Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact des processus de mutation et de recombinaison sur la diversité génomique au sein de l’espèce Escherichia coli

Escherichia coli constitue la majeure partie de la flore microbienne commensale aero-anaerobie du tube digestif de l’hote. Pourtant E. coli est aussi une des especes les plus frequemment rencontrees en pathologie humaine et animale. C’est l’une des especes bacteriennes les plus etudiees et les plus connues. L’evolution des genomes au sein de l’espece repose sur deux mecanismes distincts : la mutation et la recombinaison, qui generent une diversite genetique sur laquelle la selection naturelle peut operer. Dans notre travail, nous nous sommes interesses a ces processus et aux traces qu’ils laissent dans les genomes. Nous avons, en premier lieu, decrit une forme de mutabilite variable le long du genome car liee a l‘existence de structure secondaire locale de l’ADN : la mutabilite transcriptionnelle. Nous avons pu d’une part quantifier cette mutagenese et d’autre part reveler une reponse selective au sein du genome pour en limiter les effets. La recombinaison, quant a elle, est connue pour brouiller le signal phylogenetique de maniere importante. En second lieu, nous avons montre par une approche de genomique comparative que, malgre un taux relativement eleve de recombinaison, l’etablissement d’une phylogenie robuste etait possible. De plus, nous avons mis en evidence que les nombreuses acquisitions et pertes de genes dans le genome des differentes souches d’E. coli se situaient preferentiellement a certains sites. Enfin, nous avons utilise la structure phylogenetique de l’espece a des applications taxonomiques et epidemiologiques.
Listeria monocytogenes en alimentos: ¿son todos los aislamientos igual de virulentos?

Foodborne Listeria monocytogenes: are all the isolates equally virulent? Listeria monocytogenes is a foodborne human pathogen responsible for invasive infections presenting overall a high mortality. Despite the ubiquity of the microorganism, the actual disease rate is quite low and the disease is most often associated with an underlying predisposition. Foodborne and environmental isolates were traditionally considered of similar pathogenicity compared to clinical isolates. But the analysis of mutations in the genes encoding specific virulence factors (internalin, hemolysin, phospholipases, surface protein ActA and regulator protein PrfA), quantitative studies with cell cultures and population genetics have raised considerable concerns about virulence differences among L. monocytogenes strains. Despite this great step forward, there is not a single marker available to test the virulence of field isolates of this species. In the future, the combination of different molecular markers will probably allow the screening of food contamination by only the virulent clones of L. monocytogenes, thus improving the prevention of foodborne human listeriosis.
Le zinc dans l' alimentation du porc: oligo-element essentiel et risque potentiel pour l' environnement.

Le zinc est un oligo-element essentiel qui intervient dans la plupart des fonctions biologiques de l'animal. La perte d'appetit, la diarrhee, le retard de croissance ou la parakeratose sont les principaux symptomes d'une carence en zinc qui peuvent apparaitre chez le porc recevant une alimentation non supplementee en zinc. La meconnaissance des besoins en zinc du porc et des facteurs de variation de sa disponibilite conduit a l'incorporer de maniere excessive dans les aliments. Cette pratique genere des rejets importants et augmente le risque de pollution des sols cultives. L'ajustement des apports de zinc aux besoins de l'animal et l'amelioration de sa disponibilite sont des solutions qui permettent d'en reduire les apports. Une revue des donnees de la litterature nous permet d'estimer les besoins en zinc du porc en fonction du poids vif. L'utilisation d'additifs, notamment de phytase microbienne, permet d'ameliorer la disponibilite du zinc. A partir des resultats de la litterature, nous estimons que l'activite de 1000 unites de phytase microbienne par kg d'aliment est equivalente a une addition de 24 et 19 mg/kg de zinc sous forme de sulfate chez le porcelet de respectivement 15 et 25 kg. Ces estimations sont a valider experimentalement. D'autres voies d'amelioration de la disponibilite du zinc doivent egalement etre explorees.
Host structuring of parasite populations: Some theoretical and computational studies

9 1. HOST STRUCTURE OF PARASITE POPULATIONS 11 1.1. Motivation 11 1.2. Model Formulation and Approximation 17 1.3. Invariant Measures and Equilibrium Jump Distributions . 28 1.4. Examples 32 2. BIOLOGICAL INTERPRETATIONS 61 2.1. Sources of Transmission Bias 61 2.2. Additional Applications 67 3. TRANSMISSION BIAS AND HIV-1 VACCINE DESIGN 87 4. HOST STRUCTURE IN AN EXPANDING EPIDEMIC 101 4.1. Motivation 101 4.2. Branching Fisher-Wright Diffusions 104 4.3. Persistence and Absorption Probabilities 107 4.4. Extensions 118 5. HOST STRUCTURE, RECOMBINATION, AND HLV-1 SUPERINFECTION . 121 5.1. Background 121 5.2. Methods 127 5.3. Results 137 5.4. Discussion 141
Vitamin D3 alleviates inflammation in ulcerative colitis by activating the VDR-NLRP6 signaling pathway

Inflammation is a key factor in the development of ulcerative colitis (UC). 1,25-dihydroxyvitamin D3 (1,25(OH)2D3, VD3), as the major active ingredient of vitamin D and an anti-inflammatory activator, is closely related to the initiation and development of UC, but its regulatory mechanism remains unclear. In this study, we carried out histological and physiological analyses in UC patients and UC mice. RNA sequencing (RNA-seq), assays for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), chromatin immunoprecipitation (ChIP) assays and protein and mRNA expression were performed to analyze and identify the potential molecular mechanism in UC mice and lipopolysaccharide (LPS)-induced mouse intestinal epithelial cells (MIECs). Moreover, we established nucleotide-binding oligomerization domain (NOD)-like receptor protein nlrp6 -/- mice and siRNA-NLRP6 MIECs to further characterize the role of NLRP6 in anti-inflammation of VD3. Our study revealed that VD3 abolished NOD-like receptor protein 6 (NLRP6) inflammasome activation, suppressing NLRP6, apoptosis-associated speck-like protein (ASC) and Caspase-1 levels via the vitamin D receptor (VDR). ChIP and ATAC-seq showed that VDR transcriptionally repressed NLRP6 by binding to vitamin D response elements (VDREs) in the promoter of NLRP6, impairing UC development. Importantly, VD3 had both preventive and therapeutic effects on the UC mouse model via inhibition of NLRP6 inflammasome activation. Our results demonstrated that VD3 substantially represses inflammation and the development of UC in vivo. These findings reveal a new mechanism by which VD3 affects inflammation in UC by regulating the expression of NLRP6 and show the potential clinical use of VD3 in autoimmune syndromes or other NLRP6 inflammasome-driven inflammatory diseases.
Analyse fonctionelle de la nouvelle famille de facteur de transcription GeBP/GPL dans le contrôle du développement d'Arabidopsis thaliana

Notre equipe de recherche etudie l'action des hormones gibberellines (GA) et cytokinines (CK) dans les processus de developpement chez la plante modele Arabidopsis thaliana. En recherchant des regulateurs de l'expression d'un gene implique dans la differenciation des cellules epidermiques et dont l'expression est controlee par ces deux hormones, une nouvelle famille de quatre proteines nommees GeBP (GL1 enhancer Binding Protein), GPL1 (GeBP Protein Like 1), GPL2 et GPL3 a ete identifiee au laboratoire. Le but de ce travail de these etait de caracteriser moleculairement et fonctionnellement les membres de cette nouvelle famille multigenique. Nous avons tout d'abord verifie l'adressage nucleaire des proteines GeBP/GPL et demontre leur capacite a former des dimeres in planta via un motif Leucine-Zipper non canonique. L'analyse fonctionnelle a ete abordee par l'etude de lignees simples et multiples mutantes gebp/gpl. Differentes donnees physiologiques et moleculaires convergentes ont demontre un role redondant des genes GeBP/GPL dans le controle de la reponse aux CK. Enfin, une analyse globale des transcriptomes d'une lignee surexpresseur de GPL2 et du quadruple mutant gebp/gpl, nous a permis d'etablir un lien entre les GeBP/GPL et CPR5, un gene implique dans la reponse aux pathogenes, et le controle du cycle cellulaire. Ce lien a ete conforte experimentalement par des mesures de ploidies des noyaux des cellules foliaires montrant une deregulation du cycle cellulaire chez la lignee quadruple mutant et la lignee surexpresseur de GPL2. Les futurs travaux auront pour but de poursuivre l'etude de la fonction des GeBP/GPL et de confirmer le lien avec CPR5.
The Cell Cycle: An Introduction

In the last decade there has been a revolution in our comprehension of how cells grow and divide. Results from experiments on yeast, embryos, and cultured mammalian cells have unified seemingly disparate viewpoints into a single set of principles for normal cellular reproduction in plants, animals and bacteria. Written by two leading participants in that revolution, The Cell Cycle provides the first thorough, authoritative account of the new philosophy of normal cellular reproduction and how it emerged. It is a vivid portrayal of the molecular logic of the cell: how the cell engine induces DNA replication and chromosome replication; how the integrity of genetic information is preserved; and how cell size and environmental signals regulate the cycle of growth and division. By describing important breakthroughs in their historical and experimental context, The Cell Cycle traces the development of the new vision of cell biology and shows its relevance to other areas of modern biology. It is the ideal introduction to the current understanding of cell growth and division for advanced undergraduate and graduate level cell biology courses.
The impact of automated control of indoor air pollutants on cardiopulmonary health, environmental comfort, sleep quality in a simulated apartment: A crossover experiment protocol

Air pollution makes an impact on cardio-pulmonary health. Since people spend over 90% of their time indoors, exposures to the indoor environment make the most significant impact on health. Among indoor sources, cooking emits the most particles that disperse through the residential indoor environment and expose occupants. We use fully controlled simulated residential modules to conduct exposure experiments. In the pilot study, participants stayed in modules for 1 week, and in the main study, 14 participants will stay in the module for 4 weeks. One module is operated as a classical US house air supply recommendation. The second module has an advanced control system that, alongside the standard air supply, activates air quality interventions: stove hood, portable air cleaners, bathroom exhaust and air flush (increasing air supply ∼3 times) as a function of the PM2.5 levels in the space. Environmental sensors based on Internet of Things technology simultaneously monitored Particulate Matter (PM2.5), CO2, Total Volatile Organic Compounds Relative Humidity and air temperature in all spaces and operated air quality interventions. Participant’s scheduled activities include morning and evening tasks, Monday through Friday. Participants may leave the module during the day. They will be asked to cook breakfast and dinner using lab-provided recipes. We measured each participant’s blood pressure, heart rate, and heart rate variability. Blood and urine samples were collected 3 times per participant in the pilot and will be collected 2 times a week in the main study. Up to 20 ml of blood and a minimum of 30 ml of urine will be sampled per collection. Analysis of blood and urine was performed for 8-hydroxy-2-deoxyguanosine (8-OHdG, urine), von Willebrand Factor (vWF, blood plasma), high sensitivity C-Reactive Protein (hsCRP, blood serum), Interleukin-6 (blood plasma), CD11b (blood), Fibrinogen (blood plasma), and Myeloperoxidase (blood serum). We conducted a Pilot for 2 weeks with 3 participants to test the study protocol and data collection. We adjusted the protocol for the main study based on the pilot results. Results showed that the proposed study protocol could be completed, and the methodology adopted in this study will provide valuable insights into the relationship between exposure to cooking particles and occupants' health. Trial registration: Mayo Clinic IRB 20-007908.
The Evolutionary Constraints of HIV

HIV evolves very quickly permitting it to escape the immune system of an infected individual, limiting the effectiveness of drug treatment and making vaccine design extremely difficult. For these reasons identifying whether there are constraints on HIV evolution is of primary importance. In this thesis, I examined the relationships between sequence diversity and a number of factors including protein structure, co-evolution and RNA secondary structures, all of which contribute to evolutionary constraints. Firstly, I demonstrate that while there is an increase in sequence diversity over time, this variation has a tendency to be limited to specific structural regions. Relating the sequence variability of individual amino acid residues with three- dimensional protein structure, I find a significant difference between evolutionary rates in regions buried in the core of the protein as compared with those exposed on the surface. This result indicates that missense mutation is affected by structural constraints. Secondly, by relating recombinant breakpoint positions with the potential numbers of losses in amino acid interactions within the structure, I propose that as well as missense mutation, recombination is also affected by structural constraints, due to the need to maintain intra-molecular interactions. Thirdly, I demonstrate a relationship between conservation of RNA secondary structure and limited sequence variation in protein level, indicating RNA secondary structures are additional evolutionary constraint. This link between sequence and protein and RNA structures not only demonstrates the limits of recent HIV-1 evolution but also highlights the origins of evolutionary constraint on viral change. Lastly, I examined whether evolutionary constraints and co- evolution patterns of HIV genomes are applied in novel mosaic vaccine strategy and suggest that polyvalent mosaic vaccine sequence may generate proteins with stable structures and co-evolving units. Detailed understanding of the constraints that restrict HIV? s possible evolution will inform analysis of drug and immune escape.
Canon/archive : large-scale dynamics in the literary field

Of the novelties introduced by digitization in the study of literature, the size of the archive is probably the most dramatic: we used to work on a couple of hundred nineteenth-century novels, and now we can analyze thousands of them, tens of thousands, tomorrow hundreds of thousands. It's a moment of euphoria, for quantitative literary history: like having a telescope that makes you see entirely new galaxies. And it's a moment of truth: so, have the digital skies revealed anything that changes our knowledge of literature? This is not a rhetorical question. In the famous 1958 essay in which he hailed "the advent of a quantitative history" that would "break with the traditional form of nineteenth-century history", Fernand Braudel mentioned as its typical materials "demographic progressions, the movement of wages, the variations in interest rates [. ] productivity [. ] money supply and demand. " These were all quantifiable entities, clearly enough; but they were also completely new objects compared to the study of legislation, military campaigns, political cabinets, diplomacy, and so on. It was this double shift that changed the practice of history; not quantification alone. In our case, though, there is no shift in materials: we may end up studying 200,000 novels instead of 200; but, they're all still novels. Where exactly is the novelty?
Role of resilience and related coping in the adjustment of first year psychology students at the University of KwaZulu-Natal, Pietermaritzburg campus.

The transition to university is often a challenging process that requires students to adapt to new social and academic stresses whilst balancing the changing roles within their families, friends, academic work, leisure and often a part-time job. The ability to deal with stress in a transition regardless of challenges and still exhibit positive outcomes is crucial in order to achieve academic success along with positive mental health. The aim of the current study was to explore the role of resilience and related coping styles of first year university students’ ability to adjust to university life. A total of 142 first year students attending the University of KwaZulu-Natal in Pietermaritzburg participated in the study. Data was collected using questionnaires: The demographic information form, Resilience scale for adults (RSA), Adolescent coping scale (ACS) and Student adaption to college questionnaire (SACQ). To test the data, hierarchical multiple regression analyses were conducted composed of two models: model one: positive adjustment, model two: social adjustment. The first model outlined resilience as significant predictor for students’ adjustment at university. The second model outlined gender, diversion coping styles and resilience as significant predictors for social adjustment. It is recommended that more religious activities should be encouraged as students rely on religious beliefs to combat daily stressors.
CARACTERIZACIÓN BROMATOLÓGICA Y MICROBIOLÓGICA DE CARNES PROCEDENTES DE ESPECIES DE ANIMALES REGIONALES DE LA AMAZONIA PERUANA PARA CONSUMO HUMANO

La investigacion consistio en la caracterizacion bromatologica y determinacion microbiologica de muestras de carnes procedentes de ocho especies de animales silvestres: huangana ( Tayassu pecari ), majaz o picuro ( Agouti paca ), sajino ( Tayassu tajacu ), venado colorado ( Mazama americana ), tapir ( Tapirus terrestris ), anuje ( Dasyprota fuliginosa ), ronsoco ( Hydrochaeris hydrochaeris ) y armadillo ( Dasypus novemcinctus ); en las localidades de Puerto Belen-Roya-Utucuro, Santa Rosa de Aguaytia, Santa Luz de Abujao, Tacshitea–Sector Parinari en dos ocasiones, ubicadas en las margenes del rio Ucayali y sus afluentes, que fueron analizarlas por la empresa Servicios de Asesoramiento Tecnico S.A. C. en Lima. La caracterizacion bromatologica indico que el anuje ( Dasyprota fuliginosa ) mostro el mayor contenido en Proteina cruda seguido de la huangana ( Tayassu pecari ); en el contenido de grasa destacaron las especies armadillo ( Dasypus novemcinctus ) y la sachavaca ( Tapirus terrestris ) asi tambien en su contenido calorico. La especie venado colorado ( Mazama americana ) mostro un mayor valor en cenizas y en carbohidratos la especie huangana ( Tayassu pecari ). La determinacion microbiologica indico que todas las muestras presentaron niveles de contaminacion dentro de los limites permitidos para aerobios mesofilos viables y niveles de contaminacion por coliformes totales, coliformes fecales, algunos muy elevados y tambien de mohos y levaduras. Todos presentaron ausencia de Salmonella.
ESTUDIO DEL REGIMEN Y HABITOS ALIMENTARIOS DE LA ANCHOVETA Engruulis mordaz GIRARD (PISCES: ENGRAULIDAE), EN BAJA CALIFORNIA, MEXICO FEEDING BEHAVIOR AND DIETARY COMPOSITION OF THE NORTHERN ANCHOVY, Engruulis mordí GIRARD (PISCES: ENGRAULIDAE), OFF BAJA CALIFORNIA, MEXICO

Feeding behavior and dietary composition of northern anchovy, Etlgraulis mordaz, off the west coast of Baja California are analyzed. The visual field for prey detection is 104 mm and the basal area of the vision cone is 125 cm2. The mean number of gill rakers in the first lower branchial arch is 41; gill raker gap increases as fish grows. Diatoms, anchovy eggs, crustaceans, dinoflagellates and protozoans are the major by-number contributors to the diet of E. mordax. Filtering mechanism acts over a 0.05 to 1.50 mm range of prey length, while selective particulate feeding occurs from 1.51 to 5.00 mm prey size spectrum. The morphometric relationship between intestine length and fish length is expressed by potential functions, and the number of curvatures varies as fish grows. Although phytoplankton is the principal by-number component of the stomach conten&, zooplankton prey are consistently the major source of carbon in’ the diet. Prey size increases as predator grows.
Studies on the Morphology and Biology of Cotton Rats (Sigmodon hispidus) from Northern Mexico to Southern Nebraska

This investigation was designed to evaluate the need for retaining both Sigmodon hispidus texianus and Sigmodon hispidus berlandieri as subspecific designations. An attempt was made to demonstrate bioclimatic variation and reproductive seasonality in cotton rats. The validity of applying the results of isolated studies of cotton rat populations to the species as a whole was examined.
Analysis of local spread of metamitron‐resistant Chenopodium album patches in Belgium

Tracing spread of weeds with molecular markers can give valuable information on the importance of migration mechanisms. This study investigated the local spread of metamitron-resistant Chenopodium album patches in the west of the province West Flanders (Belgium) using amplified fragment length polymorphism (AFLP) markers. During the summer of 2009, leaf samples of C. album plants were harvested in 27 patches, distributed over 10 sugar beet fields and one maize field. The fields were grouped in four local clusters, each corresponding to a farmer who cultivated these fields. A cleaved amplified polymorphic sequence procedure identified the Ser264 to Gly mutation in the D1 protein, endowing resistance to metamitron, a key herbicide applied in sugar beet. The majority of the sampled plants within a patch (97% on average) carried this mutation. Genetic variation among the four farmers locations (12%) and among the C. album patches within the farmers locations (14%) was significant according to amova (P < 0.001). In addition, Mantel tests confirmed a positive correlation between genetic distance (linearised ? PT between pairs of patches) and the logarithm of geographic distance for the complete data set (Mantel coefficient significant at P = 0.001), suggesting isolation by distance. Nevertheless, genetic similarity between patches from different fields indicated that seed transport by agricultural machinery and manure is likely to have an important impact on the spread of metamitron-resistant biotypes. Farmers should become aware of the resistance problem as soon as possible, in order to prevent further spread in their fields.
The Mind's Eyes

Abstract The across-species genetic conservation of intercellular and extracellular chemical communication enables unicellular and multicellular organisms to functionally distinguish between self and non-self. Non-self olfactory/pheromonal input from the social environment elicits a vertebrate neuroendocrine response. The organization and activation of this neuroendocrine response modulates the concurrent maturation of the mammalian neuroendocrine system, the reproductive system, and the central nervous system during the development of sexual preferences that may be expressed in sexual behavior. Psycho-physiological mechanisms for the development of these sexual preferences include focus on unconscious affects that are detailed in reciprocal cause and effect relationships. Olfactory/pheromonal conditioning elicits neuroendocrine effects accompanied by unconscious affects on the development of sexual preferences. Integrating these unconscious affects extends to humans a developmental model of behavior that includes the development of male sexual preferences for other males. doi:10.1300/J056v18n04_03