Miracle-dz/UniFAR-FTUs huggingface dataset:
Study of the Role of mutations identified in the M27, M36, m139, m141, and m143 ORFs of the murine cytomegalovirus (MCMV) temperature-sensitive mutant tsm5

Infection with human cytomegalovirus (HCMV), usually asymptomatic in healthy individuals, can cause severe or fatal disease in infants and immunocompromised patients. The generation of a potent protective vaccine is necessary to protect vulnerable people. Because of host restriction, murine cytomegalovirus (MCMV) is used as a model for HCMV. Previously, we have generated a temperature-sensitive mutant, tsm5, which failed to replicate in mice yet protected them against virus challenge. Several mutations have been identified in this mutant by Comparative Genome Sequencing (GCS) (Roche NimbleGen); 10 synonymous and 15 non-synonymous single nucleotide polymorphisms (SNPs). Among these are m139 (Y565X) and m141 (V195M), shown to be essential for replication in macrophages but not in fibroblasts, m143 (M232I), shown to play an important role in the inhibition of the PKR-mediated host antiviral response, M27 (A658S ), involved in interference with interferon- signalling, and M36 (V54I), an anti-apoptotic protein. In the present study, the above mentioned mutations were introduced individually into the MCMV K181 (Perth) variant bacterial artificial chromosome (BAC) using RecE/T homologous recombination. An in vitro phenotypical analysis revealed that only the double (Mt[M27\(^A\)\(^6\)\(^5\)\(^8\)\(^S\)M36\(^V\)\(^5\)\(^4\)\(^I\)]) and the m139 (Mt[m139\(^Y\)\(^5\)\(^6\)\(^5\)\(^X\)]) mutants showed a temperature sensitive phenotype in MEF and/or Raw 264.7 macrophages cells
Chromatin compaction and genome reorganization during spermatogenesis in M. musculus and sporulation in S. cerevisiae

Gametogenesis is a complex process that results in a highly differentiated gamete capable of transmitting genetic and epigenetic information to the next generation. In the cases of mammalian spermatogenesis and yeast sporulation, an extreme post-meiotic compaction of the genome is key to gamete function. While genome compaction in sperm is reliant upon a histone-to-protamine transition, yeast spores accomplish compaction with a full complement of histones. Although the mechanisms behind such striking chromatin dynamics are largely unknown, several histone variants and post-translational modifications, especially acetylation of histone H4, have been implicated in these processes. The following studies elucidate the roles of two proteins, BRD4 and the linker histone (Hho1), in chromatin compaction during mouse spermatogenesis and yeast sporulation, respectively. In the post-meiotic phase of mouse spermatogenesis, BRD4 forms a ring structure around the haploid nucleus at the cytoskeletal base of the developing acrosome, which has been implicated in nuclear compaction and shaping. Chromatin immunoprecipitation followed by mass spectrometry and sequencing in post-meiotic cells revealed that BRD4, a bromodomain-containing protein, binds to acetylated histone H4 and is enriched in intergenic regions of the genome where histone replacement by protamines is most predominant in mature sperm. Thus, BRD4 may provide a structural link between the contractile force of acrosome formation and the removal of acetylated histones from the genome. In contrast to sperm, spores must use a histone-based chromatin compaction mechanism. During sporulation, Hho1 plays a dual role: transcriptional repression and nuclear compaction. Hho1 is depleted during meiosis and enriched in post-meiotic spore chromatin. Moreover, Hho1 shows a high genome-wide binding correlation with Ume6, the master repressor of meiotic genes. Meiotic depletion of both of these proteins may lead to the activation of key sporulation genes. In addition, knockout of HHO1 revealed its necessity in meiotic progression and post-meiotic genome compaction. These data provide support to the interesting hypothesis that protamines are evolutionarily derived from linker histones: Hho1 may play the role of protamines in yeast. Taken together, these studies in mouse and yeast highlight the complexity of mechanisms developed in diverse eukaryotic systems to facilitate the compaction of the gamete genome. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Shelley L. Berger
A participatory mobile application (app) development project with mental health service users and clinicians

Objective: The aim of this study was to establish the utility of a bespoke mobile app for mental health service users and clinicians. Design: Qualitative design using four focus groups. Methods: Work was conducted in three stages. The first stage involved a focus group with mental health service users and eight clinicians from a mental health early intervention service to discuss the utility of a bespoke mobile app. Visual, verbal and written prompts were used to demonstrate a mobile app and to prompt discussion. The results of the focus groups were used to create a ‘visual walk through, non-interactive mock up’ mobile app which was used to aid discussion with the same service users and clinicians in stage 2 focus groups. Stage 3 involved development of a mobile app prototype based on focus group feedback. Results: Key ideas emerging from the focus groups were adopted in the design of the app prototype. These were as follows: the use of colour to convey mood; simple mood tracking using familiar trigger icons; a calendar integrated with the service user’s care plan; a help button linked to personal support; an avatar to personalise the app; and the inclusion of evidence-based information. Conclusion: Digital health technology is an extremely important asset with scope to improve people’s lives when combined with behaviour change techniques. Co-design with service users, clinicians and digital technologists is critical to product design and adoption. The use of quality standard criteria and evidence-based content in app development and evaluation is essential.
Introduction chez brassica oleracea l. Var. Botrytis l. De genes du virus de la mosaique du chou-fleur (camv) via agrobacterium tumefaciens

L'expression de genes viraux dans des plantes transgeniques constitue une strategie efficace pour lutter contre les viroses vegetales. Afin d'obtenir une resistance au virus de la mosaique du chou-fleur (camv), la transformation genetique du chou-fleur (brassica oleracea l. Var. Botrytis l. ) a ete entreprise dans cette etude. Le gene iv (proteine de capside) et le gene vi (proteine des viroplasmes) du camv ont ete choisis pour etre transferes dans le genome de la plante. Deux strategies ont ete envisagees, soit l'expression chez la plante de la proteine de capside, soit l'expression d'un arn antisens du gene vi. Les genes viraux ont ete clones dans un vecteur binaire, puis les constructions obtenues ont ete introduites dans une souche desarmee d'a. Tumefaciens. Deux methodes de transformation via a. Tumefaciens ont ete experimentees. La premiere a ete menee sur des fragments d'hypocotyles par coculture avec une souche desarmee d'a. Tumefaciens. Aucune plante transformee n'a ete obtenue par cette approche. La deuxieme methode consistait a co-inoculer des vitroplants avec un melange d'une souche sauvage d'a. Tumefaciens, inductrice de tumeurs, et d'une souche desarmee. Les plantes transformees ont ete identifiees au moyen du test histochimique gus. Les transformants primaires obtenus ont fait l'objet d'une analyse moleculaire. L'integration de l'adn-t dans l'adn vegetal a d'abord ete verifiee chez toutes les plantes analysees. L'etude de la transcription des transgenes a ensuite ete abordee. Si l'arnm a ete detecte chez toutes les plantes analysees, la quantite d'arnm presente dans les cellules vegetales semblait tres faible chez la plupart des plantes. Concernant les plantes transformees avec le gene iv, l'expression de la proteine de capside n'a jamais pu etre mise en evidence
Short night sleeping is associated with higher risk of diabetes in older adults

Background: It remains unclear how many hours of sleep are associated with the lowest risk of diabetes type II. This meta-analysis was completed to evaluate the dose-response relationship between sleep duration and risk of diabetes type II. Methods: We conducted this meta-analysis using a comprehensive search of Medline, Pubmed, EMBASE, Cochrane database of systematic reviews, and Cochrane central register of controlled trials till 01 May 2017 for prospective observational studies that assessed the relationship of sleep duration and risk of type II diabetes. Both semiparametric and parametric methods were used. Results: Ten articles with 7 reports were eligible for inclusion in the meta-analysis. A total of 16,123 incident cases of type II diabetes were ascertained among 402,397 participants with follow-up periods ranging from 3 to 17 years. The relationship was observed between sleep duration and risk of type II diabetes, with the lowest risk observed at a sleep duration category of 7–8 h per day. Compared with 7-h sleep duration per day, the pooled relative risks for type II diabetes were 1.11 (95% CI 1.06–1.17) for each 1-h shorter sleep duration among individuals who slept <7 h per day and 1.13 (1.05–1.31) for each 1-h increment of sleep duration among individuals with longer sleep duration. Conclusions: Both short and long sleep duration are linked with a considerably increased risk of type II diabetes, underscoring the significance of appropriate sleep duration in the delay or prevention of type II diabetes.
Population Parameters: Estimation for Ecological Models

Ecologists and environmental managers rely on mathematical models, both to understand ecological systems and to predict future system behavior. In turn, models rely on appropriate estimates of their parameters. This book brings together a diverse and scattered literature, to provide clear guidance on how to estimate parameters for models of animal populations. It is not a recipe book of statistical procedures. Instead, it concentrates on how to select the best approach to parameter estimation for a particular problem, and how to ensure that the quality estimated is the appropriate one for the specific purpose of the modelling exercise. Commencing with a toolbox of useful generic approaches to parameter estimation, the book deals with methods for estimating parameters for single populations. These parameters include population size, birth and death rates, and the population growth rate. For such parameters, rigorous statistical theory has been developed, and software is readily available. The problem is to select the optimal sampling design and method of analysis. The second part of the book deals with parameters that describe spatial dynamics, and ecological interactions such as competition, predation and parasitism. Here the principle problems are designing appropriate experiments and ensuring that the quantities measured by the experiments are relevant to the ecological models in which they will be used. This book will be essential reading for ecological researchers, postgraduate students and environmental managers who need to address an ecological problem through a population model. It is accessible to anyone with an understanding of basic statistical methods and population ecology.
Effect of ammoniation of wheat straw alone or in combination with wet corn gluten feed on fibre digestion kinetics

Wet corn gluten feed (WCGF),a moist byproduct, was ammoniated with 4% urea, 50% moisture, 10 days incubation, 44.4°C alone or in combination with. wheat straw (WS) and in vitro and in situ fibre (NDF) digestion kinetics was compared with that of untreated WS (50% moisture, similarly incubated) and switch grass. In vitro fibre degradation of WS and switch grass was similar and improved by amrnoniatioll of WCGF and mixture of WS+WCGF. Shorter lag time for ammoniated mixture than ammoniated· WCGF showed the assoqiative effect of WS. Rate of fibre degradation of WCGF was highest while it was lOWest for untreated WS and switch grass, however, higher rate was. recorded in situ for untreated WS than that in vitro. PED of fibre was impTeved by 33% due to ammoniation of WS alone and 54% in mixed WS and WCGF. In a feeding trial, 3 Holstein heifers (11 months, 336 kg b.wt.) were fed on untreated WS. , 4% urea ammoniated WS alone and 4% urea ammriloniated mixture of WS and WCGF 1: 1 alongwitn concentrate ingredients in similar quality and quantity. Total DM was offered @ 2% of b.wt. in a 3x3 latin-square design. Untreated WS was supplemented with 1 g urea daily. Fungal growth and abnoxious odour were absent in the ammoniated mixture and it was consumed readlly and completely. Rate of passage ofWCGF through the GI tract was improved following the ammoniation, however, it did not affect the rate of passage ofWS which influenced digestibility of fibre fractions. It was concluded that ammoniation of mixture of WS and WCOF for 21 days is an alternative technology to harvest the double advantage i.e. improvement of nutritive value of WS and preservation and utilization of WCGF for the feeding of livestock.
Effect of chromosome 5A on gene expression during cold hardening in wheat

Changes in the transcript profile during cold hardening, a treatment necessary for achieving the full level of freezing tolerance, were monitored in a genetic system of wheat (Triticum aestivum L.) chromosome 5A substitution lines differing in their freezing tolerance. The number of cold-responsive genes in a freezing-tolerant substitution line (146) was signifi- cantly higher than in a sensitive one (97), indicating a general relationship between the overall number of genes with altered expression and the degree of freezing tolerance. The expression of 175 genes was differentially affected in the freezing-tolerant and sensitive substitution lines. Three of them, coding for a Ca-binding protein (Cab), a cold-responsive protein (Tacr7) and a protein described in a mutant deficient in embryo and meristems (Dem), were characterised in more detail. The expression of Dem was induced only by low temperature, while the transcript level of Cab was also higher following NaCl treatment and that of Tacr7 after salicylic acid and H 2 O 2 application.
Cougar Puma concolor use of wildlife crossing structures on the Trans-Canada highway in Banff National Park, Alberta

Large carnivores are vulnerable to road effects because of their great mobility and extensive spatial requirements for survival. Wildlife crossing structures have mitigated harmful effects of roads for ungulate species, but there is limited information on how effective these structures are for large predators. We investigated the response of cougars Puma concolor to wildlife crossing structures along 45 kilometers of the Trans-Canada highway in Banff National Park, Alberta, Canada. Twenty-two crossing structures were monitored year-round for wildlife passage during 1996–2000. Cougar consistently used the wildlife crossing structures more than expected during winter months and less than expected during the summer. There was a significant positive correlation between passages made by cougar through wildlife crossing structures and those made by mule deer Odocoileus hemionus and white-tailed deer O. virginianus. There was no correlation between cougar and human use of the wildlife crossing structures. Cougar use of the five structure types differed from that expected. Open-span bridge underpasses were used more than expected, whereas creek bridge underpasses were used in proportion to their availability. All other crossing structure types were used significantly less than expected. The wildlife crossing structures that received the highest numbers of cougar passages were those situated close to high quality cougar habitat. The pattern of structure use was partly explained by the quality and distribution of cougar habitat near the structures as opposed to their physical features. Our results indicated that cougars tended to use underpasses more than wildlife overpass structures, and our study documents that cougars used crossing structures in a way that ensures habitat connectivity.
A protocol for transient gene expression in Arabidopsis thaliana protoplasts isolated from cell suspension cultures

Isolation and maintenance of an Arabidopsis thaliana cell suspension culture, protoplast preparation from these cells and plasmid DNA transfection into the protoplasts by the polyethyleneglycol procedure are described. In the reported examples, the DNA contained chimaeric genes consisting on the coding region of the β-glucuronidase (GUS) reporter gene, fused to the cauliflower mosaic virus 35S promoter or to the promoter from the Arabidopsis elongation factor EF-1 α gene. Following DNA uptake into protoplasts, maximal GUS activity was observed after 50 to 60 h. The measured GUS activity indicated high transient expression of the tested chimaeric genes
Transcriptional profiling of Aspergillus niger

The industrially important fungus Aspergillus niger feeds naturally on decomposing plant material, of which a significant proportion is lipid. Examination of the A. niger genome sequence suggested that all proteins required for metabolic conversion of lipids are present, including 63 predicted lipases. In contrast to polysaccharide-degrading enzyme networks, not much is known about the signaling and regulatory processes that control lipase expression and activity in fungi. This project was aimed to gain better understanding of lipid degradation mechanisms and how this process is regulated in A. niger, primarily via assessment of its gene transcription levels. Minimizing biological and technical variation is crucial for experiments in which transcription levels are determined, such as microarray and quantitative real-time PCR experiments. However, A. niger is difficult to cultivate in a reproducible way due to its filamentous growth. In addition, the complex processing steps of transcriptomics technologies add non-experimental variation to the biological variation. To reduce this data noise, robust protocols based on a batch-fermentation setup were developed. Variation in this setup was surveyed by examining the fungal transcriptional response towards a pulse of D-xylose. The sources of non-experimental variation were described by variance components analysis. Two-thirds of total variation stems from differences in routine handling of fermentations, but in absolute terms this variation is low. As D-xylose is an inducer of the xylanolytic system, the high reproducibility of cultures for the first time allowed a detailed description of the global fungal transcriptional response towards D-xylose using microarrays. The transcriptional response towards three plant derived oils was examined in another study. Both olive oil and a wheat-gluten extracted oil induce the transcription of genes involved in lipid metabolism and peroxisome assembly, albeit with different expression profiles. The third oil, a plant membrane lipid, did not trigger a transcriptional response. Microarray data are related to the physiology of the fungus. To better understand the general principles that underlie gene regulation and gene transcription, microarray data from cultures grown under mildly and strongly perturbed conditions were analyzed for co-expression of genes. Despite the diverse culturing conditions, co-expressed gene modules could be identified. Some of these modules can be related to biological functions. For some modules, conserved promoter elements were identified, which suggests that genes in these modules are regulated on a transcriptional level. The work described in this thesis shows that (i) high-quality -omics data for A. niger can be generated; that (ii) analysis and interpretation of these data enhances our understanding of the xylanolytic and lipid metabolic regulons; and (iii) that these data give insight into the regulatory mechanisms of this fungus.
Biology and host associations of redbay ambrosia beetle, exotic vector of laurel wilt killing redbay trees in the southeastern United States

The redbay ambrosia beetle (Xyleborus glabratus Eichhoff (Coleoptera: Curculionidae: Scolytinae)) and its fungal symbiont (Raffaelea sp.), new introductions to the Southeastern United States, are responsible for the wilt of mature redbay (Persea borbonia (L.) Spreng. ) trees. In 2006 and 2007, we investigated the seasonal flight activity of X. glabratus, its host associations, and population levels at eight locations in South Carolina and Georgia where infestations ranged from very recent to at least several years old. Traps on artificially wounded trees showed that redbay ambrosia beetles were active throughout the year, but very few beetles were caught from March to late May 2006 and from mid-November 2006 through March 2007. Peak adult activity occurred in early September. Males are flightless, but a few were found at every sample date from 3 June 2006 to 30 January 2007. Based on these male emergence data, brood development appears to take 50 to 60 days. Uninfested redbay wood remained attractive to X. glabratus females for up to 70 days after being cut from live trees. Wood infested with beetles and infected with the Raffaelea sp. was similar in attraction to uninfested redbay wood, but uninfested and infested redbay wood were more attractive than a non-host species. Sassafras (Sassafras albidium (Nutt.) Nees), another species of the Lauraceae, was not attractive to X. glabratus, and very few beetle entrance holes were found in sassafras wood compared to redbay. Conversely, avocado (Persea americana Mill.) was as attractive to X. glabratus as swampbay (P. palustris (Raf.) Sarg. ), and both were more attractive than the non-host red maple (Acer rubrum L.). However, avocado had relatively few entrance holes in the wood so it is unclear whether it is a good host for brood development. In 2007, we compared X. glabratus populations in areas where all mature redbay were dead to areas where infestations were very active and more recent, as well as an area outside the known infestation. Trap catches of X. glabratus and numbers of entrance holes in trap bolts of redbay were correlated with the number of dead trees with leaves attached. Areas where mature host trees had been eliminated by the wilt had very low beetle population levels that ranged from 0.04 to 0.12 beetles/trap/day compared to areas with active infestations where catches ranged from 4 to 7 beetles/ trap/day. Our results indicate that populations of the beetle drop dramatically after suitable host material is gone, providing hope that management strategies can be developed to restore redbay trees. The lack of attraction of X. glabratus to sassafras suggests that spread of X. glabratus should slow once it is outside the range of redbay.
Early ultrastructural changes in skeletal muscle exposed to the local anaesthetic bupivacaine (Marcaine).

Abstract The local anaesthetic drug bupivacaine is known to produce a degeneration in mammalian muscle fibres which is followed by regeneration. In an attempt to define the site of action of this drug and the cell type responsible for the subsequent fibre regeneration, first lumbircal muscles of rats were exposed in vitro to concentrations of 10(-2), 5 X 10(-3), and 10(-3)M bupivacaine for periods ranging from 5 min to 3 h. An electron microscopic study of muscles exposed to 10(-2) and 5 X 10(-3)M bupivacaine revealed an initial supercontraction followed by evidence of severe and probably irreversible injury to plasma membrane, sarcoplasmic reticulum and mitochondria. Myonuclei showed signs of injury early, but satellite cells were found relatively resistant. The basal lamina remained intact throughout and myelinated axons did not suffer damage. However, both endothelial cells of capillaries and fibrocytes showed degenerative changes. Muscles exposed to 10(-3)M bupivacaine showed little change after incubation for 3 h. It is concluded that increased intracellular levels of Ca++ ions may play a part in the pathogenesis of muscle injury induced by bupivacaine and that their source may be the sarcoplasmic reticulum. The role of the satellite cell in the regeneration that follows this injury was not clearly established.