Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecology of Flying foxes and the risk of Nipah virus emergence in Cambodia : O12

Pteropid bats ( Pteropus spp ) are considered to be the main reservoir of Nipah virus (NiV) that was first identified in Malaysia in 1998 after it emerged in pigs and in hu mans causing 265 cases with 105 deaths. The virus has been re - emerging on a seasonal pattern in Bangladesh where over 200 sporadic human cases have been identified since 2001 caused by food - borne and some person - to - person transmission, with an overall case fatality exceeding 70%. In Cambodia, NiV circulation in Flying Foxes population was documented in 2000 but little is known about the epidemiology of the virus. Seasonality in infectious disease circulation can be induced by multiple climatic, environment al or host - related factors. In particular, juveniles - susceptible individuals in the absence of maternal antibodies - may amplify pathogens circulation when massively entering in contact with the general population. Therefore, a synchronized reproduction of Pteropid bats in South East Asia may trigger a peak circulation of NiV due to a pulse of juvenile after the breeding season. We monitored the reproduction phenology of a population of Lyle's flying foxes ( Pteropus Lylei ) using two different census metho ds to target the surveillance of NiV. Based on these censuses, we tested urine samples collected when a pulse of juveniles was recorded. Interviews of the local population around the roosts were also conducted to assess the potential route of transmission of the virus from the bats to humans and domestic animals. Our results showed a synchronized reproduction of the flying foxes population at our study site with a pulse of juveniles in April - May. A first batch of 129 samples collected in these months was te sted for NiV and two samples were positive. We thus detected NiV in Pteropid bats with a limited number of samples tested, showing that ecologically - targeted surveillance may help optimize the detection of emerging pathogens in wildlife. Our study suggests a peak of NiV circulation in Flying Foxes between April and June. We discuss the risk of emergence of Nipah in humans and domestic animals during that period of increased risk of transmission in relation with the potential route of transmission identifie d such as hunting, fruit contamination, market contamination or palm sap drinking. (Resume d'auteur)
Descriptors of Dolichos bean (Lablab purpureus L.)

In present study, a set of 70 characterization and evaluation descriptors of vegetative, inflorescence, fruit and seed traits is described in Dolichos bean on the basis of observed trait variation among 650 germplasm over years (2012 and 2013) at University of Agricultural Sciences (UAS), Bengaluru following the guidelines of International Plant Genetic Resources Institute. Characterization descriptors serve as diagnostic markers of germplasm accessions formaintaining their identity and purity because of their easy assaying ability, stability, simple inheritance and selectively neutral. Consequently, they also aid in identification and minimizing duplication and avoiding mistakes in labeling the germplasm accessions. Characterization descriptors along with evaluation descriptors are also useful to quantify genetic variability for economically importnat traits among germplasm accessions and conducting Distinctness, Uniformity and Stability (DUS) test, a mandatory requirement for protecting varieties under Protection of Plant Varieties and Farmers Rights (PPV& FR)Act in India.
Glutathione S-Transferase Genes Differently Expressed by Pathogen-Infection in Vitis flexuosa

Glutathione S-transferase (GST) genes from transcripts of Vitis flexuosa leaves infected with Elsinoe ampelina were characterized and analyzed for their expression using primers based on specific regions. Comparison of deduced amino acid sequences from GST transcripts of V. flexuosa showed that the score of the deduced amino acid identity ranged from 43.38% (VfGST26625 and VfGST774) to 6.67% (VfGST13892 and VfGST774). Primary and secondary structure analysis was performed using the ProtParam and Self-Optimized Prediction Method with Alignment software. A phylogenetic tree was constructed from the GST proteins by the neighbor joining method using MEGA 6.0 to investigate the relationship among VfGST, VvGST, and At GST proteins. To evaluate the differential expression pattern of GST genes by real-time polymerase chain reaction (PCR), primers specific to unique regions in each gene were obtained by alignment of the sequences. Real-time PCR revealed that GST genes were expressed differentially in the leaves of V. flexuosa infected with Botrytis cinerea, E. ampelina, and Rhizobium vitis. The expression of VfGST26625 was up-regulated, while that of others were down-regulated among five GSTs in all grapevine leaves inoculated with each pathogen. The results provided herein improve our understanding of defense responses to various pathogen attacks in grapevines.
Population Genomic Analysis of the Blue Crab Callinectes sapidus Using Genotyping-By-Sequencing

ABSTRACT Previous genetic studies of the blue crab Callinectes sapidus along the U.S. Atlantic and Gulf coasts have reported weak or temporally variable spatial structure, suggesting high gene flow among distant populations possibly facilitated by long-distance larval dispersal or other features of blue crab life history. The use of relatively few genetic markers, however, may have limited power to detect subtle but significant structure that could inform fisheries management. In this study, the potential for genome-scale datasets to uncover subtle patterns of population structure in the blue crab was examined using a high-throughput genotyping approach (genotyping-by-sequencing) that generated data for more than 9,600 single nucleotide polymorphisms (SNPs) in crabs from three populations: Panama City Beach, FL, Agawam River, MA, and Porto Alegre, Brazil. Principle components analyses among the three populations revealed very distinct clustering of the Brazilian samples from U.S. populations, likely reflecting restricted gene flow across the equator. Detailed analysis of population structure between the two U.S. populations revealed low but significant genetic differentiation (FST = 0.0103), with FST values ranging from -0.05 to 0.48. Previous studies have failed to detect significant genetic structure on a similar geographic scale. FST outlier analysis identified 242 loci (2.45% of total) with statistically extreme values at the false discovery rate α = 0.05 level, only 16 of which showed significant sequence homology to annotated proteins via BLASTx alignment. Top BLASTx hits were to crustacean or arthropod sequences and 8 of the 16 had high sequence similarity to transposable elements or related machinery. Finally, results of population assignment tests for the two U.S. populations showed that the full marker dataset provided good power to assign individuals back to their population of origin (∼83% and 92% success for Panama City Beach and Agawam River, respectively), which dropped significantly when using only 500 randomly selected SNPs (∼61% and 72% success). Overall, this study demonstrates the great utility of high-throughput sequencing technologies for characterizing fine-scale patterns of genetic structure in blue crabs, and this approach should substantially improve the delineation of stock structure and further advance our understanding of blue crab population connectivity and ecology.
SOME NEW RECORDS ON SPECIES COMPOSITION AND DISTRIBUTION OF TINTINNID CILIATES (ODER TINTINNIDA) IN THE MARINE AREA OF CON CO ISLAND

A total of 46 species belonging to 19 genera, 10 families of tintinnids were identified in the coastal waters of Con Co island, of which, 1 family, 5 genera and 14 species were the new records for tintinnids in Vietnamese waters. Family Tintinnidae was the most diverse with 7 genera (accounting for 36% of total genera recorded in studied area) and 13 species (accounting for 28% of total species). Genus Tintinnopsis was the most diverse with 9 species (accounting for 19% of total species). The species composition of Tintinnids was more diverse in the southwest, south and southeast, whereas individual density was more abundant in the west and east of the island . The species composition and density of Tintinnids were more abundant and diverse in offshore area than those in inshore area of the island. The Tintinnid density at the bottom layer was about two times higher than that in the surface layer.
Evaluation of Variability in Tunisian Olea europaea L. Accessions using Morphological Characters and Computational Approaches

The olive trees (Olea europaea L.) have been cultivated for millennia in the Mediterranean basin and its oil has been an important part of human nutrition in the region. In order to distinguish between olive accessions, morphological and biological characters have been widely and commonly used for descriptive purposes and have been used to characterize olive accessions. A comparative study of morphological characters of olive accessions grown in Tunisia was carried out and analyzed using Bayesian Networks (BN) and Principal Components Analysis (PCA). The obtained results showed that averages of fruit and kernel weights were 2.27 grams and 0.41 grams, respectively. Besides, a relatively moderate level of variation (51.22%) being explained by four Principal components. BN revealed that geographical localisation plays a role in the increase of tree habit, size of lenticels and leaf shape. A dendrogram has been carried out in the aim to classify studied olive accessions. We proposed a novel method of analysis based on the three-step scheme, in which first the data set is clustered, then olive tree features are evaluated. The studied accessions can be divided into four main groups by cutting the dendrogram at a similarity value of 0.645. Different relationships are studied and highlighted, and finally the collected features are subjected to a global principal component analysis. Obtained results confirmed that core surface was negatively correlated with geographical location (r = -0.52, p<0.05) and maturation period r = -0.539, p<0.05). Number of lenticels was positively correlated to lenticels size (r = 0.632, p<0.05). Core shape had a negative correlation with fruit shape (r = -0.759, p<0.05). On the basis of these findings, this research confirmed that morphological markers are a preliminary tool to characterize olive oil accessions.
Effect of medicinal plant extracts on inoculated Meloidogyne javanica in tomato

In this study, the inhibitory effect of medicinal plant extracts viz., marigold (Tagetes spp.), rosemary (Rosmarinus officinalis L.) and nigella (Nigella sativa L.) on root-knot nematode, Meloidogyne javanica @ 1500, 2500 and 5000 juveniles were studied on susceptible tomato cv. Karoon under greenhouse condition. Although all the treatments reduced root infections rate and significantly effect on root weight (P ≤ 0.05). It was observed that when the nematode inoculum increased, reproduction factor also increased while extract treatments effect decreased. In between treatments, rosemary extract has the greatest impact on the reduction of nematode populations @ 40% concentration as compared to control.
Complete mitochondrial DNA sequence of Pseudogastromyzon changtingensis (Osteichthyes: Gastromyzontidae)

Abstract Pseudogastromyzon changtingensis belonging to the family Gastromyzontidae is a good model for phylogeny and zoogeography research. In the present paper, the sequenced mitochondrial genome of P. changtingensis is of 16573 bp in length, and encodes 13 typical protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The result of phylogenetic analysis demonstrates that P. changtingensis is close to that of P. fasciatus.
Effects of inoculation with homolactic bacteria on the conservation of wheat silage stored in bunker-silos

Abstract This study aimed to determine the effects of a homolactic inoculant on the nutritional value, fermentation pattern, aerobic stability and dry matter (DM) loss of wheat silage stored in farm-scale bunker silos. The experiment was carried out in a completely randomised design, whereas treatments were arranged in a 2 × 3 factorial scheme: wheat silage without inoculant (WS) or treated with a homolactic inoculants (Lactobacillus plantarum plus Pediococcus acidilactici at 1 × 105 cfu/g; WSI), evaluated in three silo layers (bottom, middle and top layers) of a bunker silo. The WS silage had higher levels of acetic, propionic and butyric acids and greater fermentative DM losses. However, the homolactic inoculant (WSI) worsened the aerobic stability. As previously expected, silage stored at the top layer had lower density and higher DM losses. In conclusion, the homolactic inoculant decreased the formation of volatile fatty acids and fermentative losses, but led to worse aerobic stability of wheat silages stored in bunker silos.
The E3 ubiquitin ligase UBR5 regulates centriolar satellite stability and primary cilia formation via ubiquitylation of CSPP-L

Primary cilia are crucial for signal transduction in a variety of pathways, including Hedgehog and Wnt. Disruption of primary cilia formation (ciliogenesis) is linked to numerous developmental disorders (known as ciliopathies) and diseases, including cancer. The Ubiquitin-Proteasome System (UPS) component UBR5 was previously identified as a putative modulator of ciliogenesis in a functional genomics screen. UBR5 is an E3 Ubiquitin ligase that is frequently deregulated in tumours, but its biological role in cancer is largely uncharacterised, partly due to a lack of understanding of interacting proteins and pathways. We validated the effect of UBR5 depletion on primary cilia formation using a robust model of ciliogenesis, and identified CSPP1, a centrosomal and ciliary protein required for cilia formation, as a UBR5-interacting protein. We show that UBR5 ubiquitylates CSPP1, and that UBR5 is required for cytoplasmic organization of CSPP1-comprising centriolar satellites in centrosomal periphery. Hence, we have established a key role for UBR5 in ciliogenesis that may have important implications in understanding cancer pathophysiology.
A dynamical systems modelling framework for breast cancer cell motility and morphology analysis

Cancer is a worldwide disease and, in the UK, breast cancer is the most common. Compared to healthy cells, cancer cells migrate abnormally, associated with alterations in cell motility and morphology. The development of biomedical imaging techniques result in the production of large amounts of data. The analysis of such large data, the variety of cancer cell shapes and the potential links between cell motility and morphology present a challenge for cell migration study: how to analyse cell motility and morphology simultaneously. This thesis proposes a computational framework to address integrated cancer cell migration analysis. Firstly, automated tracking of cell boundaries is undertaken by a DWNA kinematic model of cell boundaries, described by B-spline active contours. The tracked cell states intrinsically links cell morphology to motility features. As a result, cell centroid and boundary dynamics are successfully tracked, followed by quantitative motility analysis. A module to quantitatively analyse cell morphology is proposed after tracking. Cell shapes are described by a 2D descriptor. Accordingly, cell morphodynamics are modelled as a hidden Markov process, along with three shape states: round, elongated and teardrop. In order to explore the potential interactions between cell shapes and motility, cell centroid motility characteristics are associated to the identified shape states. When the analysis was applied to breast cancer control cells, the identified shape states showed distinct motility characteristics. Finally, the proposed framework is adapted to the comparison of MDA-MB-231 cell behaviours with regulating migration-associated proteins: i) Blebbistatin and Y-27632, which are chemical inhibitors of two different proteins working on the same pathway, showed identical, but different degrees of effects on the motility and morphology characteristics of MDA-MB-231 cells. ii) The absence of FA-associated genes, including FAK, RhoE and beta-PIX, respectively showed distinct effects on cell migrations.
Assessment of genetic diversity of sorghum (sorghum bicolor) accessions from Tanzania using ssr markers: implications for conservation

Plant genetic resources are a key component of global biodiversity from which humanity derives most of its food and other essential goods and services. An understanding of the extent, distribution, and patterns of genetic variation is useful for several purposes, including selection for conservation, estimation of any possible loss of genetic diversity prior to conservation programs, understanding the genetic variability available and its potential use in breeding programs, and estimating the relative strengths of the evolutionary forces shaping natural populations. Sorghum is a subsistent and staple crop for many people living across Africa especially those in marginal arid and semi-arid tropics. The study aimed to assess the genetic diversity within as well as among 96 accessions of sorghum germplasm collected from diverse regions of Tanzania using microsatellite markers. This entailed DNA extraction whereby the CTAB method was employed, DNA quality and purity check was done and then the DNA was normalized to ensure uniformity in the amount of DNA samples used and then polymerase chain reaction was done using the 12 microsatellites. Data analysis was then carried out and different softwares were used in the data analysis and this included the genemapper version 3.7 software, allelobin software, powermarker version 3.25 software and Darwin version 5.0 software, all these were used for different stages of the analysis. The area of study included Dodoma, Morogoro, Babati, Kilimanjaro and Mtwara regions. The molecular markers revealed that there was considerable amount of genetic diversity among the Tanzania sorghum and this is indicated by the high number of alleles and the clusters generated. There are so many sub clusters dividing from the main clusters and this suggests that there is high level of diversity in these Tanzanians accessions. However this diversity was not divided according to the geographical regions and there was no appreciable diversity within the sorghum accessions but the sorghum accessions clustered according to their genotype i.e. the sorghum landraces clustered together and the varieties also clustered together. Geographical Information Systems was also used. GIS was used in this study whereby maps showing the collecting localities and the environmental conditions for those localities were generated using a combination of different GIS and computer software.
Phytochemical screening of antifungal biocompounds from fruits and leaves extract of Cerbera odollam Gaertn

Nowadays, heavy usage of fungicide in agricultural industries has resulted in environmental pollution in additional to expose a significant risk to human health. Hence, there is a need to develop alternatives to replace synthetic fungicides. In this research, phytochemical test was carried out on both fruits and leaves of Cerbera odollam Gaertn using standardized procedures to determine the antifungal compounds present in the ethanol extracts. Antifungal bioassay was performed through Kirby- Bauer disc diffusion method at various weight (0.5mg to 100mg) against fungi: Aspergillus niger, Fusarium oxysporum and Penicilium citrum. Fungi assay was assessed based on the minimum inhibitory amount of both ethanol extracts. The results of the research showed the presence of the active compounds such as alkaloid, cardiac glycoside, phenol, steroid, tannin and terpenoid in the extracts. Leaves extracts were found to have more phytoconstituents as compared to the fruits extracts. Besides, antifungal activity of leaves extract had moderate antifungal effects against Aspergillus niger (13.40mm inhibition zone) and Penicilium citrum (15.73mm inhibition zone). However, Fusarium oxysporum did not exhibit inhibition zone with this extract. Leaves extract showed best antifungal activity against Penicilium citrum, with the lowest dosage (<1mg) when compared to others. Meanwhile, fruits had showed weak antifungal activity (below 11.00mm inhibition zone) for all the tested fungi. The study on Cerbera odollam’s fruits and leaves extract indicated that they have an antifungal potential to be used as an alternative to synthetic fungicides. Investigation for its active biocompounds could be exploited further.
The Diet of the Cumberland Plateau Salamander (Plethodon kentucki) in an Old Growth Forest of Southeastern Kentucky

Abstract Examining the diet of salamanders is important for understanding their effects on invertebrate communities and the interactions among sympatric salamander species. We examined the diet of the Cumberland Plateau Salamander, Plethodon kentucki (Mittleman), in an old growth forest in southeastern Kentucky. A total of 763 prey items were recovered from 73 salamanders with an average of 10.75 prey items per stomach. The four most important prey groups were Formicidae (ants), Araneae (spiders), Coleoptera (beetles), and Collembola (springtails). Overall, we found a total of 58 different prey types in the stomach contents from 20 invertebrate orders. This study represents one of the few successful uses of nonlethal gastric lavage methods on a large plethodontid salamander and the first description of P. kentucki diet identified to family and genus. Future work should examine diet throughout the year, compare prey species composition to sympatric salamander species, and look at local prey abundances and diversity to explore salamander foraging behavior.
Sequence Detection and Comparative Analysis of the Hv1 and Hv2 Control Regions of Human Mitochondrial DNA by Denaturing High-Performance Liquid Chromatography

The objective of this research was the evaluation and forensic validation of Denaturing High-Performance Liquid Chromatography (DHPLC) as a sequencingindependent means of detecting the presence of sequence differences in pair-wise mixtures of non-concordant amplicons of human mitochondrial DNA (mtDNA). The reproducibility and efficacy of DHPLC results, including amplification reproducibility, injection reproducibility, and column-to-column reproducibility were measured, showing negligible assay-to-assay variability. In addition, cross-contamination on the DHPLC columns demonstrated very low level DNA carryover between a high-abundance sample and subsequent zero-volume injections. The accuracy with which DHPLC technology can be used to screen both evidence and control samples in the context of a forensic laboratory was evaluated. This was demonstrated by a number of pair-wise comparisons of each of the forensically relevant amplicons from 95 unrelated individuals in the study, and was in 100% agreement with sequencing data. Thus, DHPLC can be used to detect a diversity of sequence differences (transitions, transversions, insertions and deletions) in the mtDNA D-loop. Accordingly, DHPLC may have utility as a presumptive indicator of mtDNA sequence concordance samples.