Miracle-dz/UniFAR-FTUs huggingface dataset:
HIV-1 Tat induit la production de TNF-α par le monocyte humain: implication des voies du calcium et des PKC : Rôle du calcium dans la signalisation cellulaire

Dans cette etude, nous avons etudie les voies de signalisation impliquees dans la production du TNF-a par le monocyte stimule par Tat. Dans le monocyte, les voies du calcium, de la PKA et de la PKC sont tres importantes pour l'expression des genes de cytokines. Donc, ces trois voies de signalisation majeures ont ete etudiees. Nos resultats montrent que (i) le calcium extracellulaire est necessaire au signal calcium induit par Tat dans le monocyte et est requis pour la production du TNF-α, la voie de la PKC est aussi hautement impliquee, alors que la voie de la PKA ne semble pas requise (ii) en aval des PKC, l'activation de NFκB est essentielle alors que les MAP kinases ERK1/2, bien qu'activees par Tat, ne sont pas directement impliquees dans les voies de signalisation menant a la production de TNF-α.
Mangrove endophytic fungi from Sarawak: isolation of secondary metabolites and optimisation of growth conditions

Endophytic fungi are a group of organisms unique in the sense that they live virtually their entire life cycles within the tissues of a host; they have been known to confer beneficial properties to the plants they inhabit in terms of protection from predation and tolerance against abiotic stress. For all their unique properties, much work lies ahead in understanding these innocuous organisms. Mangrove endophytic fungi are the more interesting group within endophytes, this as they have adapted to not only the host plant but the extreme environment those mangrove plants are constantly subjected to. There has been limited work in Malaysia regarding mangrove endophytic fungi, with more focus being given to fungi which are associated to medicinal plants. Nevertheless, significant work has been done by countries which border the South China Sea. These works were reviewed in a bid to understand trends in mangrove endophytic fungi research on a regional scale. During the course of this research mangrove endophytic fungi were subjected to large scale fermentation to isolate natural products, as well as growth optimisation studies to discern the best growth medium for isolation and cultivation of these extreme-tolerant microbes. The well-known antioxidant trans-ferulic acid was successfully isolated from a batch of fermentation products from Phyllosticta-related strain of fungi. It appears to be the first known instance of finding this metabolite with the fungal genus tested. Growth optimisation studies revealed that the growth requirements of each strain of fungi significantly differs from each other. Salinity, nitrogenous compounds, pH, are all important factors to consider when optimising growth of mangrove endophytic fungi. Though the strains tested were limited in number and diversity, it is clear that follow-up studies will be required to reveal more about the growth behaviour of these poorly-studied life forms.
Synsepalum dulcificum extracts exhibit cytotoxic activity on human colorectal cancer cells and upregulate c-fos and c-jun early apoptotic gene expression

Objective: To explore cytotoxicity of Synsepalum dulcificum (S. dulcificum) Daniell (Sapotaceae) on human colon cancer (HCT-116 and HT-29), human monocytic leukemia (THP-1) and normal (HDFn) cell lines, and its effect on the expression of early apoptotic genes, c-fos and c-jun. Methods: Leaf, stem and berry of S. dulcificum were separately extracted by using 2 solvents, 10% ethanol (EtOH) and 80% methanol (MeOH). PrestoBlue® cell viability assay and qRT-PCR assay were conducted to examine the above objectives respectively. Results: Stem MeOH, stem EtOH, and berry EtOH extracts of S. dulcificum were cytotoxic to HCT-116 and HT-29 human colon cancer cells. For HCT-116, IC50 values of these 3 extracts were not significantly different (P>0.05) from that of the positive control bleomycin (IC50 of 33.57 μg/mL), while for HT-29, IC50 values of these 3 extracts were significantly lower (P<0.05) than that of bleomycin (IC50 of 25.24 μg/mL). None of the extracts were cytotoxic to the THP-1 monocytic leukemia cells and HDFn normal human dermal fibroblasts. For both HCT-116 and HT-29, these extracts significantly up-regulated (P<0.05) the expression of c-fos and c-jun compared to the untreated negative control. Conclusions: The results of this study suggest that cytotoxicity of stem MeOH, stem EtOH, and berry EtOH extracts of S. dulcificum on HCT-116 and HT-29 colon cancer cells is due to the induced apoptosis which is caused by the up-regulation of the expression of early apoptotic genes, c-fos and c-jun.
Simulation of the effects of photodecay on long‐term litter decay using DayCent

Recent studies have found that solar ultraviolet (UV) radiation significantly shifts the mass loss and nitrogen dynamics of plant litter decomposition in semi-arid and arid ecosystems. In this study, we examined the role of photodegradation in litter decomposition by using the DayCent-UV biogeochemical model. DayCent-UV incorporated the following mechanisms related to UV radiation: (1) direct photolysis, (2) facilitation of microbial decomposition via production of labile materials, and (3) microbial inhibition effects. We also allowed maximum photodecay rate of the structural litter pool to vary with litter’s initial lignin fraction in the model. We calibrated DayCent-UV with observed ecosystem variables (e.g., volumetric soil water content, live biomass, actual evapotranspiration, and net ecosystem exchange), and validated the optimized model with Long-Term Intersite Decomposition Experiment (LIDET) observations of remaining carbon and nitrogen at three semi-arid sites in Western United States. DayCent-UV better simulated the observed linear carbon loss patterns and the persistent net nitrogen mineralization in the 10-year LIDET experiment at the three sites than the model without UV decomposition. In the DayCent-UV equilibrium model runs, UV decomposition increased aboveground and belowground plant production, surface net nitrogen mineralization, and surface litter nitrogen pool, but decreased surface litter carbon, soil net nitrogen mineralization, and mineral soil carbon and nitrogen. In addition, UV decomposition had minimal impacts on trace gas emissions and biotic decomposition rates. The model results suggest that the most important ecological impact of photodecay of surface litter in dry grasslands is to increase N mineralization from the surface litter (25%), and decay rates of the surface litter (15%) and decrease the organic soil carbon and nitrogen (5%).
Systematic Identification of Correlates of HIV-1 Infection: An X-Wide Association Study in Zambia

Background HIV-1 remains the leading cause of death among adults in Sub-Saharan Africa, and over 1 million people are infected annually. Better identification of at-risk groups could benefit prevention and treatment programmes. We systematically identified factors related to HIV-1 infection in two nationally representative cohorts of women that participated in Zambia’s Demographic and Health Surveys (DHS). Methods We conducted a comprehensive analysis to identify and replicate the association of 1,415 social, economic, environmental, and behavioral indicators with HIV-1 status. We used the 2007 and 2013-2014 DHS surveys conducted among 5,715 and 15,433 Zambian women, respectively (727 indicators in 2007; 688 in 2013-2014; 688 in both). We used false discovery rate criteria to identify indicators that are strongly associated with HIV-1 in univariate and multivariate models in the entire population, as well as in subgroups stratified by wealth, residence, age, and history of HIV-1 testing. Findings In the univariate analysis we identified 102 and 182 variables that are associated with HIV-1 in the 2007 and 2013-2014 surveys, respectively, among which 79 were associated in both. Variables that were associated with HIV-1 status in all full-sample models (unadjusted and adjusted) as well as in at least 17 out of 18 subgroups include being formerly in a union (adjusted OR 2007 2.8, p<10−16; 2013-2014 2.8, p<10−29), widowhood (adjusted OR 2007 3.7, p<10−12; 2013-2014 4.2, p<10−30), history of genital ulcers in the last 12 months (adjusted 2007 OR 2.4, p<10−5; 2013-2014 2.2, p<10−6), and having a woman for the head of the household (2007 OR 1.7, p<10−7; 2013-2014 OR 2.1, p<10−26), while owning a bicycle (adjusted 2007 OR 0.6, p<10−6; 2013-2014 0.6, p<10−8) and currently breastfeeding (adjusted 2007 OR 0.5, p<10−9; 2013-2014 0.4, p<10−26) were associated with decreased risk. Using the identified variables, area under the curve for HIV-1 positivity ranged from 0.76 to 0.82. Interpretation Our X-wide association study in Zambian women identifies multiple under-recognized factors correlated with HIV-1 infection in 2007 and 2013-2014, including widowhood, breastfeeding, and being the head of the household. These variables could be used to improve HIV-1 testing and identification programs.
The Expansion Route of Ryegrasses (Lolium spp.) into Sandy Coasts in Japan

Although an increasing number of investigations have been made into the evolution of alien species once introduced, few studies have identified the invasion routes of these introduced species. Because multiple introductions are common in invasive species, failing to take into account the introduced lineages can be misleading when studying evolutionary change in alien species after they begin to extend their ranges. In Japan, diverse lineages of ryegrasses (Lolium spp.) were introduced as forage crops and contaminants in trading grain and have expanded to sandy coasts. We studied the expansion route of populations established along the coasts of three geographic regions within Japan by comparing variations in morphology and nuclear microsatellite and chloroplast DNA in the two habitats where ryegrasses were first introduced: croplands and international seaports. Chloroplast DNA haplotypes did not differ significantly among habitats and regions, but the coastal and seaport populations displayed similar microsatellite genetic compositions and morphological characteristics. Our results revealed that coastal populations originated from seaport populations derived from contaminants. Selective forces from the past, including domestication and naturalization, may have assisted the introduced lineages in colonizing new habitats. Nomenclature: Italian ryegrass, Lolium multiflorum L. ; rigid ryegrass, Lolium rigidum Gaudin.
Selección de bacterias ácido lácticas del queso artesanal de leche de cabra de Coahuila para su uso como cultivos iniciadores

El estado de Coahuila, Mexico, se caracteriza por la produccion de queso artesanal elaborado a partir de leche de cabra. Este estudio se enfoco enel aislamiento, identificacion y caracterizacion de bacterias acido lacticas (BAL) presentes en este tipo de queso para usarlas como cultivo iniciador. Durante la investigacion, se llevo a cabo el aislamiento e identificacion de las BAL, caracterizandolas bajo pruebas bioquimicas tales como actividadacidificante, capacidad de inhibicion, produccion de CO2 y produccion de aromas, y se seleccionaron aquellas que presentaron mejores caracteristicas en las pruebas mencionadas anteriormente. Las BAL seleccionadas fueron preparadas para ser inoculadas en leche pasteurizada de cabra y, posteriormente, en la elaboracion del queso. Losquesos se evaluaron mediante una prueba sensorial empleando la prueba diferencia de control, los resultados mostraron que los quesos enriquecidos con BAL presentaron caracteristicas sensoriales globales diferentes al queso de cabra sin adicion de BAL. Por tanto, las BAL seleccionadas podrian ser empleadas como cultivos iniciadores.
Isolation and identification of avian influenza virus H9N2 subtype.

In August 1998, the avian influenza (AI) outbreak appeared in one of the layer fanns in Tehran province. Birds on the affected fann exhibited respiratory infection and reduction of egg production with very low mortality. An agar gel precipitation (AGP) test using AIV antiserum revealed the presence of the virus in the samples from the affected birds. The sera collected from the surviving birds of the affected flocks also showed the presence of antibodies against AIV by AGP test. An avian influenza virus H9N2 subtype was isolated in embryonatedeggs from the tracheal and clocal swabs as well as pooled visceral organs of the affected birds and coded Alchicken/Iran/259/1998/H9N2.Virulence testing of the low passage virus was undertaken at the time of the outbreak in specific pathogen free (SPF) chickens. The experimentallyinfected chickens showed significant clinical signs and recovered gradually without any death. The isolated virus was characterized as nHPAI on the basis of pathotyping studies in SPF chickens. It. is the first report on isolation of AIV from the chicken flocks in Iran.
Using neural networks to bridge scales in cancer: Mapping signaling pathways to phenotypes

Cancer is an evolving system subject to mutation and selection. Selection is driven by the microenvironment that the cancer cells are growing in and acts on the cell phenotype, which is in turn modulated by intracellular signaling pathways regulated by the cell genotype. Integrating all of these processes requires bridging different biological scales. We present a mathematical model that uses a neural network as a means to connecting these scales. In particular, we consider the mapping from intracellular pathway activity to phenotype under different microenvironmental conditions.
Effect of resistance training and protein intake pattern on myofibrillar protein synthesis and proteome kinetics in older men in energy restriction

Strategies to enhance the loss of fat while preserving muscle mass during energy restriction are of great importance to prevent sarcopenia in overweight older adults. We show for the first time that the integrated rate of synthesis of numerous individual contractile, cytosolic and mitochondrial skeletal muscle proteins was increased by resistance training (RT) and unaffected by dietary protein intake pattern during energy restriction in free‐living, obese older men. We observed a correlation between the synthetic rates of skeletal muscle‐derived proteins obtained in serum (creatine kinase M‐type, carbonic anhydrase 3) and the synthetic rates of proteins obtained via muscle sampling; and that the synthesis rates of these proteins in serum revealed the stimulatory effects of RT. These results have ramifications for understanding the influence of RT on skeletal muscle and are consistent with the role of RT in maintaining muscle protein synthesis and potentially supporting muscle mass preservation during weight loss.
Estimation of the genetic parameters for test-day milk yield in Holstein cattle

The objective of this study was to determine the genetic parameters represented by heritability for test-day milk yield, the genetic correlations between test-day milk yield and the breeding value for Holstein cows. The model used was random regression test-day animal model. the data set consist of 216 test day records from 30 cows. The average number of test day per lactation was seven. The heritability estimates for test-day milk yield ranged from 0.43 at 250 th day in milk to 0.60 at 10 th day in milk. Genetic correlations between individual test-days milk yield were high and positive.
Native medicinal plants of Iran effective on memory and learning: A review

Memory and learning are considered as the most important functional levels of central nervous system (CNS) which helps to encode, store, retain, and recall information in the brain. Since the role of medicinal plants in learning and memory has attracted the attention of many researchers. Therefore, the aim of this review article is to report the native medicinal plants of Iran that are used for memory and learning. According to the findings, Rosmarinus officinale, Ficus carica, Melissa officinalis, Silybum marianum, Glycine max, Nigella sativa, Cannabis sativa, Origanum vulgare L. , and Boswellia spp. are some of the native medicinal plants of Iran that are used to improve memory and learning. The mechanism actions of these plants are not fully understood but they could be effective on learning and memory due to their phytochemical compounds and antioxidant activities. © 2016, Sphinx Knowledge House. All rights reserved.
The volatile emission of a specialist herbivore alters patterns of plant defence, growth and flower production in a field population of goldenrod

Summary Plants frequently employ induced, rather than constitutive, defences against herbivores and pathogens, presumably as an adaptive response to the unpredictability of attack by particular antagonists. Plants may further accelerate defence deployment by ‘priming’ appropriate defences in response to environmental cues that reliably predict impending attack. However, the population- and community-level ecological consequences of such priming remain relatively unexplored. We recently discovered that the volatile emissions of male Eurosta solidaginis prime the antiherbivore defences of its host plant, tall goldenrod (Solidago altissima). This co-evolved system provides a unique opportunity to study the ecological consequences of priming in a natural system. We explored effects of the priming cue on neighbouring ramets at varying distances from the emission source by quantifying subsequent levels of foliar herbivory, as well as plant growth and flower production (which might reveal trade-offs between investment in growth or reproduction and defence). We observed a linear increase in leaf damage with distance from the emission source (up to our maximal distance of 1 m), consistent with the hypothesis that the intensity of priming corresponds to the intensity of exposure to the fly emission. Unexpectedly, ramets nearest the emission source also exhibited a short-term increase in growth-rate; however, this effect did not persist to the end of the season or increase flower production. Instead, ramet's mid-distance from the emission source exhibited reduced growth and flower production compared to those nearer or farther away. Synthesis. The responsiveness of Solidago altissima ramets to herbivore-associated cues across a distance of 1 m or more is highly relevant in this system, where individual ramets frequently grow within a few cm of one another. Furthermore, the resulting mosaic of ramets primed to varying degrees might influence herbivore (and consequently predator) distributions. The unexpected decline in flower production by mid-distance ramets suggests that the effects of plant priming on ecological interactions among plants and other organisms (such as tritrophic interactions and competition) may feed back onto plant fitness in complex, and as yet unexplored, ways. A lay summary is available for this article.
La relevancia de las marcas de carne de vacuno para los consumidores. Un análisis interregional

Este estudio ha sido financiado con fondos FEDER de la UE, Programa Operativo de Cooperacion Espana Francia Andorra, 2007-2012 (POCTEFA), Proyecto OTRAC. Los autores agradecen a la coordinadora del proyecto (Pilar Santolaria) la ayuda proporcionada y al resto de investigadores su colaboracion en la realizacion de las encuestas a consumidores (Gabriela Zeballos, Ana Guerrero, Pierre Sans, Nuria) Panella-Riera, Saoussan Khliji, Maria Angels Oliver, Mari Mar Campo y Carlos Sanudo).
Introducción de tecnologías para el diagnóstico y el tratamiento del cáncer en Cuba

Cancer is a serious health problem for humanity and is expected to increase rapidly in the coming years. In Cuba, malignancies became the leading cause of death in 2012 and each year about 30 to 36 thousand new cases are diagnosed. Given the importance to our social system for medical care and the quality of life of patients, the Government and the Ministry of Health designed a project to introduce five new technologies for the diagnosis and treatment of cancer in Cuba. Two technologies are for diagnosing cancer and three for the treatment of this disease. In order to guarantee the technical requirements of this project, the planning of the introduction process of the new technology and training of human resources, working groups, made up by experts from hospitals, regulatory bodies and the Ministry of Public Health (MINSAP) were created. These working groups shall take into account the needed equipment, the regulations in force as well as staff training required by the new technologies. At present three of these technologies are already installed and by the end of 2017, the introduction of all the new technology is expected to be completed, which will have a significant social impact both on the early diagnosis of malignant diseases, and on their control in all age groups.
Solution NMR studies of HIV-1 reverse transcriptase

The human immunodeficiency virus (HIV-1) is a well-recognized threat to global public health, with current estimates of ~37 million infected individuals worldwide [1]. While efforts to develop an effective vaccine to prevent infection have not come to fruition, several FDA approved drugs targeting HIV-1 have proven effective in reducing viral replication and improving quality of life [2]. Yet, due to the increasing emergence of drug resistant variants, new HIV-1 treatments are needed as the virus continues to evolve. Structure-based drug design is a powerful approach for facilitating the development of new HIV-1 inhibitors [3], driven mainly by x-ray crystallographic studies of viral proteins [4]. However, the static nature of crystallographic studies necessitate complementary structural and dynamic studies to genuinely understand protein-ligand interactions. In this thesis, solution NMR is used to investigate HIV-1 RT, a major therapeutic target in the fight against HIV-1 infection. HIV-1 reverse transcriptase produces viral DNA from genomic RNA and is essential for the viral lifecycle [5]. Although the structure of the mature heterodimer has been well characterized, less is known about RT maturation from its p66 immature precursor, which so far has resisted crystallization. I used NMR to investigate RT maturation and to elucidate RT interactions with FDA approved inhibitors. Together the results of my thesis contribute to arrive at a more comprehensive understanding of RT maturation and RT-inhibitor interactions.
The Drosophila Y Chromosome Affects Heterochromatin Integrity Genome-Wide

The Drosophila Y-chromosome is gene poor and mainly consists of silenced, repetitive DNA. Nonetheless, the Y influences expression of hundreds of genes genome-wide, possibly by sequestering key components of the heterochromatin machinery away from other positions in the genome. To test the influence of the Y chromosome on the genome-wide chromatin landscape, we assayed the genomic distribution of histone modifications associated with gene activation (H3K4me3), or heterochromatin (H3K9me2 and H3K9me3) in fruit flies with varying sex chromosome complements (X0, XY and XYY males; XX and XXY females). Consistent with the general deficiency of active chromatin modifications on the Y, we find that Y gene dose has little influence on the genomic distribution of H3K4me3. In contrast, both the presence and the number of Y-chromosomes strongly influence genome-wide enrichment patterns of repressive chromatin modifications. Highly repetitive regions such as the pericentromeres, the dot, and the Y chromosome (if present) are enriched for heterochromatic modifications in wildtype males and females, and even more strongly in X0 flies. In contrast, the additional Y chromosome in XYY males and XXY females diminishes the heterochromatic signal in these normally silenced, repeat-rich regions, which is accompanied by an increase in expression of Y-linked repeats. We find hundreds of genes that are expressed differentially between individuals with aberrant sex chromosome karyotypes, many of which also show sex-biased expression in wildtype Drosophila. Thus, Y-chromosomes influence heterochromatin integrity genome-wide, and differences in the chromatin landscape of males and females may also contribute to sex-biased gene expression and sexual dimorphisms.