markers closely linked to the Rvi13 and Rvi5 scab resistance genes, previously mapped on apple’s chromosome 10 and 17 respectively by using the traditional linkage mapping method. Both region have been fine-mapped with various type of markers that could be used for marker-assisted selection in future breeding programs and to isolate the two resistance genes.
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Zeng, Qing-Yin. "Development of molecular techniques for fungal diagnostic research." Doctoral thesis, Umeå : Umeå universitet : Arbetslivsinstitutet, 2005. http://kb.se/resolve?urn=urn:nbn:se:umu:diva-656.
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Rhode, Clint. "Development of gene-linked molecular markers in South African abalone (Haliotis midae) using an in silico mining approach." Thesis, Stellenbosch : University of Stellenbosch, 2010. http://hdl.handle.net/10019.1/4502.
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Thesis (MSc (Genetics))--University of Stellenbosch, 2010.ENGLISH ABSTRACT: The South African abalone, Haliotis midae, is the only endemic species of commercial value. Aquaculture remains the only avenue for expanding the industry, since the closure of the fishery. The current focus is on implementing a molecular breeding programme; thus the development of molecular markers for linkage mapping and QTL analysis is a priority. Various markers, mainly anonymous, have been developed for H. midae; however emphasis is being placed on the development of gene-linked type I molecular markers. The present study investigates and demonstrates the use of public sequence collections to develop type I markers for a species with limited genomic resources, via three strategies: Surveying anonymous H. midae microsatellite markers’ flanking regions to find homology to gene sequences in public databases, cross-species marker transfer of anonymous markers from H. rubra and H. discus hannai demonstrating putative gene associations and lastly EST marker mining (SNP and microsatellites) from various Haliotids and testing transfer to the target species. Approximately 17% of H. midae anonymous markers showed significant similarity to genes. The current study also reports higher cross-species transferability from both H. rubra and H. discus hannai to H. midae (39% and 20.5%, respectively) than previously demonstrated and 15 EST-microsatellites and 16 EST-SNPs were successfully mined. Furthermore, the non-random distribution of microsatellites and high nucleotide diversity in the H. midae genome was confirmed. This is a low cost and time effective method for marker development and presents a continuous and dynamic resource that could be used for future marker development and characterisation as sequence information in public databases grow exponentially.
AFRIKAANSE OPSOMMING: Die Suid-Afrikaanse perlemoen, Haliotis midae, is die enigste van vyf inheemse spesies van kommersiële waarde. Na die noodgedwonge sluiting van die vissery, is akwakultuur die mees praktiese oplossing om die perlemoen industrie uit te brei. Die huidige fokus is gerig op die implementering van ‘n molekulêre teel-program en dus is die ontwikkeling van molekulêre merkers vir genetiese kartering en kwantitatiewe kenmerk lokus analise, van uiterste belang. Tipe II merkers is voorheen vir die perlemoen ontwikkel, maar huidige tendense lê klem op die ontwikkeling van geen-gekoppelde tipe I merkers. Die huidige studie ondersoek die gebruik van publieke databasisse vir die ontwikkeling van tipe I molekulêre merkers vir ‘n spesie met beperkte genomiese bronne. Drie strategieë is geïmplementeer: Eerstens is ‘n opname gemaak van die homologie van perlemoen tipe II merker-vleuelende volgordes met geen volgordes in databasisse. Verder is die oordraagbaarheid van tipe II merkers vanaf H. rubra en H. discus hannai wat assosiasie met gene toon ondersoek. Laastens is ‘n Uitgedrukte Volgorde Merk (UVM) (Expressed Sequence Tag, EST) merker-ontginnings metode vanaf verskeie Haliotis spesies en toetsing van oordraagbaarheid na die teiken spesie uitgevoer. Ongeveer 17% van die tipe II H. midae merkers het geniese assosiasie getoon. ‘n Hoër tussen-spesie oordraagbaarheid vanaf beide H. rubra en H. discus hannai na H. midae (39% en 20.5%, onderskeidelik) word gerapporteer in vergelyking met vorige studies en 15 UVM-mikrosatelliete en 16 UVM-enkel nukleotied polimorfismes (single nucleotide polimorphism, SNP) is ontwikkel. Verder bevestig die studie die nie-lukrake verspreiding van mikrosatelliete en hoë nukleotied diversiteit in die perlemoen genoom. Die gebruik van publieke databasise vir die ontwikkeling en karakterisering van tipe I molekulêre merkers is tyd- en koste-besparend en bied ‘n volgehoue en dinamiese bron vir toekomstige gebruik.
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Boersma, Jeffrey George. "Contributions to the molecular genetics of the Narrow-leaf Lupin (Lupinus augustifolius L.) : mapping, marker development and QTL analysis." University of Western Australia. School of Earth and Geographical Sciences, 2007. http://theses.library.uwa.edu.au/adt-WU2008.0001.
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[Truncated abstract] Narrow-leaf lupin (Lupinus angustifolius L.) was first recorded as having been introduced into Germany during the mid-19th century for use as green manuring and as fodder crops. However, it was not until post World-War I that there was any serious attempt to domesticate the species. Since that time several key domestication genes have been incorporated to enable the species to be grown as a crop over a range of climates, harvested as a bulk commodity and, the seed used for both animal and human consumption. However, the recent domestication of this species has seen a rather limited use of wild germplasm largely as a result of the difficulty in retaining these key domestication genes. To make the task of retaining these genes manageable, it was decided to resort to molecular technology. A mapping population of F8 derived recombinant inbred lines (RILs) has previously been established by the Department of Agriculture and Food, Western Australia, from a cross between a domesticated breeding line 83A:476 and a wild type P27255 in narrow-leaf lupin. The parents together with 89 RILs (of a population of 115) were subjected to DNA fingerprinting using microsatelliteanchored fragment length polymorphism (MFLP) to rapidly generate DNA markers for construction of a linkage map. Five hundred and twenty two unique markers of which 21% were co-dominant, were generated and mapped. Phenotypic data for the domestication traits: mollis (soft seeds), leucospermus (white flower and seed colour); Lentus (reduced pod-shattering), iucundis (low alkaloid), Ku (early flowering) and moustache pattern on seed coats; were included. Three to 7 molecular markers were identified within 5 cM of each of these domestication genes. The anthracnose resistance gene Lanr1 was also mapped. Linkage groups were constructed using MapManager version QTXb20, resulting in 21 linkage groups consisting of 8 or more markers. ... Five pairs of QTLs were found to be involved in epistasis, 2 of these having an effect on early vigour and another 3 influencing the time to opening of the first florets. Variation explained for each trait ranged from 28% for seed size, to 88% for days to flowering. We showed that it was possible to use this data to predict genotypes of superior progeny for these traits under Mediterranean conditions. QTL regions were compared on a second published linkage map and regions of conserved synteny with the model legume Medicago truncatula high-lighted. The work presented in this thesis demonstrates the importance of tight linkage between markers and genes of interest. It is especially important when dealing with genetically diverse material as found in the wild. One of the main problems faced by molecular scientists is the phenomenon known as linkage disequilibrium in marker populations caused by either small population size or 4 insufficient opportunity for recombination. This frequently results in the development of markers with little or no application outside of the population in which it was developed. Although the relatively small size of the population used in this study exposes it to such constraints, in this case excellent and valuable results were achieved in developing useful markers to at least 3 of the domestication traits within a relatively short time period of less then 4 years.
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Arnold, Amanda Louise. "Development of molecular markers for studying population structure in marine fishes : 'coding versus non-coding DNA' : which is best?" Thesis, University of Aberdeen, 2000. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU485291.
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This thesis set out to assess whether variants identified within either the "coding" or the "non-coding" regions of the genome were more effective in resolving population structure in marine fishes. The assessment was carried out on three marine fish species - haddock (Melanogrammus aeglefinus), the lesser sandeel (Ammodytes marinus) and the Atlantic salmon (Salmo salar). The study was extended to compare variation within the "coding and "non-coding" regions of a section of the transferrin gene directly with nucleotide sequencing of the cDNA isolated from haddock and sandeels. Variants were identified both the "coding" and "non-coding" regions of this section of the transferrin gene selected and a population analysis was carried out to assess which source of variants was more effective for resolving population differences. Overall, the findings of this study were inconclusive. In some cases variation identified within coding regions was better than variation identified in non-coding regions of the transferrin gene for resolving population structure. However, in other cases the opposite was true, or both sources of variation were found to be uninformative with regards to genetically differentiating between populations. This inconclusiveness was partially attributable to the small number of variants that were identified in coding region for both haddock and Atlantic salmon and the fact that variation within only a single gene was studied. This study did, however, indicate that the methodology employed for screening individuals has clear advantages over previous methods used for population analysis, e.g. protein electrophoresis and mini/microsatellite analysis. All the variants present in the transferrin gene were detected using nucleotide sequencing. In contrast, using protein electrophoresis only those variants that cause an amino acid change and can be detected using histochemical stains are revealed. Difficulties were, however, experienced in accurately assigning allele sizes using mini- and microsatellites and led to binning of the data. This had the disadvantage that by increasing the accuracy of the data set, much of the resolution is likely to be lost.
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Wang, Xiben 1973. "Development of a specific and reliable molecular marker to detect Stachybrotyrs [i.e. Stachybotrys] elegans, a destructive mycoparasite of Rhizoctonia solani." Thesis, McGill University, 2000. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=30766.
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Stachybotrys elegans (Pidopl.) W. Gams is a destructive mycoparasite of the soilborne plant pathogen Rhizoctonia solani. It colonizes effectively all types of cells of R. solani, and is considered as an effective biological control agent (BCA). Monitoring the presence of this mycoparasite in the field trials requires the development of a reliable and sensitive diagnostic assay that is able to detect and differentiate the BCA from their target host. To achieve this, designed SCAR (sequenced characterized amplified regions) primers designated as SE-13F and SE-13R were generated from informative RAPD markers. They were tested in conventional PCR assays alone or in conjunction with the recently developed SCAR primers (SBU-177/336) designed for Rhizoctonia solani (Kuhn) on several types of DNA. These included DNA extracted from pure cultures, co-cultures of the BCA and the pathogen, plant tissue and several types of soils inoculated with both the BCA and the pathogen. Irrespective of the type of the biological samples from which the DNA was extracted, the primers SE-13F/SE-13R successfully amplified only S. elegans. No cross-reaction was observed when the primers were used to amplify DNA of other fungi, bacteria and plant tissues. Likewise, the primer pair SBU-177/336 detected only its target organism, i.e., R. solani. The detection limit using these primers on amplified DNA was as little as 1 pg DNA extracted from pure cultures of S. elegans, 100 pg DNA extracted from greenhouse soil and 33 pg DNA extracted from natural soil. This work is the first report on the development of SCAR markers for the BCA, S. elegans. These molecular markers offer not only an alternative diagnostic assay to conventional detection methods, but also the possibility of being used in ecological studies.
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Merrill, Keith R. "Usage and Development of Molecular Markers for Investigation of the Population and Ecological Genetics of Bromus tectorum L." BYU ScholarsArchive, 2011. https://scholarsarchive.byu.edu/etd/2955.
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This thesis includes two studies: The first examined patterns of neutral genetic diversity within Bromus tectorum L. across the IMW region, and uses patterns of microsatellite (SSR) genotype distribution to make inferences about the respective roles of adaptively significant genetic variation, adaptive phenotypic plasticity, and facultative outcrossing in the ongoing invasion and recent range expansion of B. tectorum. It has been previously demonstrated that, due to extremely low outcrossing rates, it is possible to characterize individual genotypes of this species using four SSR loci. We sampled 20 individuals from each of 96 B. tectorum populations (classified by region and habitat) from throughout the IMW and used these SSR markers to characterize each individual. We found 131 four-locus SSR genotypes; however, the 14 most common genotypes collectively accounted for 79.2% of the individuals sampled. Individuals with certain SSR genotypes sorted strongly into warm or salt desert habitats (stringent habitats) and flowered earlier than individuals with genotypes from more mesic habitats, providing evidence of adaptively significant genetic variation associated with these genotypes. Other SSR genotypes were found across a wide range of habitats though they tended to be less prevalent in stringent habitats, providing evidence that adaptive phenotypic plasticity may be important for the distribution of some common genotypes. We observed very few heterozygous individuals, consistent with the highly inbreeding reproductive strategy of B. tectorum. Because specialist genotypes dominating recently invaded areas within the IMW region contained unique alleles, they are not likely to have resulted from recombination, leading us to doubt the role of facultative outcrossing as a significant mechanism facilitating the current range expansion of B. tectorum in the IMW.Previous research investigating the population and ecological genetics of Bromus tectorum L. in the North American invaded range has relied on either allozyme or microsatellite (SSR) genetic analyses, both of which have proven to have shortcomings. In order to overcome the issues associated with these other marker types, in the second study of this thesis we developed single nucleotide polymorphism (SNP) markers for B. tectorum by 1) obtaining normalized cDNA, 2) sequencing normalized cDNA using 454 sequencing, 3) aligning resultant contigs and looking for SNPs, 4) designing assays for SNP validation and genotyping using KASPar, 5) converting working KASPar assays for use with the Fluidigm EP1 platform using the 96.96 Dynamic ArrayTM IFC. Sequencing resulted in 1258041 reads, which assembled into 65486 contigs (20782 large contigs exceeding 500 base pairs). Using selection criteria of at least 10x coverage and 30% of the minor allele, 3333 putative SNPs were identified. We developed KASP assays for 255 putative SNPs, which resulted in 101 working polymorphic assays. Ninety-six assays were then successfully converted for use with KASP on the Fluidigm EP1 genotyping platform using 96.96 dynamic arrays.
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Sargison, Neil Donald. "Development of genetic crossing methods to identify genes associated with macrocyclic lactone resistance in the sheep nematode parasite, Haemonchus contortus." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/4395.
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There is a pressing need to develop strategies to reduce the emergence of macrocyclic lactone anthelmintic resistance in sheep flocks. Management practices aimed at maintaining anthelmintic susceptible nematodes in refugia while achieving a satisfactory level of production may prove to be useful. However, sensitive molecular tests are required to monitor the subtle effects of these practices on the frequency of resistance alleles within nematode populations. To-date, conventional studies of candidate genes coding for the known methods of action of macrocyclic lactone anthelmintics have produced a complex picture, highlighting the relevance of different approaches to the identification of resistance markers. This thesis describes the development of a single nematode parent genetic crossing method and discusses its application to identify molecular markers for anthelmintic resistance. Parasitological and molecular verification of successful inbreeding of the MHco3 strain of H. contortus derived from the progeny of a genetic cross between single nematode parents is described. The single parent genetic crossing method has enabled the production of diverse inbred lines of the MHco3 H. contortus and may prove useful for genome assembly, or for the development of a genetic map. The study has afforded insights to the biology of H. contortus and effects of host immunity on nematode parasites. New information is presented concerning the period during which adult female nematodes continue to shed fertilised eggs after removal of males, the development of unfertilised H. contortus eggs, and the population genetics of mixed infections of two different strains of H. contortus. Novel backcrossing experiments initially between a macrocyclic lactone resistant (MHco4 or MHco10) and a susceptible (MHco3) strain of H. contortus and then between ivermectin treated backcross generations and the parental susceptible strain are described. The resources provided by these experiments should enable comparative genomic analysis and conventional molecular biology to identify resistance genes derived from the parental resistant strains in fourth backcross generations that are the same as a parent ivermectin susceptible population, apart from the presence of alleles linked to anthelmintic resistance, derived from parent resistant strains.
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Seyfarth, Ralf. "Development of molecular markers for the adult plant leaf rust resistance genes Lr13 and Lr35 in wheat (Triticum aestivum L.) /." [S.l.] : [s.n.], 2000. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=13533.
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O'Reilly, Patrick. "Development of molecular genetic markers in Atlantic salmon (Salmo salar) and an illustration of their application to aquaculture and fisheries." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp05/nq24759.pdf.
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Kloda, Jane Margaret. "The development and utilisation of molecular genetic markers to study genetic diversity in Ononis repens, O. spinosa and related species." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615050.
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Wehbe, Katia. "Usage of FTIR spectro-imaging for the development of a molecular anatomo-pathology of cerebral tumors." Thesis, Bordeaux 1, 2008. http://www.theses.fr/2008BOR13677/document.
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Les gliomes sont des tumeurs agressives de mauvais pronostic, très angiogéniques et infiltrantes ce qui rend leur exérèse particulièrement difficile. Vu les limites des techniques actuelles d’imagerie, nous avons proposé la spectro-imagerie Infrarouge à Transformée de Fourier (IRTF), d’une résolution spatiale de 6 µm, pour apporter une information moléculaire à l’examen histologique actuel des gliomes. Nos travaux ont été fondés sur la recherche de paramètres moléculaires des vaisseaux sanguins, notamment sur la base des contenus de leur membrane basale. Celle-ci subit des altérations dûes au stress angiogénique tumoral. Nous avons mis en évidence des altérations de la structure secondaire des protéines (tels les collagènes) des vaisseaux sanguins au cours de la croissance de la tumeur. Nous avons aussi évalué les modifications des chaines d’acides gras des phospholipides membranaires, qui révélent un degré d’insaturation plus important pour les vaisseaux tumoraux. Ensuite, sur un modèle de gliome murin, nous avons établi une méthode efficace de classification des capillaires sanguins sur la base d’absorptions de leurs contenus glucidiques et lipidiques, permettant de discriminer totalement les capillaires sains et tumoraux. La combinaison de ces paramètres a été mise à profit pour assurer une histopathologie moléculaire des gliomes humains. Nos résultats ont démontré qu’il est possible de différencier entre la vasculature saine et tumorale sur ces gliomes humains, ce qui permet une bonne délimitation des zones tissulaires correspondantes. Cette technique pourrait devenir un outil analytique fiable, rapide d’une durée compatible avec la chirurgie et donc très utile pour les neurochirurgiensMalignant gliomas are very aggressive tumors with poor prognosis, highly angiogenic and invasive into the surrounding brain parenchyma, making their resection very difficult. Regarding the limits of current imaging techniques, we have proposed Fourier Transform Infrared (FTIR) spectro-imaging, with a spatial resolution of 6 µm, to provide molecular information for the histological examination of gliomas. Our work was based on the research of molecular parameters of blood vessels, notably on the basis of the contents of their basement membrane, which undergoes changes due to tumor angiogenic stress. We have identified alterations of the secondary structure of proteins (such as collagen) in blood vessels during tumor growth. We have also assessed the changes in fatty acyl chains of membrane phospholipids, which revealed a higher unsaturation level in tumor vessels. Then, on a murine glioma model, we have established an efficient method of blood vessels classification based on their carbohydrates and fats contents, allowing the differentiation between healthy and tumor blood vessels. The combination of these parameters was used to provide a molecular histopathology for the study of human gliomas. Our results have demonstrated the feasibility of differentiating between healthy and tumor vasculature in these human gliomas, which help delimitating areas of corresponding tissue. This technique could become a reliable and fast analytical tool, with duration compatible with the surgery and thus very useful for neurosurgeons
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Haddrill, Penelope R. "The development and use of molecular genetic markers to study sexual selection and population genetics in the 2-Spot ladybird, Adalia bipunctata (L.)." Thesis, University of Cambridge, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.444738.
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Makubalo, Zola. "Mutation screening of candidate genes and the development of polymorphic markers residing on chromosome 19q13.3, the progressive familial heart block I gene search area." Thesis, Stellenbosch : Stellenbosch University, 2000. http://hdl.handle.net/10019.1/51838.
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Thesis (MSc)--Stellenbosch University, 2000.ENGLISH ABSTRACT: Progressive familial heart block type I (PFHBI) is a cardiac ventricular conduction disorder of unknown cause associated with risk of sudden death, which has been described in several South African families. Clinically, PFHBI is characterised by right bundle branch block on ECG, which may progress to complete heart block, necessitating pacemaker implantation. The disease shows an autosomal dominant pattern of inheritance with evidence of genetic anticipation. Using genetic linkage analysis, the PFHBI-causative gene was mapped to a 10 eentimorgan (cM) gene-rich area of chromosome (C) 19q13.3, which has, subsequently, been reduced to 7cM by fine mapping with polymorphic dinucleotide (CA)n short tandem repeat (STR) markers. Several attractive candidate genes, including muscle glycogen synthase (GSY 1) and histidine-rich calcium binding protein (HRC), lie within this region. The aim of the present study was two-fold: 1) to identify and characterise tetranucleotide (AAAT)n STRs within the PFHBI critical region that could be developed as polymorphic markers for use in genetic fine mapping and 2) to screen selected regions of GSY 1and HRC, positional candidate genes, for the presence ofPFHBI-causing mutation(s). Cosmids harbouring CI9q13.3 insert DNA were screened for the presence of (AAAT)n STRs by dot blot and Southern blot hybridisation using a radiolabelled (AAAT)lO oligonucleotide probe. To characterise the harboured (AAAT)n STRs, the positively hybridising fragments identified by Southern blot were sub-cloned, sequenced and primers designed from the unique repeat-flanking sequences. These primers were used to genotype the (AAAT)n repeat locus to assess its polymorphic nature in a panel of unrelated individuals. Alternatively, vectorette PCR, a rapid method of identifying repeat sequences and obtaining the flanking sequences in large inserts, was employed to develop polymorphic markers from the positively hybridising clones. Selected exons of GSY1 and HRC were screened for the presence of potentially disease-causing mutations by PCR-SSCP analysis and direct sequencing, respectively, in PFHBI-affected and unaffected family members. Of the available cosmid clones that gave strong signals on dot blot and Southern blot hybridisation, three, 29395, 24493 and 20381, were located within the critical PFHBI area and were used for marker development. An interrupted (AAAT)n repeat motif (n less than 5) was identified in cosmid 29395, however, the repeat locus was not polymorphic in the tested population. No (AAAT)n motif, single or repeated was observed in the partial sequence of the sub-cloned fragment of cosmid 24493. Using vectorette peR, no repeated (AAAT)n motif was identified on sequencing the generated products in either cosmid 24493 or 2038l. However, diffuse single AAAT motifs were detected in both cosmids. Exons 4, 5, 11, 12 and 16 of GSY 1, containing domains that are conserved across species, and the conserved eterminus- encoding exons 2-6 of HRC were selected for screening for potential PFHBI-causing mutation(s). However, no sequence variations were detected. The interrupted (AAAT)n repeat identified in cosmid 29395 was not polymorphic, which confirmed reports that complex repeats, especially those containing AAAT motifs of less than 6 repeats, are not polymorphic. One possible explanation for the absence of a repeated AAAT motif in cosmids 24493 and 20381, which both gave positive hybridisation signals, is that the low annealing temperature of the AfT -rich repeat-anchored primers used in vectorette peR may have resulted in transient annealing to the diffuse single AAAT motifs detected on sequencing. The screened regions of candidate genes GSYI and HRC were excluded from carrying the disease-causing mutation(s). The availability of new sequence data generated by the Human Genome Project will influence future strategies to identify the PFHBI gene. Electronic searches will allow identification of STR sequences for development of polymorphic markers and gene annotation will allow selection of new candidate genes for mutation screening.
AFRIKAANSE OPSOMMING: Sien volteks vir opsomming
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Gan, Siou Ting. "The development and application of molecular markers for linkage mapping and quantitative trait loci analysis of important agronomic traits in oil palm (Elaeis guineensis Jacq.)." Thesis, University of Nottingham, 2014. http://eprints.nottingham.ac.uk/14197/.
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Oil palm (Elaeis guineensis) produces over five times more oil/year/hectare than oil seed rape and accounted for 33% of world vegetable oil production in 2011. Being a cross-pollinated perennial tree crop with long breeding cycles (typically 12 years) and a large planting area requirement (usually 143 palms/hectare), utilization of molecular technology could greatly improve the efficiency of oil palm breeding. In the present study, various approaches were used to develop molecular markers for genetic linkage mapping and QTL analysis, with the ultimate goal of marker-assisted selection in oil palm. Firstly, Representational Difference Analysis (RDA) and Amplified Fragment Length Polymorphism (AFLP) were coupled with Bulked Segregant Analysis (BSA) to try to identify marker(s) closely linked to the important shell-thickness gene. A novel combination of RDA with Roche 454 pyrosequencing enabled a more comprehensive study of the enrichment profiles compared to Sanger sequencing. Identification of >35% redundant sequences, repetitive sequences and organelle DNA suggested that subtractive hybridization and target enrichment of RDA were inefficient here, with the lack of elimination of common sequences masking the real difference products. The use of the AFLP method identified 29 primer pairs that yielded 49 putative shell-thickness related-polymorphic bands. A detailed analysis will need to be carried out to fully evaluate and validate these markers. The use of the relatively new Diversity Array Technology “Genotyping-By-Sequencing” (DArTSeq) platform through genotyping of two closely-related tenera self-pollinated F2 populations, 768 (n=44) and 769 (n=57), generated a total of 11,675 DArTSeq polymorphic markers of good quality. These markers were used in the construction of the first reported DArTSeq based high-density linkage maps for oil palm. Both genetic maps consist of 16 major independent linkage groups (total map length of 1874.8 and 1720.6 cM, with an average marker density of one marker every 1.33 and 1.62 cM, respectively), corresponding well with the 16 homologous chromosome pairs of oil palm (2n = 2x = 32; 14/16 chromosomes were confirmed by known location SSR markers). Preliminary quantitative trait loci (QTL) mapping of the yield and vegetative growth traits detected four significant and 34 putative as well as two significant and 30 putative QTLs for these small 768 and 769 populations, respectively. No common significant QTL were detected between the two closely-related controlled crosses which could have allowed combination of QTL across the two populations. Saturation of the shell-thickness (Sh) region with all available DArTSeq markers, as well as map integration around the Sh regions for both populations, identified 32 Single Nucleotide Polymorphism (SNP) and DArT markers mapped within a 5 cM flanking region of the Sh gene. Homology search of the DArTSeq marker sequence tag (64 bp) against the recently published oil palm genome assembly confirmed that 23 out of the 32 (72%) DArTSeq markers were located on the p5_sc00060 scaffold in which the SHELL gene was identified. The identified shell-thickness markers could be useful as molecular screening tools. This study demonstrated the potential and feasibility of using genomic resources available for genetic improvement of oil palm breeding programmes.
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Gabier, Hawwa. "Development of microsatellite (SSR) marker multiplexes for future construction of a genetic linkage map for pear (Pyrus communis L.)." Thesis, University of the Western Cape, 2012. http://hdl.handle.net/11394/4013.
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>Magister Scientiae - MScRecent advances in the field of plant genetics and application of molecular technologies has lead to greater understanding of various crop genomes and their organization.The applications of these techniques include molecular markers which have been used to examine DNA variation within crop species. This allows for the creation of further genetic variation for new and favourable traits.Molecular markers or DNA markers are short fragments of DNA that can be used to locate desirable genetic traits in the genome or show specific genetic differences. The Maloideae subfamily includes fruit species such as pear. Pears (Pyrus communis L.) are large edible fruit that are grown in cool climates, native to coastal regions in Africa, Asia and Europe. The external appearance of this fruit plays a vital role on its rate of sale potential. Thus it is important for the appearances of the pear to meet the expectations of the consumer.External factors affecting the appearance of fruit, such as shape and colour, can have a large influence on the consumer’s first impression and opinion of what the fruit may taste like(Jaeger and MacFie, et al., 2001). The South African pear industry is the fourth largest in the fruit industry after apple, citrus and grape, exporting 3.8% to Europe (Ferrandi, et al., 2005).Increase in production and export of the pear is dependant on the variety of cultivars with desired traits. New cultivars, especially ranges of new cultivars, with harvest dates from early to late in the season, can fill gaps in the marketing strategy of exporters and in the local markets (Human, et al., 2005) Therefore, development of molecular markers allows for their possible use in maker-assisted selection and for the construction of a genetic linkage map thus leading to the location of favourable traits and ultimately the improvement of the quality of the pear.In this study high throughput genomic DNA extractions were performed. The Cetyltrimethyl ammonium bromide (CTAB) method was employed as the results proved to be most promising. Furthermore the screenings of molecular markers were conducted in order to obtain DNA variation. Molecular markers were used to locate specific genetic differences.Multiplexing PCR was conducted using fluorescent primers for further screening and results proved to be useful as many variations could be observed.
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Javed, Nasir. "Development of Genetic Linkage Maps and Identification of Quantitative Trait Loci Influencing Seed Oil Content, Fatty Acid Profile and Flowering Time in Brassica napus L." Hereditary Genetics, 2012. http://hdl.handle.net/1993/30633.
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Identification of allelic variation through quantitative trait loci (QTL) mapping offers possibilities for the improvement of quantitatively inherited traits. This requires a genetic map along with the phenotypic characterization of a mapping population. A doubled haploid (DH) Polo X Topas population consisting of 194 lines and a recombinant inbred line population of 92 lines was developed. Individual genetic maps derived from each population were integrated into a consensus map. The DH-based genetic map was used for QTL mapping. The DH-based map was comprised of 620 loci that were assembled into 19 linkage groups that were anchored to the B. napus chromosomes. The DH-based map covered 2244.1 cM genomic distance with an average marker interval of 3.7 cM.
The DH population was phenotyped in four environments with each line replicated twice in a randomized complete block design. Days to flowering was recorded and oil content and fatty acid composition were determined using Near Infrared spectroscopy (NIR) and Gas Chromatography, respectively.
Fourteen QTL were identified for oil content, 33 QTL for palmitic acid content, 18 QTL for stearic acid content, 21 QTL for oleic acid content, 20 QTL for linoleic acid content, 23 QTL for linolenic acid content, 16 QTL for arachidic acid content and 14 QTL for flowering time.
Oil content QTL were identified on five linkage groups, A3, A10, C1, C5, and C6. An oil content QTL, qOIL-A10c appeared in all four environments, whereas qOIL-A10a appeared in only one environment but explained 26.99% variation. The oil content in the population ranged from 35% to 55.5% with the parents having values of 42% to 46%.
Two genomic regions on C3, with map positions at 147.83 cM and 154.55 cM harbored QTL (rQTL) for all the fatty acids studied. The additive effects of the rQTL reveal a correlation pattern which is supported by the phenotypic correlation observed between the fatty acids. This suggests rQTL have role in the fatty acid composition and possibly determine total seed oil content. The rQTL and flanking markers of the identified QTL offer utility in further development of B. napus.October 2015
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Iaffaldano, Brian. "Evaluating the Development and Potential Ecological Impact of Genetically Engineered Taraxacum kok-saghyz." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1452174223.
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Gaspari-Pezzopane, Cristiana de. "Atributos fenológicos, agronômicos e expressão gênica durante a frutificação do cafeeiro." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/11/11136/tde-14022008-170733/.
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As características relacionadas à frutificação do cafeeiro são altamente influenciadas pelo ambiente. Portanto, a associação de análises agronômicas, fenológicas e genômicas são necessárias para o entendimento desse processo. Esses estudos fazem parte do programa de melhoramento genético do café, com o objetivo de obter plantas com maior uniformidade de maturação, duração de ciclo e bebidas específicas. Nesse contexto, os objetivos desse trabalho foram estabelecer padrões agronômicos e fenológicos comparativos entre diferentes cultivares e safras de café, caracterizar genes diferencialmente expressos durante o desenvolvimento dos frutos de cafeeiro arábica e correlacionar genes diferencialmente expressos com atributos fenológicos e agronômicos. Os estudos foram realizados no Centro de Café do IAC em Campinas, SP. As cultivares de Coffea arabica utilizadas foram: Mundo Novo, Catuaí Vermelho, Icatu Vermelho, Obatã e Icatu Precoce, nas safras de 2004/2005 e 2005/2006. Os atributos fenológicos foram avaliados com base no desenvolvimento do ciclo fenológico e na porcentagem de frutos maduros na colheita. As avaliações agronômicas foram avaliadas baseadas nas características tecnológicas do produto como, produção e rendimento, tipos de sementes e tamanho dos grãos. A expressão gênica diferencial foi avaliada por método semi-quantitativo e quantitativo RT-PCR em todos os estádios de desenvolvimento dos frutos. Seqüências de genes específicos foram identificadas por buscas em bancos de dados do Programa Genoma Café e no Genbank, possibilitando a construção de oligonucleotídeos específicos para cada gene. Em geral, os resultados das análises confirmaram a influência ambiental no desenvolvimento dos frutos do cafeeiro, especialmente as variações hídricas e de temperatura. Diferenças significativas foram identificadas entre as cultivares, em relação aos atributos fenológicos e agronômicos, principalmente na safra 2005/2006 quando foi possível discriminar as cultivares quanto à duração do ciclo fenológico. A expressão gênica durante o desenvolvimento dos frutos, seguiu padrão similar entre as cultivares, mesmo comparando diferentes anos agrícolas. Conseqüentemente, essas análises permitiram a identificação de genes candidatos a serem usados como marcadores genéticos das fases de frutificação de C. arabica, como: crescimento (PAL, CHS e manB), transição do crescimento para o início da maturação (csp1, GLA e ER5), maturação e amadurecimento (CS, AAT, ACS, ACO, ETR e ICL) e transição da maturação para o amadurecimento (PAL). Esses genes marcadores em associação com atributos agronômicos e fenológicos, podem ser utilizados como parâmetros moleculares para a definição de estádios adequados à colheita, assegurando composição final específica dos frutos e da qualidade da bebida.Coffee fruit development and ripening are biological processes largely influenced by environmental conditions. Therefore, the association of agronomic, phenologic and genomic analyses is necessary for a broad comprehension of these processes. This type of approach is already part of coffee breeding programs, which aimed the development of coffee cultivars bearing maturation uniformity, controlled life cycle and specific cup qualities. In this context, the main objectives of this dissertation are to establish comparative patterns of fruit ripening among different coffee cultivars, to characterize gene expression during fruit development, and to correlate possible differential gene expression with agronomic and phenologic traits. All investigations were performed at the experimental field of the Coffee Center/IAC, Campinas, SP. The Coffea arabica cultivars Mundo Novo, Catuaí Vermelho, Icatu Vermelho, Obatã and Icatu Precoce, years 2004/2005 and 2005/2006, were evaluated regarding phenologic cycle and percentage of cherry fruits at harvesting time. Agronomic traits evaluated included productivity and outturn, type of seeds and grain size. Differential gene expression was evaluated through semi-quantitative and quantitative RT-PCR, in all stages of fruit development. Sequences of selected genes were identified through blast searches in the database of the Coffee Genome EST Project and the Genbank, and used to design gene-specific primers. In general, analyzed results confirmed the environmental influence over fruit development, especially temperature variations during evaluated seasons. Significant differences were identified among cultivars regarding phenologic and agronomic traits, especially in the year 2005/2006 where life cycle duration allowed cultivar discrimination. Gene expression during fruit development followed a similar pattern among evaluated cultivars, even when comparing different harvesting years. Therefore, these patterns allowed the identification of candidate genes for use as genetic markers of C. arabica fruit development phases, such as growing (PAL, CHS and manB), transition from growing to maturation (csp1, GLA, ER), maturation and ripening (CS, AAT, ACS, ACO, ETR, ICL) and transition from maturation to ripening (PAL). These gene-markers, in association with agronomic and phenological traits, may be used as molecular parameters for the definition of best colleting stage, ensuring specific final coffee fruit composition and cup quality.
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Dockter, Rhyan B. "Genome Snapshot and Molecular Marker Development in Penstemon (Plantaginaceae)." BYU ScholarsArchive, 2011. https://scholarsarchive.byu.edu/etd/2512.
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Penstemon Mitchell (Plantaginaceae) is one of the largest, most diverse plant genera in North America. Their unique diversity, paired with their drought-tolerance and overall hardiness, give Penstemon a vast amount of potential in the landscaping industry—especially in the more arid western United States where they naturally thrive. In order to develop Penstemon lines for more widespread commercial and private landscaping use, we must improve our understanding of the vast genetic diversity of the genus on a molecular level. In this study we utilize genome reduction and barcoding to optimize 454-pyrosequencing in four target species of Penstemon (P. cyananthus, P. davidsonii, P. dissectus and P. fruticosus). Sequencing and assembly produced contigs representing an average of 0.5% of the Penstemon species. From the sequence, SNP information and microsatellite markers were extracted. One hundred and thirty-three interspecific microsatellite markers were discovered, of which 50 met desired primer parameters, and were of high quality with readable bands on 3% Metaphor gels. Of the microsatellite markers, 82% were polymorphic with an average heterozygosity value of 0.51. An average of one SNP in 2,890 bp per species was found within the individual species assemblies and one SNP in 97 bp were found between any two supposed homologous sequences of the four species. An average of 21.5% of the assembled contigs were associated with putative genes involved in cellular components, biological processes, and molecular functions. On average 19.7% of the assembled contigs were identified as repetitive elements of which LTRs, DNA transposons and other unclassified repeats, were discovered. Our study demonstrates the effectiveness of using the GR-RSC technique to selectively reduce the genome size to putative homologous sequence in different species of Penstemon. It has also enabled us the ability to gain greater insights into microsatellite, SNP, putative gene and repetitive element content in the Penstemon genome which provide essential tools for further genetic work including plant breeding and phylogenetics.
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Sorenson, Laurie. "Molecular Marker Development for the Discrimination of Atlantic and Pacific Blue Marlin (Makaira nigricans)." W&M ScholarWorks, 2011. https://scholarworks.wm.edu/etd/1539617910.
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Collier, John Michael. "Identification and characterization of p137 a differentially regulated cardiac marker of embryonic trichloroethylene exposure." Diss., The University of Arizona, 1999. http://hdl.handle.net/10150/284051.
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Embryonic trichloroethylene (TCE) exposure was previously shown to be associated with an increased incidence of cardiac birth defects. Although embryo data are lacking exposure studies on adult animals show an association between halogenated hydrocarbon exposure and modifications in gene expression. The present study was undertaken to identify embryonic mRNA transcripts differentially expressed following TCE or metabolite exposure. This study identified numerous differentially regulated transcripts following halogenated hydrocarbon exposure. Examples of upregulated transcripts include stress responsive genes (Hsp 70, Hsp 70 cognate), a Ca²⁺-ATPase, calreticulin and serum response factor while downregulated transcripts include Midkine (RARP), numerous ribosomal proteins (8s, 18s, 24s), p137 and vimentin. p137 was a candidate sequence marked for further study to determine whether this sequence could be utilized as a molecular marker of TCE exposure. p137 showed a correlation between increased levels of maternal TCE exposure and decreased levels of transcript expressed in E11 fetal tissue. Immunohistochemical staining using an affinity purified antibody to p137 demonstrates widespread expression in rat E11 and chicken St. 17 embryos. p137 protein is broadly expressed in chicken St. 13 through St. 22 heart, but by St. 29 becomes more restricted in the ventricular myocardium with continued endocardial expression. At stages between St. 13 and St. 17 in chick embryos the ectodermal epithelium, yolk sac epithelium, dermatome, developing optic vesicle and neural tube express p137 protein. To explore potential function of p137, atrioventricular explants were exposed to affinity purified p137 antibody. Results show that p137 antibody treatment blocks epithelial-mesenchymal transformation of endothelial cells in-vitro. This study shows that p137 is expressed during rat and chicken mid-gestation in heart and other epithelial tissue derivatives and appears to play a role in the epithelial-mesenchymal transformation of the cardiac atrioventricular cushions. p137 is identified as a useful marker of developmental exposure to halogenated hydrocarbons and its altered expression may contribute to the phenotype of the affected heart.
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Mazaheri, Lucy. "Development of a Molecular Marker to Track APA G40199 Introgression in Common Bean for Bruchid Resistance." Thesis, North Dakota State University, 2018. https://hdl.handle.net/10365/29300.
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In common bean (Phaseolus vulgaris), the main seed storage pests are the bruchid beetles. Damage done to the seed by the larvae has a large impact on seed quality and yield. Arcelin (ARC), phytohaemagglutinin (PHA), and α-amylase inhibitor (α-AI) are linked seed storage proteins that form the APA locus on chromosome Pv04 and are associated with resistance. A major breeding objective is to introduce bruchid resistance into common bean from a resistant tepary genotype, G40199, by introgressing the resistant APA locus into susceptible common bean backgrounds. Here we developed a molecular marker that tracks the introgression. A set of PCR primers to the α-amylase inhibitor locus amplified a DNA fragment that showed a 45 base pair insertion in the middle of a lectin Leg_b domain. This enhanced locus characterization and insertion/deletion marker may preclude the need for bruchid resistance screening early in the breeding.United States. Agency for International Development
United States. Global Hunger and Food Security Initiative (Cooperative Agreement No. EDH-A-00-07-00005-00)
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Morel, Alexandre. "Physiologie moléculaire du développement des embryons somatiques de pin maritime (Pinus pinaster Ait.) : approches transcriptomique et protéomique." Phd thesis, Université d'Orléans, 2014. http://tel.archives-ouvertes.fr/tel-01069408.
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Chez le pin maritime l'embryogenèse somatique, méthode de multiplication végétative performante, n'est pas optimisée la limite étant le contrôle du développement des embryons somatiques (ES). Nos objectifs ont été 1) d'étudier les mécanismes physiologiques, cellulaires et moléculaires précoces contrôlant la différenciation des ES en réponse à une disponibilité en eau réduite 2) d'évaluer pour l'ES cotylédonaire de 12 semaines son état de maturité, son protéome afin de les comparer à l'embryon zygotique (EZ). 1) Pour le 1er objectif, le rapprochement de données de transcriptomique et de protéomique a été entrepris. Nous avons observé une réponse physiologique et moléculaire ABA-dépendante entrainant une transition précoce de la prolifération vers la différenciation des ES (surexpression de protéines impliquées dans la division cellulaire, l'embryogenèse et la synthèse de l'amidon). Une protéine de type germine et une ubiquitine ligase apparaissent comme marqueurs potentiels de l'embryogenèse somatique précoce du pin maritime, alors que la protéine phosphatase 2C marque la réponse adaptative à l'environnement de culture. 2) La maturité de l'ES cotylédonaire a été étudiée aux niveaux physiologiques (masse sèche, teneur en eau) et biochimiques (teneur en protéines totales, en sucres solubles). Des ES de 10, 12 ou 14 semaines se révèlent semblables. Une méthode de classification hiérarchique ascendante basée sur 9 variables explicatives, montre que l'ES est similaire à l'EZ cotylédonaire frais (protéomes présentant 94% d'homologie). Parmi les protéines communes, 3 familles ont été identifiées (protéines de réserve, protéines de réponse au stress HSP, protéines LEA) ainsi que l'aldose réductase et l'adénosine kinase. Nous les proposons comme marqueurs génériques du stade cotylédonaire de l'embryogenèse tardive du pin maritime. L'ensemble des résultats contribue à une meilleure compréhension de l'embryogenèse somatique du pin maritime.
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Olsson, Magnus. "Nuclear pore membrane glycoprotein 210 as a new marker for epithelial cells." Doctoral thesis, Uppsala University, Department of Cell and Molecular Biology, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3265.
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Epithelial cell polarisation is a prerequisite for the branching morphogenesis in several organs. Differential screening techniques were used to identify genes, which are upregulated during induction of epithelium in early kidney development. This investigation revealed two separate genes, Nuclear localising protein 1 (Nulp1), a previously undescribed gene with sequence characteristics of the basic helix-loop-helix transcription factor family, and glycoprotein 210 (gp210, POM210), an integral membrane protein constituent of the nuclear pore complex (NPC). Of these, gp210 was found to be upreglated during conversion of mesenchyme to epithelium.
The nuclear envelope, which demarcates the nuclear region in the eukaryotic cell, consists of an inner and an outer membrane that are fused at the locations for NPCs. These large macromolecular assemblages are tube like structures connecting the cytoplasmic and nuclear compartments of the cell. NPCs serve as the only conduits for exchange of molecular information between these cellular rooms. Electron microscopy techniques have revealed detailed information about the NPC architecture. A number of proteins (nucleoporins) have been characterised and embodied as components of the NPC structure. Active, energy dependent nucleocytoplasmic transport of RNAs and proteins is mediated by a group of soluble receptor proteins, collectively termed karyopherins.
Gp210 has been suggested to be important for nuclear pore formation. Nevertheless, our analyses showed a limited expression pattern of gp210, with its mRNA and protein largely confined to epithelial cells in the mouse embryo. Furthermore, in several cell lines, gp210 was undetectable. The expression pattern of gp210 was not synchronised with some other nucleoporins, indicating NPC heterogeneity. Characterisation of the structure of the human gp210 gene, including its promoter region, gave insight about possible cell-type specific gene regulatory mechanisms.
Regulation of molecular traffic between the nucleus and the cytoplasm leads to transcriptional control. Cell specific configuration of the NPC structure, due to diffential expression of gp210, could be involved in this control. Gp210 could be of importance for the development of epithelial cell polarisation.
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Wang, Xiben. "Development of a specific and reliable molecular marker to detect Stachybrotyrs elegans, a destructive mycoparasite of Rhizoctonia solani." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0030/MQ64477.pdf.
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Johnson, Frank Orlando. "Behavioral outcomes and molecular marker modulation during learning and memory formation following developmental exposure to organophoshorus insecticides." Diss., Mississippi State : Mississippi State University, 2007. http://library.msstate.edu/etd/show.asp?etd=etd-03122009-143101.
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Moulay, Mohammed [Verfasser]. "Expression of stem cell marker genes in canine prostate cancer cell lines as basis for the development of molecular therapeutic tools / Mohammed Moulay." Hannover : Bibliothek der Tierärztlichen Hochschule Hannover, 2014. http://d-nb.info/1065263368/34.
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Souza, Carla dos Anjos de. "Investigação de polimorfismos nos genes dos fatores Miogênicos e Miostatina como marcadores moleculares para características quantitativas em Gallus gallus." Universidade de São Paulo, 2005. http://www.teses.usp.br/teses/disponiveis/11/11139/tde-12052005-170339/.
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O presente trabalho teve como objetivo identificar polimorfismos em cinco genes candidatos (MyoD, Myf5, miogenina, MRF4 e miostatina) que atuam no desenvolvimento muscular de galinhas, e avaliar os efeitos de suas variantes alélicas sobre características quantitativas de crescimento e desenvolvimento muscular. Os genes MyoD e Myf5 são essenciais para a determinação da linhagem miogênica de células precursoras das fibras musculares na etapa inicial da miogênese, enquanto que a miogenina e MRF4 são requeridos na diferenciação final destas células. A miostatina por sua vez, atua como um potente regulador negativo do crescimento muscular esquelético durante a miogênese, persistindo por toda a fase adulta. Os produtos amplificados dos cinco genes foram clonados e seqüenciados a partir de pools de DNA dos parentais de duas linhagens divergentes desenvolvidas pela Embrapa - Suínos e Aves, uma de corte (TT) e outra de postura (CC). Os polimorfismos identificados foram validados e genotipados em uma população experimental F2, originada do cruzamento entre machos da linhagem TT e fêmeas da linhagem CC. Para avaliação dos efeitos dos polimorfismos sobre características quantitativas foram genotipados os genes da miostatina, miogenina e MyoD. Os polimorfismos dos genes da miostatina e MyoD não apresentaram efeito sobre nenhuma das características avaliadas. Dentre os sítios polimórficos detectados no gene da miogenina, um identificado como T455C apresentou associação estatisticamente significativa com as características: peso vivo ao 42 dias (P = 0,0263), ganho de peso do nascimento aos 42 dias de idade (P = 0,0291), ganho de peso dos 35 aos 42 dias de idade (P = 0,0368), peso da carcaça (P = 0,0245), peso das asas (P = 0,0099) e da carcaça residual (P = 0,0056), peso da gordura abdominal (P = 0,0320), do fígado (P = 0,0373) e do pulmão (P = 0,0262). Novas investigações poderão ser feitas no intuito de validar este polimorfismo como possível marcador genético para seleção de aves com maior capacidade de desenvolvimento muscular. Embora inúmeros polimorfismos tenham sido detectados nos genes Myf5 e MRF4, não foi possível estabelecer condições ideais para realização da genotipagem destes genes.The aim of this work was to identify polymorphisms in five candidate genes (MyoD, Myf5, Myogenin, MRF4 and Myostatin) which act in chicken muscle development and evaluate the effects of its allelic variants on growth and muscle development quantitative traits. MyoD and Myf5 are essential for the determination of the myogenic lineage of muscle precursor cells in early stages of myogenesis, whereas myogenin and MRF4 are required for the final differentiation of these cells. Myostatin acts as a potent negative regulator of skeletal muscle growth during myogenesis and continues to be expressed in adult animals. PCR products of these five genes were cloned and sequenced from DNA pools of parental individuals from two distinct lineages developed by Embrapa - Suínos e Aves, a broiler sire line (TT) and a layer line (CC). The polymorphisms identified were validated and genotyped in a F2 experimental population originated from a crossing of TT line sires ands CC line dams. Polymorphisms of Myostatin, Myogenin and MyoD genes were genotyped to evaluate their effects on quantitative traits. The effects of Myostatin and MyoD polymorphisms were not significant on any traits. Among the polymorphic sites detected in the myogenin gene one, identifyed as T455C, was significantly associated with the following traits: body weight at 42 days of age (P = 0,0263), body weight gain between birth and 42 days of age (P = 0,0291), body weight gain between 35 and 42 days of age (P = 0,0368), carcass weight (P = 0,0245), weight of drums (P = 0,0099), residual carcass (P = 0,0056), abdominal fat (P = 0,0320), liver (P = 0,0373) and lungs (P = 0,0262). New investigations should be conducted to validate this polymorphism as a possible genetic marker for selection of chickens with increased muscle development potential. Although many polymorphisms were detected in Myf5 and MRF4 genes, it was not possible to establish ideal conditions for their genotyping.
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GARCIA, Odair Scatolin Rossafa. "Utiliza??o de marcadores moleculares na an?lise da caracter?stica de qualidade da carne em caprino (Capra hircus)." Universidade Federal Rural do Rio de Janeiro, 2017. https://tede.ufrrj.br/jspui/handle/jspui/2413.
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Goat meat has lower levels of fat than those found in other types of meat such as beef, pork, sheep and deer, but the lack of selection criteria for slaughter, storage and commercialization of meat leads to a low level because of the lack of standardization of the product presenting unpleasant sensory characteristics. A study of polymorphism, variation in gene expression and the association of these variations with the desired phenotype allows to broaden the understanding of the physiological processes, which helps in the strategies aimed at improving the characteristic of interest, resulting in the expected final phenotype. The objective of the present study was to evaluate polymorphisms and gene expression among some of the most promising genotypes of pleiotropic genes, comparing the polymorphism and expression among groups of animals with greater and lesser weight at slaughter to verify if there is any relation with the weight difference Or softness of the flesh. For this purpose, genotypes of 40 goats from the Saanen and Alpina breeds for the growth hormone (GH) gene, diacylglycerol acyltransferase 1 gene (DGAT1), myostatin gene (MSTN), growth factor gene Similar to insulin 1 (IGF1), fatty acid carrier protein (FATP1) gene, nuclear factor 1 (NF1) gene, gamma peroxisome proliferator activated receptor (PPAR?) gene. After analyzing the association of the different genotypes with the slaughter weight (AP), carcass weight (PC) and meat softness expressed in shear force (FC), some genes were selected for the analysis of expression and association with them Variables. The GH, NF1 and PPAR genes were not evaluated for expression, the first for not having presented a good result for the efficiency analysis of the other two primers due to the lack of substantial data for the preparation of the primers. For the softness test, previously performed in another study by the same team, the longissimus lumborum muscle was used. Polymerase chain reaction (PCR) technique was used for the genotyping and later, for some genes, the digestion of the fragments amplified by restriction enzymes, a technique known as PCR-RFLP. Gene expression was conducted using the Real Time PCR technique (qPCR) and the meat tenderness phenotype was analyzed in a texturometer. The data were statistically related using the SAS GLM procedure. The UNIVARIATE procedure was used to verify the normality of residues of expression of the genes under study (expressed as 2-?Ct) and softness data. The averages were compared by the Tukey test and the Pearson correlations tested by the t test. The polymorphism already described in the GH was also detected in the population studied in the present study, the genotype heterozygous AB presented a mean 2.78kg at slaughter weight more than the AA individuals, for the MSTN the individuals with heterozygous M1M2 genotype presented higher scores for weight at slaughter, while for the IGF1 gene the heterozygous AB animals present less tender meat. The group with lower weight at slaughter showed higher expression of the DGAT1 and FATP genes, which may reflect a higher deposition of fat in the carcass and greater softness, in comparison with the group of higher weight.
A carne caprina apresenta teores de gordura abaixo dos encontrados em outros tipos de carne como a de bovino, su?no, ovino e veado. Entretanto, a falta de crit?rio de sele??o para o abate, estocagem e comercializa??o da carne, acaba por gerar um baixo n?vel de consumo, devido ? falta de padroniza??o do produto apresentando caracter?sticas sensoriais desagrad?veis. Estudo de polimorfismo, varia??o na express?o g?nica e associa??o destas varia??es com o fen?tipo desejado permite ampliar a compreens?o sobre os processos fisiol?gicos, al?m de auxiliar programas de melhoramento gen?tico animal para a sele??o de animais com fen?tipos superiores para a caracter?stica de interesse. O objetivo do presente trabalho foi avaliar a associa??o de polimorfismos e express?o g?nica com a caracter?stica peso ao abate e verificar se h? rela??o entre a diferen?a de peso e a maciez da carne. Para este prop?sito foram identificados inicialmente os gen?tipos de cabritos das ra?as Saanen e Alpina para os seguintes genes: horm?nio do crescimento (GH), diacilglicerol aciltransferase 1 (DGAT1), miostatina (MSTN), fator de crescimento semelhante ? insulina 1 (IGF1), prote?na transportadora de ?cidos graxos (FATP1), fator nuclear 1 (NF1), receptor ativado por proliferadores de peroxissomas gama (PPAR?). Ap?s a an?lise de associa??o dos diferentes gen?tipos com o peso ao abate (PA), peso da carca?a (PC) e maciez da carne expressa em for?a de cisalhamento (FC), foram selecionados alguns genes para a an?lises de express?o e associa??o com as mesmas vari?veis. Os genes GH, NF1 e PPAR n?o foram avaliados quanto a express?o, o primeiro por n?o ter apresentado um bom resultado para as analise de efici?ncia dos primers os outros dois devido ? problemas no genoma refer?ncia para a confec??o dos primers. Para o teste de maciez foi utilizado o m?sculo longissimus lumborum. Para a genotipagem foi utilizada a t?cnica da rea??o em cadeia pela polimerase (PCR) e posteriormente, para alguns genes, digest?o dos fragmentos amplificados por enzimas de restri??o (PCR-RFLP). A express?o g?nica foi conduzida utilizando a t?cnica de PCR em Tempo Real (qPCR) e o fen?tipo de maciez da carne foi analisado em textur?metro. Os dados foram analisados estat?sticamente utilizando o procedimento GLM do SAS. O procedimento UNIVARIATE foi utilizado para verificar a normalidade dos res?duos da express?o dos genes em estudo (expressos com 2-?Ct) e dados de maciez. As m?dias foram comparadas pelo teste de Tukey e as correla??es de Pearson testadas pelo teste de t. O polimorfismo j? descrito no GH foi tamb?m detectado na popula??o estudada no presente trabalho, o gen?tipo heterozigoto AB apresentou m?dia 2,78kg a mais de peso ao abate do que os indiv?duos AA, para a MSTN os indiv?duos com gen?tipo heterozigoto M1M2 apresentaram maiores escores para peso ao abate, enquanto para o gene IGF1 os animais heterozigotos AB apresentam carne menos macia. O grupo com menor peso ao abate apresentou maior express?o dos genes DGAT1 e FATP, o que pode refletir maior deposi??o de gordura de gordura na carca?a e maior maciez, em compara??o com o grupo de maior peso.
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Enjin, Anders. "Neural Control of Movement : Motor Neuron Subtypes, Proprioception and Recurrent Inhibition." Doctoral thesis, Uppsala universitet, Genetisk utvecklingsbiologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-147361.
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Movement is central for life, and all animals depend on accurate regulation of movement for purposeful behavior. There is great diversity of movements, ranging between simple and vital breathing movements to minute and subtle movements of the face used to communicate emotions. Consequently, motor neurons, which are the only route of central nervous system output, are essential for all motor behaviors. To control the many motor behaviors expressed by an animal, motor neurons are exposed to a large number and variety of modulating synaptic inputs and have evolved into subtypes with specific functions. In this thesis, motor neuron subtypes and the synaptic input to motor neurons from Renshaw cells and Ia afferents have been studied. Novel molecular markers that identify subtypes of motor neurons are described. Three markers, Chodl, Calca and ERRβ, have been used to study the degeneration of subtypes of motor neurons in a mouse model of the neurodegenerative disease amyotrophic lateral sclerosis (ALS). Another marker, 5-ht1d, has been used to record the electrophysiological character of gamma motor neurons. In mice that lack 5-ht1d, motor neurons develop with reduced proprioceptive input. Remarkably, these mice had fewer foot faults than control animals when challenged to cross a narrow beam suggesting that the amplitude of monosynaptic proprioceptive input to motor neurons is not essential for motor coordination. In a final set of experiments, genetic removal of vesicular transport of neurotransmitter from Renshaw cells suggest that Renshaw cells are not integral for motor circuit function or motor behaviors. However, they are involved in the development of motor circuits in the spinal cord. Together, this thesis provides novel molecular tools for studies of motor neuron subtypes and novel data regarding the development and function of spinal motor circuits.
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Tong, Xiao. "Co-registration of fluorescence diffuse optical tomography (fDOT) with Positron emission tomography (PET) and development of multi-angle fDOT." Thesis, Paris 11, 2012. http://www.theses.fr/2012PA112251/document.
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Ce travail de thèse concerne le traitement d’image fDOT (fDOT pour fluorescence diffuse optical tomography) suit vers deux axes. Le recalage d'images fDOT à l’aide de l’imagerie TEP (tomographie par émission de positons) et l’amélioration des reconstructions fDOT à l’aide de miroirs pour collecter des projections complémentaires. Il est présenté en deux parties : Dans la première partie, une méthode automatique pour recaler les images de fDOT avec les images de Tomographie par Emission de Positons (TEP) développée dans le but de corréler l’ensemble des informations issues de chaque modalité. Cette méthode de recalage est basée sur une détection automatique de marqueurs fiduciaires présents dans les deux modalités. La particularité de cette méthode est l’utilisation de l’image de surface obtenue en fDOT, qui sert à identifier la position en Z des marqueurs fiduciaires dans les images optiques. Nous avons testé cette méthode sur un modèle de souris porteuses de xénogreffes de tumeurs de cellules cancéreuses MEN2A qui imitent un carcinome thyroïdien médullaire humain, après une double injection de traceur radioactif : [18F]2-fluoro-2-Deoxy-D-glucose (FDG) pour l’imagerie TEP et un traceur optique d’infrarouge fluorescent, le Sentidye. Grâce à la précision de notre méthode, nous arrivons à démontrer que le signal Sentidye est présent à la fois dans la tumeur et les vaisseaux environnants [1]. La qualité des images fDOT est dégradée selon l’axe Z du fait d’un nombre limité de projections pour la reconstruction. Dans la deuxième partie, le travail s’est orienté vers une nouvelle méthode de reconstruction d’images fDOT à partir d’un nouveau système d’acquisition multi-angulaire avec deux miroirs placés de chaque côté de l’animal. Ce travail a été mené en collaboration avec le département CS d’University College London (UCL), partenaire du projet Européen FMT-XCT. Le logiciel TOAST développé par cette équipe a été utilisé comme source pour l’algorithme de reconstruction, et modifié pour s’adapter à notre problématique. Après plusieurs essais concernant l’ajustement des paramètres du programme, nous avons appliqué cette méthode sur un fantôme réaliste des tissus biologiques et chez la souris. Les résultats montrent une amélioration de l’image reconstruite d’un fantôme semi-cylindrique et de l’image de rein chez la souris, pour lesquelles la méthode des miroirs est supérieure à la méthode classique sans miroir. Malgré tout, nous avons observé que les résultats étaient très sensibles à certains paramètres, d’où une performance de reconstruction variable d’un cas à l’autre. Les perspectives futures concernent l’optimisation des paramètres afin de généraliser l’approche multi-angleThis thesis concerns the image processing of fluorescence diffuse optical tomography (fDOT), following two axes: FDOT image co-registration with PET (positron emission tomography) image and improvement of fDOT image reconstructions using mirrors to collect additional projections. It is presented in two parts:In the first part, an automatic method to co-register the fDOT images with PET images has been developed to correlate all the information from each modality. This co-registration method is based on automatic detection of fiducial markers (FM) present in both modalities. The particularity of this method is the use of optical surface image obtained in fDOT imaging system, which serves to identify the Z position of FM in optical images. We tested this method on a model of mice bearing tumor xenografts of MEN2A cancer cells that mimic a human medullary thyroid carcinoma, after a double injection of radiotracer [18F] 2-fluoro-2-Deoxy-D-glucose ( FDG) for PET imaging and optical fluorescent infrared tracer Sentidye. With the accuracy of our method, we can demonstrate that the signal of Sentidye is present both in the tumor and surrounding vessels.The fDOT reconstruction image quality is degraded along the Z axis due to a limited number of projections for reconstruction. In the second part, the work is oriented towards a new method of fDOT image reconstruction with a new multi-angle data acquisition system in placing two mirrors on each side of the animal. This work was conducted in collaboration with the CS Department of University College London (UCL), a partner of the European project FMT-XCT. TOAST software developed by this team was used as source code for the reconstruction algorithm, and was modified to adapt to the concerned problem. After several tests on the adjustment of program parameters, we applied this method on a phantom that simulating the biological tissue and on mice. The results showed an improvement in the reconstructed image of a semi-cylindrical phantom and the image of mouse kidney, for which the reconstruction of the mirrors geometry is better than that of conventional geometry without mirror. Nevertheless, we observed that the results were very sensitive to certain parameters, where the performance of reconstruction varies from one case to another. Future prospectives concern the optimization of parameters in order to generalize the multi-angle approach
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Yang, Yi-Zhen, and 楊依臻. "Method Development for Haploid Maize Identification Using Molecular Markers." Thesis, 2017. http://ndltd.ncl.edu.tw/handle/56667090720960742099.
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碩士國立臺灣大學
農藝學研究所
105
The doubled haploid technique is a method to develop inbred lines quickly in maize breeding programs. Because the haploid induction rate is only around 10%, efficient markers to identify haploid plant precisely are required. In the current study, DNA markers were developed for the combination of the RWS derived haploid inducer and the cross of G6 and C18 both of which are sweet corns. These DNA markers were also used to evaluate accuracy of two morphological markers R1-nj and Purple1. Two InDel markers ID1 and ID4 were used to screen a total of 2849 seedlings. Additional three KASP markers ZMKASP_002, ZMKASP_008, and ZMKASP_009 were also able to distinguish haploid individuals from hybrids of inducer lines. Based on the genotypes of 2849 seedlings, the R1-nj marker had 48% FDR(false discovery rate) and 25.7 % FNR(false negative rate). In contract, the genotypes of the Purple1 marker showed 100% matches to the genotypes of DNA markers while expressivity of the Purple1 marker were sometimes very low.
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Rahman, Md Mukhlesur. "Development of molecular markers for marker assisted selection for seed quality traits in oilseed rape." 2007. http://hdl.handle.net/1993/2846.
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Molecular markers for seed quality traits including erucic acid content genes, seed coat color genes in Brassica napus and seed coat color genes in B. rapa were developed. A single base change in the Bn-FAE1.1 gene in the A genome and a two-base deletion in the Bn-FAE1.2 gene in the C genome produce the nearly zero content of erucic acid observed in canola. The single base change was detected as single nucleotide polymorphic (SNP) marker with an ABI SNaPshot kit. A multiplexing primer set was designed by adding a polyT to the 5´ primer end to increase SNP detection throughput through sample pooling. The two-base deletion in the C genome gene was detected as a sequence characterized amplified region (SCAR) marker in an ABI 3100 Genetic analyzer. To increase the throughput, one genome specific primer was labeled with four fluorescence dyes and combined with 20 different primers to produce PCR products with different fragment sizes. These multiplexed high throughput molecular markers have been successfully implemented in our canola/rapeseed breeding programs. Trigenic inheritance was observed for seed coat color in B. napus. Three Sequenced Related Amplified Polymorphism (SRAP) markers very closely linked to the three different seed coat color genes were developed. Chromosome-walking technology was used to convert the SRAP marker into a SCAR marker and a SNP marker. Subsequently, the first seed coat color gene (Bn1) marker was converted into a SCAR marker, and the second seed coat color gene (Bn2) marker was converted into a SNP marker. Digenic inheritance was observed for seed coat color genes in B. rapa. A SRAP marker was identified as being tightly linked to the major seed coat color gene (Br1). The SRAP marker was sequenced and extended sequences were obtained using chromosome-walking technology. The flanking sequences of the SRAP marker contained 24 SNPs and a 12-bp deletion position that allowed the marker to be converted into a co-dominant SNP marker and a co-dominant SCAR marker, respectively. The SCAR marker was detected in the ABI 3100 genetic analyzer with four fluorescently labeled M13 primers integrated with different SCAR primers, which permitted pooling of PCR samples for high throughput detection.October 2007
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Lee, Teng-Yu, and 李騰裕. "Molecular Markers in the Development and Outcome of Gastric Cancer." Thesis, 2014. http://ndltd.ncl.edu.tw/handle/6bn6hf.
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博士中國醫藥大學
臨床醫學研究所博士班
102
Aim: Early diagnosis in gastric cancer remains a challenge due to the limitations of screening tools, and most patients already suffer from advanced tumors when gastric cancers are newly diagnosed. Some novel molecular markers have been related to gastric cancer development, such as osteopontin (OPN), matrix metalloproteinase-9 (MMP-9) and folate. We aimed to investigate the associations between these molecular markers and gastric cancer and to develop a personalized risk prediction tool that might facilitate cancer risk stratifications for patients. Method: Using prospectively collected data and blood samples from the gastric cancer patients and the healthy controls, we conducted case-control studies for investigations. Deoxyribonucleic acid was extracted from peripheral blood leucocytes. Single-nucleotide polymorphisms (SNPs) in the OPN promoter (-66, -156, -443, -616, -1748, and -1776) were analyzed by pyrosequencing and direct sequencing methods. MMP-9 genotyping was analyzed by PCR-RFLP method. For serum folate analysis, blood samples were obtained after overnight fasting, and serum folate concentrations were measured by microbiological assay. The associations between molecular markers and clinicopathological features were analyzed by multivariate regression analysis. In addition, we collected data from the National Health Insurance Research Database in Taiwan on 278,898 patients with a primary diagnosis of peptic ulcer disease, and we used the data to develop a nomogram, which we validated by discrimination and calibration, and in a test cohort. Results: SNP -443 C/C and -616 T/T of the OPN promoter were significantly associated with gastric cancer (OR 2.88; 95% CI: 1.16–7.12, and OR 1.95; 95% CI: 1.35–2.82, respectively). Analysis of the combined effect of OPN promoter SNPs revealed that the combination of SNP -443 (T/C or C/C) and SNP -616 (T/T or T/G) had the most significant association with gastric cancer (OR 3.95; 95% CI: 1.58–9.90). There was significant correlation between female patients with MMP-9 -1562 C/T or T/T genotype and higher risk of gastric cancer (OR 2.12, 95% CI: 1.13–3.96). On stratified analysis, only elderly females with T allele had higher risk of gastric cancer (OR 2.64, 95% CI: 1.02–6.84). The mean serum folate level was significantly lower in gastric cancer patients than that in controls (3.71 ± 0.30 vs. 8.00 ± 0.54 ng/mL). In the patient cohort of gastric cancer, the respective cutoff values showed that low serum folate was significantly associated with serosal invasion (OR 2.54, 95% CI: 1.23–5.23), lymphatic invasion (OR 2.23, 95% CI: 1.17–4.26), and liver metastasis (OR 6.67, 95% CI: 1.28–34.91). We developed a nomogram according to independent risk factors associated with gastric cancer developemnt, and the concordance index for the nomogram was 0.78. Study subjects were divided in quartiles of predicted risk scores; from lowest score quartile to highest, cumulative incidences at 2 years were 9.3, 20.9, 38.0, and 135.7 per 10,000 people. The nomogram was validated in an independent cohort and similar incidence values were determined. Conclusion: Polymorphisms in the OPN promoter were associated with the development of gastric cancer, and the combination of SNP -443 and -616 most significantly increased susceptibility to gastric cancer. MMP-9 -1562 promoter polymorphism with T allele might be used as a marker to predict gastric cancer development in female subjects, especially in the elderly. Lower serum folate levels were significantly associated with gastric cancer development and invasive phenotypes. The clinical applications of these molecular markers warrant further study. In addition, we developed a nomogram to predict risk for gastric cancer development one and two years after diagnosis of peptic ulcer disease, and the nomogram could facilitate cancer risk stratifications for patients.
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Yaw-Yuan, Wang, and 王照元. "Molecular Markers and Development of Diagnostic Oligo Chips for Colorectal Cancer." Thesis, 2003. http://ndltd.ncl.edu.tw/handle/383v3x.
Full textAbstract:
博士高雄醫學大學
醫學研究所
91
Colorectal cancer (CRC) is one of the leading causes of malignancies worldwide and is the second most frequent cause of cancer death in developed countries. Even with the recent advances in diagnostic and surgical techniques, the outcome remains poor in cases of advanced disease and only CRC diagnosed at an early stage are likely to be cured by surgical resection. According to analyses from the Department of Health of Taiwan, CRC is the second most frequent malignancy in 1999, leading to over 6000 new cases and 3000 deaths per year. Because distant metastases are major problems in the treatment of CRC, development of a sensitive, specific and convenient diagnostic method for detecting CRC at a very early stage could ultimately affect future patient prognosis. Nowadays, there are still no reliable and simple methods in the early diagnosis and postoperative follow-up for CRC. At present, the clinical diagnostic tools used for CRC diagnosis are stool occult blood test, tumor marker, image study and colonoscopy. However, the high false positive and negative rates limit the stool occult blood test to be a rough screening tool. The conventional tumor marker assays require that tumors have a significant volume of cancer cells, and have the shortcoming of limited sensitivity and specificity. The accurate interpretation by image studies needs that a tumor grows up to be a considerable mass. Colonoscopy is an invasive and a low cost-benefit procedure; thus, it is not feasible for mass screening and regular follow-up at short intervals in CRC patients following operations. Recent improvements in molecular biological techniques have been used to clarify the genetic alterations associated with the development and metastasis of CRC and to assess the possibility of using oncogenes and tumor suppresser genes to predict the cancer prognosis in clinic. For the rapid and accurate diagnosis in CRC, it is necessary to find out the genes associated with CRC carcinogenesis, and to elucidate the roles of these oncogenes and tumor suppressor genes in the development of CRC before their clinical application. Furthermore, the understanding of molecular pathogenesis in CRC would be essential in the development of CRC diagnostic gene chips. A series of genetic alterations have been associated with CRC, and a multistep model of tumorigenesis involving activation of protooncogenes and inactivation of tumor suppressor genes has been proposed. Of the genes characterized to date, inactivation of tumor suppressor genes APC and p53, as well as activation of the oncogene K-ras are thought to be particularly important determinants of tumor initiation and progression. To assess the prevalence and spectrum of APC, K-ras and p53 gene mutations in Taiwanese patients with CRC, we analyze these three gene mutations in tumors tissues from 104 patients in Taiwan. Our results showed that 46 of 104 (44.2%) CRC patients have the APC gene mutations in tumor tissues, 47 of 104 (45.2%) have the K-ras gene mutations, and 38 of 104 (36.5%) have the p53 gene mutations. Overall, 78 of 104 patients (75%) have at least one gene mutations in cancer tissues. Due to high frequency of these genes mutations in CRC, we further use these target genes as molecular markers in the early diagnosis of CRC. Nevertheless, conventional diagnostic procedures do not always give an accurate preoperative evaluation of the extent of the disease or a complete postoperative follow-up. Moreover, tumor markers such as CEA used at present in clinical follow-up are not satisfactorily sensitive and specific. Therefore, looking for a powerful and reliable tumor marker for the patients with CRC is mandatory. Application of molecular markers is based on the apoptosis of tumor cells during the tumorigenesis, and subsequently trace tumor DNA is released into circulation. It is earlier to detect the recurrence and metastasis of malignancies than conventional tumor markers by the amplification of circulating nucleic acid through the molecular biology. Therefore, more aggressive therapies could be advised at the micrometastasis stage to improve the survival rate of patients. Following our observation of APC, K-ras, and p53 gene mutations in the same series of patients, we performed a paired comparison between tumor tissues and serum in individual patients, as a potential approach to a noninvasive method for the detection of micrometastasis. APC, K-ras, and p53 mutations were detected in serum samples in 30.4% (14/46), 34.0% (16/47), and 34.2% (13/38) of patients, respectively with tumors harboring the same mutations. The presence of at least one molecular alteration in serum was observed in 46.2% (36/78) of the cases. With regard to tumor stage, we observed a tendency toward a stage-dependent difference in the occurrence of APC, K-ras, and p53 mutations in the serum samples of CRC patients. The incidence of tumor DNA detectable is increasing from 0% in Dukes stage A to 66.7% in Dukes stage D in serum and the higher detection rate is observed in the more advanced stage. The detection of tumor DNA as molecular markers is practicable; therefore, we are anticipating searching for new target genes through understanding genetic alterations in the adenoma-carcinoma model in CRC for diagnostic and therapeutic subjects. We combine suppression subtractive hybridization and cDNA microarray to analyze genes that are involved in the carcinogenesis of colorectal polyps to CRC. The significantly up-regulated genes were then further confirmed by Northern blot and subsequently sequenced. Northern analysis of each set of cDNA genes on the chip revealed that 36 genes were detected as up-regulated in adenoma compared to normal and 54 genes were detected as up-regulated in carcinoma as compared to normal control. A set of 23 genes with serial increase of gene expression from adenoma to carcinoma was identified. Of the 23 genes identified as being gradually overexpressed, which were then evaluated by Human Tumor MTNTM Blot 1 (Clontech, #7792-1), three clones were considered as function-unknown genes and 20 were shown as function-known genes. Of these 20 function-known genes, 6 genes have previously been shown to be overexpressed in carcinogenesis of CRC; however, 14 genes had not yet been reported to be correlated to CRC. Subsequently, we selected some genes overexpressed both in polyp and CRC tissues, and negative control genes to produce a prototype of diagnostic chips containing 71 genes. One hundred CRC patients and 90 patients of negative control were evaluated using the prototype of gene chips. The sensitivity rate of the chip was 88% (88/100), the specificity rate was 92% (83/90), the positive predictive rate was 92% (88/95), and the negative predictive rate was 88% (83/95). Our preliminary results indicated that diagnostic gene chips would provide clinicians a rapid, effective and early diagnostic tool, and then in the prevention and early therapy for CRC, and finally increase the survival rate and response rate for CRC patients. We believe that gene diagnostic chips would play a very important role in the diagnosis of clinical oncology, and expand its application in the preventive medicine in the near future.