Miracle-dz/UniFAR-FTUs huggingface dataset:
Modèle murin invalidé pour les LXRs : dyslipidémie et impact sur la maturation post-testiculaire des gamètes

L’obtention de spermatozoides fecondants est un processus long et multi etapes, debutant par la production des gametes mâles dans le testicule. Les spermatozoides sont ensuite successivement matures au cours du transit epididymaire puis lors de leur passage dans les voies genitales femelles au cours du processus de capacitation. Ces etapes de maturation post-testiculaires concernent notamment la composition lipidique du gamete pour lui permettre d’acquerir une fluidite membranaire essentielle a la fecondation. Les resultats presentes dans cette these mettent en evidence l’importance de l’homeostasie lipidique epididymaire pour la maturation lipidique des spermatozoides et l’acquisition du pouvoir fecondant. Au niveau moleculaire cette homeostasie lipidique est regulee par les isoformes α et β des LXRs, les recepteurs nucleaires des oxysterols (NR1H3 et NR1H2, respectivement). Un regime alimentaire enrichi en cholesterol chez des souris jeunes invalidees pour les LXRs entraine une infertilite avec une atteinte specifique de l’epididyme. La maturation epididymaire des spermatozoides est alors alteree, entrainant des defauts de compositions lipidiques et proteiques de la membrane plasmique spermatique. Ces defauts ont des repercussions deleteres sur la capacitation, issues de perturbations des flux calciques et de la tyrosine phosphorylation. En plus de leurs repercussions endocriniennes, les dyslipidemies semblent egalement affecter la maturation post-testiculaire. Ces resultats sont a considerer dans le cadre des protocoles de PMA puisque le bilan lipidique plasmatique ne fait pas partie des examens classiques des couples en PMA. Or en France, 55% des hommes entre 30 et 54 ans sont atteints d’une dyslipidemie. Ces desordres metaboliques lipidiques pourraient alterer la maturation post-testiculaire des gametes, provoquant un certain nombre d’infertilites et/ou d’echecs en PMA.
A multilevel statistical toolkit to study animal social networks: Animal Network Toolkit (ANT) R package

How animals interact and develop social relationships regarding, individual attributes, sociodemographic and ecological pressures is of great interest. New methodologies, in particular Social Network Analysis, allow us to elucidate these types of questions. However, the different methodologies developed to that end and the speed at which they emerge make their use difficult. Moreover, the lack of communication between the different software developed to provide an answer to the same/different research questions is a source of confusion. The R package Animal Network Toolkit (ANT) was developed with the aim of implementing in one package the many different social network analysis techniques currently used in the study of animal social networks. Hence, ANT is a toolkit for animal research allowing among other things to: 1) measure global, dyadic and nodal networks metrics; 2) perform data randomization: pre-network and network (node and link) permutations; 3) perform statistical permutation tests. The package is partially coded in C++ for an optimal coding speed, and it gives researchers a workflow from raw data to the achievement of statistical analyses, allowing for a multilevel approach: from individual position and role within the network, to the identification of interaction patterns, and the analysis of the overall network properties.
Effects of Land Use on Hellbenders (Cryptobranchus alleganiensis) at Multiple Levels and Efficacy of Artificial Shelters as a Monitoring Tool

Understanding how species respond to anthropogenic changes and why species respond in the way that they do can help focus conservation planning. Hellbenders (Cryptobranchus alleganiensis) are a freshwater species of increasing conservation concern that are suspected to have declined due to loss of forest cover. However, quantitative evidence of land use effects on hellbenders is lacking. I used a multilevel approach to understanding whether hellbenders respond to land use by examining physiological indices, demographics and patterns of species occurrence as endpoints. My study area included two major river drainages in Virginia which mark a largely understudied portion of the species’ range. In Chapter I, I described hellbender distribution and tested the hypothesis that hellbenders would be more likely to occur in heavily forested landscapes. Surprisingly, hellbenders occupied a relatively wide land use gradient (range = 50-90% forest in an upstream catchment) and current land use was an unreliable predictor of occurrence. In Chapter II I examined hellbender abundance and demographics at a subset of study sites stratified across a land use gradient. Abundance of sub-adult/adult hellbenders increased as forest cover increased in collective upstream riparian areas, primarily as the result of increased recruitment of new adults to local populations (rather than increased apparent survival of adults). Populations in lesser forested areas were declining and composed largely of relatively old adults, indicating that land use can lead to changes in hellbender distribution given sufficient time. In Chapter III, I examined three indices of
Regulation of Chromosome Segregation and Cohesion by the deubiquitinase USP37

During the cell cycle, replicated chromosomes must remain paired until cell division in mitosis. This pairing is mediated by the conserved cohesin complex. During mitosis, a bipolar spindle facilitates the equal transmission of genetic material to two daughter cells. This fidelity in chromosome segregation protects cells against chromosomal instability and aneuploidy, which can contribute to development and progression of a variety of diseases, including cancer and Down syndrome. In this thesis, I present an RNA interference screen for novel regulators of bipolar spindle assembly, which led to the finding that the deubiquitinase USP37 regulates chromosome segregation during mitosis. Although the role of ubiquitin ligases (e.g. APC/C, SCF complex) in cell cycle regulation is known, the role of deubiquitinases is less well characterized. Accordingly, my thesis focuses on understanding the molecular mechanisms by which USP37 regulates chromosome segregation. In Chapter 3, I present evidence that USP37 regulates the NDC80 (HEC1) complex in kinetochore-microtubule attachment during chromosome segregation in mitosis. In Chapter 4, I present evidence that USP37 regulates chromatid cohesion. Specifically, USP37 regulates the deubiquitylation and stability of chromatinassociated WAPL, a protein required for removal of cohesin from chromosome arms in early
Patrones de diversidad y estructura genética en especies antárticas y subantárticas de Nacella (Nacellidae)

Resumen La biogeografia del Oceano Austral es el resultado de la compleja interaccion de distintas fuerzas macroevolutivas sobre su particular biota en el tiempo y en el espacio. Los procesos de tectonica de placas que derivaron en la separacion de los continentes junto al establecimiento de la Corriente Circumpolar Antartica y el enfriamiento paulatino de la region desde el Eoceno se han asociado directamente a la composicion, abundancia y distribucion de su fauna marina bentonica. Mas recientemente, los procesos glaciales del Cuaternario impactaron fuertemente la distribucion de la variacion genetica intraespecifica en una variedad de taxones. El genero Nacella (Patellogastropoda: Nacellidae) incluye 11 especies nominales que se distribuyen en distintas provincias del Oceano Austral. En este estudio se compararon los patrones de diversidad y estructura genetica a nivel del DNA mitocondrial de cuatro especies de Nacella provenientes de Antartica maritima (Nacella concinna), Sudamerica (Nacella magellanica) y de dos islas ubicadas en el sector Indico del Oceano Austral: Kerguelen (Nacella edgari) y Marion (Nacella delesserti). Bajos niveles de diversidad genetica y ausencia de estructura caracterizan a cada una de las especies analizadas lo que muestra el tremendo impacto del avance y retroceso de los hielos sobre la demografia de todas ellas. Baja diversidad haplotipica, genealogias cortas y las demografias especificas sugieren la ocurrencia de efectos poblacionales mas severos en Antartica maritima e Isla Marion que en el resto de las regiones subantarticas. Abstract The biogeography of the Southern Ocean is the result of the complex interaction of different macroevolutionary forces over its particular biota in space and time. Plate tectonics processes derived in the separation of the continents, together with the establishment of the Antarctic Circumpolar Current and the gradual cooling of the region since the Eocene, are directly associated to the composition, abundance, and distribution of its marine benthic fauna. More recently, glacial processes of the Quaternary strongly impacted the distribution of the intraspecific genetic variation in different taxa. The genus Nacella (Patellogastropoda: Nacellidae) includes 11 nominal species that are distributed in different provinces of the Southern Ocean. In this study, we compared mitochondrial DNA patterns of genetic diversity and structure in four Nacella species from maritime Antarctica (Nacella concinna), South America (Nacella magellanica), and two islands located in the Indian sector of the Southern Ocean: Kerguelen (Nacella edgari), and Marion (Nacella delesserti). Low levels of genetic diversity and absence of genetic structure characterize each one of the analyzed species showing the major impact of ice advances and retreats over the species’ demographies. Low haplotypic diversity, short genealogies and specific demographies suggest the occurrence of more severe population effects in maritime Antarctica and Marion Island than in the rest of the subantarctic provinces.
Characteristics of Fruit Quality of Peach Cultivars and Hybrids in the Steppe Crimea

The study of peach fruit quality and biochemical composition of cultivars and hybrids were conducted in terms of the steppe zone of Crimea. A total of 40 cultivars and hybrids from five periods of ripening were analyzed for content of basic biochemical components: solids, sugars, acids, polyphenolic compounds and vitamin C. The main fruit quality parameters: the size, the attractive appearance, the consistency flesh, the stone adherence to flesh, taste and others have been evaluated. As a result of studies peach cultivars with a high content of sugar in the fruit under the steppe Crimea have highlighted: Kremlyovskiy (13.6), Regina (13.2), Velvet (12.9), hybrids C7/38 (13.1) and C4/57 (12.9). Cultivars and hybrids of peach 10607, C1/227 C7/38, C7/6, C8/162, С4/147, C16/87, C4/64, Early Red Haven, Miorita, 7/221, Kremlyovskiy, 10848 are characterized by the best biochemical and morphological indices of fruits. They are recommended for State cultivar testing or use in breeding work to improve the quality of peach fruits.
Phylommand - a command line software package for phylogenetics

Phylogenetics is an intrinsic part of many analyses in evolutionary biology and ecology, and as the amount of data available for these analyses is increasing rapidly the need for automated pipelines to deal with the data also increases. Phylommand is a package of four programs to create, manipulate, and/or analyze phylogenetic trees or pairwise alignments. It is built to be easily implemented in software workflows, both directly on the command prompt, and executed using scripts. Inputs can be taken from standard input or a file, and the behavior of the programs can be changed through switches. By using standard file formats for phylogenetic analyses, such as newick, nexus, phylip, and fasta, phylommand is widely compatible with other software.
Valoración de cepas silvestres de Azospirillum sp. y Gluconacetobacter sp. como promotoras de crecimiento vegetal

Los esquemas actuales de nutricion vegetal implican el uso extensivo de fertilizantes quimicos que acarrean consigo numerosos efectos secundarios entre los cuales destacan la contaminacion de los mantos freaticos y la progresiva erosion del suelo, lo cual refleja la imperiosa necesidad de alternativas que permita reemplazar de forma eficiente aquellos esquemas. La alternativa propuesta por este trabajo, desarrollado en las instalaciones de la Universidad Tecnologica de Izucar de Matamoros en 2013, es impulsar el uso de biofertilizantes elaborados a base de bacterias autoctonas de la region, para lo cual, se realizaron ensayos in vitro e in planta que demuestran su efecto como promotores de crecimiento vegetal por medio de mecanismos como la fijacion biologica de nitrogeno (FBN) y la produccion de reguladores de crecimiento. Se aislaron dos cepas empleando medios de cultivo carentes de nitrogeno, ambas caracterizadas de forma parcial, la primera de ellas pertenece al genero Azospirillum denominada M1 aislada de raices de Jatropha, la segunda del genero Gluconacetobacter denominada G1 aislada de raices de cana de azucar. En los ensayos realizados en esquejes de pitahaya, plantas de maiz y cana de azucar tanto in vitro como in planta se observo que ambas cepas poseen la capacidad de promover la formacion de raices laterales y que el numero de estas es mayor en comparacion con testigos no inoculados, del mismo modo, se observo que la cepa M1 posee un efecto semejante en rizogenesis al de la cepa G1 y que la coinoculacion de ambas cepas en estos modelos vegetales.
The eggspots of cichlids: Evolution through sensory exploitation? Die Eiflecken bei Cichliden: Evolution durch Nutzung der Sinne?

Many cichlid species independently evolved mouthbreeding as a highly specialised brood care behavior. Egg dummies, resembling the ova of the corresponding species, formed of various parts of the body can be found in different lineages of mouthbreeding cichlids. Most abundant are eggspots, which are conspicuously yellow spots developed on the anal fin of males. Eggspots were believed to have evolved to deceive the females during spawning, thus maximising the fertilisation rates of the males, but empirical studies showed that the presence of eggspots has no effect on fertilisation rates. However, eggspots seem to play a role during mate choice of females. Here, the role of sexual selection in the evolution of eggspots is reviewed and eggspots are hypothesised to have evolved through sensory exploitation. The sensory exploitation hypothesis can explain the shortcomings of previously suggested hypotheses on the evolutionary origin of eggspots.
Upper range limit establishment after wildfire of an obligate-seeding montane forest tree fails to keep pace with 20th century warming

How species respond to climate change at local scales will depend on how edaphic and biological characteristics interact with species physiological limits and traits such as dispersal. Obligate seeders, those species that depend on fire for recruitment, have few and episodic opportunities to track a changing climate envelope. In such cases, long-distance seed dispersal will be necessary to take advantage of rare recruitment opportunities. We examine recruitment patterns and seedling growth below, at and above the timberline of an obligate-seeding Australian montane forest tree (Eucalyptus delegatensis) after stand-replacing fire, and place these changes in the context of regional warming. We use two methods to detect whether E. delegatensis can establish and persist above the timberline after stand-replacing wildfire in montane forests in south-east Australia. First, we examine establishment patterns by using belt transects at six sites to quantify how changes in post-fire recruit density with increasing distance above the timberline seven years post-fire. Second, to determine whether dispersal or physiological constraints determine post-fire establishment patterns, we transplanted seedlings and saplings into bare ground above (100 m elevation), at, and below (50 m elevation) timberline 18-months after fire. We monitored seedling growth and survival for one growing season. There was minimal upslope migration of the species after fire with most saplings observed near seed-bearing timberline trees, with only occasional outpost saplings. Transplanted seedlings and saplings survived equally well across one growing season when planted above existing timberlines, relative to saplings at or below the timberline. Seedling and sapling growth rates also did not differ across these location, although seedlings grew at much faster rates than saplings. These findings suggest that upslope growing season conditions are unlikely to limit initial range expansion of trees after fire. Instead, it is more likely that seed traits governing dispersal modulate responses to environmental gradients, and global change more generally.
A proposed framework for participatory forest restoration in semiarid areas of North Africa

Ecological restoration is a suitable tool to revert land degradation in semiarid areas. Social participation is increasingly considered as a guarantee for the long‐term success and sustainability of restoration projects. In rural areas of North African countries, experiences of participatory restoration are still not frequent, and poverty and illiteracy with top‐down approaches boost land‐use conflicts and raise skepticism toward restoration programs. We developed a framework for forest restoration based on knowledge share, trust, and active stakeholder participation in all restoration steps. The framework was tested through a demonstrative project aimed at restoring Tetraclinis articulata forests in a semiarid area of North Morocco, in which scientists, managers, and local stakeholders were involved in all steps of the restoration process: identification of restoration priorities, assessment of land‐use options, definition of the restoration procedure, participatory plantation, evaluation, surveillance, and monitoring. In a 1 ha plot, 250 plants were planted by 90 participants in a spirit of knowledge exchange, mutual aid, environmental education, and social solidarity. After 2 years, the plot remains intact, free of any act of vandalism and grazing, and shows signals of improved ecosystem functioning. A wider application of the proposed framework in current restoration strategies will enhance our understanding of the factors behind social acceptance and support for restoration projects.
Temperature and precipitation effects on breeding productivity of some passerines – a multivariate analysis of constant effort mist-netting data

Abstract The relationship between the temperature, the precipitation of the breeding season’s months, and the annual proportions of the first year birds such as the indicators of the breeding success were examined by canonical correspondence analysis (CCA) having targeted nine common passerine species. The results of our study have shown that the high April and May temperature has been favourable for the breeding of the partial and the short-distance migrants, the common blackbird (Turdus merula) and the Eurasian blackcap (Sylvia atricapilla). This is confirmed by the fact that the highest annual capture (164) of the hatching year of the Eurasian blackcap was in 2009, when there was the mildest April during the study period (13.57°C), while the lowest annual capture (15) was in 2002, when there was the second coolest April (9.78°C). The common chiffchaff (Phylloscopus collybita) was a wet spring-tolerant species. There was negative correlation between April, May, June temperature and proportion of young great tit. The relationships between the annual captures of first year birds and the climate variables could not be identified with the methods used for the European robin (Erithacus rubecula), the common whitethroat (Sylvia communis), the lesser whitethroat (Sylvia curruca) and the blue tit (Parus caeruleus). The temperature in July was the most important climate factor for the breeding success of the long-distance migrant European pied flycatcher (Fycedula hypoleuca).
Age Related Tissue Fibrosis During Fracture Repair Is Mediated by Wnt/β-catenin Signaling

The regenerative potential of tissue injury declines with age. Recently, a significant role for Wnt/β-catenin signaling has been shown in tissue specific stem cell aging, leading to increased tissue fibrosis. Wnt/β-catenin signaling regulates the differentiation of multipotent mesenchymal stem cells into osteoblasts during fracture repair. We investigated the potential role of dysregulated Wnt/β-catenin signaling in delayed fracture union and tissue fibrosis in the elderly. Old mice displayed increased total β-catenin protein levels at 4 and 7 days post-fracture and tissue fibrosis at 14 and 21 days post-fracture compared to young mice. Furthermore, treatment with a pharmalogical agent decreased total β-catenin protein levels in the fracture callus at 4 days post-fracture and prevented tissue fibrosis at 21 days post-fracture. Our data suggests that dysregulated Wnt/β-catenin signaling in the elderly contributes to delayed fracture repair and tissue fibrosis and offers a potential therapeutic strategy to improve fracture outcome in the
An Overview of Purification Strategies

A New Look at Xylanases Interest on xylanases from different sources has increased markedly in the past decade, in part because of the application of these enzymes in the pulp and paper industry. Purity and purification costs are becoming important issues in modern biotechnology as the industry matures and competitive products reach the mar- ketplace. Thus, new paths for successful and efficient xylanase recovery have to be followed. This article reviews the isolation and purification methods used for the recovery of microbial xylanases. Origins and applications of xylanases are described, highlighting the special features of this class of en- zymes, such as the carbohydrate-binding domains (CBDs) and their importance in the development of affin- ity methodologies to increase and facilitate xylanase purification. Implications of recombinant DNA technology for the isolation and purification of xylanases are evaluated. Several purification procedures are analyzed, taking into consideration the sequence of the methods used in each and the number of times each method is used. New directions to improve xylanase separation and purification from fermentation media are described. Index Entries: Xylanase; purification strategies; CBD; biospecific affinity.
In Vitro Testing of the Insecticide Reldan 22 on Swine Oocyte Maturation

Chlorpyrifos (Reldan 22) is an widely used insecticide for the control of insect pests in agricultureand in residential areas. It is classified as moderately toxic by the United States Environmental Protection Agency and has been quantified in human biological fluids. Given that the use of porcine and bovine models for testing chemicals has increased recently we designed an experiment to test the toxicity of several Chlorpyrifos concentrations and investigate its effects on maturation of swine oocytes. Swine oocytes from ovaries harvested in a commercial slaughterhouse were cultured for 44-45h in M199 supplemented with the following Reldan 22 concentrations: 0.1, 0.5, 1 or 2 Âµg/ml. Cumulus oophorous expansion was assessed and oocytes were denuded and stained with 1 Âµg/ml fluorescein diacetate to estimate viability. Afterwards, oocytes were fixed in a 60% methanol/DPBS solution and stained with 50 Âµg/ml propidium iodide to observe the DNA stage. Differences were analysed by the analysis of variance and interpreted using the Tuckey test. Our research shows that the insecticide Reldan 22 Â® stimulated cumulus expansion to an extent but reduced oocyte viability which was accompanied by an increase in the number of immature oocytes and a decrease in the percentages of gametes that resumed meiosis. This leads us conclude that its presence in the oocyte environment is toxic for development at concentrations 0.5, 1 and 2 Âµg/ml.