Miracle-dz/UniFAR-FTUs huggingface dataset:
Soil Conservation Practices and Stakeholder’s Participation in Research Projects—Empirical Evidence from Southern Italy

Adoption of soil conservation practices is promoted by increased engagement between researchers and stakeholders. By reporting a case study from southern Italy where farmers have been involved in research projects dealing with soil conservation over several years, we demonstrated that the rate of adoption of conservative technologies is positively linked to the degree of stakeholder participation in the project and that farmers (and other stakeholders) have been driven toward more conscious perception of the complex link between agricultural practices, environmental impacts and socioeconomic effects. The results of this study reinforce the pivotal role of effective participatory processes in soil conservation—evidencing the importance of (i) time required to build relationships and (ii) intensity (and persistence) of collaboration among similar initiatives. Empirical evidence highlights the need to combine different approaches to deal with soil degradation. As well as the participatory time length, the synergies between the methods utilized, and the range of interacting mind sets are also very important.
Molecular Diversity Analysis of Some Chilli (Capsicum spp.) Genotypes Using SSR Markers

Chilli belongs to the genus Capsicum which possesses enormous wealth of genetic diversity. Extent of genetic diversity determines the success level of crop improvement programme. Simple sequence repeats (SSRs) are the most widely used marker system for molecular diversity analysis especially in cultivated species. The aim of our present study was to assess the molecular genetic diversity of 20 local chilli genotypes of Bangladesh using SSR markers. Genomic DNA was extracted from young leaves and PCR reactions were performed. Eleven SSR primers were used in PCR amplification. Total 10 alleles were detected for the five polymorphic SSR loci, with a mean of 2.00 alleles per primer. Gene diversity ranged from 0.333 to 1.00 with an average of 0.567. Polymorphic Information Content (PIC) values of the SSR primers ranged from 0.255 to 0.500 with an average value of 0.371. The similarity index matrix ranged from 0.00 to 1.000. It was highest in several germplasms viz. Pop-2 vs Pop-18; Pop-3 vs Pop-5 vs Pop-19 vs Pop-20 and the lowest in the germplasm Pop-8 vs Pop-18. Dendrogram based on Nei’s genetic distance using Unweighted Pair Group Method of Arithmetic Means (UPGMA) indicated the segregation of 20 chilli genotypes into two main clusters. The SSR markers showed genetic variability in the studied pepper genotypes and they are powerful tools for estimating molecular diversity of chilli. The findings of the present study have potential applications in future breeding programme for the genetic improvement of chilli.
Pup Provisioning in the Cooperatively Breeding African Wild Dog, Lycaon pictus, is Driven by Pack Size, Social Status and Age

Division of labour, in terms of providing for offspring, in obligate cooperatively breeding mammalian species is poorly understood. To understand offspring provisioning in a cooperatively breeding canid, we analysed a long-term dataset comprising 22 African wild dog, Lycaon pictus, denning events (nine packs over nine consecutive years). We investigated the effects of sex, age class, social status, and pack size on the likelihood and frequency of regurgitating food to pups at the den. We found that the interaction of social status and pack size affected the likelihood of regurgitation. Specifically, when in a large (≤15) pack, dominant individuals were less likely to regurgitate than subordinate individuals. However, in smaller (≤ 15) packs, dominant individuals were more likely to regurgitate than subordinate individuals. We also found that the interaction of age and pack size affected the frequency of regurgitation. Specifically, in large packs, yearlings regurgitated more frequently per observation period than adults. Contrastingly, in smaller packs, adults regurgitated more frequently. Sex did not affect pup provisioning. We suggest that these contrasting patterns of helping are best explained by a strong selection pressure for individual behaviour that results in larger pack sizes in this species. When in larger packs, costs are shared as the division of labour spreads amongst individuals. In smaller packs, a division of labour requires individuals that already experience costs (such as reproduction) to be further burdened by provisioning. Overall, our results support that the need for more helpers to care for offspring contributes to the evolutionary consequence of an inverse density dependence.
Arsenite exposure inhibits histone acetyltransferase p300 for attenuating H3K27ac at enhancers in low-dose exposed mouse embryonic fibroblast cells

Epidemiological investigations have validated the positive relationships between arsenic in drinking water and several cancers, including skin, liver and lung cancers. Besides genotoxicity, arsenic exposure-related pathogenesis of disease is widely considered through epigenetic mechanisms; however, the underlying mechanistic insight remains elusive. Herein we explore the initial epigenetic changes via acute low-dose arsenite exposures of mouse embryonic fibroblast (MEF) cells and Dot1L knockout MEF (Dot1L-/- for abbreviation) cells. Our RNA-seq and Western blot data demonstrated that, in both cell lines, acute low-dose arsenite exposure abolished histone acetyltransferase p300 at the RNA level and subsequent protein level. Consequently, p300-specific main target histone H3K27ac, a marker separating active from poised enhancers, decreased dramatically as validated by both Western blot and ChIP-seq analyses. Concomitantly, H3K4me1 as another well-known marker for enhancers also showed significant decreases, suggesting an underappreciated crosstalk between H3K4me1 and H3K27ac involved in arsenite exposure. Significantly, arsenite exposure-reduced H3K27ac and H3K4me1 inhibit the expression of genes including EP300 itself and Kruppel Like Factor 4(Klf4), a tumor suppressor gene. Collectively, our investigations identify p300 as an internal bridging factor within cells to sense external environmental arsenite exposure to alter chromatin, thereby changing gene transcription for disease pathogenesis.
Advantages and challenges of advanced biotech used in assisted equine reproduction

Some reports suggest the equine species as the first one to be subjected to the artificial insemination. Despite this fact, the development of assisted reproduction in this species has been slow when compared to other production species. The authorization of the use of embryo transfer by some breed associations stimulated the development and expansion of several reproductive techniques for use in horses. The present study aimed to address the advanced biotechnologies currently available for this species, such as superovulation, transfer of oocytes, gamete intrafallopian transfer, in vitro production of embryos and cloning, emphasizing their practical and clinical applications, as well as certain challenges that still need to be overcome in each biotech.
Disease and Demography in the Americas.

This volume is a product of one in a series of symposia produced as part of the National Museum of Natural Historys commemoration of the Columbus Quincentenary which was held November 2-3 1989 in Washington D.C. This particular symposium was entitled Disease and Demography in the Americas Changing Patterns Before and After 1492. The 27 papers included examine both the impact of imported diseases on the Native American population as well as the diseases that affected that population before European arrival. The general approach is interdisciplinary. Several papers focus on questions of population size and the demographic impact of the European conquest including such questions as "the size of the aboriginal population fluctuation in population size prior to European contact the extent to which disease impact preceded actual population contact the magnitude and severity of the epidemics and regional or local variability in the timing and rate of population decline. " (EXCERPT)
Mononuclear phagocyte activation and its role in HIV-1 pathogenesis

Three decades into the HIV-1 pandemic, it is increasingly apparent that generalized immune activation is a key pathogenic determinant of AIDS. Studies of immune activation, in the setting of HIV-1, have focused primarily on the adaptive immune response despite the role of monocytes and macrophages as key regulators of inflammatory responses. In this thesis, I focused on the relationships between mononuclear phagocyte activation and HIV-1 pathogenesis, both in vitro using model systems and in vivo in African patients with AIDS, Using a monocyte-derived macrophage (MDM) model of Ml and M2a polarization, I found that activation transiently altered the capacity of macrophages to support productive HIV-1 infection and that the level of viral inhibition was dependant on the polarization phenotype. Ml and M2a polarized MDM also differed in the capacity to transmit virus to CD4+ T cells with M2a cells efficiently transmitting HIV-1 via a DC-SIGN dependant mechanism. In a cohort of treatment-naive AIDS patients, in vivo activation of circulating monocytes and intestinal macrophages was strongly associated with HIV-1 pathogenesis. Monocyte activation in these patients was differentially regulated by HIV-1 and circulating LPS (marker of microbial translocation) and was associated with two clearly distinct activation profiles. At the tissue level, HIV-1 was associated with alterations in intestinal macrophage distribution, frequency and phenotype. In the colon, macrophage activation was negatively correlated with viral load and positively correlated with microbial translocation suggesting that, although inflammatory macrophages in the intestine may contribute to the control viral replication, they may also enhance microbial translocation and systemic activation.
A Monte Carlo method for in silico modeling and visualization of Waddington’s epigenetic landscape with intermediate details

Waddington’s epigenetic landscape is a classic metaphor for describing the cellular dynamics during the development modulated by gene regulation. Quantifying Waddington’s epigenetic landscape by mathematical modeling would be useful for understanding the mechanisms of cell fate determination. A few computational methods have been proposed for quantitative modeling of landscape; however, to model and visualize the landscape of a high dimensional gene regulatory system with realistic details is still challenging. Here, we propose a Monte Carlo method for modeling the Waddington’s epigenetic landscape of a gene regulatory network (GRN). The method estimates the probability distribution of cellular states by collecting a large number of time-course simulations with random initial conditions. By projecting all the trajectories into a 2-dimensional plane of dimension i and j, we can approximately calculate the quasi-potential U(xi, xj) = −ln P(xi, xj), where P(xi, xj) is the estimated probability of an equilibrium steady state or a nonequilibrium state. A state with locally maximal probability corresponds to a locally minimal potential and such a state is called an attractor. Compared to the state-of-the-art methods, our Monte Carlo method can quantify the global potential landscape of GRN for a high dimensional system. The same topography of landscape can be produced from deterministic or stochastic time-course simulations. The potential landscapes show that not only attractors represent stability, but the paths between attractors are also part of the stability or robustness of biological systems. We demonstrate the novelty and reliability of our method by plotting the potential landscapes of a few published models of GRN. Besides GRN-driven landscapes of cellular dynamics, the algorithm proposed can also be applied to studies of global dynamics of other dynamical systems.
Genome-wide Association Study for Noise-induced Cochlear Synaptopathy

In order to elucidate the genetic architecture of the auditory hair cell synapse and the susceptibility to noise-induced cochlear synaptopathy, we are providing the first genome-wide association study with 111 strains (n=695) of the Hybrid Mouse Diversity Panel based upon the strain variation of the wave 1 P1-N1 amplitude of the auditory brainstem responses both before and after noise exposure. Based on this association analysis and our cochlear gene expression data, we identified several novel loci and prioritized positional candidate genes related to cochlear synaptopathy, especially after exposure to noise. Abstract This is the first genome-wide association study (GWAS) with the Hybrid Mouse Diversity Panel (HMDP) to define the genetic landscape of the auditory hair cell synapse and the susceptibility to noise-induced cochlear synaptopathy. We tested 5-week old female mice (n=695) from 111 HMDP strains (n= 6-7/strain) at baseline and post noise exposure using ABR wave 1 suprathreshold amplitudes (P1-N1 at 80 dB SPL) at 8, 12, 16, 24 and 32 kHz tone burst stimuli. Mice were exposed for 2 hours to 10 kHz octave band noise (OBN) at 108 dB SPL. A broad range of suprathreshold ABR wave 1 amplitude were detected across the HMDP strains. At the genome-wide significance threshold (-logP = 5.39), associations on Chr. 3 and Chr. 16 were identified at baseline. Also, association peaks on Chr. 2 and Chr. 13 were determined post noise exposure. In order to prioritize candidate genes, we generated gene expression microarray profiles using RNA isolated from cochleae in 64 HMDP strains (n =3 arrays per strain). We then used EMMA to perform an association analysis between all SNPs and array probes mapping within each region. A total of 17 genes (2 within Chr. 3 association, 6 within Chr. 2 association and 9 within Chr. 13 association) of these 3 loci were identified with at least 1 probe whose expression was regulated by a significant cis eQTL in the cochlea. Also, the genetic architecture of noise induced cochlear synaptopathy is distinct from that of baseline auditory nerve/synapse integrity. In summary, from this GWAS and our eQTL data, we identified 4 novel loci and prioritized positional candidate genes related to cochlear synaptopathy at baseline and after exposure to noise.
Etude comparative des activités antioxydantes d’extraits éthanoliques de feuilles, d’écorces et de racines de Cassia sieberiana

Dans cet article, les 3 organes de C. sieberiana recoltee au Togo ont fait l’objet d’une etude comparative pour la determination de leur composition phytochimique, teneur en phenols et flavonoides totaux, et activites antioxydantes. Le tri phytochimique a ete realise grâce aux reactions de colorimetrie et precipitation. La teneur en phenols totaux a ete determinee grâce au reactif du Folin-Ciocalteu et celle des flavonoides par AlCl 3 . L’activite antioxydante a ete evaluee par les methodes de DPPH et FRAP. Les resultats obtenus ont montre que les 3 organes de la plante contiennent des grands groupes chimiques, tels que les flavonoides, tanins et saponosides. Les teneurs en phenols totaux des extraits ethanoliques sont (en mg EAG/g) de 276,62 ± 26,120 (feuilles) ; 345,04 ± 3,160 (ecorces) ; 327,16 ± 3,990 (racines). Celles des flavonoides totaux sont (en mg EQ/g) de 34,134 ± 4,324 (feuilles) ; 36,430 ± 2,022 (ecorces) et 37,270 ± 2,216 (racines). Les extraits ethanoliques des 3 organes ont un pouvoir antioxydant appreciable. En conclusion, les resultats obtenus revelent que les racines et ecorces ont des activites antioxydantes semblables, toutefois ne permettent pas a ce stade de la recherche de preciser l’organe approprie pouvant remplacer les racines. © 2017 International Formulae Group. All rights reserved. Mots cles: Cassia sieberiana ; composition phytochimique activite antioxydante ; phenols totaux English Title: Comparative antioxidant potential study of different part of Cassia sieberiana English Abstract In this article, the 3 organs of C. sieberiana harvested in Togo were the subject of a comparative study for the determination of their phytochemical composition, content of total phenols and flavonoids, and antioxidant activities. Phytochemical composition was carried out by colorimetric and precipitation reactions. The total phenol content was determined by Folin-Ciocalteu reagent and total flavonoids by AlCl 3 . Antioxidant activity was evaluated by DPPH and FRAP methods. The results obtained showed that the 3 organs of the plant contain large chemical groups, such as flavonoids, tannins and saponosides. The total phenol contents of the ethanolic extracts are (in mg EAG / g) of 276.62 ± 26.120 (leaves); 345.04 ± 3.160 (barks); 327.16 ± 3.990 (roots). Those of the total flavonoids are (in mg Eq / g) 34,134 ± 4,324 (leaves); 36,430 ± 2,022 (barks) and 37,270 ± 2,216 (roots). The ethanolic extracts of the 3 organs have an appreciable antioxidant power. In conclusion, the results obtained reveal that the roots and barks have similar antioxidant activities, however do not allow at this stage of research to specify the appropriate organ that can replace the roots. © 2017 International Formulae Group. All rights reserved. Keywords: Cassia sieberiana ; phytochemical composition; antioxidant activity; total phenols
Importance of Chromosomal Architecture to Organize Promoter-Enhancer Long-Range Interactions in c-Myc locus

In metazoans the regulation of transcription commonly relies on multiple types of regulatory elements. Often these elements are separated from their target promoters by great genomic distance and can even have other genes in between. Current models propose the chromosomes to be folded following a specific topology in order to allow these long-range interactions to occur. In addition to the locus topology, chromatin environment and DNA accessibility play an important role to determine the activity of regulatory elements. Thanks to genome-wide studies these layers of regulation have been shown to correlate with gene expression to different extents, however it is still not clear how chromatin, DNA topology and genetic components integrate in order to carry out this process. With this project we aim to understand basic mechanisms organizing promoter–regulatory elements communication in a defined model locus. A previous project from the laboratory used chromosomal deletions and in vivo reporter assays to identify and characterize regulatory elements in c-Myc locus. This study, performed by Veli Uslu showed that during mouse embryonic development, at 11.5 days of gestation, different enhancers coordinate c-Myc transcription in the facial tissues and embryonic liver. We analyzed the distribution inside c-Myc locus of histone modifications enriched at enhancer sites, restricting to few smaller putative regions the genetic position of facial and liver enhancers. We also assessed the occupancy of the architectural protein CTCF, enriched at sites involved in long- range interactions and on insulators, finding both tissue-invariant and tissue-specific binding sites at different parts of the locus. To study if the topology of the locus influences enhancer promoter communication and how it does this, we created three lines of mice carrying different chromosomal inversions. Each of which reshuffles the relative positions of the different genetic elements: c-Myc promoter, enhancers and CTCF binding sites. The observed effects of the genetic engineering include significant reductions of c-Myc expression in the facial tissues and redirection of regulatory activity to other 1 genes. In the liver we saw instead milder and non-significant effects of the inversions on c-Myc regulation. We investigated the occupancy of CTCF and the Cohesin complex subunit RAD21 (another architectural protein) in the facial mesenchyme and liver, on the engineered lines, detecting in c-Myc locus just some minor changes compared to the Wt. Our data suggest that the architecture of the loci may have a functional role in organizing promoters-regulatory elements interactions, and, if altered, can lead to genes misexpression. In case architectural proteins are involved in this process, our data suggests that their binding to the genome, not significantly altered by genetic reshuffling, may be mostly determined by the DNA sequence (genetics). On the other hand, it is possible that the long-range interactions engaged by these proteins may be influenced more by their working context.
Potential effects of climate change on canopy communities

This study aims to map the spatial distribution of Atlantic cloud forest and assess its protection status in the Serra da Mantiqueira, southeastern Brazil, using a combination of predictive distribution modelling and remote sensing techniques. The potential distribution of cloud forests in the Serra da Mantiqueira was predicted using a combination of three algorithms for different environmental variables, including climatic, hydrometeorological, a topographic variable and a fog-related variable. After estimating the potential cloud forest distribution, remote sensing mapping techniques were used to approximate actual cloud forest area. Four land-use classes were distinguished: cloud forest, plantation forest, a ‘high-altitude complex’, and ‘other covers’. Actual mapped cloud forest areas were compared with locations of existing protected areas to assess the status of regional cloud forest protection. Predicted cloud forest distribution was excellent, with conditions above 1500 m.a.s.l. generally the most suitable for cloud forest occurrence. Actual cloud forest occurrence mapped with remote sensing imagery was 52% of the predicted potential area with differences likely due to past forest loss and the presence of non-forest (‘high-altitude complex’) vegetation. Much of the mapped cloud forest area is under nominal protection, with most areas falling into the ‘Protected Area with Sustainable Use of Natural Resources’ category. The combined use of predictive distribution modelling and remotely sensed observations successfully mapped cloud forest extent in the study area. The results reinforce the need to assign high conservation priority to the Serra da Mantiqueira as a whole and to create a core area with full protection status. m.a.s.l. et al., 2005). occurs frequently at during winter, but is rare 1999b).