Miracle-dz/UniFAR-FTUs huggingface dataset:
Climatic Correlates of White Pine Blister Rust Infection in Whitebark Pine in the Greater Yellowstone Ecosystem

Whitebark pine, a foundation species at tree line in the Western U.S. and Canada, has declined due to native mountain pine beetle epidemics, wildfire, and white pine blister rust. These declines are concerning for the multitude of ecosystem and human benefits provided by this species. An understanding of the climatic correlates associated with spread is needed to successfully manage impacts from forest pathogens. Since 2000 mountain pine beetles have killed 75% of the mature cone-bearing trees in the Greater Yellowstone Ecosystem, and 40.9% of monitored trees have been infected with white pine blister rust. We identified models of white pine blister rust infection which indicated that an August and September interaction between relative humidity and temperature are better predictors of white pine blister rust infection in whitebark pine than location and site characteristics in the Greater Yellowstone Ecosystem. The climate conditions conducive to white pine blister rust occur throughout the ecosystem, but larger trees in relatively warm and humid conditions were more likely to be infected between 2000 and 2018. We mapped the infection probability over the past two decades to identify coarse-scale patterns of climate conditions associated with white pine blister rust infection in whitebark pine.
Activation of the liver X receptors alters CD4+ T cell membrane lipids and signalling through direct regulation of glycosphingolipid synthesis

Liver X Receptors (LXRs) are important transcriptional regulators of intracellular cholesterol, fatty acid, and phospholipid levels. LXRs can dampen inflammation in macrophages by promoting cholesterol efflux and altering plasma membrane lipid rafts; microdomains enriched for cholesterol and glycosphingolipids that regulate immune-cell signalling. However, little is known about the impact of LXR activators on T cell plasma membrane lipid rafts, which are critical for T-cell antigen receptor (TCR) signalling. Here we show that the LXR synthetic agonist GW3965 significantly increases glycosphingolipid levels and reduces cholesterol and lipid order (stability) in the plasma membrane of human CD4+ T cells. Moreover, the GSL biosynthesis enzyme UGCG was identified as a novel direct target of LXR activation. Importantly, LXR-mediated changes in T cell lipid composition were associated with altered spatiotemporal distribution of lipids and signalling molecules at the immune synapse. Crucially, LXR activation altered the kinetics of proximal TCR-signalling events in activated T cells, reduced T cell proliferation and enhanced the production of IL-2 and IL-4. Thus, LXR activation influences T cell function via alteration of the plasma membrane lipid profile. Finally, the expression of UGCG and other LXR-regulated genes and lipids was significantly dysregulated in T-cells isolated from people with multiple sclerosis. Overall, a novel action of LXR has been characterised that involves modulation of lipid raft-associated cholesterol and glycosphingolipids in CD4+ T-cells, which could be of therapeutic relevance in multiple sclerosis.
INVESTIGATION OF PARASITIC INFECTION AMEBIASIS AMONG A POPULATION IN AL-SAMAWAH CITY/ AL-MUTHANNA PROVINCE BY USING MOLECULAR METHOD REAL-TIME POLYMERASE CHAIN REACTION

Entamoeba histolytica parasite is widely distributed throughout the world, but prevalence rates are highest in developing countries . E.histolytica infection ,Amebiasis, is consistently present among the poor developing countries, this study aim to investigate the amoeba parasites in the city of Al-Muthanna province using microscopic and molecular methods to explain the spread of the disease in this city because of its importance to the health of individuals in society where we use microscopic examination and PCR technology to investigate the amoeba parasites and found the percentage of amoeba parasites was 69.2307690 % and the negative samples were 30.769231% from the 286 total sample, a significant difference below the significant level p≤00.05 in the incidence of parasitic infection.
Autonomous emergence of connectivity assemblies via spike triplet interactions

Non-random connectivity can emerge without structured external input driven by activity-dependent mechanisms of synaptic plasticity based on precise spiking patterns. Here we analyze the emergence of global structures in recurrent networks based on a triplet model of spike timing dependent plasticity (STDP) which depends on the interactions of three precisely-timed spikes and can describe plasticity experiments with varying spike frequency better than the classical pair-based STDP rule. We describe synaptic changes arising from emergent higher-order correlations, and investigate their influence on different connectivity motifs in the network. Our motif expansion framework reveals novel motif structures under the triplet STDP rule, which support the formation of bidirectional connections and loops in contrast to the classical pair-based STDP rule. Therefore, triplet STDP drives the spontaneous emergence of self-connected groups of neurons, or assemblies, proposed to represent functional units in neural circuits. Assembly formation has often been associated with plasticity driven by firing rates or external stimuli. We propose that assembly structure can emerge without the need for externally patterned inputs or assuming a symmetric pair-based STDP rule commonly assumed in previous studies. The emergence of non-random network structure under triplet STDP occurs through internally-generated higher-order correlations, which are ubiquitous in natural stimuli and neuronal spiking activity, and important for coding. We further demonstrate how neuromodulatory mechanisms that modulate the shape of triplet STDP or the synaptic transmission function differentially promote connectivity motifs underlying the emergence of assemblies, and quantify the differences using graph theoretic measures.
Shiga toxigenic, enteroinvasive and enteropathogenic Escherichia coli in fish from experimental fish farm (Layo), Cte dIvoire

The objective of this study was to know the sanitary quality of fish coming from Layo farm. Twenty fishes (Oreochromis niloticus), were selected in four ponds and Escherichia coli were isolated in gills and viscera according to microbiological methods. One hundred and twenty strains of E. coli were isolated, and their virulence was performed by polymerase chain reaction (PCR) using specific primers. Eleven (11) strains (9.16%) including 7 strains of gills (11.66%) and 4 strains of viscera (6.66%) had virulence genes eae, Stx1, Stx2 or ial. Atypical Enteropathogenic E. coli (EPEC, eae+, lack of bfp) was isolated from gills (5%) and viscera (1.66%). Shiga toxigenic E. coli (STEC) with genes eae + Stx2, Stx1 and Stx2 were isolated in viscera (5%) and gills (3.33%). For Enteroinvasive E. coli (EIEC), ial gene was isolated in gills (3.33%) but no ipah gene. Enterotoxinogen E. coli (ETEC) with lt gene and Enteroaggregating E. coli (EAEC) with aggA gene were not detected in this study. This study revealed that some fish from Layo farm are carriers of virulent E. coli that can cause serious human diseases and can lead to consumer death if cooking is insufficient or by cross-contamination. This therefore poses a real public health problem. Key words: Escherichia coli pathogens, fish, ponds, public health.
Dynamic measurement of cytosolic pH and [NO3-] uncovers the role of the vacuolar transporter AtCLCa in the control of cytosolic pH

Ion transporters are key players of cellular processes. The mechanistic properties of ion transporters have been well elucidated by biophysical methods. Meanwhile the understanding of their exact functions in the whole cell homeostasis is limited by the difficulty to monitor their activity in vivo. The development of biosensors to track subtle changes in intracellular parameters provides an invaluable key to tackle this challenging issue. Here, we adapted the use of a dual biosensor using guard cells as experimental model to visualize the impact on the cytosol of anion transport from intracellular compartments. To image the activity of AtCLCa, a vacuolar NO3-/H+ exchanger regulating stomata aperture in Arabidopsis thaliana, we expressed a genetically encoded biosensor, ClopHensor allowing monitoring the dynamics of cytosolic anion concentration and pH. We first show that ClopHensor is not only a Cl- but also a NO3- sensor. We were then able to unravel and quantify the variations of NO3- and pH in the cytosol. Our data show that AtCLCa activity modifies cytosolic pH and NO3-, demonstrating that the transport activity of a vacuolar exchanger has a profound impact on cytosolic homeostasis. We propose that a major function of this endomembrane transporter is to adjust cytosolic conditions to cellular needs. This opens a novel perspective on the function of intracellular transporters of the CLC family in eukaryotes: not only controlling the intra organelle lumen but also actively modifying cytosolic conditions. Significance Intracellular transporters are key actors in cell biological processes. Their disruption causes major physiological defects. The role of intracellular ion transporters is usually seen through an “intra organelle” lens, meanwhile their potential action on cytosolic ion homeostasis is still a black box. The case of a plant CLC is used as a model to uncover the missing link between the regulation of conditions inside the vacuole and inside the cytosol. The development of an original live imaging workflow to simultaneously measure pH and anion dynamics in the cytosol reveals the role of an Arabidopsis thaliana CLC, AtCLCa, in the modification of cytosolic pH. Our data highlight an unsuspected function of endomembrane transporters in the regulation of cytosolic pH.
Bayesian Linear Mixed Models with Polygenic Effects

We considered Bayesian estimation of polygenic effects, in particular heritability in relation to a class of linear mixed models implemented in R (R Core Team 2018). Our approach is applicable to both family-based and population-based studies in human genetics with which a genetic relationship matrix can be derived either from family structure or genome-wide data. Using a simulated and a real data, we demonstrate our implementation of the models in the generic statistical software systems JAGS (Plummer 2017) and Stan (Carpenter et al. 2017) as well as several R packages. In doing so, we have not only provided facilities in R linking standalone programs such as GCTA (Yang, Lee, Goddard, and Visscher 2011) and other packages in R but also addressed some technical issues in the analysis. Our experience with a host of general and special software systems will facilitate investigation into more complex models for both human and nonhuman genetics.
Commensal bacteria differentially shape the nutritional requirements of Drosophila during juvenile growth

The interplay between nutritional and microbial environments is one of the decisive environmental inputs that determine juvenile growth trajectory. Nutritional deficiencies contribute to developmental delays, and an immature gut microbiota is a hallmark of pathologies related to childhood undernutrition. However, how commensal bacteria modulate the impact of nutrition on juvenile growth remains elusive. Here, using gnotobiotic Drosophila melanogaster larvae independently associated with two major commensal strains, Acetobacter pomorumWJL (ApWJL) and Lactobacillus plantarumNC8 (LpNC8), we performed a large-scale, systematic nutritional screen based on larval growth in 40 different and precisely controlled nutritional environments. We combined these results with in silico metabolic network reconstruction to define the biosynthetic capacities of Drosophila germ-free larvae and the two commensals. We first establish that ApWJL or LpNC8 differentially fulfills the nutritional requirements of the ex-GF larva and parsed such difference down to individual amino acids, vitamins, other micronutrients and trace metals. We found that Drosophila commensal bacteria not only fortify the host’s diet with essential nutrients but in specific instances, they functionally compensate for host auxotrophies even if the bacteria fail to synthetize the missing nutrient. Our systematic work reveals that beyond the molecular dialogue engaged between the host and its commensal partners, Drosophila engage into an integrated nutritional network with its facultative commensals centered around the sparing and utilization of nutrients. We thus uncover a novel facet of the facultative nutritional mutualism engaged between Drosophila and its commensal bacteria, which allows the juvenile host to better cope with changes in nutrients availability during the critical phase of post-natal growth; hence ensuring optimal host fitness.
Temporal dynamics of mycorrhizal fungal communities and co‐associations with grassland plant communities following experimental manipulation of rainfall

Climate models project overall a reduction in rainfall amounts and shifts in the timing of rainfall events in mid‐latitudes and sub‐tropical dry regions, which threatens the productivity and diversity of grasslands. Arbuscular mycorrhizal (AM) fungi may help plants to cope with expected changes but may also be impacted by changing rainfall, either via the direct effects of low soil moisture on survival and function or indirectly via changes in the plant community. In an Australian mesic grassland (former pasture) system, we characterized plant and AM fungal communities every 6 months for nearly 4 years to two altered rainfall regimes: (a) ambient, (b) rainfall reduced by 50% relative to ambient over the entire year and (c) total summer rainfall exclusion. Using Illumina sequencing, we assessed the response of AM fungal communities sampled from contrasting rainfall treatments and evaluated whether variation in AM fungal communities was associated with variation in plant community richness and composition. We found that rainfall reduction influenced the fungal communities, with the nature of the response depending on the type of manipulation, but that consistent results were only observed after more than 2 years of rainfall manipulation. We observed significant co‐associations between plant and AM fungal communities on multiple dates. Predictive co‐correspondence analyses indicated more support for the hypothesis that fungal community composition influenced plant community composition than vice versa. However, we found no evidence that altered rainfall regimes were leading to distinct co‐associations between plants and AM fungi. Overall, our results provide evidence that grassland plant communities are intricately tied to variation in AM fungal communities. However, in this system, plant responses to climate change may not be directly related to impacts of altered rainfall regimes on AM fungal communities. Synthesis. Our study shows that arbuscular mycorrhizal (AM) fungal communities respond to changes in rainfall but that this effect was not immediate. The AM fungal community may influence the composition of the plant community. However, our results suggest that plant responses to altered rainfall regimes at our site may not be resulting via changes in the AM fungal communities.
Biology of Danaus chrysippus L. (Lepidoptera: Danaidae): feeding potentials in the larval host plants and adult nectar plants

The biology and feeding potential of plain tiger butterfly, Danaus chrysippus L. (Lepidoptera: Danaidae) were examined in both field and laboratory conditions from July 2011 to June 2012. Field collected singly laid eggs on host plant (Asclepias curassavica) were reared in the laboratory at room temperature (25 ± 3 °C) and 70 ± 5% RH. Various life stages of the butterfly, viz. egg, larvae, pre-pupa, pupa and adult have been described. The egg incubation period was 4.6 ± 0.8 days; the duration of larval stages from 1st to 5th instars were 1.7 ± 0.2, 2.2 ± 0.2, 2.5 ± 0.3, 2.7 ± 0.2 and 3.1 ± 0.4 days, respectively; pre-pupal period was 1.4 ± 0.4 days; pupal period was 8.6 ± 1.1 days; the longevity of the adult females was 7.8 ± 0.3 days and of the males was 10.4 ± 0.7 days. The larval lengths of each of the five instars were 3.7 ± 0.84, 8.7 ± 1.09, 14.3 ± 1.20, 23.2 ± 2.36 and 38.5 ± 2.54 mm, respectively. The feeding potential rates of the five instar larvae were 5.5 ± 1.11%, 22.8 ± 2.96%, 67.7 ± 2.99%, 96.8 ± 4.09% and 293.6 ± 15.9%, respectively. The weights (in gram) of the excreta of five larval instars were 0.06 ± 0.02, 0.13 ± 0.03, 0.54 ± 0.06, 0.81 ± 0.06 and 1.96 ± 0.09, respectively. A total of 187 individuals was observed on 16 potential nectar plants in the Butterfly Research Park (BRP), Gazipur. These were Lantana camara, Asclepias curassavica, Duranta plumeri, Hibicus rosa sinensis, Duranta repens, Tagetes patula, Ixora chinensis, Heliotropium indicum, Cosmos bipinnatus, Wedelia calendulaca, Punica hybrida, Spilanthes calva, Leucas linifolia, Helianthus annus, Euphorbia pulcherrima and Gomphera globosa. Among these, L. camara was visited most frequently (16.58%) and L. linifolia was least frequently (1.60%) by this butterfly. No Danaus chrysippus was observed visiting H. annus and E. pulcherrima plants. J. Biodivers. Conserv. Bioresour. Manag. 2019, 5(1): 121-132
Ground-Dwelling Arthropod Community Responses to Recent and Repeated Wildfires in Conifer Forests of Northern New Mexico, USA

The increasing frequency and severity of wildfires in semi-arid conifer forests as a result of global change pressures has raised concern over potential impacts on biodiversity. Ground-dwelling arthropod communities represent a substantial portion of diversity in conifer forests, and could be particularly impacted by wildfires. In addition to direct mortality, wildfires can affect ground-dwelling arthropods by altering understory characteristics and associated deterministic community assembly processes (e.g., environmental sorting). Alternatively, disturbances have been reported to increase the importance of stochastic community assembly processes (e.g., probabilistic dispersal and colonization rates). Utilizing pitfall traps to capture ground-dwelling arthropods within forest stands that were burned by one or two wildfires since 1996 in the Jemez Mountains of northern New Mexico, United States (USA), we examined the potential influences of deterministic versus stochastic processes on the assembly of these diverse understory communities. Based on family-level and genera-level arthropod identifications, we found that the multivariate community structures differed among the four fire groups surveyed, and were significantly influenced by the quantities of duff, litter, and coarse woody debris, in addition to tree basal area and graminoid cover. Taxon diversity was positively related to duff quantities, while taxon turnover was positively linked to exposed-rock cover and the number of logs on the ground. Despite the significant effects of these understory properties on the arthropod community structure, a combination of null modeling and metacommunity analysis revealed that both deterministic and stochastic processes shape the ground-dwelling arthropod communities in this system. However, the relative influence of these processes as a function of time since the wildfires or the number of recent wildfires was not generalizable across the fire groups. Given that different assembly processes shaped arthropod communities among locations that had experienced similar disturbances over time, increased efforts to understand the processes governing arthropod community assembly following disturbance is required in this wildfire-prone landscape.
Independent transposon exaptation is a widespread mechanism of shadow enhancer evolution in the mammalian genome

Many regulatory networks involve (possibly partially) redundant cis-regulatory elements. These elements are commonly referred to as shadow enhancers and have been assumed to mainly originate by sequence duplication. An alternative mechanism that has not been examined involves the independent exaptation of transposons. Here, we identified 2,117 and 2,787 pairs of shadow enhancers in the human and mouse genomes, respectively, and found that 34% and 18% of these pairs derive from transposons. Moreover, we show that virtually all the enhancer partners of these transposon-derived shadow enhancer pairs are independent exaptations from different transposon types and hypothesize that the increase in the expression and tissue-specificity of their targets as compared to those of non-shadow enhancers facilitates their fixation in the genome. Finally, we provide evidence that the regulatory redundancy observed in many mammalian regulatory networks is predominantly driven by convergent evolution, since shadow enhancers are hardly ever conserved across species.
In vitro behavior of tendon stem/progenitor cells on bioactive electrospun nanofiber membranes for tendon-bone tissue engineering applications

Purpose In order to accelerate the tendon-bone healing processes and achieve the efficient osteointegration between the tendon graft and bone tunnel, we aim to design bioactive electrospun nanofiber membranes combined with tendon stem/progenitor cells (TSPCs) to promote osteogenic regeneration of the tendon and bone interface. Methods In this study, nanofiber membranes of polycaprolactone (PCL), PCL/collagen I (COL-1) hybrid nanofiber membranes, poly(dopamine) (PDA)-coated PCL nanofiber membranes and PDA-coated PCL/COL-1 hybrid nanofiber membranes were successfully fabricated by electrospinning. The biochemical characteristics and nanofibrous morphology of the membranes, as well as the characterization of rat TSPCs, were defined in vitro. After co-culture with different types of electrospun nanofiber membranes in vitro, cell proliferation, viability, adhesion and osteogenic differentiation of TSPCs were evaluated at different time points. Results Among all the membranes, the performance of the PCL/COL-1 (volume ratio: 2:1 v/v) group was superior in terms of its ability to support the adhesion, proliferation, and osteogenic differentiation of TSPCs. No benefit was found in this study to include PDA coating on cell adhesion, proliferation and osteogenic differentiation of TSPCs. Conclusion The PCL/COL-1 hybrid electrospun nanofiber membranes are biocompatible, biomimetic, easily fabricated, and are capable of supporting cell adhesion, proliferation, and osteogenic differentiation of TSPCs. These bioactive electrospun nanofiber membranes may act as a suitable functional biomimetic scaffold in tendon-bone tissue engineering applications to enhance tendon-bone healing abilities.
Relationship of estrogen beta (ERβ) receptor genes polymorphism with epithelial ovarian cancer

Ovarian cancer is the leading cause of death among all uterine diseases. Ovarian cancer is affected by exogenous and endogenous estrogen factors. Beta estrogen receptors are predominant estrogen receptors in the normal ovary. Polymorphisms in the beta estrogen receptor gene (ERβ) can affect the risk of epithelial ovarian cancer through regulation of cell proliferation and apoptosis. The purpose of this study was to determine the relationship of beta estrogen receptor gene polymorphism (ERβ) with epithelial ovarian cancer incidence. Method: a case-control study, there were 60 samples. A single nucleotide polymorphism in the beta estrogen receptor (RsaI/rs1256049) is selected. Genotyping using PCR-RFLP. Data were analyzed by Chi-square, considered significant if the p-value is less than 0.05. Results: there is no significant difference in the characteristics of respondents. Genotypic frequency in the case group was 56.7% GG, 43.3% GA/AA and control group was 23.2% GG, 76.7% GA/AA. The frequency of alleles in the case group was 78.3% G, 21.7% A and control which was 50% G, 50% A allele. ERβ polymorphism is associated with epithelial ovarian cancer (p 0.018). Allele A in RsaI was associated with epithelial ovarian cancer (p 0.002). Polymorphism of the beta estrogen receptor gene associated with epithelial ovarian cancer.