Miracle-dz/UniFAR-FTUs huggingface dataset:
Linking fish consumption patterns and health risk assessment of mercury exposure in a coastal community of NW Mexico

ABSTRACT We aimed at characterizing the methylmercury (MeHg) exposure through fish consumption in two populations (common general and fishing-related population (FRP)) using a probabilistic health risk assessment in children, women of childbearing age, and adults in Mazatlán. The hazard quotients (HQs) were obtained from fish consumption, defined through a survey, and the levels of mercury in fishery products, obtained from published information. The average fish ingestion rate (IRfood) was higher in the FRP (167.85 g d−1) than in the general population (GP) (140.9 g d−1). However, HQs were significantly (p < 0.05) higher in the GP (ranging from 0.18 to 10.91) compared to the FRP (0.20 to 2.48); significant differences were also found among groups of both populations. Remarkably, children in both populations exhibited the highest proportions of risk, reaching up to 97% in GP. For all populations, fish consumption was the most important variable influencing MeHg exposure. Overall, for MeHg exposure, there is no safe level of fish consumption without risk, and actions should be taken to mitigate possible risk; further research with current data is needed to assess potential health risks associated with MeHg exposure, particularly in children.
Evidence of cytotoxic activity against mammalian red blood cell of Na+ channel neurotoxin (AE1) from sea anemone (actinia equina)

The diversification of anthozoan toxins played an important role in the ability to colonize various ecological niches. In this study we evaluated the hemolytic activity of HPLC separated fraction of tentacle extracts of sea anemone Actinia equina. Toxic components from acid tissue tentacle extracts were investigated by size exclusion and reverse phase HPLC to characterize cytolytic molecules. A novel low molecular weight active fraction was sequenced by MALDI TOF analysis and a protein correspondent to 5.4 kDa Sodium channel neurotoxin (Ae1) from A. equina was identified. Synthetic Ae1 was assayed and it showed an hemolytic activity against mammalian erythrocytes in a dose dependent manner. Cytolytic activity in addition to neuro-inhibitory function could be a further property of Ae1 toxin repertoire.
Dynamical Formalism for Assessment and Projection of Carrying Capacity in Different Socio-Climatic Scenarios

Increase in demand, decline in primary resources and impact of climate change make agricultural sustainability a complex function of many variables. A major gap is a consistent and quantitative formulation for assessment and projection of sustainability. We consider agricultural self-sustainability, defined as the condition of minimum food requirement from domestic production, and present a dynamical model of evolution of its constrained dynamics. The model is then applied to estimate and project agricultural self-sustainability, carrying capacity and import requirement with India as a case study in different socio-climatic scenarios. Unconstrained productivity is considered to determine technology demand for different scenarios.
Organochlorine pesticides in green sea turtles (Chelonia mydas) with and without fibropapillomatosis caught at three feeding areas off Brazil

Many factors threaten the survival of marine turtles, such as incidental capture by fisheries, habitat degradation, pollution and diseases. One of the most important diseases is fibropapillomatosis (FP), characterized by the development of benign skin tumours. FP predominantly affects juvenile green sea turtles (Chelonia mydas) and involves a complex multifactorial aetiology. For several years, it has been noted that the prevalence of FP tends to be higher in marine environments under the influence of human activities, leading to the hypothesis that environmental pollutants play a role in the epidemiology of this disease. Organochlorine compounds (OCs) are persistent organic pollutants with immunosuppressive and carcinogenic effects in humans and wildlife. OC levels (α-BHC, β-BHC, α-endosulphan, β-endosulphan, endosulphan sulphate, pp′-DDD, op′-DDD, pp′-DDE, op′-DDE, heptachlor, dicofol and mirex) were quantified through gas chromatography with a micro-electron capture detector (GC-μECD) in liver and fat samples from 64 juvenile green sea turtles. Specimens with and without FP were analysed, after being caught at three feeding areas off the Brazilian coast: Ubatuba, Praia Grande and Vitória. OC levels were comparable to those observed in similar studies, and no consistent difference was observed between sea turtles with and without FP. This study helps to elucidate the contamination profile in sea turtles caught at feeding areas off Brazil and confirms that green sea turtles are exposed to OCs, which may play a negative role in the health of this species.
Global proteome response of Escherichia coli BL21 to production of human basic fibroblast growth factor in complex and defined medium

The global proteome response toward recombinant protein production in Escherichia coli BL21 (DE3) grown in complex and defined medium was analyzed. Overproduction of human basic fibroblast growth factor (hFGF‐2), a difficult‐to‐fold protein, led to a reconstruction of the bacterial proteome. For example, heat shock chaperones were highly upregulated, especially when production occurred during fast growth in complex medium. Although heat shock chaperones increased to higher levels in complex medium more hFGF‐2 accumulated within inclusion bodies indicating that the capacity to chaperone protein folding was not sufficient for high speed production. In both types of media, cellular proteins from substrate transport systems, central metabolic pathways, and by‐product uptake (e.g. acetate) were downregulated. This downregulation was connected to growth inhibition and metabolic perturbations. For example, during production in complex and defined medium acetate reassimilation and glucose uptake, respectively, were severely hampered. Cellular proteins for degradation of less favorable substrates, elimination of reactive oxygen species, and DNA protection were also downregulated in response to hFGF‐2 production. The decrease of proteins involved in transport, central metabolic pathways, and general cell protection was more pronounced in the fast producing culture in complex medium than in the slow producing culture in defined medium. In general, production of hFGF‐2 seems to interfere with the adaptation process to changing growth conditions, in this case the adaptation from exponential growth to stationary phase.
Improved coastal hydrodynamic model offers insight into surface and groundwater flow and restoration objectives in Biscayne Bay, Florida, USA

Biscayne Bay, a marine lagoon along the southeast Florida coast, has been affected by altered freshwater input due to water management construction features and operations. The Comprehensive Everglades Restoration Plan aims to improve the quantity, quality, timing, and distribution of freshwater flow through central Florida to the southern coasts and to restore nearshore estuarine conditions in Biscayne Bay. The Biscayne Bay Simulation Model (BBSM) is used to evaluate the effects of proposed changes to freshwater flow on salinity in the bay. However, a recent version of the model has left out the groundwater component due to uncertainty in its quantity, a critical shortcoming considering the porous substrate connecting the bay to inland freshwater sources and historic evidence of fresh groundwater discharge. As a result, the BBSM had been unable to reproduce mean salinity and salinity variability along the shoreline. In the present effort, salinity data from an expanded set of monitoring stations were used to estimate the quantity of the fresh groundwater discharge component. Adjustments in friction in the shallow nearshore regions were also made to increase salinity variability to mimic natural conditions. The result, referred to as BBSM version 4, has improved salinity behavior in the critical nearshore region while maintaining previous salinity performance mid-bay. A substantial coastal freshwater component was required to simulate nearshore salinity during portions of the year. This is an interesting finding that suggests groundwater and other freshwater sources along the coast, including convection driven precipitation events, may have been underestimated and require further investigation.
Seasonal variation and potential roles of dark septate fungi in an arid grassland

ABSTRACT High temperatures and extended drought in temperate and tropical arid ecosystems promote the colonization of diverse microenvironments by dark septate fungi (DSF). These fungi contribute to soil nutrient cycling, soil stabilization, and plant survival, but the roles of individual DSF species, their distributions, and their community diversity are poorly understood. The objective of this study was to evaluate the distribution, seasonal variation, and potential roles of DSF on plant growth. We collected biocrust (lichen-, moss-, and cyanobacterium-dominated biocrusts) soils at different depths and rhizosphere soils from two grasses, Bromus tectorum and Pleuraphis jamesii, in an arid grassland near Moab, Utah, USA. Seasonal variation of DSF was evaluated using culture-based approaches and compared with fungal community profiles from next-generation sequencing (NGS). Culturing showed that DSF were 30% more abundant in biocrusts compared with the focal rhizospheres. The abundance of DSF varied seasonally in belowground samples (rhizosphere and below-biocrust), with a significant increase during the summer months. Pleosporales was the dominant order (35%) in both biocrust and rhizosphere soils out of 817 isolated fungi. Dominant DSF genera in culture included Alternaria, Preussia, Cladosporium, Phoma, and an unknown Pleosporales. Similar results were observed in biocrust and rhizosphere soils NGS. Further, seed germination experiments using dominant taxa were conducted to determine their potential roles on germination and seedling growth using maize as a model plant. Cladosporium and unknown Pleosporales isolates showed plant growth–promoting ability. The variation in abundance of DSF, their differential occurrence in different microenvironments, and their ability to grow in a xerotolerant medium reflect adaptations to summer environmental conditions and to changes in the abundance of organic matter, as well as a potential increase in plant investment in these fungi when heat and drought stresses are more severe.
Identification and characterization of transcription factors involved in morphogenesis in the human fungal pathogen Candida albicans

Candida albicans est un champignon commensal de l’homme, mais aussi l'un des agents pathogenes fongiques les plus repandus. C. albicans alterne entre formes levure et filamenteuses (pseudohyphes ou hyphes), une transition morphologique declenchee par divers signaux environnementaux et jouant un role important dans la virulence. Un reseau de regulation complexe, faisant intervenir de nombreux facteurs de transcription, gouverne la transition levure-hyphe. L’objectif de ce travail de these etait d’etudier la fonction et l’interaction avec ce reseau de regulation de deux facteurs de transcription, Skn7 et Orf19 . 217. L’identification des circuits de transcription gouvernes par Skn7, par des approches globales d’etude de la transcription et de la fixation a la chromatine, indique un double role dual dans la regulation de la reponse au stress osmotique/oxydatif et de la croissance filamenteuse. L’analyse des interactions genetiques a revele des relations fonctionnelles entre Skn7 et les principaux regulateurs de la morphogenese. En outre, Skn7 est indispensable pour limiter l'accumulation d'especes reactives a l'oxygene (ROS) pendant la croissance filamenteuse sur milieu solide. La caracterisation de mutants specifiques de Skn7 a mis en evidence un decouplage de cette derniere fonction et de la fonction de Skn7 dans la morphogenese.Orf19.217 est implique dans la virulence de C. albicans, mais sa fonction biologique reste incertaine. Notre etude montre que Orf19.217 regule divers processus, tels que la morphogenese, la modification de la paroi cellulaire et la reponse au stress. D'autres experiences sont en cours pour elucider son role dans la virulence
Sexual differences in the effect of previous breeding performance on nest-box reuse and mate retention in White-rumped Swallows (Tachycineta leucorrhoa)

ABSTRACT In birds, the selection of nesting sites and mates has a profound influence on the daily interactions of individuals. Both behaviours are energetically costly and time-consuming and can strongly affect the Darwinian fitness of individuals. Using a 12-year dataset on banded returning breeders, we explored variables associated with nest-box choice and mate choice in the White-rumped Swallow, a socially monogamous migratory passerine. Females reusing nest-boxes, but not males, produced significantly more fledglings than did those that changed nest-boxes. Females and males that retained mates produced significantly more fledglings than did those that divorced. General linear mixed models revealed that the number of fledglings produced in previous seasons significantly explained the reuse of particular nest-boxes by females, but not by males. Mate choice by females was not strongly affected by either past breeding performance or nest-box reuse, but nest-box reuse alone predicted mate choice by males. Nest-box reuse by males was apparently more related to retention of female partners. This study revealed that sexual differences in the nesting and mating decisions were guided by the use of information on past breeding performance in a subtropical, secondary cavity nester.
Long‐term fertilizer regimes have both direct and indirect effects on arthropod community composition and feeding guilds

Vegetation species composition and structure are known to affect taxonomic composition and life‐history characteristics of arthropod communities. Soil conditions alter vegetation composition and structure, and thus, soils have indirect effects on arthropods. Whilst grassland management affects soil properties, and hence vegetation, the direct effects of soil on arthropod communities within the sward are less clear. We used a long‐term hay meadow experiment to assess both direct and indirect effects of various fertilizer regimes on arthropod community composition and feeding guilds. Arthropods were sampled via pitfall traps and sweep nets and then analysed using principal components and redundancy analyses (RDA) to determine relationships between soil properties, vegetation community, forage quality and arthropod community. Vegetation community composition, measured by the first vegetation principal component, was used as a constraining variable in partial RDA, to estimate direct effects of soil on the arthropods. Variance partitioning quantified the relative roles of vegetation and soil on the arthropod community. Our results indicate that available soil nitrogen and carbon–nitrogen ratios are important determinants of arthropod community composition. Once the effects of the vegetation were removed, it was found the soil acidity and the available potassium altered arthropod community composition. Further research is required to determine the mechanisms by which these soil properties affect arthropod communities.
Effect of inbreeding in productive traits in Nellore cattle

Inbreeding coefficients were estimated using the diagonal elements of genomic matrix (FGRM), runs of homozygosity (FROH), and pedigree data (FPED) of a Nellore cattle population. Genotypic data were obtained using a panel of 700,000 SNPs, out of a total of 2,569 animals. The genomic matrix was calculated using the VanRaden (2008) formula and the runs of homozygosity were calculated using the Plink program. The noticeable peaks on chromosome 7, 12, and 21 present hotspots of autozygosity (> 40%) putatively hovering selective pressure. The pedigree had 1,535,678 animals. The mean values for FPED, FROH and FGRM were 0.48%, 6.05% and 0.96% respectively. Indicating that the pairings between relatives is reduced in this population. Using one mixed model we found a negative effect of FROH on postweaning weight gain, muscularity and conformation and a negative effect of FPED in the postweaning weight gain. In the rest of the studied traits, we found no effect.
Patterns of Arabidopsis gene expression in the face of hypobaric stress

Extreme hypobaria is a novel abiotic stress that is outside the evolutionary experience of terrestrial plants. In natural environments, the practical limit of atmospheric pressure experienced by higher plants is about 50kPa or about 0.5 atmospheres; a limit that is primarily imposed by the combined stresses inherent to high altitude conditions of terrestrial mountains. However, in highly controlled chambers, and within projected extra-terrestrial greenhouses, the atmospheric pressure component can be isolated from the associated high altitude stresses such as temperature, desiccation and even hypoxia. Such chambers allow the exploration of hypobaria as a single variable that can be carried to extremes beyond what is possible in terrestrial biomes. Here, we examine the organ-speciﬁc progression of transcriptional strategies for the physiological adaptation to various degrees of hypobaric stress, as well as the response to severe hypobaria over time. An abrupt transition from a near-sea level pressure of 97kPa to a mere 5kPa is accompa-nied by the differential expression of hundreds of genes, primarily those associated with drought, hypoxia and cell wall metabolism. However, pressure transitions between these two extremes reveals that plants respond with complex, organ-speciﬁc transcriptomic responses, which also vary over time. These responses are not linear; neither with respect to the gradient of hypobaric severity from 75, 50, 25 to 10kPa, nor with the duration of exposure of up to 3 days at 10kPa. In the ﬁrst few hours of hypobaria, plants engage changes in basic metabolism and hormonally mediated growth and development. After 12 or more hours of hypobaria, the gene expression patterns are more indicative of hypoxia and drought environmental responses. The hypobaria transcription patterns were highly organ speciﬁc, and roots appeared to be more sensitive to hypobaria than shoots in that the number of differentially expressed genes was higher in roots than in shoots. The patterns of gene expression among organs, across a gradient of atmospheric pressures and over time suggest that plants adapt to the novel stress of pure hypobaria by using recognizable metabolisms to meet appropriately interpreted hypoxia stresses, while engaging drought responses that are seemingly inappropriate to the wet and humid environment of the chambers.
Aquatic insect functional diversity and nutrient content in urban streams in a medium‐sized city

Aquatic insects play a large role in the processing of organic matter in headwater streams; however, anthropogenic disturbances associated with watershed urbanization can impact the biodiversity and abundance of these insects. Aquatic insects function on multiple trophic levels (i.e., shredders, collectors, scrapers, and predators) and interact in the nutrient cycling within lotic systems. The degradation or loss of any of these functional groups could disrupt stream biogeochemistry and the ﬂ ow of energy in stream ecosystems. We used a paired reach site design to assess the insect functional group representation in ﬁ ve streams impacted by urbanization with downstream urban and upstream rural reach sites. We also sampled two non-urban reference streams with rural upstream and rural downstream reach sites. We assessed functional group richness and abundance and measured insect biomass, insect body nitrogen (N) content, phosphorus (P) content, and N:P ratio. We found that collectors were numerically the most abundant and taxonomically the richest insect group in all site types. There were much fewer insects collected from urban sites than rural sites and individual insects were generally smaller in the urban sites. Collectors represented the most insect biomass in urban sites and predators the most insect biomass in rural sites. Insect N and P concentrations were not affected by urban landuse, ranging from 88.45 (cid:1) 12.50 to 121.74 (cid:1) 15.80 mg/g and 10.60 (cid:1) 2.10 to 18.36 (cid:1) 7.05 mg/g, respectively; and N:P ratios from 3.48 to 20.97. However, lower total insect biomass, particularly of predators and shredders, led to signi ﬁ cantly lower total N and P mass in urban sites. Urbanization had clear effects on the diversity of functional groups, insect and their nutrient mass in this medium-sized city.
The Amino Acid Content of Rumen Microbes, Feed, Milk and Tissue after Multiple Hydrolysis Times and Implications for the CNCPS

Nutrient supply and requirement models such as the Cornel Net Carbohydrate and Protein System (CnCpS) (Higgs et al., 2015; Van Amburgh et al., 2015) and the NRC (NRC, 2001) predict post-ruminal flows of nutrients from feed proteins that escape rumen fermentation and rumen microbes. Feed and microbial protein flow has an AA content, AA profile, and a digestibility of individual AA to calculate supply of metabolizable AA. The CNCPS has been updated into a new dynamic framework (v. 7; Higgs, 2014; Higgs et al. submitted) where all amino acids and other protein components are described by their nitrogen (N) content and the model uses a more mechanistic approach then previous versions as it accounts for protozoa and endogenous AA contributions to total aA flow in addition to bacteria and feed. To improve this model, accurate representations of the AA content and digestibility of all sources of AA were needed to understand sources of error in predictions of particular AA. On an N basis, the predictions of non-ammonia nitrogen (NAN) in CNCPS v. 7 were reasonably accurate and precise. However, predictions of individual AA such as Lys, Met, Ile, Leu, and Val were biased, suggesting there was a lack of information about the true content those AA in both microbes and feeds and possibly their digestibility (Fessenden et al., 2017; Higgs, 2014; Higgs et al., submitted).
Dosage Compensation of Trisomy 21 and Its Implications for Hematopoietic Pathogenesis in Down Syndrome

Down Syndrome (DS), the most common aneuploidy seen in live-borns, is caused by trisomy for chromosome 21. DS imposes high risks for multiple health issues involving various systems of the body. The genetic complexity of trisomy 21 and natural variation between all individuals has impeded understanding of the specific cell pathologies and pathways involved. In addition, chromosomal disorders have been considered outside the hopeful progress in gene therapies for single-gene disorders. Here we test the feasibility of correcting imbalanced expression of genes across an extra chromosome by expression of a single gene, XIST, the key player in X chromosome inactivation. We targeted a large XIST transgene into one chromosome 21 in DS iPS cells, and demonstrated XIST RNA spreads and induces heterochromatin and gene silencing across that autosome in cis. By making XIST inducible, this allows direct comparison of effects of trisomy 21 expression on cell function and phenotypes. Importantly, XIST-induction during in vitro hematopoiesis normalized excess production of differentiated blood cell types (megakaryocytes and erythrocytes), known to confer high risk for myeloproliferative disorder and leukemia. In contrast, trisomy silencing enhances production of iPS and neural stem cells, consistent with DS clinical features. Further analysis revealed that trisomy 21 initially impacts the endothelial hematopoietic transition (EHT) to generate excess CD43 progenitors, and also increases their colony forming potential. Furthermore, results provide evidence for a key role for enhanced IGF signaling, involving over-expression of non-chromosome 21 genes controlled by trisomy 21. Finally, experiments to examine trisomy effects on angiogenesis showed no effect on