Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomics and physiological evolution of cold tolerance in Drosophila melanogaster

Thermal stress impacts animals around the globe and understanding how organisms adapt to changes in temperature is of particular interest under current climate change predictions. My research focuses on the evolutionary genetics involved in cold tolerance and plasticity of cold tolerance using both artificially selected and naturally segregating populations, while tying the genes of interest to their physiological components. First I address cross-tolerance of stress traits following artificial selection to a non-lethal cold tolerance metric, chill-coma recovery. Using these artificial selection populations, we found that stress traits such as desiccation tolerance, starvation tolerance, acclimation, and chronic and acute cold tolerance do not correlate with level of cold tolerance as defined by chill-coma recovery time. We next assessed lifetime fitness of these different cold tolerance lines and found that only at low temperatures did fitness differ among cold tolerance levels. We then analyzed gene expression differences between resistant and susceptible populations at three time points to understand where selection pressures are hypothesized to act on genomic variation. Our gene expression analyses found many differences between resistant and susceptible lines, primarily manifesting themselves in the recovery period following cold exposure. We next utilized a community resource, the Drosophila melanogaster reference panel, to identify naturally segregating variation in genes associated with cold acclimation and fitness. We specifically asked if longand short-term acclimation ability had overlapping genetic regions and if plasticity values from constant rearing environments were associated with demographic parameters in fluctuating environments. We found that longand short-term acclimation are under unique genetic control and functionally tested several genes for acclimation ability. We also found that acclimation ability in constant environments and fitness in fluctuating environments do not correlate, but that genotypes are constrained in their fitness abilities between a warm and cool environment. Our analyses describe several novel genes associated with cold tolerance selection and longand short-term acclimation expanding our knowledge of the complex relationship between demographic components and survivorship as well as a unique investigation of the change in gene expression during cold exposure. GENOMICS AND PHYSIOLOGICAL EVOLUTION OF COLD TOLERANCE IN DROSOPHILA MELANOGASTER
Total phenolics and flavonoids content in ripened and unripened fruits of different mulberry (Morus alba) varieties

The results of the experiment indicated that K 2 mulberry variety have shown maximum flavonoid and phenolic content in un-ripened fruits, while AR 14 variety have maximum total phenolic content in ripened fruits. The BR 2 mulberry variety has highest total flavonoids content in ripened fruits. The high contents of functional compounds in mulberry juice, fruits, and leaves implied that they might be potential resources for the development of functional drinks and food. Considering the advantages of potential medicinal properties of flavonoids and phenols enriched fruits of mulberry it can be utilized to treat several diseases of animals and human being.
Comparative genomics of trypanosome metabolism.

(1) Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK, (2) Division of Biological Chemistry & Molecular Microbiology, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, Scotland, UK, (3) Research Unit for Tropical Diseases and Laboratory of Biochemistry, Ch. de Duve Institute of Cellular Pathology, Université catholique de Louvain, B-1200 Brussels, Belgium,
Health-Related Internet Usage and Design Feature Preference for E-Mental Health Programs Among Men and Women

Background Major depressive episodes (MDEs) are prevalent in the workplace and affect workers’ health and productivity. Therefore, there is a pressing need for innovation in the prevention of MDEs in the workplace. Electronic mental (e-mental) health programs are a cost-effective approach toward the self-management of stress and emotional issues. E-mental health dropout rate, MDE prevalence, and symptoms greatly vary by sex and age. Thus, the development and implementation of e-mental health programs for the prevention of MDEs need to be examined through a sex and age lens to enhance program use and effectiveness. Objective This study aimed to examine design feature preferences based on sex and age for an e-mental health program targeted toward depression prevention. Methods Household residents across Canada were contacted using the random digit dialing method. 500 women and 511 men who were 18 years and older and who were at high risk of having MDEs were interviewed. Internet use was assessed using questions from the 2012 Canadian Internet Use Survey conducted by Statistics Canada, and preferred design features of e-mental health program questions were developed by the BroMatters team members. The proportions of likely use of specific features of e-mental health programs in women were estimated and compared with those in men using chi-square tests. The comparisons were made overall and by age groups. Results Men (181/511, 35.4%) and women (211/500, 42.2%) differed significantly in their likelihood of using an e-mental health program. Compared with men (307/489, 62.8%), women (408/479, 85.2%) were more likely to use the internet for medical or health-related information. Women were more likely to use the following design features: practices and exercises to help reduce symptoms of stress and depression (350/500, 70.7%), a self-help interactive program that provides information about stress and work problems (302/500, 61.8%), the ability to ask questions and receive answers from mental health professionals via email or text message (294/500, 59.9%), and to receive printed materials by mail (215/500, 43.4%). Men preferred to receive information in a video game format (156/511, 30.7%). Younger men (46/73, 63%) and younger women (49/60, 81%) were more likely to access a program through a mobile phone or an app, and younger men preferred having access to information in a video game format. Conclusions Factors such as sex and age influenced design feature preferences for an e-mental health program. Working women who are at high risk for MDEs preferred interactive programs incorporating practice and exercise for reducing stress, quality information about work stress, and some guidance from professionals. This suggests that sex and age should be taken into account when designing e-mental health programs to meet the needs of individuals seeking help via Web-based mental health programs and to enhance their use.
Review of AbleData: Tools & Technologies to Enhance Life

ABSTRACT Assistive technology (AT) can significantly enhance quality of life for people with disabilities. AbleData, produced by the National Institute on Disability, Independent Living and Rehabilitation Research (NIDILRR), provides comprehensive, unbiased information about a broad range of assistive technology products for use by a variety of populations with disabilities. The database search function is intuitive and simple to use, and is augmented by browsing features and indexing links. Additional helpful resources are linked from the site.
Teaching and training in orthopaedics

This article aims to review the current trends in the pedagogy of orthopaedic surgery, with specific reference to teaching philosophies, training methods and assessments tools that may be used. Our expanding knowledge base and the complexity of skills required, combined with the pressure created by medical negligence litigation increases the emphasis on knowledge of disease in contrast to pure competency in practical procedures. At specialist level, the drive now appears stronger than ever to develop lessor non-invasive ways to treat musculoskeletal disease. As a disease specialist the trainee, therefore, needs to develop a wider vision than one held by a competent technician. A combination of educational philosophies can be employed to achieve these objectives. Cognitive task analysis (CTA) and constructivism may be useful strategies for skills acquisition. In terms of theoretical knowledge, the emphasis remains on an evidence-based approach, delivered in an active student-centred environment. Clinical teaching as a whole, however, demands the promotion of critical thinking and a problem-oriented approach in a situated learning setting. The pedagogy of skill and knowledge assessment in orthopaedics remains unresolved. However, the educational impact of assessment through its value as a driver for learning has been recognised. Level of evidence: Level 5
Caractérisation du phénotype associé à la mutation masculinisante "mal" chez la truite arc-enciel, Oncorhynchus mykiss

La truite arc-en-ciel a un determinisme du sexe strictement genetique de type XX/XY. Pourtant des femelles genetiques se sont spontanement masculinisees apres une gynogenese endomitotique. Ce phenotype masculinise a penetrance incomplete serait du a une mutation inconnue appelee " mal ". Afin d'identifier le gene causal porteur de cette mutation, une meilleure caracterisation de son phenotype est necessaire. Pour cela, nous avons procede a la caracterisation du phenotype gonadique en utilisant a la fois des approches histologiques et moleculaires. Tous les animaux XXmal presentent une differenciation sexuelle tres perturbee autant sur le plan histologique que sur le plan de leurs profils d'expression geniques. Parmi ces perturbations, l'inhibition de l'expression du gene de l'aromatase gonadique (cyp19a1a), une enzyme de synthese des œstrogenes, pourrait etre un facteur explicatif de cette masculinisation. De plus des temperatures d'elevage elevees (18°C) augmentent fortement la masculinisation de ces animaux XXmal. Enfin, la croissance des animaux XXmal est affectee negativement selon le degre de perturbation. En consequence, la masculinisation de ces animaux serait le resultat d'une deregulation profonde en amont du gene cyp19a1a, avec comme consequence une instabilite precoce de la differenciation ovarienne suivie par la masculinisation effective d'une partie des animaux XXmal. Cette instabilite serait amplifiee par des temperatures elevees qui affecteraient a la fois le developpement global des animaux XXmal et la transcription de cyp19a1a. Nos resultats suggerent fortement que le phenotype "mal" est plus complexe qu'un simple phenotype "femelle masculinisee".
Functional analysis of Group 2 chaperonins from archaeal species in E. coli

The chaperonin proteins form a ubiquitous family of molecular chaperones and are absolutely required for correct folding or assembly of a subset of proteins in the cell. They are divided into two groups based on phylogeny: Group 1 found in bacteria and eukaryotic-organelles and Group 2 found in eukaryotic-cytoplasma and archaea. The two groups share a significant degree of conservation but differ in structure and mechanism and are believed to have evolved to serve specific client proteins. Using archaeal chaperonin from M. maripaludis (MmCCT) as a representative, we report here for the first time that a Group 2 chaperonin can partially replace the function of a Group 1 chaperonin from E. coli (GroEL). We have also identified and characterized two functional variants of MmCCT that show better GroEL complementation and have utilized them for a preliminary mutational analysis of potential client binding residues of MmCCT. We further demonstrate an initiative using a tagging approach for identification of bacterial proteins that interact with MmCCT in vivo. We suggest that our findings provide a novel platform for genetic dissection of MmCCT using a comparatively simple host, E. coli, which in turn can help identify properties of this archaeal chaperonin and provide insights for structure-function co-relations of Group 2 chaperonins in general.
Antimicrobial resistance pattern of clinical isolates of Pseudomonas aeruginosa and Escherichia coli on carbapenems

Background : Carbapenems are the most effective and important therapeutic options to serious infections caused by Enterobacteriaceae and Pseudomonas aeruginosa isolates. However, Carbepenems resistant isolates of Enterobacteriaceae and Pseudomonas aeroginosa are increasing worldwide. This study, therefore, was carried out to determine the resistance pattern of clinical isolates of Pseudomonas aeruginosa and Escherichia coli to Carbapenems. Methods : Fifty (50) E. coli and forty seven (47) Pseudomonas aeruginosa isolates were studied. Antibiotic Susceptibility test was performed as recommended by the CLSI. The antibiotics used were Ertapenem, Imipenem, Colistin Sulphate, Levofloxacin, and Piperacillin/Tazobactam. Results : Out of 97 clinical isolates subjected to drug susceptibilities test, Pseudomonas aeruginosa showed resistance to Ertapenem (87.2%); followed by Levofloxacin (19.1%), Colistin sulphate (12.8%), Piperacillin/tazobactan (4.3%) and Imipenem (2.1%) while E.coli displayed resistance to Ertapenem (30%), Levofloxacin (20%) and Colistin sulphate (4%). Interestingly, E coli was susceptible to Imipenem (0%) and Piperacillin/tazobactan (0%). A significant effect of Ertapenem on Pseudomonas aeruginosa was recorded. Also a significant effect of Piperacillin/Tazobactam was recorded on E coli . No significant effect was recorded among the other antibiotics on P aeruginosa or E coli . Conclusion : There is a high level of Carbapenems resistance among the clinical isolates of Pseudomonas aeruginosa compared to Escherichia coli in this study. Considering the therapeutic value of Carbapenems as one of the last options for the treatment of Enterobacteriaceae and Pseudomonas aeruginosa infections, rational Carbapenems usage is essential to reduce selective pressure over Enterobacteriaceae and Pseudomonas aeruginosa clinical isolates. Keywords : Carbapenems, Antibiotics, Nosocomial, Susceptibility
Dengue viral infections and shock syndromes: An overview

Abstract Dengue viral infections are caused by one of four single stranded RNA viruses of the family Flaviviridae. They can occur virtually throughout the tropics and are transmitted by their mosquito vector, Aedes aegypti. Dengue, the most common arboviral disease in the world, has become more prevalent now than ever before and its prevalence is expected to increase. The risk for severe disease is determined by a complex interplay of epidemiological, virus and host factors. The clinical syndromes caused by dengue viral infections occur in an iceberg fashion along a severity continuum. Most cases are asymptomatic and a much smaller proportion present with severe forms of the disease-dengue hemorrhagic fever/dengue shock syndrome-that are characterized by sudden increase in vascular permeability and consequent shock. The traditional WHO classification and grading of dengue fever, dengue hemorrhagic fever and dengue shock syndrome are described along with a discussion of the timing and methods of laboratory diagnosis. Management is predominantly supportive. In patients with severe shock, treatment strategies are double pronged and include methods to judiciously resolve shock and control bleeding while simultaneously preventing fluid overload and its complications, including the need for assisted ventilation. These considerations are especially relevant in resource limited tropical countries where dengue viral infections are amongst the leading causes of childhood hospitalization, morbidity and death.
Investigation of the biochemistry and function of neutrophil serine protease 4 (NSP4)

Serine proteases in cytoplasmic granules of neutrophils (NSPs), namely neutrophil elastase, cathepsin G (CG) and proteinase 3, have been under intense investigation for several decades. They are mainly known for their role in intracellular killing of pathogens and are also increasingly recognized as key regulators of innate immune responses. In 2009, I identiﬁed a fourth serine protease in neutrophils that has been completely overlooked and neglected so far. The aim of this thesis was an in-depth biochemical and functional characterization of this novel serine protease 4 (NSP4) of human neutrophils. Using monoclonal antibodies to NSP4, the distribution of NSP4 in normal human tissues was studied. NSP4 was observed only in neutrophils and neutrophil precursors of the bone marrow. The content of NSP4 in neutrophil lysates was about 20-fold lower compared to CG. Nevertheless, NSP4 was found to be released into the supernatant upon neutrophil activation. NSP4 could be further identiﬁed as a novel azurophil granule protein of neutrophils by Western blot analyses of subcellular fractions. For the functional analysis, the production and yield of recombinant NSP4 was clearly improved using different expression systems and DNA construct modiﬁcations. The proteolytic speciﬁcity was analyzed using E. coli peptide libraries, mass spectrometry and several synthetic peptide libraries. All these analyses clearly revealed an arginine speciﬁcity for NSP4. Consistent with this, NSP4 was strongly inhibited by heparin-accelerated antithrombin and C1 inhibitor and, with lower efﬁcacy, by α1-proteinase inhibitor (α1PI). The data allowed me to generate an NSP4-speciﬁc α1PI variant that was shown to form covalent complexes with all NSP4 of neutrophil lysates and supernatants of activated neutrophils. This ﬁnding strongly indicated that NSP4 is fully processed and stored as an already activated enzyme in azurophil granules. In addition, dipeptidyl peptidase I (DPPI) was identiﬁed as the activator of NSP4 in vivo, as DPPI deﬁciency resulted in complete absence of NSP4 in a Papillon-Lefevre patient. Analysis of cell-based calcium assays revealed that proteinase-activated receptor-2 may represent a potential natural substrate of NSP4. So far, NSP4-deﬁcient mice did not show an abnormal phenotype under clean housing conditions. Activation of isolated neutrophils by phorbol esters or immune complexes was also not impaired. This study establishes NSP4 as the only arginine-speciﬁc pre-activated serine protease stored in azurophil granules of neutrophils that may fullﬁl a quite distinct, supportive role in neutrophil responses to tissue damage and bacterial infections.
Anterior Endomesoderm Specification in Xenopusby Wnt/-catenin and TGF- Signalling Pathways

Abstract InXenopus, XHexandcerberusare early marker genes of the anterior endomesoderm (AE), a subset of endoderm cells fated to form the liver and foregut and implicated in head induction. UsingXHexandcerberusas markers we have examined the signals underlying AE induction. We show that the AE is specified by the early blastula in the absence of mesodermal signals but that cell–cell contact between presumptive AE cells is required. In overexpression experiments maternal Wnt/β-catenin and TGF-β signals (Vg1, Xnr1–2) can induce ectopicXHexandcerberus.Inhibiting these pathways with dominant interfering signalling components blocks endogenousXHexandcerberusexpression. We assess the role of signals from the organiser and show that the BMP antagonists noggin and chordin are important for maintainingXHexandcerberusexpression. Finally, ventral injection ofXHexmRNA can induce ectopiccerberus.Our results indicate that endodermal and mesodermal patterning are closely coordinated and that the AE is likely to be specified by the combined action of dorsal Wnt/β-catenin signals and endoderm-specific factors mediated by TGF-β signalling. These results provide a starting point for understanding the molecular events underlying the progressive determination of endodermally derived organs, such as the liver and foregut.
Root rot biocontrol for indoor poinsettia with Trichoderma spp.

In Morelos, root rot caused by Fusarium spp. , is one of the main diseases of indoor poinsettia. In order to prevent or control its devastating effect, frequent applications of chemical products are performed, with inherent risks to human health and environment. In quest for alternative biorational options, an essay in which three commercial strains of Trichoderma spp. , was done, in three different substrates: S1= "organic soil" (70% v/v)+thick tezontle (15% v/v)+thin tezontle (10% v/v)+agrolita (5% v/v); S2= peat moss (80% v/v)+ coconut fiber (20% v/v); S3= "organic soil" (70%)+"tepojal" (30%), in most common commercial varieties, Freedom Red and Prestige Red. A factorial design of 4 x 3 x 2 treatment was used and resulting treatments were evaluated in a completely random design with six repetitions. Regards root rot incidence, commercial strains of Trichoderma spp. , did not show differences between them, either with chemical control. Root rot was associated with S2, due low aeration capacity, and only it was seen in Prestige Red. Population of Trichoderma spp. ,(UFC g -1 ) in the substrate at end of cycle was the same (p≤ 0.05) between commercial strains and between them and the control (without inoculation), due presence of native strains of Trichoderma in organic components of substrates ("organic soil", peat moss and coconut fiber).
Regulation of the Kcnq1ot1 Imprinting Domain in Mouse

II KEYWORDS. III CO-­‐AUTHORSHIP STATEMENT. IV ACKNOWLEDGMENTS. V ETHICS APPROVAL . VI LIST OF TABLES . IX LIST OF FIGURES . X LIST OF APPENDICES . XV CHAPTER 1: INTRODUCTION . 1 1.1 EPIGENETICS . 1 1.1.1 General Introduction . 1 1.1.2 Mechanisms of Epigenetic Regulation . 2 1.1.3 Histone Modifications . 2 1.1.4 DNA Methylation . 5 1.1.5 Non-­‐coding RNAs . 5 1.1. 6 Nucleosome Remodelers . 9 1.2 GENOMIC IMPRINTING . 12 1.2. 1 Overview of Genomic Imprinting . 12 1.2. 2 Epigenetic Reprogramming.16 1.2. 3 Imprinting Domains . 17 1.2. 4 Kcnq1ot1 Domain.24 1.2. 5 Models of Kcnq1ot1 Domain Regulation.27 1.3 RATIONALE.33 1.4 HYPOTHESIS . 33 1.5 OBJECTIVES . 34
Dense Non-Natural Sequence Peptide Microarrays for Epitope Mapping and Diagnostics

Antibodies play an important role in modern science and medicine. They are essential in many biological assays, and have emerged as an important class of therapeutics. Unfortunately, current methods for mapping antibody epitopes require costly synthesis or enrichment steps, and no low cost universal platform exists. In order to address this, we tested a random sequence peptide microarray consisting of over 330,000 unique peptides sequences sampling 83% of all possible tetramers and 27% of pentamers. It is a single, unbiased platform capable of performing many different types of tests, it does not rely on informatic selection of peptides for a particular proteome(s), and it does not require iterative rounds of selection. In order to optimize the platform, we developed an algorithm that considers the significance of k-length peptide subsequences (k-mers) within selected peptides that come from the microarray. We tested eight monoclonal antibodies and seven infectious disease cohorts. The method correctly identified 5/8 monoclonal epitopes, and identified both reported and unreported epitope candidates in the infectious disease cohorts. This algorithm may greatly enhance the utility of random-sequence peptide microarrays, by enabling rapid epitope mapping and antigen identification.