Rozprawy doktorskie: „QTR 1”

1

Kurt, Aslihan. "The Regulatory Effect Of Ccar Activator On The Cephamycin C Gene Cluster Of Streptomyces Clavuligerus". Phd thesis, METU, 2011. http://etd.lib.metu.edu.tr/upload/12614004/index.pdf.

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Streptomyces clavuligerus produces industrially important secondary metabolites such as cephamycin C (a &beta
-lactam antibiotic) and clavulanic acid (a potent &beta
-lactamase inhibitor). Cephamycin C is active against penicillin-resistant bacteria due to presence of methoxyl group in C-7 position of cephalosporin nucleus. Clavulanic acid is prescribed in combination with &beta
-lactams for treatment of various bacterial infections. Cephamycin C and clavulanic acid gene clusters form &beta
-lactam supercluster in S. clavuligerus genome. CcaR (Cephamycin C-Clavulanic Acid Regulator), encoded by ccaR, located in cephamycin C gene cluster, is a positive regulator of &beta
-lactam supercluster. Previous studies on cephamycin C gene cluster have used different techniques, such as S1 nuclease (Paradkar et al., 1994), Northern blot (Perez-Llarena et al., 1997), and Western blot (Alexander and Jensen, 1998) to determine expression of cephamycin C genes at mRNA level and to identify their functions at protein level, and they have studied on different parts of the cluster. Hence, a comprehensive study is needed to understand molecular mechanisms of pathway-specific regulation of cephamycin C production by S. clavuligerus. In this study, time-dependent expression levels of cephamycin C gene cluster in a ccaR-disrupted mutant and ccaR-overexpressed recombinant strain of S. clavuligerus as compared to those in the wild strain were analysed by RT-PCR and qRT-PCR. In addition, DNA-binding sequences of CcaR on cephamycin C gene cluster were examined by EMSA. The effect of ccaR disruption and overexpression on cephamycin C and clavulanic acid yields were determined by bioassay and HPLC. Three polycistronic and two monocistronic transcripts were obtained by RT-PCR. CcaR regulation showed its effect on mostly ccaR, lat, cmcI, cefD, blp and cefF expression levels. qRT-PCR data was supported by EMSA showing CcaR binding to lat, cefD&ndash
cmcI and ccaR promoters. ccaR overexpression from multi-copy recombinant plasmid resulted in significant increase in cephamycin C and clavulanic acid yields, making the respective recombinant strain as an attractive industrial strain. qRT-PCR data presented herein constitute the first that reveal the effect of CcaR activator on the expression of cephamycin C genes in a time-dependent manner.

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2

Attilio, Dênia Borges. "Testes de associação em região de QTL ligados do cromossomo 1 da galinha doméstica". Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/11/11139/tde-30042014-104202/.

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Atualmente, o Brasil é considerado o maior exportador mundial e terceiro maior produtor mundial de carne de frango. Este destaque é resultado, principalmente, do melhoramento animal baseado na estimação do valor genético a partir da mensuração de fenótipos e informações de pedigree. Entretanto, é comum que a seleção não seja feita para cada característica isoladamente devido à correlação genética entre elas. Esta correlação tem como causas a pleiotropia ou a ligação genética. Com este trabalho objetivou-se detectar associações entre características fenotípicas de interesse para a avicultura e SNPs em uma região do cromossomo 1 (168 - 208 cM e 57 - 71 Mbp), onde possíveis QTL ligados foram previamente mapeados. Utilizou-se o Beadchip de SNPs de 60k para genotipar 14 animais da geração Parental (machos TT e fêmeas CC) e 28 F1 da população TCTC desenvolvida pela Embrapa Suínos e Aves. A linhagem TT apresentou maior variabilidade genotípica que CC, porém, os F1 foram superiores às linhagens Parentais com base no número de heterozigotos e MAF. O polimorfismo com maior ocorrência em ambas as gerações foram as transições com 84,3%. Foram selecionados 144 SNPs mais informativos com base na heterozigosidade dos cinco casais F1 que geraram os 453 F2. Houve redução de heterozigotos e MAF em F2, em função da média de F1, decorrente de certo grau de parentesco e endogamia entre os animais que compuseram esta geração. Os blocos de haplótipos construídos demonstraram que os machos TT apresentaram 25 blocos, fêmeas CC (17), F1 (32) e F2 (23) com tamanho médio de 278, 467, 242 e 160 kpb, respectivamente. Foi evidenciado que 236 (42,7%) correlações fenotípicas foram significativas, das quais o maior número constatado foi entre PB_MS e outras 17 características e, o maior valor estimado foi entre PB_MS e EE_MS (-0,90). Do total esperado de 3.456 testes de associação, 609 (17,6%) foram considerados significativos (p < 0,05), sendo 424 (69,6%) com efeito aditivo e 185 com efeito de dominância (30,4%). PV41 apresentou maior número de associações (123), enquanto DOR não foi associado a nenhum SNP. Proporcionalmente, o maior número de SNPs foi associado próximo ao QTL pleiotrópico 2 para 17 características. Já os maiores níveis de significância (p < 9,59 x 10-8) para o efeito aditivo foram evidenciados para SNPs localizados próximos ao QTL pleiotrópico 1 e associados somente com PV41, a saber: Gga_rs13869715 (A < C), Gga_rs13870613 (T < C), Gga_rs14827719 (A < G), GGaluGA019336 (T < C) e GGaluGA019533 (A < C). Foram detectadas associações ainda não descritas na literatura para GP3541, CA3541, INT, PES, CAB, FIG, COR, MOE, PUL, HEM, COL, TRI, TC, PB_MS, EE_MS, CZ_MS. Finalmente, foram indicados possíveis genes candidatos posicionais e funcionais, tais como, IGF1, MYBPC1, MTPN, SOX-5, FGFR1OP2 e TTLL12 que poderão ser empregados na análise de expressão gênica.
Actually, Brazil is considered the world\'s first- and third-biggest exporter and producer of poultry meat, respectively. These performances are mainly consequence of animal breeding based on the estimation of breeding value combining phenotypes and pedigree information. However, usually the selection is not carried out for each trait separately due to genetic correlation between them. This correlation is caused by pleiotropy or linkage. We aimed to detect associations between phenotypic traits of interest to poultry industry and SNPs on a region of chromosome 1 (168 - 208 cM and 57 - 71 Mbp), where putative linked-QTL were previously mapped. A chicken 60k SNP BeadChip was used to genotype 14 animals from Parental generation (TT males and CC females) and 28 F1 of the TCTC population that was developed by Embrapa Swine and Poultry. The TT line showed greater genotypic variability than CC, however, F1 were higher than Parental generation based on the number of heterozygotes and MAF. The polymorphism more frequent in both generations was the transitions with 84.3%. The 144 most informative SNPs were selected based on heterozygosity of the five F1 couples which generated the 453 F2. There was a reduction of heterozygotes and MAF in F2, based on the F1 mean value, as consequence of some degree of relationship and inbreeding between animals that formed this generation. Haplotype blocks demonstrated that the TT males showed 25 blocks, CC female (17) F1 (32) and F2 (23) with an average size of 278, 467, 242 and 160 kbp, respectively. It was observed that 236 (42.7%) phenotypic correlations were significant. Out of these, the highest number was found between PB_MS and other 17 traits and the highest estimated value was between PB_MS and EE_MS (-0.90). Out of 3,456 expected association tests, 609 (17.6 %) were considered significant (p < 0.05), being 424 (69.6%) with additive effect and 185 with dominance effect (30.4%). PV41 presented the highest number of associations (123), while DOR was not associated to any SNP. Proportionally, the highest number of SNPs was associated close to the pleiotropic QTL 2 with 17 traits. On the other hand, the highest significance levels (p < 9.59 x 10-8) for the additive effect were evidenced for SNPs located close to the pleiotropic QTL 1 and associated only with PV41 (Gga_rs13869715 (A < C), Gga_rs13870613 (T < C), Gga_rs14827719 (A < G), GGaluGA019336 (T < C) and GGaluGA019533 (A < C)). Novel associations were detected for GP3541, CA3541, INT, PES, CAB, FIG, COR, MOE, PUL, HEM, COL, TRI, TC, PB_MS, EE_MS, CZ_MS when we compared our results with literature. Finally, putative positional and functional candidate genes were indicated such as IGF1, MYBPC1, MTPN, SOX-5, FGFR1OP2 and TTLL12, which may be used in gene expression analysis.

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3

Bauman, Lara Elizabeth. "QTL variance component models". Diss., Restricted to subscribing institutions, 2007. http://proquest.umi.com/pqdweb?did=1464110531&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.

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4

Watkins, Gemma L. "A comparison of HIV-1 and HIV-2 gag gene expression". Thesis, University of Warwick, 2012. http://wrap.warwick.ac.uk/45902/.

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Despite being closely related viruses with similar replication cycles, HIV-2 replicates more slowly than HIV-1 and produces fewer particles, resulting in a lower plasma viral load. Expression of the major structural gene, gag, from HIV-1 and HIV-2 proviruses was compared to investigate whether this could play a role in the difference in particle production observed between HIV-1 and HIV-2 infection. Using quantitative RT-PCR, significantly less full-length HIV-2 gag mRNA was found to be transcribed from its provirus than for HIV-1. Sub-cellular fractionation allowed us to determine HIV-1/2 gag mRNA levels in the nucleus and cytoplasm throughout a time course. RNA export of HIV-2 gag mRNA was shown to be slower than for HIV-1 gag mRNA. HIV-2 full-length gag RNA was shown to be translated much less efficiently than HIV-1 in a range of cell lines. Both HIV-1 and HIV-2 Gag have been proposed to be translated by internal ribosome entry. Shutting down capdependent translation (by poliovirus-mediated eIF4G cleavage) significantly reduced translation from both HIV-1/2 gag RNAs, with no evidence of compensatory IRES activity. This suggests that cap-dependent translation is the predominant mechanism for translation of both HIV-1 and HIV-2 RNA. Additional work explored HIV RNA-protein interactions by UV cross-linking experiments using cellular proteins. Several proteins differentially binding to HIV-1/2 5’ UTR RNAs were identified and, in particular, a 45 kDa protein binding only to the HIV-1 5’ UTR. Attempts were made to characterise the proteins binding with different affinities to HIV-1 and HIV-2 RNAs. Confocal microscopy was used to visualise HIV-1/2 Gag expression within the cell. Both HIV-1 and HIV-2 Gag expression was shown to be reduced when siRNA was used to inhibit the cellular clathrin adaptor protein AP-1. In conclusion, HIV-2 Gag gene expression was found to be less efficient than HIV-1 at the level of transcription, RNA export and translation. Future work will continue to investigate the mechanisms behind these differences.

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5

Lea, Nicholas. "Processing and trafficking of Shiga-like toxin 1 in eukaryotic cells". Thesis, University of Warwick, 1996. http://wrap.warwick.ac.uk/79995/.

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Shiga toxin (ST) and the Escherichia coli Shiga-like toxins (SLTs) are type 11 ribosome inactivating proteins (RIPs). All members of this group exhibit specific RNA N-glycosidase activity, the prototype being the plant toxin ricin. ST and the SL Ts are bipartite toxins composed of a catalytic A subunit and a pentamer of cell binding B subunits. These toxins show overall structural similarities to ricin, which is also a bipartite toxin with a catalytic A chain and a single cell binding B chain. The A chains of ST and SL T 1 show homology to ricin A chain, particularly in the active site region, and appear identical in their enzymatic mechanism. The respective B chains however are structurally very different and interact with quite different cellular components. In this study, the role of intracellular proteolytic activation of SLT 1 is addressed using a molecular biological approach. The biological characteristics of several mutant SL Ts has been investigated both in vitro, by addition of exogenous protease, and in vivo by comparing the relative cytotoxicities of mutant and wild type proteins in Vero cells. The intracellular processing of these mutant toxins has also been examined. In parallel, the biological properties of a ricin A chain SL T 1 chimeric protein has been investigated. The ultimate aim of this study was to extend our knowledge of the proteolytic processing requirements of SL T 1 and it has led to the conclusion that proteolytic removal ofthe A2 portion of SL T 1 is not an essential prerequisite for intoxication of Vero cells with SLT 1.

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Abioye, Jumai Adeola. "Engineering chimaeric recombinases for HIV-1 proviral DNA excision". Thesis, University of Glasgow, 2018. http://theses.gla.ac.uk/9143/.

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‘Cutting out’ HIV-1 proviral DNA could potentially cure a person of the infection. Genome editing approaches have been proffered for eradicating the provirus in infected persons by activating all latent viral reservoirs for further antiretroviral therapy or for the excision of the proviral DNA from memory T- cells. Previous approaches to do this have used nuclease-based tools or reprogrammed tyrosine recombinases; the former presenting unpredictable therapeutic outcomes and the latter, lengthy design time for newer tool variants if viral mutability erodes their effectiveness. Unlike nuclease-based tools that only cut DNA and rely on host-mediated repair mechanisms, chimaeric recombinases (CRs) cut DNA and carry the inherent ability to re-ligate cut ends at the cleavage site. The modular domain architecture of small serine recombinases can be redesigned to mediate site-specific recombination on non-cognate sites, by replacing the C-terminal DNA binding domains (DBDs) of serine recombinases with programmable DBDs such as Zinc Finger (ZF) proteins, TAL effector proteins and CRISPR-dCas9. For HIV-1 proviral DNA excision, CR requirement for the interaction of two recombinase-bound sites, and the lack of necessity for host cell-encoded factors should maximize the fidelity and efficiency of provirus removal. In this work, the engineering and characterization of CRs with the specificity to recognize and promote site-specific recombination at highly conserved regions within the HIV-1 proviral DNA is explored. This research provides a solid proof-of-concept for the use of CRs to target divergent novel target sequences, expanding their applicability for applied genome editing and wider biotechnological applications.

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7

McGeehan, John Edward. "Molecular characterisation of Herpes simplex virus type 1 deoxyuridine triphosphatase". Thesis, University of Glasgow, 1998. http://theses.gla.ac.uk/6104/.

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Analysis of primary sequence data revealed a subset of open reading frames that were predicted to encode HSV-I dUTPases based on five areas of local primary sequence conservation. The differences in the primary sequence organisation of these motif regions allowed the description of two distinct dUTPase classes. The class I dUTPases are encoded by a diverse range of organisms and are characterised by a trimeric arrangement with subunit protein lengths approximating 150 amino acids. The class II dUTPases are specific to the herpesviruses and are characterised by a monomeric arrangement with a protein chain length approximately double that of their class I counterparts. It has been proposed that the class II dUTPases arose by the intragenic duplication of the class I open reading frame. In this thesis the class I structures were used as a basis to investigate the HSV-1 class II dUTPase in terms of structural and evolutionary relationships. To allow a defined approach to functional analysis of the HSV-1 dUTPase a tertiary structural model was generated for the class II enzymes. Following intensive primary sequence analysis a method was devised for comparing class I and class II sequences directly. Secondary structure prediction programs were utilised to judge the basic structural similarities between the two classes allowing the proposition of several defined hypotheses. The available class I structural information was utilised in order to characterise highly conserved structural elements within the class I group. In was then possible to relate this data set to class I primary sequences and subsequently to the generation of a class II model. Various modelling techniques were used based on the constraints on the structural organisation that could achieve a functionally active monomer plus the set of hypotheses defined in the earlier work. Mutagenic analysis of the HSV-1 dUTPase was then possible using the class II model as a reference. Several targets were investigated based on predicated functionally important regions. Analysis of these mutant enzymes was performed using purified recombinant HSV-1 dUTPase expressed from the T7 E.coli expression system.

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8

Mantovani, Paola <1978&gt. "Identificazione di un QTL principale per resistenza a ruggine bruna sul cromosoma 7B di frumento duro". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2009. http://amsdottorato.unibo.it/1748/1/Mantovani_tesi.pdf.

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Leaf rust caused by Puccinia triticina is a serious disease of durum wheat (Triticum durum) worldwide. However, genetic and molecular mapping studies aimed at characterizing leaf rust resistance genes in durum wheat have been only recently undertaken. The Italian durum wheat cv. Creso shows a high level of resistance to P. triticina that has been considered durable and that appears to be due to a combination of a single dominant gene and one or more additional factors conferring partial resistance. In this study, the genetic basis of leaf rust resistance carried by Creso was investigated using 176 recombinant inbred lines (RILs) from the cross between the cv. Colosseo (C, leaf rust resistance donor) and Lloyd (L, susceptible parent). Colosseo is a cv. directly related to Creso with the leaf rust resistance phenotype inherited from Creso, and was considered as resistance donor because of its better adaptation to local (Emilia Romagna, Italy) cultivation environment. RILs have been artificially inoculated with a mixture of 16 Italian P. triticina isolates that were characterized for virulence to seedlings of 22 common wheat cv. Thatcher isolines each carrying a different leaf rust resistance gene, and for molecular genotypes at 15 simple sequence repeat (SSR) loci, in order to determine their specialization with regard to the host species. The characterization of the leaf rust isolates was conducted at the Cereal Disease Laboratory of the University of Minnesota (St. Paul, USA) (Chapter 2). A genetic linkage map was constructed using segregation data from the population of 176 RILs from the cross CL. A total of 662 loci, including 162 simple sequence repeats (SSRs) and 500 Diversity Arrays Technology markers (DArTs), were analyzed by means of the package EasyMap 0.1. The integrated SSR-DArT linkage map consisted of 554 loci (162 SSR and 392 DArT markers) grouped into 19 linkage blocks with an average marker density of 5.7 cM/marker. The final map spanned a total of 2022 cM, which correspond to a tetraploid genome (AABB) coverage of ca. 77% (Chapter 3). The RIL population was phenotyped for their resistance to leaf rust under artificial inoculation in 2006; the percentage of infected leaf area (LRS, leaf rust susceptibility) was evaluated at three stages through the disease developmental cycle and the area under disease progress curve (AUDPC) was then calculated. The response at the seedling stage (infection type, IT) was also investigated. QTL analysis was carried out by means of the Composite Interval Mapping method based on a selection of markers from the CL map. A major QTL (QLr.ubo-7B.2) for leaf rust resistance controlling both the seedling and the adult plant response, was mapped on the distal region of chromosome arm 7BL (deletion bin 7BL10-0.78-1.00), in a gene-dense region known to carry several genes/QTLs for resistance to rusts and other major cereal fungal diseases in wheat and barley. QLr.ubo-7B.2 was identified within a supporting interval of ca. 5 cM tightly associated with three SSR markers (Xbarc340.2, Xgwm146 e Xgwm344.2), and showed an R2 and an LOD peak value for the AUDPC equal to 72.9% an 44.5, respectively. Three additional minor QTLs were also detected (QLr.ubo-7B.1 on chr. 7BS; QLr.ubo-2A on chr. 2AL and QLr.ubo-3A on chr. 3AS) (Chapter 4). The presence of the major QTL (QLr.ubo-7B.2) was validated by a linkage disequilibrium (LD)-based test using field data from two different plant materials: i) a set of 62 advanced lines from multiple crosses involving Creso and his directly related resistance derivates Colosseo and Plinio, and ii) a panel of 164 elite durum wheat accessions representative of the major durum breeding program of the Mediterranean basin. Lines and accessions were phenotyped for leaf rust resistance under artificial inoculation in two different field trials carried out at Argelato (BO, Italy) in 2006 and 2007; the durum elite accessions were also evaluated in two additional field experiments in Obregon (Messico; 2007 and 2008) and in a green-house experiment (seedling resistance) at the Cereal Disease Laboratory (St. Paul, USA, 2008). The molecular characterization involved 14 SSR markers mapping on the 7BL chromosome region found to harbour the major QTL. Association analysis was then performed with a mixed-linear-model approach. Results confirmed the presence of a major QTL for leaf rust resistance, both at adult plant and at seedling stage, located between markers Xbarc340.2, Xgwm146 and Xgwm344.2, in an interval that coincides with the supporting interval (LOD-2) of QLr.ubo-7B.2 as resulted from the RIL QTL analysis. (Chapter 5). The identification and mapping of the major QTL associated to the durable leaf rust resistance carried by Creso, together with the identification of the associated SSR markers, will enhance the selection efficiency in durum wheat breeding programs (MAS, Marker Assisted Selection) and will accelerate the release of cvs. with durable resistance through marker-assisted pyramiding of the tagged resistance genes/QTLs most effective against wheat fungal pathogens.

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9

Martinez, Ascanio Ana Karine <1979&gt. "Fine Mapping of qroot-yield-1.06, a QTL for Root, Plant Vigor and Yield in Maize". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2015. http://amsdottorato.unibo.it/7160/1/Martinez_Ascanio_Ana_Karine_Tesi.pdf.

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Root-yield-1.06 is a major QTL affecting root system architecture (RSA) and other agronomic traits in maize. The effect of this QTL has been evaluated with the development of near isogenic lines (NILs) differing at the QTL position. The objective of this study was to fine map qroot-yield-1.06 by marker-assisted searching for chromosome recombinants in the QTL interval and concurrent root phenotyping in both controlled and field conditions, through successive generations. Complementary approaches such as QTL meta-analysis and RNA-seq were deployed in order to help prioritizing candidate genes within the QTL target region. Using a selected group of genotypes, field based root analysis by ‘shovelomics’ enabled to accurately collect RSA information of adult maize plants. Shovelomics combined with software-assisted root imaging analysis proved to be an informative and relatively highly automated phenotyping protocol. A QTL interval mapping was conducted using a segregating population at the seedling stage grown in controlled environment. Results enabled to narrow down the QTL interval and to identify new polymorphic markers for MAS in field experiments. A collection of homozygous recombinant NILs was developed by screening segregating populations with markers flanking qroot-yield-1.06. A first set of lines from this collection was phenotyped based on the adapted shovelomics protocol. QTL analysis based on these data highlighted an interval of 1.3 Mb as completely linked with the target QTL but, a larger safer interval of 4.1 Mb was selected for further investigations. QTL meta-analysis allows to synthetize information on root QTLs and two mQTLs were identified in the qroot-yield-1.06 interval. Trascriptomics analysis based on RNA-seq data of the two contrasting QTL-NILs, confirmed alternative haplotypes at chromosome bin 1.06. qroot-yield-1.06 has now been delimited to a 4.1-Mb interval, and thanks to the availability of additional untested homozygous recombinant NILs, the potentially achievable mapping resolution at qroot-yield-1.06 is c. 50 kb.

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Kulkarni, Anurag. "The role of VIF in overcoming the APOBEC3G block to HIV-1 replication". Thesis, University of Warwick, 2011. http://wrap.warwick.ac.uk/36847/.

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This project focuses on the Virus Infectivity Factor protein of HIV-1 and its relief of the block to virus replication exerted by the APOBEC3G component of the innate immune response. Virus Infectivity Factor (vif) is an accessory gene of HIV, deletion of which leads to large drops in virus infectivity. This decrease in infectivity was found to be due to APOBEC3G, an inhibitor of HIV replication which is constitutively expressed in peripheral blood mononuclear cells (PBMCs), the natural host cells for HIV in humans. Vif is indispensable to block the inhibitory effects of APOBEC3G thereby allowing normal viral replication to continue inside the host. This recognition of the critical role played by Vif in the viral replication cycle has centred studies on characterising the interactions of Vif with both APOBEC3G as well as other virus encoded proteins. Stimulation of proteasomal degradation of APOBEC3G is currently believed to be the primary anti-APOBEC3G effect induced by Vif. However recent reports, particularly those showing that Vif remains able to block the inhibitory actions of degradation resistant APOBEC3G, question the validity of this hypothesis. The recognition that both APOBEC3G and Vif become incorporated into HIV particles through an interaction with the precursor of the virion structural proteins, Pr55GAG has raised the possibility that they may compete with each other for this incorporation. Using techniques such as mammalian two-hybrid assays, sucrose gradient analysis of GAG virus-like particles (VLPs) and confocal imaging, the interactions of these proteins with Pr55GAG have been analyzed and the results obtained indicate that Vif competes with APOBEC3G for Pr55GAG binding leading to its displacement and exclusion from the budding HIV virions. This potentially important pathway for Vif activity and its significance in the development of novel antiretroviral drugs in the future will be discussed.

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Graziani, Marta <1983&gt. "Mappaggio fine di un QTL principale per la resa in granella sul cromosoma 3B di frumento duro". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2012. http://amsdottorato.unibo.it/4283/1/graziani_marta_tesi.pdf.

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In durum wheat, two major QTL for grain yield (Qyld.idw-2B and Qyld.idw-3B) and related traits were identified in a recombinant population derived from Kofa and Svevo (Maccaferri et al. 2008). To further investigate the genetic and physiological basis of allelic variation for this important trait, the fine mapping of Qyld.idw-2B e Qyld.idw-3B was done during the PhD. In this regard, new molecular markers were added to increase the map resolution in the target interval. For Qyld.idw-2B region COS markers derived from the synteny between wheat and rice/ sorghum /brachypodiu genomes were screened. While for Qyld.idw-3B region SSR, ISBP and COS markers obtained from BAC end-sequences and BAC sequences generated during the construction of the 3B physical map (Paux et al., 2008) were screened. In the RIL population a final map resolution of 2,8 markers/cM for Qyld.idw-2B and 0,6 markers/cM for Qyld.idw-3B were obtained. Eighteen pairs of near-isogenic lines (NILs) for Qyld.idw-3B were obtained from F4:5 heterogeneous inbred families. In order to confirm the phenotypic effect of the QTL all pairs were evaluated in field trials (2010 and 2011) for all traits. Three pairs of NILs, with contrasted haplotypes at the target region, were crossed to produce a large F2 population (ca. 7,500 plants in total) that was screened for the identification of recombinants. A total of 233 homozygous F4:5 segmental isolines were obtained and the phenotypic and genotypic characterization of these materials were done. A fine mapping for Qyld.idw-3B was obtained and the QTL peak was identified in a interval of 0,4 cM. All markers were anchored to the Chinese Spring physical map of chr. 3B, which allowed us to identify the BAC Contigs spanning the QTL region and to assign the QTL peak to Contig 954. Sequencing of this contig has revealed the presence of 42 genes.

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Milner, Sara Giulia <1985&gt. "A multiparental cross population for mapping QTL for relevant agronomic traits in durum wheat (Triticum durum Desf.)". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amsdottorato.unibo.it/6648/1/Milner_Sara_Giulia_tesi.pdf.

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Multiparental cross designs for mapping quantitative trait loci (QTL) in crops are efficient alternatives to conventional biparental experimental populations because they exploit a broader genetic basis and higher mapping resolution. We describe the development and deployment of a multiparental recombinant inbred line (RIL) population in durum wheat (Triticum durum Desf.) obtained by crossing four elite cultivars characterized by different traits of agronomic value. A linkage map spanning 2,663 cM and including 7,594 single nucleotide polymorphisms (SNPs) was produced by genotyping 338 RILs with a wheat-dedicated 90k SNP chip. A cluster file was developed for correct allele calling in the framework of the tetraploid durum wheat genome. Based on phenotypic data collected over four field experiments, a multi-trait quantitative trait loci (QTL) analysis was carried out for 18 traits of agronomic relevance (including yield, yield-components, morpho-physiological and seed quality traits). Across environments, a total of 63 QTL were identified and characterized in terms of the four founder haplotypes. We mapped two QTL for grain yield across environments and 23 QTL for grain yield components. A novel major QTL for number of grain per spikelet/ear was mapped on chr 2A and shown to control up to 39% of phenotypic variance in this cross. Functionally different QTL alleles, in terms of direction and size of genetic effect, were distributed among the four parents. Based on the occurrence of QTL-clusters, we characterized the breeding values (in terms of effects on yield) of most of QTL for heading and maturity as well as yield component and quality QTL. This multiparental RIL population provides the wheat community with a highly informative QTL mapping resource enabling the dissection of the genetic architecture of multiple agronomic relevant traits in durum wheat.

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Bagnato, Alessandro <1961&gt. "Identification of CNV and QTL for productive and functional traits in dairy cattle using dense SNP chips". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2015. http://amsdottorato.unibo.it/6931/1/Bagnato_Alessandro_Tesi.pdf.

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The thesis identify CNV structural variants as possible markers for genomic selection and identify QTL regions for Fatty Acid Content in the Italian Brown Swiss population. Additionally it maps the QTL for mastitis resistance in the Valdostana Red Pied cattle.

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McCaig, Lesley. "Study on the roles of O-acetylserine (thiol) lyase and thiol dependent reductase 1 of Leishmania". Thesis, University of Glasgow, 2009. http://theses.gla.ac.uk/1281/.

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Thiol dependent reductase 1 (TDR1) of Leishmania has been implicated in both the activation of pentavalent antimonial drugs and in the generation of drug-thiol conjugates facilitating drug-resistance. Reverse genetic studies were carried out on TDR1 to elucidate the role of the enzyme and to assess its potential value as a drug target against Leishmania. In a similar study, O¬acetylserine (thiol) lyase (OAS-TL), a key enzyme for the de novo synthesis of cysteine in Leishmania, was investigated as a potential target for new antileishmanial drugs. TDR1 of Leishmania is a 49.9 kDa protein of which the physiological role remains unclear. The protein has shown both thiol transferase activity and dehydroascorbate reductase activity. Due to its ability to reduce pentavalent antimonials to the active trivalent form in vitro, TDR1 has been suggested as playing a vital role in antimonial resistance in Leishmania. This part of the study was undertaken to clarify the role TDR1 plays in the parasite by investigating the effects of deleting the gene. Attempts were made to generate Δtdr1 null mutants in Leishmania donovani, but these were unsuccessful despite the fact that Δtdr1 null mutants exist for L. major and L. infantum. The mutants of these latter lines were studied to discover more on the roles of the proteins. L. major and L. infantum Δtdr1 null mutant promastigotes grow normally and do not display any change in total intracellular levels of cysteine, glutathione and trypanothione. The L. major Δtdr1 null mutants were able to survive and proliferate in parasitophorous vacuoles of peritoneal macrophages in vitro, with significantly higher numbers of parasites per infected macrophage compared to L. major wild-type. This suggests that the loss of TDR1 is beneficial to L. major when establishing an infection in macrophages. However the loss of TDR1 also causes hypersensitivity to the antimonial drug sodium stibogluconate, under the conditions tested. The data generated in this study indicate that the physiological function of TDR1 does not lie in the activation of pentavalent antimonials as has been previously suggested. The sulfur-containing amino acid cysteine plays a vital role in the synthesis of low molecular weight thiols, e.g. glutathione and trypanothione, as well as redox active thiol-containing proteins. In addition, cysteine is important for the stabilisation of tertiary and quaternary protein conformation due to its ability to form inter- and intra-chain disulfide bonds with other cysteine residues. In mammals, cysteine can either be taken up from the environment, or synthesised via the reverse trans-sulfuration pathway, involving the action of the enzymes cystathionine β-synthase and cystathionine γ-lyase, to generate cysteine from the essential amino acid methionine. In contrast, Leishmania parasites can synthesise cysteine in two ways but appear unable to salvage it effectively. They contain the reverse trans-sulfuration pathway, similar to mammals, and additionally, can generate cysteine through the sulfhydrylation pathway from serine, coenzyme A and sulfide, by utilising the enzymes serine acetyltransferase and O-acetylserine (thiol) lyase (OAS-TL). The aim of this study was to assess the suitability of OAS-TL as a potential drug target against Leishmania. In this study, Δoas-tl null mutants were generated in L. donovani, thus negating the sulfhydrylation pathway. The Δoas-tl null mutant promastigotes displayed a slight growth defect as well as a severe morphological alterations directly affecting cell body and flagellum length. In addition, the Δoas-tl null mutants were unable to survive in the parasitophorous vacuoles of peritoneal macrophages in vitro, suggesting that the exogenous supply of a source of cysteine (such as methionine) was not sufficiently high to support parasite proliferation. The finding that addition of high methionine concentrations to the medium facilitates parasite survival supports this idea. The data show that either differentiation of promastigotes into amastigotes or proliferation of amastigotes is detrimentally affected by the deletion of OAS-TL. Lines re-expressing OAS-TL were also generated in the Δoas-tl null mutants and were found to complement the phenotypes of the Δoas-tl null mutants identified in this study. The inability of Leishmania Δoas-tl null mutants to survive within macrophages, together with the absence of OAS-TL in the mammalian host, make it a suitable candidate for the identification of new drug targets in the search for novel chemotherapeutic agents against leishmaniasis.

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15

Dewar, Emma Louise. "Alpha-1-acid glycoprotein as a potential biomarker of breast cancer in 'at risk' individuals". Thesis, Edinburgh Napier University, 2015. http://researchrepository.napier.ac.uk/Output/9835.

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The identification of a blood-based diagnostic biomarker for breast cancer (BC) would be particularly beneficial to those at increased risk of developing BC and could result in earlier detection which may increase survival rates due to earlier treatment. Alterations in α-1-acid glycoprotein (AGP) glycosylation levels occur during disease and this study sought to determine the diagnostic potential of AGP glycan variation in triple negative breast cancer (TNBC) compared to BC of unknown type and healthy controls as well as women at increased risk of developing BC compared to age-matched healthy controls. AGP was isolated from blood of two different sample populations using low pressure chromatography. AGP purity was confirmed using SDS-PAGE and concentration determined using spectrophotometry. Structural analysis of AGP glycan monosaccharide and oligosaccharide content was undertaken using high pH anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD). Increased AGP concentrations were observed, in comparison to their controls, in BC of unknown type, TNBC and “at-risk” samples. Quantitative alterations in monosaccharide composition were also present. N-acetylgalactosamine (GalNAc) was present in over 88% of TNBC samples and was inversely correlated with age. For the TNBC groups, GalNAc was also present at higher levels in samples of individuals with family history of BC. There was an overall increase in GlcNAc levels compared to age-matched healthy controls and GalNAc presence in 81% of “at risk” samples. Oligosaccharide analysis revealed increased branching in BC of unknown type and TNBC < 35 years of age, whereas the “normal” healthy population and TNBC >35 possessed less branching. A similar trend was observed between the “at risk” samples and the age-matched controls. These branching patterns aligned well with the corresponding monosaccharide data. Overall, this study indicated that alterations in AGP levels and glycosylation exist between TNBC compared to BC of unknown type and “normal” healthy controls as well as an “at risk” population and age-matched healthy controls. The data could underpin the development of a new diagnostic BC biomarker.

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16

Castelletti, Sara <1981&gt. "Approcci molecolari e bioinformatici volti alla caratterizzazione di Vgt1, QTL coinvolto nella regolazione dell'epoca di fioritura in Zea Mays". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2011. http://amsdottorato.unibo.it/3668/1/Castelletti_Sara_Tesi.pdf.

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The genetic control of flowering time has been addressed by many quantitative trait locus (QTL) studies. A survey of the results from 29 independent studies reporting information on 441 QTLs led to the production of a QTL consensus map, which enabled the identification of 59 chromosome regions distributed on all chromosomes and shown to be frequently involved in the genetic control of flowering time and related traits. One of the major QTLs for flowering time, the Vegetative to generative transition 1 (Vgt1) locus , corresponds to an upstream (70 kb) non-coding regulatory element of ZmRap2.7, a repressor of flowering. A transposon (MITE) insertion was identified as a major allelic difference within Vgt1. One of the hypotheses is that Vgt1 might function by modifying ZmRap2.7 chromatin through an epigenetic mechanism. Therefore, the methylation state at Vgt1 was investigated using an approach that combines digestion with McrBc, an endonuclease that acts upon methylated DNA, and quantitative PCR. The analyses were performed on genomic DNA from leaves of six different maize lines at four stages of development. The results showed a trend of reduction of methylation from the first to the last stage with the exception of a short genomic region flanking the MITE insertion, which showed a constant and very dense methylation throughout leaf development and for both alleles. Preliminary results from bisulfite sequencing of a small portion of Vgt1 revealed differential methylation of a single cytosine residue between the two alleles. ZmRap2.7 expression was assayed in the four developmental stages afore mentioned for the six genotypes, in order to establish a link between methylation at Vgt1 and ZmRap2.7 transcription. To assess the role of Vgt1 as a transcriptional enhancer, two reporter vectors for stable transformation of plants have been developed.

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17

Richbourg, Henry L. "QTL analysis for genes conferring tolerance to drought stress and damage from UV-B radiation". View electronic thesis, 2008. http://dl.uncw.edu/etd/2008-1/r1/richbourgh/henryrichbourg.pdf.

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Bruschi, Martina <1986&gt. "Fine mapping of QSbm.ubo-2BS, a major QTL for resistance to Soil-Borne Cereal Mosaic Virus (SBCMV) in durum wheat". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2018. http://amsdottorato.unibo.it/8564/1/Bruschi_Martina_tesi.pdf.

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QSbm.ubo-2BS, a major QTL controlling the response to Soil-Borne Cereal Mosaic Virus in durum wheat, maps within a 2 cM-wide interval in the distal region of chromosome arm 2BS. The consensus map developed by Maccaferri et al. (2015) allowed to enrich QSbm.ubo-2BS interval with SNPs from the 90K Illumina array common to several linkage maps. Eleven SNPs were successfully converted to KASP markers, which provided fluorescent high-throughput assays spanning the QTL region. Marker-assisted selection was performed on ~3,000 RILs from the Svevo (resistant) x Ciccio (medium-susceptible) population with two KASP markers flanking the QTL interval, KUBO 9 and KUBO 13. MAS identified a total of 521 lines recombinant between the two markers. In particular, 320 and 189 of these lines were characterized for SBCMV response in a field nursery under severe and uniform SBCMV infection in 2016 and 2017, respectively. The lines were scored for symptom severity on a 0 to 5 scale, where 0 = very resistant and 5 = very susceptible. The same lines were genotyped with six KASP markers distributed along the QTL interval (KUBO 1, KUBO 3, KUBO 27, KUBO 29, KUBO 40 and KUBO 41) and with the DArT marker wPt-2106. The fine mapping conducted on Svevo x Ciccio allowed to locate the most probable QSbm.ubo-2BS support interval to 0.2 cM between the markers KUBO 27 and KUBO 41. Single-marker analysis showed that all markers in the interval are strongly associated with the QTL. Markers order was confirmed through genotyping of Meridiano x Claudio RILs with recombinant events in the interested interval. QSbm.ubo-2BS support interval corresponds to 3.2 Mb on the physical map of Svevo genome, a region that harbors 93 genes, including defensins, proteins belonging to NBS-LRR family and NBS-LRR-like resistance proteins. This work provides the foundation for the positional cloning of QSbm.ubo-2BS.

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19

Vera, Ortega Walter. "Approaching a Tat-Rev independent HIV-1 clone towards a model for research". Thesis, University of Glasgow, 2018. http://theses.gla.ac.uk/30755/.

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Human immunodeficiency virus type 1 (HIV-1) is responsible for the acquired immunodeficiency syndrome (AIDS), a leading cause of death worldwide infecting millions of people each year. Despite intensive research in vaccine development, therapies against HIV-1 infection are not curative and the huge genetic variability of HIV-1 challenges drug development. Current animal models for HIV-1 research present important limitations, impairing the progress of in vivo approaches. Macaques require CD8+ depletion or large portions of the genome to be replaced by sequences derived from simian immunodeficiency viruses to progress to AIDS, and the maintenance cost is high. Mice are a cheaper alternative, but need to be 'humanized' and breeding is not possible and knockout experiments are difficult. The development of an HIV-1 clone able to replicate in mice is a challenging proposal. The lack of human co-factors in mice impedes function of the HIV-1 accessory proteins Tat and Rev, hampering HIV-1 replication. The Tat and Rev function can be replaced by constitutive/chimeric promoters, codon-optimized genes and the constitutive transport element (CTE), generating a novel HIV-1 clone able to replicate in mice without disrupting the amino acid sequence of the virus. By minimally manipulating the genomic 'identity' of the virus, we propose the generation of an HIV-1 clone able to replicate in mice to assist in antiviral drug development. My results have determined that murine NIH 3T3 cells are able to generate pseudotyped HIV-1 particles, but they are not infectious. Codon-optimized HIV-1 constructs are efficiently made in human HEK-293T cells in a Tat and Rev independent manner and capable of packaging a competent genome in trans. CSGW (an HIV-1 vector genome) efficiently generates infectious particles in the absence of Tat and Rev in human cells when 4 copies of the CTE are placed preceding the 3’LTR. HIV-1 replication competent genomes lacking tat expression and encoding different promoters are functional during the first cycle of replication when Tat is added in trans. Finally, we developed a replication competent HIV-1 clone lacking tat and rev genes and encoding 4CTEs that could be a future candidate for HIV research. My results shown that the development of an HIV-1 Tat-Rev independent clone could become a candidate for HIV research in a near future, but further investigations are necessary before proposing our model as an alternative yet.

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Silva, Filho Miguel Inácio da. "Detecção de locos de características quantitativas com efeito da origem parental dos alelos nos cromossomos 1, 2 e 4 de suínos". Universidade Federal de Viçosa, 2010. http://locus.ufv.br/handle/123456789/4726.

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Data from an F2 swine population, consisting of 600 animals derived from crosses between Piau sires and Commercial dams were used in order to detect QTL with parent-of-origin effects. Phenotypic data on performance, carcass, internal organs, viscera, carcass cuts and meat quality traits were collected in the F2 animals. The population was genotyped for 16 microsatellite loci covering the chromosomes 1, 2 and 144. Based on the genotypes a specific linkage map was constructed for this population. Association analyses were performed using interval mapping by regression for QTL detection. A decision tree for identifying QTL with parent-of-origin effects based on tests against the Mendelian mode of expression was used. Twenty three QTL were detected using the Mendelian model of analysis, three on the chromosome one, five on chromosome two and 15 on chromosome four. It was also detected 12 QTL with parentof-origin effects. Six of these QTL were identified on chromosome one, where three were paternally expressed and three were maternally expressed. Three QTL were detected on chromosome two, where one was paternally expressed and the other two were maternally expressed. The remaining three QTL were identified on chromosome four, all of them were paternally expressed. None of the QTL with parent-of-origin effects was detected by the Mendelian model. The results generated in this study may contribute to a better understanding of the genetic mechanisms involved in the control of quantitative traits.
Com o objetivo de detectar QTL com efeito da origem parental dos alelos, foram utilizados dados de uma população F2 de suínos, composta de 600 animais, obtidos a partir do cruzamento de machos Piau e fêmeas comerciais. Nos animais F2, foram avaliadas características de desempenho, carcaça, órgãos e vísceras, cortes de carcaça e qualidade de carne. Para a genotipagem de todos os animais, foram utilizados 16 locos de microssatélites distribuídos nos cromossomos 1, 2 e 4. Com o resultado da genotipagem, foi construído o mapa de ligação específico dos marcadores para a população desenvolvida. As análises de associação foram baseadas no mapeamento por intervalo usando métodos de regressão. Para identificar QTL com efeito da origem parental dos alelos, foi utilizada uma árvore de decisão baseada em testes contra o modelo de expressão Mendeliana. Usando o método de análise para esse tipo de expressão, foram detectados 23 QTL mendelianos: três no cromossomo 1, cinco no cromossomo 2 e 15 no cromossomo 4. Foram detectados também 12 QTL com efeito da origem parental dos alelos: seis no cromossomo 1 (três de expressão paterna e três de expressão materna), outros três no cromossomo 2 (um de expressão paterna e os outros dois de expressão materna) e três no cromossomo 4 (todos de expressão paterna). Nenhum dos QTL com efeito da origem parental dos alelos foi identificado pelo modelo Mendeliano. Os resultados obtidos podem contribuir para o melhor entendimento dos mecanismos genéticos envolvidos no controle das características quantitativas.

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21

Li, Kai <1993&gt. "QTL mapping identifies novel major loci for ear fasciation, ear prolificacy and tillering in maize (ZEA MAYS L.)". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2022. http://amsdottorato.unibo.it/10465/1/Thesis_Kai%20Li.pdf.

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Maize ear fasciation originates from excessive or abnormal proliferation of the ear meristem and usually manifests as multiple-tipped ear, ear flatness and/or disordered kernel arrangement. Ear prolificacy expresses as multiple ears per node. Both traits can affect grain yield. In this study, the genetic control of the two traits was analyzed using two recombinant inbred lines (RIL) populations (B73 × Lo1016 and Lo964 × Lo1016) with Lo1016 and Lo964 as donors of ear fasciation and prolificacy, respectively. Four ear fasciation-related traits (ear fasciation, kernel distribution and ear ovality indexes and ratio of ear diameters), number of kernel rows, ear prolificacy and number of tillers were phenotyped in multi-year field experiments. Ear fasciation traits and number of kernel rows showed relatively high heritability (h2 > 0.5) except ratio of ear diameters, and showed correlation. Prolificacy and tillering h2 ranged 0.41 - 0.78 and did not correlate. QTL mapping identified four QTL for ear fasciation, on chr. 1 (two QTLs), 5 and 7, the latter two overlapping with QTLs for number of kernel rows. However, the strongest effect QTL for number of kernel rows mapped on chr. 2 independently from ear fasciation. Four and five non-overlapping QTLs were mapped for ear prolificacy and tillering, respectively. Two ear fasciation QTLs from this study, qFas1.2 and qFas7, overlapped with formerly known fasciation QTLs and spanned candidate genes expressed in ear meristems namely compact plant2 and ramosa1. Our study identified novel ear fasciation, ear prolificacy and tillering loci which are unexpectedly still segregating in elite maize materials, and provides foundation for genomics-assisted breeding for yield components

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22

Grimes, Leanne M. "Using fruit fly eyes as membrane protein factories : expression of rat P2X2 and pannexin-1 in Drosophila melanogaster". Thesis, Cardiff University, 2015. http://orca.cf.ac.uk/70779/.

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P2X receptors and pannexins (Panx) are eukaryotic ion channels that are implicated in a range of diseases and conditions including cancer, inflammation and pain sensation and as a result, are important therapeutic targets. Deducing their 3D-structures would enable the use of structure-based drug design to identify novel agonists or antagonists. However, solving eukaryotic membrane protein structures is a significant challenge due to the requirement for high yields of purified folded, functional protein, which are not readily obtainable with conventional over-expression systems. By using P2X receptors and pannexins as model ion channel targets, this thesis aims to test Drosophila melanogaster as a system for the over-expression and functional analysis of eukaryotic ion channels. A number of epitope-tagged P2X and Panx protein constructs were generated and first expressed in HEK-293 cells (rat P2X2-GFP, human P2X4-GFP, rat Panx1-GFP and human P2X4-int-CBD (chitin binding domain)) to allow their expression, glycosylation and oligomeric states to be investigated as markers of protein folding and quality. Subsequently, rat P2X2-GFP and rat Panx1-GFP constructs were successfully expressed in the photoreceptor cells of Drosophila melanogaster, where the photoreceptive membrane in the visual system is organised into a densely packed brush of microvilli, the rhabdomere. This system provides a large surface area of membrane for protein expression. Although the yields of purified protein were lower than expected, rat Panx1-GFP was successfully purified and used for low resolution structural studies with transmission electron microscopy. Rat P2X2-GFP was also expressed in the nervous system of Drosophila under control of a pan-neural, C155-Gal4 driver and was shown to be functional by measuring ATP-evoked action potentials using electrophysiological recordings of the Drosophila taste sensilla. This system was also used to test the activity of an adenosine nucleotide library of 80 compounds. Three nucleotides were identified that elicited responses similar to ATP; these were 2F-ATP, ATPαS and ATPγS.

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Hidalgo, André Marubayashi. "Fine mapping and single nucleotide polymorphism effects estimation on pig chromosomes 1, 4, 7, 8, 17 and X". Universidade Federal de Viçosa, 2011. http://locus.ufv.br/handle/123456789/4753.

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Mapeamento de loci de caracaterística quantitativas (QTL) geralmente resultam na detecção de regiões genômicas que explicam parte da variação quantitativa da característica. Entretanto essas regiões são muito amplas e não permitem uma acurada identificação dos genes. Dessa forma, torna-se necessário o estreitamento dos intervalos onde os QTL estão localizados. Com a seleção genômica ampla (GWS), foram desenvolvidas ferramentas estatísticas de forma a se estimar os efeitos de cada marcador. A partir dos valores desses efeitos, pode-se analisar quais são os marcadores de maiores efeitos. Assim, objetivou-se realizar o mapeamento fino dos cromossomos suínos 1, 4, 7, 8, 17, e X, usando marcadores microsatélites e polimorfismo de base única (SNP), em uma população F2 produzida pelo cruzamento de varrões da raça naturalizada brasileira Piau com fêmeas comerciais, associados com características de desempenho, carcaça, orgãos internos, cortes e qualidade de carne. Também objetivou-se estimar os efeitos dos marcadores SNP nas características que tiveram QTL detectados, analisar quais são os mais expressivos e verificar se eles estão localizados dentro do intervalo de confiança do QTL. Os QTL foram identificados por meio do método regressão por intervalo de mapeamento e as análises foram realizadas pelo software GridQTL. O efeito de cada marcador foi estimado pela regressão de LASSO Bayesiano, usando o software R. No total, 32 QTL foram encontrados ao nível cromossômico de significância de 5%, destes, 12 eram significativos ao nível cromossômico de 1% e 7 destes eram significativos ao nível genômico de 5%. Seis de sete QTL apresentaram marcadores de efeito expressivo dentro do intervalo de confiança do QTL. Resultados deste estudo confirmaram QTL de outros trabalhos e identificaram vários outros novos. Os resultados encontrados utilizando marcadores microsatélites junto com SNPs aumentaram a saturação do genoma levando a um menor intervalo de confiança dos QTL encontrados. Os métodos usados foram importantes para estimar os efeitos dos marcadores, e também para localizar aqueles com efeitos mais expressivos dentro do intervalo de confiança do QTL, validando os QTL encontrados pelo método da regressão.
Quantitative Trait Loci (QTL) mapping efforts often result in the detection of genomic regions that explain part of the quantitative trait variation. However, these regions are very large and do not allow accurate gene identification, hence the interval must be narrowed where the QTL was located. With the genome wide selection (GWS), many statistical tools have been developed in order to estimate the effects for each marker. With the marker effects values it is possible to analyze which markers have large effects. Hence, the objective of this investigation was to fine map pig chromosomes 1, 4, 7, 8, 17 and X, using microsatellites and SNP markers, in a F2 population produced by crossing naturalized Brazilian Piau boars with commercial females, associated with performance, carcass, internal organs, cut yields and meat quality traits. A further aim was to estimate the effects of single nucleotide polymorphism (SNP) markers on traits with detected QTL, analyze the most expressive ones and verify whether the markers with larger effects were indeed within the QTL confidence interval. QTL were identified by regression interval mapping using the GridQTL software. Individual marker effects were estimated by Bayesian LASSO regression using the R software. In total, 32 QTL for the studied traits were significant at the 5% chromosome-wide level, including 12 significant QTL at the 1% chromosome-wide level and 7 significant at the 5% genome-wide level. Six out of seven QTL with genome-wide significance had markers of large effect within their confidence interval. These results confirmed some previous QTL and identified numerous novel QTL for the investigated traits. Our results have shown that the use of microsatellites and SNP markers that increase the genome saturation lead to QTL of smaller confidence intervals. The methods used were also valuable to estimate the marker effects and to locate the most expressive markers within the QTL confidence interval, validating those QTL found by the regression method.

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Miranda, Alexandra de Sousa Montenegro. "Characterisation of LVI-1 (WDR76) as a candidate tumour suppressor gene". Thesis, University of Glasgow, 2006. http://theses.gla.ac.uk/4967/.

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The central aim of this study was to characterise the expression of the candidate tumour suppressor gene, LV/-J (lentivirus integration-I) and its products. The LVI-J gene (WDR76) was discovered as a target for disruption by proviral insertional mutagenesis in a case of pre-B cell lymphoma in a FIV infected cat {Beatty, 1998 5 lid; Beatty, 2002 7 lid}. As LV/-J is highly conserved, my work focused on the human and murine orthologues to take advantage of the superior resources available for these species. My work showed potentially important differences in expression of the human and mouse genes with respect to promoter use and length of 3' untranslated sequences. The murine gene is transcribed mainly from the distal PI promoter, which appears to be a bi-directional element shared with the adjacent MJapJ gene, while the human gene transcripts are derived exclusively from the proximal P2 promoter. Direct analysis by RT-PCR showed that the murine gene could also be expressed from the P2 promoter. These findings have significant implications for Lvi-l protein expression as the P2 transcripts are predicted to express larger proteins with a distinct N-terminal sequence. To characterise the LV/-J gene products, rabbit polyclonal antisera were raised to GST fusion proteins expressed in bacteria. Use of the murine anti-ml.vi-I antiserum in Western blotting identified a protein of the expected size (58 kDa) based on translation of the major mRNA species from the PI promoter. Immunofluorescence and confocal microscopy suggested that this protein is localised mainly in the cytoplasm. Although the function of LVI-I is unknown, its closest relative in the human genome is DDB2, a protein involved in repair of UV-induced DNA damage. Regulation of LVI-I expression was examined after UV irradiation, providing preliminary evidence of responses at transcriptional and post-transcriptional levels. Further leads were followed by analogy with the yeast orthologue of LVI-I, YDLI56W, but no evidence of a complex between LVI-I and MSH6 was found. In conclusion, while function of the LVI-I gene remains to be establishes, it provides the basis for future characterisation of this highly conserved and potentially important eukaryotic gene.

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Palmer, Elizabeth Ann. "Studies on the herpes simplex virus type 1 UL32 DNA packaging protein". Thesis, University of Glasgow, 2010. http://theses.gla.ac.uk/1987/.

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The work presented in this thesis is concerned with the characterisation of the UL32 gene of herpes simplex virus type 1 (HSV-1). UL32 encodes an essential 596 amino acid cysteine-rich, zinc-binding protein that is highly conserved throughout the herpesviruses. The UL32 protein is essential for the cleavage of concatemeric viral DNA into monomeric genomes and their packaging into preformed capsids. Conservation is highest at the C-terminus and three CxxC motifs are present in almost all known herpesvirus UL32 sequences The UL32 antibodies available in the laboratory at the beginning of the project were incapable of detecting small amounts of UL32 protein and so new rabbit antisera were created. Soluble extracts from insect cells infected with a UL32-expressing baculovirus (AcUL32) were fractionated by anion exchange chromatography and the UL32-containing fractions used to immunise rabbits. The resultant antisera successfully recognised UL32 from transfected, HSV-1 infected and baculovirus infected cells on western blots, and UL32 in transfected cells by immunofluorescence. I performed random mutagenesis of the UL32 gene in an effort to examine structure-function relationships within this protein, and generated a panel of 37 mutants containing 5 amino acid insertions at distinct positions. The abilities of these mutants to complement the DNA packaging and growth defects of a virus lacking a functional copy of UL32 (the null mutant hr64) were examined and 15 of the mutants retained functionality in both assays. A complete correlation was found between the ability of mutants to support growth and DNA packaging, suggesting that the key functions of UL32 are confined to the DNA packaging pathway. There was also good correlation with the degree of amino acid conservation within UL32, with most of the mutants which abolished functionality being located in the highly conserved regions, and the functional mutants in less conserved regions. A number of site-specific mutants were also created, in which the paired cysteine residues were replaced with serines (i.e. CxxC to SxxS). Mutation of the first and third cysteine pairs (from the N-terminus) completely abrogated growth and packaging, whereas significant functionality was maintained following mutagenesis of the central pair. Finally, removal of the C-terminal 4 amino acids also resulted in generation of a non-functional protein. Generation of an HA-tagged UL32 construct and the introduction of this into HSV-1 allowed the localisation of UL32 in infected cells to be studied. In contrast to previous reports, I detected UL32 predominantly in the nuclei of infected cells, co-localising with ICP8 in replication compartments. DNA packaging has previously been shown to occur within the replication compartments and a number of the other packaging proteins also localise to these sites. It was previously reported that UL32 played a role in the localisation of capsids to the replication compartments. However, work presented in this thesis shows this not to be the case, and that capsid proteins VP5 and VP19C were correctly localised in replication compartments during infections with the UL32 mutant hr64. I found no evidence of UL32 interaction with the UL6, UL25 or UL17 DNA packaging proteins in HSV-1 infected or transfected cells, or using immunoprecipitation from baculovirus-expressed cells. Immunofluorescence studies of co-transfected cells showed that UL15 could direct the partial re-localisation of UL32 from the cytoplasm to the nucleus. The addition of the other terminase subunits UL28 and UL33 caused the complete re-localisation of UL32 to the nucleus, suggesting that UL32 might interact with the terminase complex. Fifteen of the insertional mutants were completely re-localised to the nucleus in the presence of UL15, UL33 and UL28, with eleven further mutants showing an intermediate phenotype of partial nuclear localisation. The ability to at least partially co-localise with the terminase complex appeared necessary for the ability of the mutants to support virus growth and DNA packaging, suggesting that this interaction may be essential for the function of UL32. However, no interaction could be demonstrated between UL32 and any of the individual terminase subunits using immunoprecipitation from insect cells. A series of experiments was undertaken to further characterise the UL32 protein. A new UL32 mutant virus (Δ32EP) was generated by insertion of a kanamycin resistance cassette in place of a large portion of the UL32 gene. This mutant had an indistinguishable phenotype from hr64, confirming that the main function of UL32 is within DNA packaging. The functional conservation between HSV-1 UL32 and the homologues from HCMV and VZV was examined, but neither protein could support the growth of Δ32EP. DNA fragments from replicated concatemeric DNA from Δ32EP infected cells behaved similarly to wt HSV-1 fragments in PFGE, suggesting that UL32 is not involved in the resolution of branched structures within the genome prior to packaging. UL32 had previously been reported to bind zinc, and this was confirmed using a zinc-release colourimetric assay. The amount of zinc bound to soluble baculovirus-expressed UL32 was quantified, showing that UL32 bound zinc in a 1:1 molar ratio. UL32 does not share all of the characteristics of a zinc finger motif, but the results of the mutagenesis experiments suggest that the outer CxxC/CxxxC motifs may be important for zinc binding. Because of its zinc-binding properties and potential interaction with the terminase complex, the DNA binding properties of UL32 were also investigated. It was found that UL32 did not bind to dsDNA containing either the minimal packaging sequence (Uc-DR1-Ub) or an unrelated non-HSV-1 sequence using an electrophoretic mobility shift assay (EMSA).

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26

Noakes, Karen. "Exploiting the retrograde transport of disarmed toxins for the delivery of exogenous antigens into MHC class 1 presentation pathway". Thesis, University of Warwick, 1999. http://wrap.warwick.ac.uk/4371/.

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The targeting of exogenous antigen into the MHC class 1-restricted presentation pathway is required for the induction of cytotoxic T lymphocytes (CTL) which have been shown to be an important component of the protective response to intracellular antigens and also induce immunity to tumour cells. Thus, induction of a CTL response is an important goal in vaccine research and a number of delivery systems are being investigated. Certain cytotoxic proteins that catalytically modify substrates in the cytosol of mammalian cells undergo retrograde vesicular transport from the cell surface to the endoplasmic reticulum before translocating into the cytosol. In this study, Shiga-like toxin 1 (SLT) from Escherichia coil 0157: H7 was used to deliver an antigenic peptide for presentation by major histocompatibility complex (MHC) class I molecules. The SLT A chain was genetically fused with a nonamer peptide derived from influenza virus Matrix protein, positioned at either the N- or C-terminus of the toxin (designated SLT N-Ma or C-Ma). The SLT coding sequence was also mutated to convert an active site glutamate into aspartate to significantly reduce ribosome-inactivating activity, and hence the inherent cytotoxicity of the toxin chimeras. Recombinant holotoxins carrying the viral peptide were expressed in E. coil and purified to homogeneity before use. HLA-A2-transfected HeLa cells were allowed to internalize the disarmed toxin-peptide chimeras and were used as targets of influenza Matrix-specific cytotoxic T lymphocytes (CTL). HLA-A2-matched cells, unable to internalize SLT, were used as negative controls. Results from this study show that SLT N-Ma but not SLT C-Ma is capable of sensitizing HeLa A2 cells for lysis by cytotoxic T -lymphocytes (CTL) whilst no killing of SLT-resistant cells has been observed. Treatment of cells with the Golgi stack-disrupting agent brefeldin A successfully blocked the presentation of the M58- 66 epitope at the cell surface, confirming that the antigenic peptide was liberated intracellularly. This strategy was repeated for ricin A-chain, placing a nonamer peptide derived from influenza virus nucleoprotein at either the N-terminus or within an external loop of the toxin A-chain (designated RTA N-NP or Clal-NP). Fusion proteins were expressed in E. coli and purified, followed by reassociation with ricin B-chain. Preliminary results have failed to show the delivery of peptide antigen to class-i molecules by the ricin chimeras. This work is ongoing. This thesis demonstrates that Shiga-like toxin-1, known to be endocytosed from the cell surface to the ER lumen and then transferred to the cytosol of eukaryotic cells, can intersect the MHC class 1 presentation pathway and effectively carry antigenic peptide to class 1 molecules in vitro. This approach opens up new possibilities for the generation of CD8+ T-cell vaccines for use against infectious agents, cancer and autoimmune disorders.

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27

Eno-Ibanga, Cheryl K. "The analysis of a conserved RNA structure in the 3D polymerase encoding region of human parechovirus 1". Thesis, University of Essex, 2016. http://repository.essex.ac.uk/19097/.

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Picornaviruses are important causes of human illness and it is necessary to understand more about how these viruses function. Human parechoviruses (HPeV) are common pathogens and studies have shown that 95% of people become infected with HPeV at a very early age, usually with symptoms such as mild diarrhoea and fever. However, one virus type HPeV3, is implicated in much more serious cases of neonatal disease and so it is important to understand HPeVs to increase the opportunity to develop drugs or vaccines against the infection. The HPeV1 genome encodes a single polyprotein that is cleaved into structural and non-structural proteins. Analysis of one region of the genome (encoding the polymerase, 3Dpol) shows that some codons are perfectly conserved, suggesting functions in addition to protein coding. This region seems to fold into an RNA secondary structure made up of three stem-loops and a tertiary structure “kissing” interaction. The structure was validated by comparing all the available HPeV sequences and found to be highly conserved. To investigate if the structure has a role in RNA stability, an EGFP fluorescent assay was used. Sequences containing the structure was added to the 3’ UTR of the EGFP gene. A mutant with 21 mutations which completely destroys the RNA structure was also used. A FACS-based method was used to measure expression levels of EGFP. The results showed that there was a significant reduction in fluorescence from the mutant construct. The effect of the structure was also investigated in infected cells and in cells exposed to different stresses which could mimic virus infection. The results suggest that the structure can positively affect RNA stability/translation. Further investigation on other possible roles such as RNA replication and translation should be performed to improve the understanding of the biology of the structure in HPeVs and a Renilla Luciferase reporter gene system was assembled to facilitate the studies in the future.

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28

Das, Elif. "Effect Of Controlled Atmosphere Storage, Modified Atmosphere Packaging And Gaseous Ozone Treatment On The Survival Characteristics Of Salmonella Enteritidis At Cherry Tomatoes". Master's thesis, METU, 2004. http://etd.lib.metu.edu.tr/upload/12605337/index.pdf.

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iv In recent years, outbreaks of infections associated with raw and minimally processed fruits and vegetables have been reported. Possible sources for contamination are irrigation water, manure, wash water, handling by workers and contact with contaminated surfaces. Pathogens can occur on raw and minimally processed produce at populations ranging from 103 to 109 CFU/g and able to survive and sometimes grow under various storage conditions. The objective of this study was to analyse the growth/survival of Salmonella Enteritidis at spot-inoculated or stem-injected cherry tomatoes during passive modified atmosphere packaging (MAP), controlled atmosphere (CA) and air storage at 7 and 22°
C. Low density polyethylene (LDPE) with a package size of 10x10 cm2 for 25±
2 g tomatoes was used for MAP storage in which the gas composition equilibrated to 6% O2/ 4% CO2 and a carbon dioxide incubator was used for CA storage in which the CO2 level was monitored and maintained as 5% through the term of storage at 7 and 22°
C. During the research, the effect of ozone treatment (5-30 mg/L ozone gas for 0-20 min) was also considered for surface sanitation. The results demonstrate that S.Enteritidis can survive and/or grow during the storage of tomatoes depending on the location site of the pathogen on fruit, suspension cell density and storage temperature. During MAP, CA and air storage, S.Enteritidis with initial population of 7.0 log10 CFU/tomato survived on tomato surfaces with an approximate decrease of 4.0-5.0 log10 CFU/tomato in population within the storage period
however, in the case of initial population of 3.0 log10 CFU/tomato, cells died completely on day 4 during MAP storage and on day 6 during CA and air storage. The death rate of S.Enteritidis on the surfaces of tomatoes that were stored in MAP was faster than that of stored in air. Storage temperature was effective on the survival of S.Enteritidis for the samples stored at ambient atmosphere
cells died completely on day 6 at 7°
C and on day 8 at 22°
C. Stem scars provided protective environments for Salmonella
an approximate increase of 1.0 log10 CFU/tomato in stem-scar population was observed during MAP, CA and air storage at 22°
C within the period of 20 days. Cells survived with no significant change in number at 7°
C. The development of the microbial association in tomatoes was dominated by lactic acid bacteria (LAB). The pH values of the tomatoes changed approximately from 4.0 to 3.0 during the storage period. LAB grew well under all atmospheric conditions with or without the presence of S.Enteritidis. Gaseous ozone treatment has bactericidal effect on S.Enteritidis, inoculated on the surface of the tomatoes. 5 mg/L ozone gas treatment was not effective. 30 mg/L ozone gas treatment affected surface color.

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29

Ceylan, Cagatay. "The Evaluation Of High Hydrostatic Pressure Effects On Bovine Blood Constituents And The Microbial Survival". Phd thesis, METU, 2005. http://etd.lib.metu.edu.tr/upload/3/12605943/index.pdf.

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The main objective of this study was to investigate the effects of high hydrostatic pressure on the stability of blood constituents for the purpose of an effective reduction of viral and bacterial count. The effect of HHP treatment on the several blood constituents were analyzed at different HHP levels at 25 0C for 5 minutes. The bovine blood as the model material was separated into two major parts
namely, serum and blood cells by centrifugation. Erythrocytes were found to be mostly stable up to 220 MPa pressure treatment displaying only surface modifications, but the cells lose their morphology at 350 MPa. White Blood Cells and platelets were found to be more sensitive, being degraded at around 110 MPa pressures putting an upper limit for the HHP treatment for the whole blood. But serum components and parameters studied showed much higher stability up to 220 MPa pressure level. The HHP treated blood cells were analyzed by FTIR spectroscopic technique and found to be stable in the macromolecular level. HHP treated proteins display only minimal changes in their secondary structures shown by the artificial neural network and curve fitting studies. Changes in the lipid bands indicated the changes in the membranes of the blood cells. In the microbiologic part of the study, Listeria innocua was found to be more stable than Bovine Herpes Virus type 1 as the model bacterium and virus respectively and their inactivation levels were compared with that of blood constituents.

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30

Jones, Lim Stephen. "Mobile genetic elements associated with blaNDM-1 in Acinetobacter spp. and Vibrio cholerae". Thesis, Cardiff University, 2015. http://orca.cf.ac.uk/74109/.

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NDM-producing bacteria are associated with extensive antimicrobial resistance (AMR). This thesis reports on detailed molecular analysis, including whole genome sequencing, of Acinetobacter spp. and Vibrio cholerae isolates. A study of clinical Acinetobacter baumannii isolates from India, demonstrated spread of a single strain containing blaNDM-1 but with evidence of significant genetic plasticity between isolates. A novel plasmid, pNDM-32, was fully characterised in isolate CHI-32. This contained multiple AMR genes including blaNDM-1 and the aminoglycoside methyltransferase gene armA. A repAci10 replicase gene was identified but no conjugation machinery and the plasmid could not be transferred in conjugation experiments. A single isolate of Acinetobacter bereziniae from India contained plasmid, pNDM-40-1, harbouring blaNDM-1, which was closely related to plasmids from NDM-producing Acinetobacter spp. isolated in China, and was readily transferred into Escherichia coli and Acinetobacter pittii by conjugation. Five blaNDM-1 positive Acinetobacter spp. isolated from a faecal screening study in Pakistan also included three, clonal, Acinetobacter haemolyticus isolates harbouring a similar plasmid. Three environmental V. cholerae strains from India and a blood isolate from a traveller returning to the UK from India were found to include three distantly related strains. 2 isolates of a single strain contained an IncA/C plasmid, pNDM-116-17, harbouring AMR genes including blaNDM-1. In one isolate pNDM-116-17 had become integrated into a chromosomal region containing a SXT-like element. In the other isolates blaNDM-1 and other AMR determinants were localised to a large plasmid, pNDM-116-14, with a novel replicase and a full complement of conjugative transfer genes, and a novel genomic island, SGI-NDM-1. Most previous studies have focused on Enterobacteriaceae. Thecurrent work contributes to an understanding of the full extent of the genetic diversity of blaNDM-1 contexts, and their dissemination. Such knowledge should help to infer factors which contribute to the spread of AMR in bacterial pathogens.

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31

Cané, Maria Angela <1978&gt. "Heterosis in maize (Zea mays, L.): characterization of heterotic quantitative trait loci (QTL) for agronomic traits in near isogenic lines (NILs) and their testcrosses". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2011. http://amsdottorato.unibo.it/3945/1/cane_mariaangela_tesi.pdf.

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In a previous study on maize (Zea mays, L.) several quantitative trait loci (QTL) showing high dominance-additive ratio for agronomic traits were identified in a population of recombinant inbred lines derived from B73 × H99. For four of these mapped QTL, namely 3.05, 4.10, 7.03 and 10.03 according to their chromosome and bin position, families of near-isogenic lines (NILs) were developed, i.e., couples of homozygous lines nearly identical except for the QTL region that is homozygote either for the allele provided by B73 or by H99. For two of these QTL (3.05 and 4.10) the NILs families were produced in two different genetic backgrounds. The present research was conducted in order to: (i) characterize these QTL by estimating additive and dominance effects; (ii) investigate if these effects can be affected by genetic background, inbreeding level and environmental growing conditions (low vs. high plant density). The six NILs’ families were tested across three years and in three Experiments at different inbreeding levels as NILs per se and their reciprocal crosses (Experiment 1), NILs crossed to related inbreds B73 and H99 (Experiment 2) and NILs crossed to four unrelated inbreds (Experiment 3). Experiment 2 was conducted at two plant densities (4.5 and 9.0 plants m-2). Results of Experiments 1 and 2 confirmed previous findings as to QTL effects, with dominance-additive ratio superior to 1 for several traits, especially for grain yield per plant and its component traits; as a tendency, dominance effects were more pronounced in Experiment 1. The QTL effects were also confirmed in Experiment 3. The interactions involving QTL effects, families and plant density were generally negligible, suggesting a certain stability of the QTL. Results emphasize the importance of dominance effects for these QTL, suggesting that they might deserve further studies, using NILs’ families and their crosses as base materials.

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32

Eser, Unsaldi. "Medium Optimization For Cephamycin C Overproduction And Comparison Of Antibiotic Production By Ask, Hom, And Ask+hom Recombinants Of Streptomyces Clavuligerus". Master's thesis, METU, 2010. http://etd.lib.metu.edu.tr/upload/12612421/index.pdf.

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Streptomyces clavuligerus is well-known for synthesizing several &beta
-lactam antibiotics like cephamycin C which is produced through aspartic acid pathway initiated by aspartokinase (Ask) enzyme encoded by ask. Four different strains were constructed in our laboratory to increase cephamycin C production by S. clavuligerus. TB3585 and BA39 contained extra copies of ask gene on a multicopy plasmid, control strains TBV and BAV contained vector only in wild type strain NRRL3585 and hom-minus background, AK39, respectively. In this study, the effects of carbon and nitrogen sources incorporated into chemically defined medium were investigated for optimum growth and cephamycin C production by AK39. A modified-chemically defined medium (mCDM) was obtained by increasing the asparagine concentration two-fold and replacing glycerol with sucrose. Subsequently, growth and cephamycin C production by recombinant S. clavuligerus strains (TB3585, AK39, BA39, BAV, TBV) in Tryptic Soy Broth (TSB) and mCDM were compared. The specific antibiotic production in mCDM by TB3585 was 3.3- and 3.2-fold higher than TBV at 72h and 96h, respectively. Aspartokinase activity of S. clavuligerus recombinants was measured to verify the ask overexpression. TB3585 showed the highest activity at 48h. Finally, intracellular amino acid pools of the strains were measured to relate the Ask activity and antibiotic production to the amino acid content within the cells. AK39 was shown to have the highest intracellular levels of lysine, leading to cephamycin C precursor synthesis
lysine plus threonine, exerting concerted feedback inhibition on Ask enzyme
methionine, which cannot be produced by AK39 like threonine due to hom disruption.

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33

Geymüller, Philipp von, i Anton Burger. "Assessing the effects of quality regulation in Norway with a quality regulated version of dynamic DEA". Forschungsinstitut für Regulierungsökonomie, WU Vienna University of Economics and Business, 2007. http://epub.wu.ac.at/990/1/document.pdf.

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In order to find out why energy-not-supplied in Norway - the most important indicator for the quality of service in the quality-regulation regime there - decreased more pronounced before the introduction of quality-regulation in 2001 than after it, we develop a dynamic quality-DEA-model and apply it to a representative sample of distribution-net operators. Our model enables us to calculate a counter-factual and thus to tentatively answer the question: What would have happened, had there been no quality-regulation? This way we find strong evidence that the quality-regulation in Norway did not have an effect on the behavior of the firms. (author's abstract)
Series: Working Papers / Research Institute for Regulatory Economics

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34

Trippl, Michaela, Franz Tödtling i Lukas Lengauer. "The Vienna software cluster: local buzz without global pipelines?" Institut für Regional- und Umweltwirtschaft, WU Vienna University of Economics and Business, 2007. http://epub.wu.ac.at/550/1/document.pdf.

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The goal of this paper is to examine innovation activities in the Vienna software industry and to get a better understanding of the nature and geography of knowledge linkages in this sector. In the literature there seems to be a growing consensus that innovation rests on both informal local knowledge linkages and formal global networks, i.e. a combination of "local buzz" and "global pipelines". Recent studies on the software sector, however, show that the importance of different types of knowledge sources, the spatial dimension of knowledge transfer and the relevance of different channels of knowledge exchange in the software industry remain poorly understood. Drawing on a firm survey and qualitative face-to-face interviews with companies we will show that in the Vienna software industry the transfer and exchange of knowledge is highly localised and strongly informal in nature, pointing to a high significance of "local buzz" and a lack of "global pipelines". This specific pattern raises the question whether the Vienna software sector is exposed to a danger of lock in. (author´s abstract)
Series: SRE - Discussion Papers

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35

Zvokelj, Alexander. "Logistische Instrumente zur Förderung innerstädtischer Nachhaltigkeit". Institut für Transportwirtschaft und Logistik, WU Vienna University of Economics and Business, 2009. http://epub.wu.ac.at/720/1/document.pdf.

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Commercial transportation and all its related stakeholders are faced with new challenges, both from the increasing concentration of urban population and areas, as well as from the ever increasing competition in the transportation services industry. Because the causes of the necessary restructuring in commercial transportation are very complex, this paper will define the parameters, influencing factors and resulting consequences as it applies to commercial transportation in the Vienna metropolitan area. It will include a systematic analysis of the interrelated effects on an economic and ecocologic, as well as on a social level. This method of analysis, using these three supporting elements, allows for a holistic approach that makes possible alternative logistic concepts that are both economically efficient and sustainable. Because small carriers, due to their supply function especially within the Vienna city limits, play such an important role in Vienna commercial transportation, they have been chosen as the starting point for this analysis. The conclusions resulting from this analysis are intended to provide the conceptual basis for an internet based order processing service with the project name "KTAK" ("Kleintransporteure auf Knopfdruck"). The "KTAK" concept can be viewed as an instrument that promotes both an increase in the operating efficiency for the service provider and an increase in the sustainability of innercity areas. (author's abstract)
Series: Schriftenreihe des Instituts für Transportwirtschaft und Logistik - Logistik

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36

Maier, Gunther, i Shanaka Herath. "Real Estate Market Efficiency. A Survey of Literature". Institut für Regional- und Umweltwirtschaft, WU Vienna University of Economics and Business, 2009. http://epub.wu.ac.at/402/1/document.pdf.

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In this paper, we discuss the question whether or not the real estate market is efficient. We define market efficiency and the efficient market hypothesis as it had been developed in the literature on financial markets. Then, we discuss the empirical evidence that exists concerning the efficiency or inefficiency of financial markets, usually seen as the reference markets as far as market efficiency is concerned. In a separate section, we turn to the real estate market. There, we define the real estate market and discuss various aspects that are decisive for the efficiency of that market. As it turns out, the result found in the literature is inconclusive. Majority of studies provide evidence supporting inefficiency of the real estate market while several studies maintain the notion of real estate market efficiency.
Series: SRE - Discussion Papers

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37

Andruchowitz, Ingo Albin. "Politik - Kunst - Wirtschaft. Über die "intimen" Beziehungen selbstreferenzieller sozialer Systeme in Wien. Eine systemtheoretische Studie". WU Vienna University of Economics and Business, 2011. http://epub.wu.ac.at/3457/1/creativeindustries5andruchowitz.pdf.

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Zielsetzung des im Rahmen vom WWTF geförderten Projektes "Creative Industries in Vienna" durchgeführten Forschungsvorhabens ist es, die Entwicklung der Kunst als soziales System und Medium der Kommunikation in Europa und in Wien exemplarisch herauszuarbeiten. Damit wird der vorherrschende CI-Diskurs um eine systemtheoretische Perspektive erweitert. Im hier präsentierten Vorbericht werden die dafür aufbereiteten theoretischen Ausgangspositionen, Fragestellungen und Zielsetzungen dargestellt. Zu diesem Zweck wird zunächst in der Einleitung das Gesamtprojekt im internationalen CI-Diskurs verortet und der Mainstream der Diskussion aus systemtheoretischer Perspektive in Frage gestellt. Die Entscheidung, einen systemtheoretischen Zugang zu wählen, wird bereits in der Einleitung begründet und durch die Gliederung der Gesamtarbeit vorgestellt. Im Kapitel 1. Theorie wird die angewandte Theorie der sozialen Systeme im Kontext des sogenannten radikalen Konstruktivismus verortet und die übergeordnete Fragestellung der Zusammenhänge von Kunst Politik und Wirtschaft aus systemtheoretischer Perspektive aufbereitet. Im abschließenden Kapitel zur sogenannten Habermas-Luhmann-Kontroverse wird schließlich die Entscheidung für die Systemtheorie noch einmal veranschaulicht und reflektiert.
Series: Creative Industries in Vienna: Development, Dynamics and Potentials

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38

Ertl, Sylvia. "Frauen in der Logistik - Ursachenforschung zum geringen Anteil an Frauen mit Führungsfunktion in der Logistik- und Transportbranche". Institut für Transportwirtschaft und Logistik, WU Vienna University of Economics and Business, 2010. http://epub.wu.ac.at/2996/1/ertl.pdf.

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The Austrian economy is characterised by a very low proportion of women in leading positions. Although women's employment is as high as never before and women are very well-trained, top management consists predominantly of male executives. There is no progress with regard to a balanced proportion during the last fifteen years. In some industries, as logistics and information technology, the percentage to women in leading positions is particularly low. The diploma thesis includes causal research regarding the low proportion of women in leading positions in logistics and the transport industry. The aim of the paper is to find out if the responsible factors are within the industry sector, the economic system or they are gender related. At first, a theoretical framework of the concept of logistics management, human resource development and gender mainstreaming which has impacts on career developments of the employees in logistics, is provided, followed by an analysis of the contemporary situation of women in the Austrian economy, especially in logistics. Subsequently, a qualitative research was conducted. Different experts of the transport industry, such as university professors, human resource managers and employees, have been consulted. The evaluation of the interviews shows that 1) the acceptance of female managers is low, 2) it is difficult to set up a work-life-balance for working mums, 3) sociopolitical conditions disadvance women 4) the knowledge about gender mainstreaming is low and 5) some female employees have low self-esteem. Concluding, the final results are summarized and recommendations are presented. (author's abstract)
Series: Schriftenreihe des Instituts für Transportwirtschaft und Logistik - Logistik

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39

Michael, Georghia. "Repolarisation reserve and the development of torsade de pointes in models of long QT syndrome 1, 2 and 3". Thesis, University of Strathclyde, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.444406.

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40

Izuagbe, Rhys E. "A prostate cell line model of persistent Zika virus infection". Thesis, Queensland University of Technology, 2019. https://eprints.qut.edu.au/129570/1/Rhys_Izuagbe_Thesis.pdf.

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This study investigates how Zika virus can persist and replicate in the human prostate. It establishes a human prostate cell line model to address this question and examines the replication of three different virus strains in the cells. It also characterises the gene expression changes that occur in prostate cells during persistent Zika virus infection.

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41

Burger, Anton, i Philipp von Geymüller. "Can we measure Welfare? Dynamic Comparisons of Allocative Efficiency before and after the Introduction of Quality Regulation for Norwegian Electricity Distributors". Forschungsinstitut für Regulierungsökonomie, WU Vienna University of Economics and Business, 2008. http://epub.wu.ac.at/624/1/document.pdf.

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We investigate empirically the usefulness of price-cap and quality regulation in terms of allocative efficiency and welfare. An analytical framework allows us to determine sufficient conditions for an increase in welfare. We propose Malmquist productivity indices and their decomposition to check the conditions and to see whether it was a better-solved trade off between quality and costs that caused the welfare increase. The application of this method to a representative sample of Norwegian distribution system operators yields strong evidence for a positive effect of quality regulation on welfare. (author's abstract)
Series: Working Papers / Research Institute for Regulatory Economics

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42

Ogulur, Ismail. "The Effects Of Twelve Quorum-sensing Gene Products On The Expression Of Bacabcde Operon In Bacillus Subtilis". Master's thesis, METU, 2008. http://etd.lib.metu.edu.tr/upload/12609983/index.pdf.

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In Bacillus subtilis, genetic competence, sporulation and antibiotic production are controlled by quorum-sensing global regulatory mechanism. Bacilysin, being produced and excreted by certain strains of Bacillus subtilis, is a dipeptide antibiotic composed of L-alanine and L-anticapsin. We showed that the biosynthesis of bacilysin is under the control of quorum sensing global regulatory pathway through the action of ComQ/ComX, PhrC (CSF), ComP/ComA in a Spo0K (Opp)-dependent manner. Recently, the ywfBCDEF genes of B. subtilis 168 were shown to carry biosynthetic core function and renamed as bacABCDE operon. The objective of the present study is to elucidate the effects of previously-identified genes srfA, oppA, comA, phrC, phrF, phrK, comQ (comX), comP, spo0H, spo0A, abrB and codY on the expression of bacilysin biosynthetic operon bacABCDE. In order to monitor the expression of bac operon a B. subtilis strain, namely OGU1, containing a transcriptional bacA-lacZ fusion at bacA locus was constructed. Subsequently, each of the above-mentioned genes of cell density signaling was insertionally inactivated by transforming the competent cells of OGU1 with chromosomal DNA of the corresponding blocked mutant strains. The resulting strains and OGU1 as the control were cultured in PA medium and bacA-directed &
#946
-galactosidase activities were monitored. bacA-lacZ expression was severely impaired in the srfA, oppA, comA, phrC, phrF, phrK, comQ (comX), comP, spo0H and spo0A disrupted mutants. On the other hand, in the abrB single mutant bacA expression level increased nearly 2-fold during exponential growth and in the codY mutant it severely decreased during the stationary phase.

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43

Aras, Taskin Asli. "Proteome-wide Analysis Of Functional Roles Of Bacilysin Biosynthesis In Bacillus Subtilis". Master's thesis, METU, 2010. http://etd.lib.metu.edu.tr/upload/12612409/index.pdf.

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The members of the genus Bacillus produce a wide variety of secondary metabolites with antimetabolic and pharmacological activities. Most of these metabolites are small peptides that have unusual components and chemical bonds and synthesized nonribosomally by multifunctional enzyme complexes called peptide synthetases. Bacilysin, being produced and excreted by certain strains of Bacillus subtilis, is one of the simplest peptide antibiotics known. It is a dipeptide with an N-terminal L-alanine and an unusual amino acid, L-anticapsin, at its C-terminal. Recently, ywfBCDEF operon of B. subtilis 168 was shown to carry bacilysin biosynthesis function, the genes of this operon were renamed as bacABCDE. The first member of bac operon, bacA gene was proved to encode the function of L-alanine &ndash
L-anticapsin amino acid ligation. Bacilysin production is regulated at different levels, negatively by GTP via the transcriptional regulator CodY and AbrB while positive regulation occurs by guanosine 5

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Dincel, Sezen. "Chemical And Rheological Properties Of Yoghurt Produced By Lactic Acid Cultures Isolated From Traditional Turkish Yoghurt". Master's thesis, METU, 2012. http://etd.lib.metu.edu.tr/upload/12614484/index.pdf.

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Yoghurt is a fermented milk product which is produced by Streptococcus thermophilus and Lactobacillus delbrueckii spp. bulgaricus. The production of yoghurt has started in Middle East and spread all over the world. The aim of this study is to select the culture combination which is appropriate to Turkish taste and have the best yoghurt characteristics by means of post-acidification and whey separation properties, texture of gel formation, exopolysaccharide and acetaldehyde content
and to observe the effect of freeze-drying of cultures on these yoghurt properties. At the first part of this study, six L.delbrueckii spp. bulgaricus isolates and six S.thermophilus isolates were used with different combinations to produce 36 yoghurt samples. These isolates were selected among a strain collection which contains 111 L.delbrueckii spp. bulgaricus and 56 S.thermophilus isolates which were isolated from traditional Turkish yoghurt according to their acidification activity and acetaldehyde production properties. In addition, two commercial S.thermophilus isolates and one commercial L.delbrueckii spp. bulgaricus isolate were used to produce two commercial yoghurt samples. 38 yoghurt samples were examined in terms of pH and total titratable acidity changes during 21-day storage, syneresis and hardness. According to these three analyses, six yoghurt samples were chosen, which give the best results, for the determination of exopolysaccharide and acetaldehyde content. In addition, two yoghurt samples produced by commercial cultures and one sample, which gives average results in experiments, were also examined for these compounds to provide a good comparison. In the second part of the study the amount of exopolysaccharide and acetaldehyde of nine yoghurt samples were determined. In addition, sensory analysis was conducted to see consumer perception. According to the results, one culture combination was obtained as the best combination which produces the appropriate yoghurt to Turkish taste with the closest chemical analysis results to the commercial samples. In the last part, freeze drying process was examined if this has a significant effect on the selected LAB combination as well as yoghurt produced by using this.

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45

Zambruni, Andrea <1974&gt. "Prolungamento dell'intervallo QT nei pazienti con cirrosi in corso di emorragia digestiva: ipotesi patogenetiche e significato prognostico". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2009. http://amsdottorato.unibo.it/2245/1/Zambruni_Andrea_tesi.pdf.

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46

Briglauer, Wolfgang, Georg Ecker i Klaus Gugler. "Regulation and Investment in Next Generation Access Networks: Recent Evidence from the European Member States". Forschungsinstitut für Regulierungsökonomie, WU Vienna University of Economics and Business, 2012. http://epub.wu.ac.at/3447/1/wp_nga_eu.pdf.

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Fibre-deployment of future telecommunications networks ("Next Generation Access" - NGA) is a major challenge for sector-specific regulators as well as for investing firms. Although the future socioeconomic importance of new telecommunications networks is uncontroversial, the related investment activities vary substantially in international comparison. This work identifies the most important determinants of NGA deployment, using data from the EU27 member states for the years 2005 to 2010. Our results indicate that stricter previous broadband access regulation has a negative impact on NGA deployment, while competitive pressure from broadband and mobile affects NGA deployment in an inverted U-shaped manner. We further find that there are severe adjustment costs and stickiness towards the desired long-term level of NGA infrastructure. It appears that the approach of the European Commission of strict cost-based access regulation will not elicit the huge new investment needed for a comprehensive NGA roll-out. (authors' abstract)
Series: Working Papers / Research Institute for Regulatory Economics

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47

Beattie, Debra. "The wrong crowd : an online documentary and analytical contextualisation". Thesis, Queensland University of Technology, 2003. https://eprints.qut.edu.au/15874/1/Debra_Beattie_Thesis.pdf.

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This doctoral study comprises two parts. 75 per cent of the total weight of the submission consists of the creative component, the writing, directing and producing of a moving-image documentary in an online environment (supplementary material includes the script). Cutting edge technology (QTVR 'movies' and Live Stage Professional software) was used to create an immersive cinematic experience on the net. The Wrong Crowd can be viewed either online at www.abc.net.au/wrongcrowd or offline via a CD Rom (the latter includes the radio play 'Death of a Prostitute' which was excised from the version published via ABC Online because of legal concerns on the part of the ABC lawyers). The second part of the doctorate is the analytical contextualisation, comprising 25 per cent of the submission. This part examines the critical literature on the nature of the documentary form, documentary as history, cultural memory and the autobiography as history. Documentary exists as a truth-claim. History also embraces the search for evidence. The history documentary has a television form from which the online version is derived. The nature of the internet as a delivery platform for the moving image is discussed with reference to he truth claim as founded in the visible evidence - the news coverage - the 'this really happened'. The evidence however is open to interpretation for the historical record and is retold to suit the present power relations (the funding bodies, the commissioning editors, etc). In a CD Rom and more so online, this tendency towards individual interpretation is amplified to the point where the viewer can participate in the construction of the argument via a navigable database. Visually, the change from the temporal montage of the linear television documentary to spatial montage of the windows interface has led us to reconnect with computer-based moving images as a form of animated painting. Conventional screen theories of engagement and reception are invoked to aid in the discussion of modified cinematic conventions of editing and framing within the online form. The case-study of one of the inaugural Australian Film Commission funded online documentaries, The Wrong Crowd: Inside the Family Outside the Law, is a personal history narrative that intersects with Queensland police history from the 1950s to the late 1970s at the moments of inquiries into issues of police brutality and corruption.

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48

Zuzarte, Ian Jeromino. "A Principal Component Regression Analysis for Detection of the Onset of Nocturnal Hypoglycemia in Type 1 Diabetic Patients". University of Akron / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=akron1226955083.

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Baloglu, Mehmet Cengiz. "Expression Analysis Of Nac Type Transcription Factors On Wheat Seedlings Under Abiotic Stress Conditions". Phd thesis, METU, 2011. http://etd.lib.metu.edu.tr/upload/12613501/index.pdf.

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Wheat is the most important grain crop grown in our country providing greatest part of the daily nutritional requirement. Abiotic factors including salinity, drought, cold and heat stresses affect quality and yield of wheat varieties used for the production of both bread and pasta flour. NAC proteins form one of the widest families of plant specific transcription factors. Members of this family are related with development, defense and abiotic stress responses. TaNAC69-1 and TtNAM-B2 genes were isolated from T.aestivum and T.turgidum, respectively. Then they were cloned into different monocot and dicot expression vectors to be used for further wheat and tobacco genetic transformation studies. To understand effects of salinity, drought, cold and heat stresses on expression profiles of TaNAC69-1 and TtNAM-B2 genes, quantitative real time PCR was performed. The time series expression profiles of TaNAC69-1 show that it was signi

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50

Farah, Michel Marques. "Simula??o em n?vel de gene e de indiv?duo aplicada ao melhoramento animal". UFVJM, 2010. http://acervo.ufvjm.edu.br/jspui/handle/1/771.

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Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior (CAPES)
A simula??o de dados apresenta diversas vantagens, como proporcionar a obten??o de respostas ? sele??o e diminuir o tempo necess?rio para a avalia??o das metodologias estudadas no melhoramento gen?tico animal. Por?m, os trabalhos que utilizam simula??o empregam v?rios termos como simula??o estoc?stica, simula??o determin?stica, simula??o de Monte Carlo, simula??o em n?vel de gene e simula??o em n?vel de indiv?duo e, muitas vezes, estes termos s?o utilizados de maneiras diferentes ou em outras condi??es, causando uma diverg?ncia nos termos utilizados. Assim, os objetivos deste trabalho foram agrupar, definir e diferenciar os termos t?cnicos utilizados nos trabalhos de simula??o em melhoramento gen?tico animal e comparar e definir as propriedades dos procedimentos de simula??o em n?vel de indiv?duo e em n?vel de gene. Foram desenvolvidos tr?s cen?rios de simula??o, em n?vel de indiv?duo, em n?vel de gene com e sem marcador utilizando o software LZ5. Foram simuladas tr?s popula??es de su?nos para cada cen?rio e com diferentes herdabilidades (0,12, 0,27 e 0,47). A popula??o-base foi constitu?da de 1500 animais, sendo 750 machos e 750 f?meas e para as duas simula??es em n?vel de gene foi considerado um genoma de 2800 cM e 18 cromossomos de tamanhos aleat?rios, as caracter?sticas foram governadas por 500 locos polig?nicos dial?licos, com freq??ncias al?licas iguais e taxa de recombina??o de 0,01. Para a simula??o em n?vel de gene com marcadores, ainda foram distribu?dos marcadores distanciados igualmente a 50 cM e distribu?dos aleatoriamente 5 QTLs por todo o genoma. Os valores amostrados apresentaram bem semelhantes para os tr?s tipos de simula??o, apresentando um aumento das vari?ncias aditiva e fenot?pica e da herdabilidade nas primeiras gera??es e depois decrescendo ao longo das gera??es. J? para a m?dia fenot?pica, houve um ganho gen?tico por gera??o, indicando que todos os m?todos utilizados s?o eficientes para a obten??o de dados simulados. Assim, a vantagem da simula??o em n?vel de gene ? que ? poss?vel simular marcadores moleculares e QTLs, enquanto a simula??o em n?vel de indiv?duo ? muito eficiente para obten??o de dados como o valor gen?tico do indiv?duo e da m?dia fenot?pica da popula??o em um per?odo de tempo muito menor, pois demanda menos recursos computacionais e de algoritmos estruturados para desenvolver quando comparado com a simula??o em n?vel de gene. Portanto, define-se simula??o em n?vel de indiv?duo como uma metodologia de simula??o que consiste em gerar valores gen?ticos (G) a partir de uma distribui??o normal com m?dia e vari?ncia previamente definidas; enquanto para a simula??o em n?vel de gene a metodologia consiste em gerar os valores dos efeitos de cada loco polig?nico e seus QTLs, a partir de uma distribui??o normal com m?dia e vari?ncia previamente definidas para cada componente, e pela soma destes, obt?m-se o G de cada indiv?duo da popula??o. Para a gera??o do efeito residual (E) as duas metodologias de simula??o s?o feitas da mesma forma, gerando-se um efeito aleat?rio amostrado, tamb?m, de uma distribui??o normal e assim obt?m-se os valores fenot?picos (P) de cada indiv?duo pela soma destes dois componentes (G+E).
Disserta??o (Mestrado) ? Programa de P?s-Gradua??o em Zootecnia, Universidade Federal dos Vales do Jequitinhonha e Mucuri, 2010.
ABSTRACT The simulation data has several advantages, such as providing the obtaining responses to selection and reduce the time required for evaluation methodologies studied in animal breeding. However, simulation studies employ various terms such as simulation stochastic, deterministic simulation, Monte Carlo simulation, simulation level of gene and simulation at the individual level and often these terms are used in different ways or in other conditions, causing a divergence in the terms used. Thus, the objectives were cluster, define and differentiate the technical terms used in the work of simulation in animal breeding and compare and define the properties procedures for simulation-level and individual-level gene. There had been developed three scenarios for simulation at the individual-level and level gene, with and without marker, using the software LZ5. There had been simulated three pig populations for each scenario, with different heritabilities (0.12, 0.27 and 0.47). The base population consisted of 1500 animals, 750 males and 750 females and for both simulations at the level of the gene was considered a genome of 2800 cM, and 18 chromosomes in random sizes, the characteristics were governed by 500 loci diallelic polygenic, with equal allele frequencies and recombination rate of 0.01. For the simulation Level with gene markers, were also distributed bookmarks equally spaced at 50 cM and five QTL distributed randomly across the genome. The sampled values were very similar for the three types of simulation, an increase of additive variance and phenotype and heritability in the first generations and then decreasing to over the generations. As for the average phenotype was a genetic per generation, indicating that all methods used are efficient for obtain simulated data. Thus, the advantage of gene-level simulation is that it can simulate molecular markers and QTLs, while the simulation at individual level is very efficient for obtaining data as the individual's genetic value and phenotypic average of the population over a period of much less time, since it requires less computational resources and algorithms structured to develop, when compared with the simulation-level gene. Therefore, it is defined as the individual level simulation a methodology simulation that generates breeding values (G) from a normal distribution with mean and variance as previously defined; and the gene level simulation is defined as a methodology that generates the values of effects of each locus and their polygenic QTLs from a normal distribution with mean and variance previously defined for each component, and the sum of these gives the G of each individual in the population. For the generation of residual effect (E) the two simulation methodologies are made in the same way, generating a random effects sampled also a normal distribution and so it was obtained the phenotypic values (P) of each individual by summing these two components (G+E).

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