Miracle-dz/UniFAR-FTUs huggingface dataset:
ARN régulateurs de Staphylococcus aureus : Rôle de RsaA dans la formation du biofilm et de la capsule, niveaux d'expression des ARN dans les prélèvements cliniques

Staphylococcus aureus est responsable de nombreuses infections nosocomiales etcommunautaires dont la diversite est liee a l’expression de nombreux facteurs de virulence.L’expression de ces facteurs est temporellement coordonnee au cours de l’infection par desfacteurs de transcription, des systemes a 2 composants et des ARN regulateurs (ARNnc). Ungrand nombre d’ARNnc potentiels a ete predit dans le genome de S. aureus mais leur fonctionreste meconnue.L’objectif premier de ce travail a ete de caracteriser le role dans la regulation de la virulence del’un des ARNnc identifies par notre equipe, RsaA. Des approches phenotypiques in vitro ontpermis de demontrer que RsaA active la formation du biofilm et reprime la synthese de lacapsule bacterienne, avec une incidence sur l’opsonophagocytose de la bacterie et sur soninternalisation dans les macrophages. Au niveau moleculaire, RsaA reprime la traduction dufacteur de transcription MgrA, represseur de la formation de la biofilm et activateur de lacapsule, par un mecanisme de type antisens entre RsaA et l’ARNm mgrA. Parallelement, RsaAreprimerait l’operon yabJ-spoVG, activateur de la synthese de capsule. Ainsi, RsaA active laformation de biofilm et reprime la synthese de capsule.Le second objectif de ce travail a ete de caracteriser l’expression in vivo de RsaA, E, G, H ainsique l’ARN III dans des prelevements d’infections aigues (abces cutanes), chroniques (crachatsde patients mucoviscidiques) ou de portages nasales. L’etude de l’expression de ces ARN parRT-PCR, a permis de montrer que tous ces ARN sont exprimes avec une grande variabilite dansles prelevements infectieux par rapport aux prelevements de portages.
Knowing but not doing: Quantifying the research-implementation gap in conservation paleobiology

Conservation paleobiology aims to provide a longer-term perspective on environmental problems to inform decisions about natural resource conservation. As such, conservation paleobiology research falls short when geohistorical data and insights do not inform conservation practice, contributing to the well-known idea that a “gap” exists between the production and use of science in the environmental realm. Our study quantified the extent of this research-implementation (or knowing-doing) gap through a systematic literature review and survey questionnaire. We determined whether empirical studies in conservation paleobiology with a link to conservation, management, or restoration documented the use of geohistorical data to implement some form of action or if there was a specific mention of how the geohistorical data could be used in theory. Results indicate that “applied” conservation paleobiology has a poor record of translating research into action. Tangible conservation impacts were evident in only 10.8% of studies. Over half of these studies included coauthors affiliated with a conservation organization. Among the studies coded as having a theoretical application, 25.2% specified how the geohistorical data could be implemented to enhance conservation, management, or restoration actions. All studies documenting action used geohistorical data from the geologically recent past where the species and habitats are familiar to those found today. Drawing insights from the bright spots we identified, we offer some practical suggestions to narrow the gap between knowing and doing in conservation paleobiology.
Papel del coactivador PGC-1α en el balance energético. Importancia en la producción de bovinos de engorda.

The importance of dietary fat in the expression of multiple genes is clear, in the case of beef cattle, fat in the form of fatty acids (saturated or unsaturated), vitamin A (mainly retinoic acid), or carotenoids (β-carotene, lutein, licopen and their metabolites), is obtained constantly from the dietary feed or from pasture. This review tries to summarize the advances in the study of some of the transcription factors and their co-regulators, specifically coactivator PGC-1, which has been observed to affect the transcription of genes involved in energy homeostasis. The capacity of dietary lipids or their metabolic products, to influence on PGC-1α, due in part to the presence of an element of answer to PPAR in its genic promoter, which appears to be conserved in different species of mammals including bovines. It might be important to find nutrients or other types of compounds, that could act as ligands of the factors of transcription of specific genes, that control metabolic processes such as gluconeogenesis and lipolysis in rumiants so in a near future they would contribute to improve the production in the specie.
The characterization of the caleosin gene family in Triticeae and their role in G-protein signalling and Identification and characterization of rye genes silenced in allohexaploid triticale: A bioinformatic study

ABSTRACT The characterization of the caleosin gene family in Triticeae and their role in G-protein signalling and Identification and characterization of rye genes silenced in allohexaploid triticale: A bioinformatic study Hala Badr Abdel-Sadek Khalil, Ph.D. Concordia University, 2013 The caleosin genes encode proteins with a single conserved EF hand calcium-binding domain and comprise small gene families found in a wide range of plant species. In this study, Clo3, a member of caleosin family in hexaploid wheat (Triticum aestivum), has been shown to play an important role in signaling by both in vivo and in vitro analyses of its interaction with Gα, the alpha subunit of heterotrimetric GTP binding protein. This interaction increased the GTPase activity of Gα by approximately 25%. Eleven paralogous groups of caleosins, which comprise a total of thirty-four caleosin genes, have been assembled and identified using the T. aestivum GenBank EST database and ten gene family members were assembled from Secale cereale 454-cDNA sequences. The analysis of caleosin gene expression was assayed by RNA-Seq analysis of 454 sequence sets and members of the gene family were found to have diverse patterns of gene expression in the nine tissues that were sampled in rye and in triticale, a synthetic polyploid species derived from durum wheat (Triticum turgidum) and rye (Secale cereale). The impact of the polyploidization event on rye genes in the triticale background was investigated using both caleosin genes and whole transcriptome comparisons. The high-throughput cDNA sequence comparison between the diploid rye and the hexaploid triticale detected suppression of expression of approximately 2% of the rye genes surveyed in the triticale. The expression of 23503 rye cDNA contigs was analyzed in 454-cDNA libraries obtained from anther, root and stem from both triticale and rye as well as in five 454-cDNA data sets created from ovary, pollen, seed, seedling shoot and stigma from triticale. Among these, 112 rye cDNA contigs were found to be totally suppressed in all triticale tissues, although their expression was relatively high in rye tissues. Suppressed rye genes were found to have strikingly low similarity to their closest BASTN matches in a current draft of the wheat genome available through the International Wheat Genome Survey Consortium, IWGSC. The comparison of rye silenced genes to wheat database revealed that 89% of rye genes silenced in triticale do not have a best match in T. aestivum with sequence identity higher than 90%, whereas 59% of random rye contigs had a best hit of 90% or higher in T. aestivum. The comparisons to the draft genomes of Triticum. urartu, and Aegilops. tausshii, the A and D genome donors to T. aestivum, respectively, support the previous observation. PCR assays found that 6 out of 10 candidate suppressed genes were deleted from the triticale genome.
Rhombomere boundaries and hindbrain patterning in the zebrafish.

The vertebrate hindbrain is a segmented structure, divided into repeating segments called rhombomeres, at the interface of which boundary cells are induced as a specific cell type. Previous work has found that, in the zebrafish hindbrain, there is a distinctive organisation of glia and neurons along the anterior-posterior axis within each rhombomere, with specific neurons at the centre or boundary regions, separated by a glial curtain adjacent to the boundary. Using molecular markers, I have characterised the organisation of several cell types within each rhombomeres, and found that from 24 hours of development, neurogenesis occurs predominantly adjacent to the rhombomere boundaries, which suggests a role for boundaries in establishing this pattern. The aim of this work was to test a possible patterning role of boundaries, and to establish a genetic hierarchy between boundary genes by carrying out knockdowns of boundary-specific genes. The secreted factor wntl is expressed in dorsal boundaries and is a candidate mediator of a potential signalling role of boundaries. From many lines of evidence in previous work, wntl was known to promote proliferation of neural progenitors and inhibit neuronal differentiation. I found that in the zebrafish hindbrain, however, knockdown of wntl or of the Wnt pathway effector tcj3b causes expansion of boundary-specific markers and loss of neurogenesis in non- boundary regions. Knockdown of rfng, a component of the Notch pathway required for boundary expression of wntl also causes expansion of boundary markers. Wntl is necessary for the expression of ash and ngnl proneural genes, and of delta genes, which in turn block ectopic boundary marker expression. Thus, wntl mediates a lateral inhibition of boundary fate by regulating neurogenesis in hindbrain segments. Taken together with concurrent work in the lab, the model derived from this is remarkably similar to the regulatory interactions occurring at the dorso-ventral boundary of the Drosophila wing imaginal disc, and indicates recruitment of a conserved network of genes in non homologous tissues.
p38δ controls Mitogen- and Stress-activated Kinase-1 (MSK1) function in response to toll-like receptor activation in macrophages

Mitogen- and Stress-activated Kinase (MSK) 1 is a nuclear protein, activated by p38α Mitogen-Activated Kinase (MAPK) and extracellular signal-regulated kinase (ERK1/2), that modulate the production of certain cytokines in macrophages. Using knockout cells and specific kinase inhibitors, we show that, besides p38α and ERK1/2, another p38MAPK, p38δ, mediates MSK phosphorylation and activation, in LPS-stimulated macrophages. Additionally, recombinant MSK1 was phosphorylated and activated by recombinant p38δ, to the same extent than by p38α, in in vitro experiments. Moreover, the phosphorylation of the transcription factors CREB and ATF1, that are MSK physiological substrates, and the expression of the CREB-dependent gene encoding DUSP1, were impaired in p38δ-deficient macrophages. Also, the transcription of IL-1Ra mRNA, that is MSK-dependent, was reduced. Our results indicate that MSK activation can be one possible mechanism by which p38δ regulates the production of a variety of inflammatory molecules involved in immune innate response.
Morphometric characters of the freshwater American crayfish, Orconectes limosus Raf., from the Vistula Lagoon [Poland]

The aim of the present study was to perform an initial characterization of the morphometric parameters of the American crayfish, Orconectes limosus, that occur in the brackish waters of the Polish coastal zone, as well as to present its range of occurrence and rate of expansion in Polish waters. The size of O. limosus occurring in the Vistula Lagoon (2-4 psu) varied from 77.0 mm to 118.0 mm (mean 95.0 ± 8.0 mm). The most numerous class was comprised of specimens measuring from 90.1 to 95.0 mm; this class represented 23% of animals collected. Males and females had similar dimensions and body ratios, while the abdomen width (23.6 ± 2.7 mm) of females was wider than that of males (20.3 ± 2.0 mm). The males had longer and higher chelae that did females of comparable length. Individuals from Vistula Lagoon (4 psu) exhibited a larger maximum body length in comparison with those caught in the freshwater habitats (Lake Wdzydze). The relationship between carapace length and specimen dry weight is represented by the following formula: DW = 0.0072L (r = 0.69). Anna Szaniawska, Monika Normant, Monika Michałowska, Agnieszka Kami ska 196
A função retórica Suporte em português

The paper now presented aims to investigate the relations established by clauses and phrases initiated by the structure alem de [aside from in Portuguese]. Therefore, it assumes as theoretical apparatus the Functional Discourse Grammar (HENGEVELD; MACKENZIE, 2008), in order to analyze occurrences of spoken language, extracted from the "Portugues oral" [oral Portuguese] corpus, organized by the Center of Linguistics of the University of Lisbon, in partnership with the University of Toulouse-le-Mirail and the University of Provence-Aix-Marseille.
A novel signature constructed by super-enhancer-related genes for the prediction of prognosis in hepatocellular carcinoma and associated with immune infiltration

Background Super-enhancer (SE) refers to a regulatory element with super transcriptional activity, which can enrich transcription factors and drive gene expression. SE-related genes play an important role in the pathogenesis of malignant tumors, including hepatocellular carcinoma (HCC). Methods The SE-related genes were obtained from the human super-enhancer database (SEdb). Data from the transcriptome analysis and related clinical information with HCC were obtained from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) database. The upregulated SE-related genes from TCGA-LIHC were identified by the DESeq2R package. Multivariate Cox regression analysis was used to construct a four-gene prognostic signature. According to the median risk score, HCC patients were divided into high-risk and low-risk group patients. Results The Kaplan-Meier (KM) curve showed that a significantly worse prognosis was found for the high-risk group (P<0.001). In the TCGA-LIHC dataset, the area under the curve (AUC) values were 0.737, 0.662, and 0.667 for the model predicting overall survival (OS) over 1-, 3-, and 5- years, respectively, indicating the good prediction ability of our prediction model. This model’s prognostic value was further validated in the LIRI-JP dataset and HCC samples (n=65). Furthermore, we found that higher infiltration level of M0 macrophages and upregulated of CTLA4 and PD1 in the high-risk group, implying that immunotherapy could be effective for those patients. Conclusion These results provide further evidence that the unique SE-related gene model could accurately predict the prognosis of HCC.
Chemoreception in coho salmon (Oncorhynchus kisutch) : aspects of behavior, physiology, and toxicology

approved: Carl B. Schreck Detection of L-serine and D,L-alanine by juvenile coho salmon (Oncorhynchus kisutch) was measured in a twochoice Y-trough. Threshold concentration for olfactory detection of L-serine was 10-8 M for zero-age parr, iO-7 M for yearling parr, 10-5 M for smolts in late April-early May, and 10-6 M for smolts in June. Threshold for the detection of D,L-alanine was 10-7 M for yearling parr, 10-6 M for smolts in late April-early May, and 10-5 M for smolts in June. Zero-age fish adapted to either freshwater or seawater were able to detect L-serine at 10-9 M. In vitro olfactory receptor assays and behavioral experiments were used to examine the specificity of Lserine detection by coho salmon. Of the 10 amino acids tested, L-serine, L-alanine and L-threonine were similar Redacted for Privacy in their ability to compete for the serine receptor site. All three of these amino acids as well as L-histidine elicited behavioral avoidance responses in a 2-choice Ytrough. Behavioral cross-adaptation experiments indicated that the detection of L-serine was inhibited by the adapting amino acids L-serine, L-alanine, and glycine but not by L-threonine, L-aspartic acid, or L-histidine. Classical conditioning experiments showed that serine and alanine were not discriminated from each other although either could be discriminated from L-histidine. These results, taken together, indicate that coho salmon perceive L-serine and L-alanine as identical odors. The olfactory detection of L-serine in a 2-choice Ytrough was inhibited by 2 hr exposures to mercury (Hg) or copper (Cu) but not by zinc (Zn). Upstream swimming behavior, however, was depressed by the presence of Zn as well as Hg or Cu. Of these metals, only Hg strongly inhibited the binding of L-serine to its olfactory receptor. The inability to detect L-serine in the presence of Cu did not result from Cu masking the presence of serine. Chemical speciation calculations suggest that serine-metal complexation was not extensive enough to compromise olfactory detection. Thus, the mechanism of action of Cu is unclear whereas Hg appears to act at the level of the olfactory receptor. The ability to detect and avoid L-serine was not inhibited by a continuous exposure to Zn at 100 or 500 ug/L for 21 days. CHEMORECEPTION IN COHO SALMON (ONCORHYNCHUS KISUTCH): ASPECTS OF BEHAVIOR, PHYSIOLOGY, AND TOXICOLOGY
Effect of Rate, Carrier Volume, and Surfactant on Imazamethabenz Efficacy

Imazamethabenz is a selective herbicide used to control wild oat in small grains. The effects of rate, volume of carrier, and surfactant concentration on the efficacy of this herbicide in controlling wild oat were studied in field experiments. As each of the variables increased, wild oat control increased; the greatest degree of wild oat growth inhibition occurred at the highest herbicide rate, highest volume of carrier, and highest surfactant concentration.
ROLE OF REACTIVE OXYGEN SPECIES IN PLATELET FUNCTION IN NORMAL STATES AND CHRONIC MYELOPROLIFERATIVE DISORDERS

Platelets play a crucial role in physiological and pathophysiological processes such as primary hemostasis and arterial thrombosis. Growing evidence indicates that reactive oxygen species, mainly superoxide generated by transmembrane NAD(P)H oxidase, have a key regulatory role in platelets. They mediate the intracellular signaling pathways activated by growth factors through tyrosine kinase receptors and the bidirectional signaling through integrins, influencing thus platelet activation and subsequent aggregation. In chronic myeloid leukemia, the BCR-ABL tyrosine kinase receptor is constitutively active, kinase inhibitors being currently used as anti-mieloproliferative drugs.
Immunogenetics and polymorphism in a natural population of field voles (Microtus agrestis)

Most of our understanding of immunity has been gained through studies of humans or laboratory rodents. However, such studies do not allow the immune system to be studied in the ecological context in which it has evolved and, as such, they provide a poor model for studying the variation in infectious disease resistance and immune function observed in natural settings. Studies of natural populations have provided fresh insights into the evolution and phenotypic consequences of immunogenetic variation, but have thus far concentrated almost exclusively on genes of the major histocompatibility complex (MHC). As these genes form only a fraction of the vertebrate immune repertoire, there is a need to broaden research in natural populations to include non-MHC genes, in order to gain a more comprehensive understanding of natural selection and immunity. In this thesis, the genetic diversity of a range of non-MHC immune genes was examined in a natural population of field voles (Microtus agrestis L.) in Kielder Forest, UK, which are subject to infection by a range of pathogens. Cytokine genes were the primary focus of this study as they play a central role in regulating the immune response but have rarely been studied in wild species. I examined the hypothesis that, as cytokines are crucial to immunity, variation within these genes may be under selection within populations and between species, and may mediate phenotypic differences between individuals in parasite resistance and immune function. Coding regions from nine cytokine and three other non-MHC vole genes were sequenced, yielding 6.6 Kb of sequence data and 26 SNPs (1 per 255 bp). Three cytokine genes (Il1b, Il2, and Tnf) exhibited patterns of polymorphism consistent with balancing selection maintaining genetic diversity, including an excess of intermediate frequency mutations and more even allele frequencies than one would expect under neutrality. Polymorphism within Il1b and Il2 was also consistently associated with variation in parasite resistance, providing evidence that pathogens are the selective force driving the maintenance of genetic diversity at these loci. In addition, Il1b and Il2 exhibited repeated associations with variation in host immune phenotype, while the Il12b gene was associated both with variation in pathogen resistance and with altered expression levels of Il1b and Il2. Variation in immune function, mediated through the cytokine network, is therefore likely to contribute to parasite resistance in the field vole. This work is the first to show that variation in cytokine genes of a natural population can be maintained by selection, and that this variation can lead to phenotypic variation in parasite resistance and immune function. More broadly, this thesis demonstrates that wild rodents are an excellent model to help us bridge the gap in our understanding between the mechanistic insights gained through studies on laboratory rodents and the variation in infectious disease susceptibility and immune function observed in nature.
Distinct Roles of the IκB Kinase α and β Subunits in Liberating Nuclear Factor κB (NF-κB) from IκB and in Phosphorylating the p65 Subunit of NF-κB*

Phosphatidylinositol 3′-kinase (PI3K) and the serine/threonine kinase AKT have critical roles in phosphorylating and transactivating the p65 subunit of nuclear factor κB (NF-κB) in response to the pro-inflammatory cytokines interleukin-1 (IL-1) and tumor necrosis factor (TNF). Mouse embryo fibroblasts (MEFs) lacking either the α or β subunit of IκB kinase (IKK) were deficient in NF-κB-dependent transcription following treatment with IL-1 or TNF. However, in contrast to IKKβ-null MEFs, IKKα-null MEFs were not substantially defective in the cytokine-stimulated degradation of Iκβα or in the nuclear translocation of NF-κB. The IKK complexes from IKKα- or IKKβ-null MEFs were both deficient in PI3K-mediated phosphorylation of the transactivation domain of the p65 subunit of NF-κB in response to IL-1 and TNF, and constitutively activated forms of PI3K or AKT did not potentiate cytokine-stimulated activation of NF-κB in either IKKα- or IKKβ-null MEFs. Collectively, these data indicate that, in contrast to IKKβ, which is required for both NF-κB liberation and p65 phosphorylation, IKKα is required solely for the cytokine-induced phosphorylation and activation of the p65 subunit of NF-κB that are mediated by the PI3K/AKT pathway.