Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi‐scale habitat modelling identifies spatial conservation priorities for mainland clouded leopards (Neofelis nebulosa)

Deforestation is rapidly altering Southeast Asian landscapes, resulting in some of the highest rates of habitat loss worldwide. Among the many species facing declines in this region, clouded leopards rank notably for their ambassadorial potential and capacity to act as powerful levers for broader forest conservation programmes. Thus, identifying core habitat and conservation opportunities are critical for curbing further Neofelis declines and extending umbrella protection for diverse forest biota similarly threatened by widespread habitat loss. Furthermore, a recent comprehensive habitat assessment of Sunda clouded leopards (N. diardi) highlights the lack of such information for the mainland species (N. nebulosa) and facilitates a comparative assessment.
Molecular pathogenic and host range determinants of reassortant Egyptian low pathogenic avian influenza H9N2 viruses from backyard chicken

ABSTRACT Since the introduction of H9N2 low pathogenic avian influenza virus in Egypt, it became an endemic disease causing considerable economic losses in different poultry sectors especially in the presence of other secondary bacterial and viral infections. The H9N2 viruses in Egypt are in continuous evolution that needs deep analysis for their evolution pattern based on the genetic constitutions of the pathogenic determinant genes (HA, PB2, PB1, PA, and NS). In this work, samples were collected from the backyard chickens from 3 Egyptian governorates. Five selected viruses were sequenced and analyzed for the hemagglutinin gene which showed genetic relatedness to the Asian G1 lineage group B, similar to the circulating H9N2 viruses in Egypt since 2013. The sequence for PB2, PB1, PA, HA and NS genes of the selected five viruses indicate a natural re-assortment event with recent Eurasian subtypes and similar to Egyptian H9N2 virus isolated from pigeon in Egypt during 2014. The Egyptian viruses of our study possess amino acids signatures including S42, V127, L550, L672 and V504 in the internal genes NS1, PA, and PB2, of respectively of an impact on virus transmission and replication. This work indicates that the H9N2 is in continuous evolution with alarming to the reassortment occurrence.
Interactions between Climate and Nutrient Cycles on Forest Response to Global Change: The Role of Mixed Forests

Forest ecosystems are undergoing unprecedented changes in environmental conditions due to global change impacts. Modification of global biogeochemical cycles of carbon and nitrogen, and the subsequent climate change are affecting forest functions at different scales, from physiology and growth of individual trees to cycling of nutrients. This review summarizes the present knowledge regarding the impact of global change on forest functioning not only with respect to climate change, which is the focus of most studies, but also the influence of altered nitrogen cycle and the interactions among them. The carbon dioxide (CO2) fertilization effect on tree growth is expected to be constrained by nutrient imbalances resulting from high N deposition rates and the counteractive effect of increasing water deficit, which interact in a complex way. At the community level, responses to global change are modified by species interactions that may lead to competition for resources and/or relaxation due to facilitation and resource partitioning processes. Thus, some species mixtures can be more resistant to drought than their respective pure forests, albeit it depends on environmental conditions and species’ functional traits. Climate change and nitrogen deposition have additional impacts on litterfall dynamics, and subsequent decomposition and nutrient mineralization processes. Elemental ratios (i.e., stoichiometry) are associated with important ecosystem traits, including trees’ adaptability to stress or decomposition rates. As stoichiometry of different ecosystem components are also influenced by global change, nutrient cycling in forests will be altered too. Therefore, a re-assessment of traditional forest management is needed in order to cope with global change. Proposed silvicultural systems emphasize the key role of diversity to assure multiple ecosystem services, and special attention has been paid to mixed-species forests. Finally, a summary of the patterns and underlying mechanisms governing the relationships between diversity and different ecosystems functions, such as productivity and stability, is provided.
First Record of Leptocybe invasa and Ophelimus maskelli Eucalyptus Gall Wasps in Tunisia

Dhahri, S. , Ben Jamaa, M. L. , and Lo Verde, G. 2010. First record of Leptocybe invasa and Ophelimus maskelli eucalyptus gall wasps in Tunisia. Tunisian Journal of Plant Protection 5: 231236. Two Australian gall wasps were detected for the first time in Tunisia on the foliage of Eucalyptus camaldulensis trees. Leptocybe invasa was detected in 2004, while Ophelimus maskelli in 2006. L. invasa makes galls on petioles, leaf midribs and young branches whereas O. maskelli induces galls on limbs. Vigilance is recommended when seedlings are carried to plantation.
Pontoniine shrimps from Papua New Guinea, with designation of two new genera, Cainonia and Colemonia (Crustacea: Decapoda: Palaemonidae)

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Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago

Indonesia is the world’s fourth most populous country, host to striking levels of human diversity, regional patterns of admixture, and varying degrees of introgression from both Neanderthals and Denisovans. However, it has been largely excluded from the human genomics sequencing boom of the last decade. To serve as a benchmark dataset of molecular phenotypes across the region, we generated genome-wide CpG methylation and gene expression measurements in over 100 individuals from three locations that capture the major genomic and geographical axes of diversity across the Indonesian archipelago. Investigating between- and within-island differences, we find up to 10% of tested genes are differentially expressed between the islands of Mentawai (Sumatra) and New Guinea. Variation in gene expression is closely associated with DNA methylation, with expression levels of 9.7% of genes strongly correlating with nearby CpG methylation, and many of these genes being differentially expressed between islands. Genes identified in our differential expression and methylation analyses are enriched in pathways involved in immunity, highlighting Indonesia tropical role as a source of infectious disease diversity and the strong selective pressures these diseases have exerted on humans. Finally, we identify robust within-island variation in DNA methylation and gene expression, likely driven by very local environmental differences across sampling sites. Together, these results strongly suggest complex relationships between DNA methylation, transcription, archaic hominin introgression and immunity, all jointly shaped by the environment. This has implications for the application of genomic medicine, both in critically understudied Indonesia and globally, and will allow a better understanding of the interacting roles of genomic and environmental factors shaping molecular and complex phenotypes.
Entomocidal Efficacy of Different Botanical Extracts against Cotton Mealybug, Phenacoccus solenopsis Tinsley (Sternorrhyncha: Pseudococcidae)

Use of botanicals is an age-old practice where people used to utilize the extracts from the plant parts to control the insects. In the present study entomocidal effect of different plant extracts was studied against cotton mealybug, Phenacoccus solenopsis (Tinsley), Hemiptera, Pseudococcidae. Two experiments were carried out in the laboratory of Entomology Department, Gomal University, Dera Ismail Khan, Pakistan. Five treatments, viz. Neem (Azadirachta indica), Ak (Calotropis procera), Bitter Cress (Cardamine hirsuta), Ajwain (Trachyspermum ammi), Hareer (Terminalia chebula) and Garlic (Allium sativum) were evaluated at three different concentrations of 1, 2 and 3% and replicated three times. The adults or 3 instar nymphs of mealybugs were exposed to botanical extracts on Hibiscus rosasinensis leaves in glass petri dishes at constant conditions of 27±2C, 65± 5% R.H. In both experiments, A. indica extracts showed a higher mortality of both adult and 3 instar of cotton mealybug at all the tested concentrations as compared to other treatments. The efficacy of the evaluated plant extracts increased by increasing the exposure period. From the overall mean results, A. indica (Neem) seed extract at 2% registered highest (51.37%) mortality of the adult cotton mealybug. Similarly, A. indica seed extract at 3% registered highest (45.00%) mortality of 3 instar of cotton mealybug, whereas, lowest mortality was recorded in C. procera extracts at all the tested concentrations. The present results might help in getting better and safer control of cotton mealybug.
Cortical remodelling in childhood is associated with genes enriched for neurodevelopmental disorders

Cortical development during childhood and adolescence has been characterised in recent years using metrics derived from Magnetic Resonance Imaging (MRI). Changes in cortical thickness are greatest in the first two decades of life and recapitulate the genetic organisation of the cortex, highlighting the potential early impact of gene expression on differences in cortical architecture over the lifespan. It is important to further our understanding of the possible neurobiological mechanisms that underlie these changes as differences in cortical thickness may act as a potential phenotypic marker of several common neurodevelopmental and psychiatric disorders. In this study, we combine MRI acquired from a large typically-developing childhood population (n=768) with comprehensive human gene expression databases to test the hypothesis that disrupted mechanisms common to neurodevelopmental disorders are encoded by genes expressed early in development and nested within those associated with typical cortical remodelling in childhood. We find that differential rates of thinning across the developing cortex are associated with spatially-varying gradients of gene expression. Genes that are expressed highly in regions of accelerated thinning are expressed predominantly in cortical neurons, involved in synaptic remodeling, and associated with common cognitive and neurodevelopmental disorders. Further, we identify subsets of genes that are highly expressed in the prenatal period and jointly associated with both developmental cortical morphology and neurodevelopmental disorders.
Expression profiles of TRAIL and its receptors in normal, hyperplastic, and malignant endometrial tissues: Hints on endometrial cancer biology

1Bucak School of Health, Mehmet Akif Ersoy University, Burdur, Turkey 2Department of Medical Biology And Genetics, Faculty of Medicine, Akdeniz University, Antalya, Turkey 3Department of Medical Genetics, Faculty of Medicine, Cukurova University, Adana, Turkey 4Department of Pathology, Faculty of Medicine, Akdeniz University, Antalya, Turkey 5Department of Gynecology And Obstetrics, Faculty of Medicine, Akdeniz University, Antalya, Turkey
Unbiased global proteomic profiling of patient-derived meningiomas of all grades to identify molecular signatures of differentially expressed proteins and phosphoproteins.

Meningioma is the most frequent primary intracranial tumour. Surgical resection remains the main therapeutic option as pharmacological intervention is still hampered by the poor knowledge of the molecular signature of these tumours. In order to elucidate the proteomic profiling of meningiomas and identify proteins involved in their pathogenesis, we completed a comparative mass spectrometry analysis of meningioma tissue of all WHO grades, analysing global proteins, phosphoproteins and phosphopeptides. We performed differential expression analyses and functional annotation studies to identify commonly upregulated proteins and phosphoproteins in all grades of meningioma compared to meningeal tissue as well as grade-specific candidates relevant for tumour progression. Top candidates were validated by Western blotting and immunohistochemistry in an independent sample set, confirming for example significant overexpression of proteins including EGFR, STAT2 and EPS8L2 across all grades, as well as the aberrant activation of the PI3K/AKT/mTOR pathway. Further, we validated upregulation in all grades of the total and activated phosphorylated form of the NIMArelated kinase, NEK9, involved in mitotic progression and of the transmembrane protein CKAP4. Novel proteins identified in meningioma and validated as commonly overexpressed in all grades were the nuclear proto-oncogene SET and the splicing factor SF2/ASF, while another newly identified protein that was specific for high-grade meningiomas was the glycolytic enzyme hexokinase-2, involved in cellular metabolism.
Resolution and co-occurrence patterns of Gardnerella leopoldii, Gardnerella swidsinskii, Gardnerella piotii and Gardnerella vaginalis within the vaginal microbiome

Background Gardnerella vaginalis is a hallmark of vaginal dysbiosis, but is found in the microbiomes of women with and without vaginal symptoms. G. vaginalis encompasses diverse taxa differing in attributes that are potentially important for virulence, and there is evidence that ‘clades’ or ‘subgroups’ within the species are differentially associated with clinical outcomes. The G. vaginalis species description was recently emended, and three new species within the genus were defined (leopoldii, swidsinskii, piotii). 16S rRNA sequences for the four Gardnerella species are all >98.5% identical and no signature sequences differentiate them. Results We demonstrated that Gardnerella species can be resolved using partial chaperonin-60 (cpn60) sequences, with pairwise percent identities of 87.1-97.8% among the type strains. Pairwise co-occurrence patterns of Gardnerella spp. in the vaginal microbiomes of 413 reproductive aged Canadian women were investigated, and several significant co-occurrences of species were identified. Abundance of G. vaginalis, and swidsinskii was associated with vaginal symptoms of abnormal odour and discharge. Conclusions cpn60 barcode sequencing can provide a rapid assessment of the relative abundance of Gardnerella spp. in microbiome samples, providing a powerful method of elucidating associations between these diverse organisms and clinical outcomes. Researchers should consider using cpn60 in place of 16S RNA for better resolution of these important organisms.
Physicochemical and Phytochemical Analysis of Different Plant Parts of Annona muricata L. (Annonaceae)

Background: Annona muricata L. possesses multitudinous curative benefits and used traditionally to treat diverse ailments including cancer. The current study was undertaken to assess and investigate the physicochemical and phytochemical profile in different parts (rind, pulp, seed, leaf, bark and root) of Annona muricata L. collected from the State of Goa to determine requisite pharmacognostic standards for evaluating the plant material. Methods: Comparative assessment of physico-chemical parameters of plant parts viz. moisture loss, total ash, water soluble ash, acid insoluble ash and extractives were determined according to WHO recommended parameters for standardization. Phytochemical analysis to evaluate the effect of extractive solvents to determine difference of solvent polarity to phytochemical content, using aqueous, methanol, ethanol, ethyl acetate, chloroform, petroleum ether and hexane as solvents. Results: Physicochemical parameters revealed constants for identification and authentication of plant parts of A. muricata. Phytochemical analysis manifested the presence of salient classes of phytoconstituents. Among the solvents used for extraction, methanol showed the maximum yield of extract for all plant parts. Interestingly, major phytochemicals has polar properties largely extracted by methanol and part of them had semi-polar properties extracted by other polar and semi-polar solvents including alkaloids, flavonoid, saponin, phenol, tannin, proteins, amino acids, quinones and reducing sugars. Phytosterols, coumarins, fixed oils and fats were largely detected in non-polar solvents such as chloroform, petroleum ether and hexane. Conclusion: The findings of the present study form referential data for identification and standardization of the plant material for pharmaceutical applications.
RNA Polymerase II CTD phosphatase Rtr1 prevents premature transcription termination

RNA Polymerase II (RNAPII) transcription termination is regulated by the phosphorylation status of the C-terminal domain (CTD). Using disruption-compensation (DisCo) protein-protein interaction network analysis, interaction changes were observed within the termination machinery as a consequence of deletion of the serine 5 RNAPII CTD phosphatase Rtr1. Interactions between RNAPII and the cleavage factor IA (CF1A) subunit Pcf11 were reduced in rtr1Δ, whereas interactions with the CTD and RNA-binding termination factor Nrd1 were increased. These changes could be the result of altered interactions between the termination machinery and/or increased levels of premature termination of RNAPII. Transcriptome analysis in rtr1Δ cells found decreased pervasive transcription and a shift in balance of expression of sense and antisense transcripts. Globally, rtr1Δ leads to decreases in noncoding RNAs that are linked to the Nrd1, Nab3 and Sen1 (NNS)-dependent RNAPII termination pathway. Genome-wide analysis of RNAPII and Nrd1 occupancy suggests that loss of RTR1 leads to increased termination at noncoding genes and increased efficiency of snRNA termination. Additionally, premature termination increases globally at protein-coding genes where NNS is recruited during early elongation. The effects of rtr1Δ on RNA expression levels were erased following deletion of the exosome subunit Rrp6, which works with the NNS complex to rapidly degrade terminated noncoding RNAs. Overall, these data suggest that Rtr1 restricts the NNS-dependent termination pathway in WT cells to prevent premature RNAPII termination of mRNAs and ncRNAs. Additionally, Rtr1 phosphatase activity facilitates low-level elongation of noncoding transcripts that impact the transcriptome through RNAPII interference. AUTHOR SUMMARY Many cellular RNAs including those that encode for proteins are produced by the enzyme RNA Polymerase II. In this work, we have defined a new role for the phosphatase Rtr1 in the regulation of RNA Polymerase II progression from the start of transcription to the 3’ end of the gene where the nascent RNA from protein-coding genes is typically cleaved and polyadenylated. Deletion of the gene that encodes RTR1 leads to changes in the interactions between RNA polymerase II and the termination machinery. Rtr1 loss also causes early termination of RNA Polymerase II at many of its target gene types including protein coding genes and noncoding RNAs. Evidence suggests that the premature termination observed in RTR1 knockout cells occurs through the termination factor and RNA binding protein Nrd1 and its binding partner Nab3. Additionally, many of the prematurely terminated noncoding RNA transcripts are degraded by the Rrp6-containing nuclear exosome, a known component of the Nrd1-Nab3 termination coupled RNA degradation pathway. These findings suggest that Rtr1 normally promotes elongation of RNA Polymerase II transcripts through preventation of Nrd1-directed termination.
Variability of physical attributes in tropical weathered soil cultivated with irrigated beans (Phaseolus vulgaris L.)

Soil physical attributes are affected by several events. The ability to identify the variation of those attributes can be used to decide the best crop management. Although it is known that smaller grids are more representative, predicting the least number of points while maintaining accuracy is a tool that might reflect a gain in yield and time. The aims of this study were to evaluate the spatial physical variability and to define the minimum sampling density in a tropical Typic Haplustults soil using a scaled semivariogram in a central pivot area with pinto bean (Phaseolus vulgaris L.) after the eighth bean harvest in Cristalina, Goias State. Soil samples were collected at a regular grid of 10-m intervals, totaling 180 points, and at depths of 0.00–0.10 m, 0.10–0.20 m, and 0.20–0.30 m to determine total sand content (TS), silt (SIL), clay (CL), water-dispersed clay (WDC), mean weight diameter of soil aggregates (MWD), soil penetration resistance (PR), soil macroporosity (Ma), soil microporosity (Mi), and soil bulk density (BD). The results demonstrated that management promoted superficial soil compaction with increasing BD and Mi and decreasing Ma and TP. The scaled semivariogram demonstrated similarity between attributes in the three studied soil layers, evidencing strong spatial dependency. The sample density showed a strong influence of WDC in the irrigated soil properties. Adoption of a scaled semivariogram is a strategy that can be used to determine a minimum number of points that represents the spatial variability of soil physical attributes and to assist the best management in irrigated soils.
Pan African phylogeography and palaeodistribution of rousettine fruit bats: Ecogeographic correlation with Pleistocene climate vegetation cycles

The impact of Pleistocene climatic oscillations on tropical biomes is associated with changes in the extent of forest cover. Fruit bats have played a role in woodland dynamics via pollination and seed dispersal. We hypothesized that phylogeographic patterns of Rousettus on continental Africa and adjacent islands should show a signature of pluvial‐drought cycles, involving demographic expansions and contractions.
Histomorphology of exocrine pancreas of large white Yorkshire pigs (Sus scrofa)

The present study provides a baseline data on histology of exocrine part of the pancreas of large white Yorkshire pigs. Histological study revealed that the gland was covered by a thick connective tissue capsule in splenic lobe and a thin capsule in duodenal and connecting lobes. The capsule of all the pancreatic lobes consisted of collagen, elastic, reticular fibres, adipose tissue, blood vessels and nerves. The interlobular and intersublobular septa divided the gland into lobules and sublobules. Each sublobule consisted of exocrine pancreatic acini and endocrine islets of Langerhans. The exocrine portion of pancreas consisted of many serous acini which were lined by pyramidal cells. At the basal portion of pyramidal acinar cells, spherical shaped condensed and vesicular types of nuclei were noticed. Numerous zymogen granules were observed in the apical cytoplasm of all the acinar cells. Centroacinar cells were also observed in the lumen of pancreatic acini. The duct system of exocrine pancreas was consisted of intercalated duct lined by squamous cells, intralobular duct lined by cuboidal epithelium, interlobular and main ducts lined by columnar epithelium. Numerous goblet cells among the columnar epithelial cells and small serous glands in the lamina propria were observed in the main duct.