Miracle-dz/UniFAR-FTUs huggingface dataset:
An African Bat Hotspot: The Exceptional Importance of Mount Nimba for Bat Diversity

Mount Nimba, covering 674 km2, straddles Liberia, Guinea and Côte d'Ivoire (Ivory Coast) in West Africa and is situated in the transition zone between the tropical forest zone to the south and moist woodlands to the north. Mount Nimba supports an exceptional biodiversity, with a number of endemic plants, invertebrates and vertebrates restricted to the massif, including the bat Hipposideros lamottei. Previous surveys suggested a high bat richness of 41 species associated with the mountain. During a series of surveys conducted in 2008–2012, we found that the bat diversity in this region far surpasses earlier figures and currently is 59 species. At least one bat species is entirely restricted to the mountain, with several other near-endemics or Upper Guinea forest endemics. Three species are listed as threatened by the IUCN, including one Critically Endangered. Furthermore, the conservation statuses of nine taxa have yet to be evaluated by the IUCN, several of which are recently described species and are likely to be threatened. This study highlights the irreplaceability of Mount Nimba for the conservation of bat diversity on the African continent, and draws attention to its protection.
Multiple ecological strategies explain the distribution of exotic and native C4 grasses in heterogeneous early successional sites in Hawai’i

Aims Biotic homogenization results in novel communities containing multiple exotic species. Many attributes that contribute to the dominance of invaders and increase invasibility of communities have been identified, but rarely have factors governing the dominance of co-occurring invaders been considered. Here we assess the presence and performance of five exotic and one native C4 grass species across local (microsite) and more broad-scale variation in fire history, soil age, altitude and precipitation. We ask whether species show preferences for the same conditions, whether all are constrained by poor soil development, and how their performance changes when alone versus co-occurring. In addition to providing information useful to managers who want to control some of these species, such information can help to predict how distributions might change with climate change Methods We measured percent cover and plant height of each grass species in 64 plots in each of 15 sites, located in young volcanic substrates across environmental gradients in Hawai’i Volcanoes National Park, Hawai’i, USA. Sites varied in fire history and soil age, across altitudinal and precipitation gradients. We estimated microsite heterogeneity by measuring rock cover and soil depth, where each species was present and in plots as a whole. We analyzed effects of possible controlling variables using chi-square tests and Generalized Additive Mixed Models. Important Findings Two species (Schizachyrium condensatum and Hyparrhenia rufa) were absent in shallow soil, restricted to more mesic sites and showed increasing performance with soil depth. By contrast, two other species (Andropogon virginicus and Melinis repens) tended to occur in shallow soil with high rock cover across a wide range of sites. One additional species (Melinis minutiflora) was weakly affected by soil depth and was the dominant at higher elevation (more mesic) and on burned sites, especially in old soil. This species was largely absent from lower elevation sites, where the more widespread and opportunistic congener, M. repens, and a drought tolerant native grass, Heteropogon contortus, were more abundant. The latter was confined to this low hot zone. Introduced C4 grasses in this region of Hawai’i are distributed according to an interaction between soil requirements, climate (correlated with elevation), competitive ability and fire response. No one strategy can explain the distributions, which will likely persist unless climate changes toward warmer and drier conditions or new fires occur. The latter would promote dominance of M. minutiflora in more mesic sites, while the former would promote either native (H. contortus) or other exotic grasses (M. repens, A. virginicus).
Development of AHP-embedded Deng’s hybrid MCDM model in micro-EDM using carbon-coated electrode

Abstract The use of thin film-coated micro-tool electrode introduced a new technical solution to bring the best technical–economic efficiency in the field of non-conventional machining processes. Multi-objective optimization of process parameters in micro-electrical discharge machining (EDM) is very limited with the help of thin film-coated micro-tool, which brought benefits for the industry. In this research work, the technological parameters such as voltage (V), spindle rotation, and capacitance (C) in micro-EDM using carbon-coated electrode were optimized, and Z-coordinate depth of cut and tool wear rate were selected as response variables. Taguchi is combined with Deng’s method to solve this multi-objective decision problem. The results showed that Taguchi–Deng’s method is the right solution for multi-target decision in micro-EDM using the coated electrode. C is the strongest influence on optimal efficiency, and it is the smallest with V. The machining quality under optimal conditions is improved.
A New Leaf-Mining Dark-Winged Fungus Gnat (Diptera: Sciaridae), with Notes on Other Insect Associates of Marsh Marigold (Ranunculaceae: Caltha palustris L.)

Abstract. The known insect associates of Caltha palustris L. (Ranunculaceae) in North America are reviewed. Zygoneura calthella new species (Sciaridae) is described from western Massachusetts, USA. Larvae bore in petioles and stems of C. palustris and mine into the basal portions of the leaves. DNA barcodes of the new and other Zygoneura species are presented. Inquilines and parasitoids in the larval galleries of Z. calthella include an undescribed species of Elachiptera Macquart (Chloropidae); Megaselia limburgensis (Schmitz) (Phoridae); Scaptomyza pallida (Zetterstedt) (Drosophilidae); and a species of Neurateles Ratzeburg (Ichneumonidae). Larvae of Prasocuris boreella (Schaeffer) (Chrysomelidae) feed externally on foliage of the same plants.
Chemical and nutritional constituents of sea buckthorn (Hippophae rhamnoides ssp. turkestanica) berries from Pakistan

Sea buckthorn (Hippophae rhamnoides L. ssp. turkestanica) is a very important multipurpose plant in areas of northern Pakistan. The berry of sea buckthorn is rich in nutrients and medicinal compounds such as vitamins, carotenoids, flavonoids, oil, carbohydrates, organic acids, amino acids and minerals. The chemical composition and nutritive value of sea buckthorn berries from eight populations from different areas of northern Pakistan were compared. The concentration of vitamin C in the berries was 250-333 mg/100 g; the seed oil was 7.69-13.7%, oil in dried pulp was 19.2-29.1% and the pytosterol content of the seed oil was 3.3-5.5%; there were 0.5-25 mg/L anthocyanins in the fruit juice. The potassium (2.8-7.2 g/kg), sodium (0.065-0.8 g/kg), calcium (0.7-1.25 g/ kg), magnesium (139-240 mg/kg), iron (40-225 mg/kg) and phosphorus (110-133 mg/kg) contents were high in dried berries. Sea buckthorn berries from Pakistan are a good source of phytonutrients and minerals.
Morphogenesis and structure of Tifton 85 cultivated in subtropical climate and fertilized with nitrogen

The experiment evaluated the morphogenesis and structure of Tifton 85 ( Cynodon spp. ) cultivated in subtropical climate and fertilized with nitrogen (N). The experiment was a completely randomized design with four levels of N (Zero; 75; 150 or 225 kg ha -1 ) in nine replicates per area. The experimental animals were Suffolk female lambs. The grazing method was continuous to maintain the sward height at 15 cm ± 10%. The stem expansion increased by 0.000027 cm degree-days -1 to each kg N applied (linear model). According to nonlinear model, the highest stem expansion (0.0226 cm degree-days -1 ) was observed with the use 220.1 kg ha -1 N. The leaf lifespan fitted a linear regression model, with increase of 50 degree-days leaf -1 , comparing the levels zero and 225 kg ha -1 of N. According to nonlinear regression model, the longest leaf lifespan (407.1 degree-days) was observed with the use 208.8 kg ha -1 N. With the maintenance of sward height at approximately 15 cm, we recommended to use 200 kg ha -1 N in Tifton 85 cultivated in subtropical climate.
Isolation of Streptomyces sp. YU100 producing extracellular phospholipase D

Soil samples were screened for actinomycete strains capable of producing phospholipase D, and a strain, Streptomyces sp. YU100, showing a high transphosphatidylation activity was isolated. This strain secreted phospholipase D in a culture broth after 12 h of cultivation, and its productivity continued to increase for 36 h of fermentation. In addition, its transphosphatidylation rate of phosphatidylcholine to phosphatidylserine was almost 68% within 1 h. The morphological and chemotaxonomical characteristics showed that this strain could be classified as a number of the Streptomycetaceae family, particularly due to the spiral form of its spore chain consisting of 60-70 smooth spores (0.75×1.0 μm) on an aerial mycelium, FA-2c type of fatty acid profile in the cell wall, and LL-DAP component in the cell wall peptidoglycan. A phylogenetic analysis of the 16S rDNA provided a clue that the strain YU100 was actually a member of the genus Streptomyces, because the determined sequence exhibited a higher homology with Streptomyes sp. ASB27, S. peucetius JCM9920, and S. griseus ATCC10137. A dendrogram based on the 16S rDNA sequences also showed a phylogenetic relationship between the strain YU100 and these strains. However, the strain YU100 has not yet been assigned to a particular species, because of absence of any other classified species with a high matching score.
AN ANTIBACTERIAL POTENTIAL OF TRAGIA INVOLUCRATA L. AGAINST OPPORTUNISTIC BACTERIAL PATHOGENS OF HIV/AIDS POSITIVE PATIENTS OF KARUR DISTRICT

Various synthetic antibiotics are in use to treat diseases caused by human pathogenic microorganisms. It is being observed that the invented medicines are not much effective in treatment, as the infection causing microbes are becoming resistant and modifying themselves into multidrug resistant strains. To fight against these human pathogens there is a need of introduction of Phytomedicines having antimicrobials action are needed to be evaluated. So the present study aims to determine the antibacterial potential of Tragia involucrata on opportunistic bacterial pathogens. Antibacterial activity of petroleum ether, acetone, chloroform, ethanol and methanol extract of Tragia involucrata was investigated by disc diffusion method on both gram positive and gram negative pathogens. Methanolic and ethanolic leaf extract showed significant activity against tested
Nucleotide-Free Crystal Structure of Nucleotide-Binding Domain 1 from Human Abcc1 Supports a 'General-Base Catalysis' Mechanism for ATP Hydrolysis.

ATP-binding cassette (ABC) transporters are molecular motors that transport substrates through biological membranes, using the energy of ATP binding and hydrolysis to foster a series of conformational changes that follow the alternating access mechanism principles. While this general scheme of substrate transport is well accepted, details about the ATP hydrolysis mechanism itself are still a matter of debate. Decades of biochemical and structural studies have identified well-conserved key residues involved in the enzymatic reaction, but their actual role, or order in the hydrolytic process, differ according to the mechanism involved. Here, we investigate the fundamental mechanisms of ATP hydrolysis, by reporting the nucleotide-free structure of the N-terminal nucleotide-Binding Domain (NBD1) of human Multidrug Resistance Protein 1 (MRP1/ABCC1), a transporter of chemotherapeutic drugs. Comparison with the nucleotide-bound structure clearly identified movements of H827 associated with nucleotide binding and release of the active site. These results, put in the context of other structural information and mutational studies of ABC transporters, support the general-base catalysis mechanism for ATP hydrolysis for ABCC1.
Evolution in Light of Mitonuclear Landscapes: An Examination of Mitochondrial Replacement in Killifish (Fundulus Spp.)

ii ACKNOWLEDGMENTS . iv LIST OF TABLES . viii LIST OF ILLUSTRATIONS . ix CHAPTER I – INTRODUCTION TO THE MITO-NUCLEAR LANDSCAPE . 1 1.1 The Mitochondrion . 1 1.2 Fitness Consequences of Cytonuclear Incompatibilities . 3 1.3 Mitochondrial Introgression. 6 1.4 Marker Types . 9 1.5 Literature Cited . 12 CHAPTER II – WIDESPREAD INTROGRESSION OF FUNDULUS OLIVACEUS MITOCHONDRIAL DNA INTO FUNDULUS EURYZONUS . 21 2.1 Abstract . 21 2.2 Introduction . 21 2.3 Methods. 24 2.4 Results . 30 2.5 Discussion . 34 2.6 Acknowledgments. 37 2.7 Literature cited . 38 vi CHAPTER III – LANDSCAPE GENETICS OF FUNDULUS OLIVACEUS AND FUNDULUS EURYZONUS IN THE LAKE PONTCHARTRAIN DRANIAGE . 45 3.1 Abstract . 45 3.2 Introduction . 45 3.3 Methods. 47 3.3.1 Sampling Locations . 47 3.3.2 Environmental data . 48 3.3.3 Fish collection and preservation . 49 3.3.4 Analyses . 50 3.4 Results . 52 3.4.2 Species identification and hybrids . 54 3.4.3 Population differentiation . 56 3.5 Discussion . 68 3.6 Acknowledgments. 71 3.7 Literature cited . 72 CHAPTER IV – LANDSCAPE GENOMICS OF FUNDULUS SPP. IN THE LAKE PONTCHARTRAIN DRAINAGE . 78 4.1 Abstract . 78 4.2 Introduction . 78 4.3 Methods. 80 vii 4.4 Results . 83 4.5 Discussion . 100 4.6 Acknowledgments. 103 4.7 Literature cited . 104 CHAPTER V – BODY SHAPE VARIATION ASSOCIATED WITH SIZE, SEX, AND RIVER OF ORIGIN IN THE FUNDULUS NOTATUS SPECIES COMPLEX. 109 5.1 Abstract . 109 5.2 Introduction . 109 5.3 Methods. 112 5.4 Results . 115 5.4.1 Sexual dimorphism and species differentiation . 115 5.4.2 Position Along the River Continuum . 119 5.4.3 River of Origin Effect . 122 5.5 Discussion . 129 5.6 Acknowledgments. 131 5.7 Literature cited . 132 APPENDIX A – IACUC Letter . 139
foxQ2 evolved a key role in anterior head and central brain patterning in protostomes

Anterior patterning of animals is based on a set of highly conserved transcription factors but the interactions within the protostome anterior gene regulatory network (aGRN) remain enigmatic. Here, we identify the foxQ2 ortholog of the red flour beetle Tribolium castaneum as novel upstream component of the insect aGRN. It is required for the development of the labrum and higher order brain structures, namely the central complex and the mushroom bodies. We reveal Tc-foxQ2 interactions by RNAi and heat shock-mediated misexpression. Surprisingly, Tc-foxQ2 and Tc-six3 mutually activate each other forming a novel regulatory module at the top of the insect aGRN. Comparisons of our results with those of sea urchins and cnidarians suggest that foxQ2 has acquired functions in head and brain patterning during protostome evolution. Our findings expand the knowledge on foxQ2 gene function to include essential roles in epidermal development and central brain patterning. Author summary The development of the anterior most part of any animal embryo – for instance the brain of vertebrates and the head of insects – depends on a very similar set of genes present in all animals. This is true for the two major lineages of bilaterian animals, the deuterostomes (including sea urchin and humans) and protostomes (including annelids and insects) and the cnidarians (e.g. the sea anemone), which are representatives of more ancient animals. However, the interaction of these genes has been studied in deuterostomes and cnidarians but not in protostomes. Here, we present the first study the function of the gene foxQ2 in protostomes. We found that the gene acts at the top level of the genetic network and when its function is knocked down, the labrum (a part of the head) and higher order brain centers do not develop. This is in contrast to the other animal groups where foxQ2 appears to play a less central role. We conclude that foxQ2 has acquired additional functions in the course of evolution of protostomes.
Glucose-6-phosphate dehydrogenase deficiency: A possible risk factor for neurodegeneration associated with aging and amphetamine use

Glucose-6-phosphate dehydrogenase (G6PD) regenerates the reduced form of nicotinamide adenine dinucleotide phosphate (NADPH), which is important for reactive oxygen species (ROS) detoxification. ROS have been implicated in the development of neurodegenerative diseases in aging as well as the neurotoxic effects of amphetamine analogs. Using a mutant G6PD-deficient mouse model, we investigated the potential neuroprotective role of G6PD in aging-related and amphetamine-initiated neurotoxicity. Aging G6PD-deficient mice exhibited increased DNA damage along with neurodegenerative changes including a marked loss of Purkinje cells. Locomotor
Editorial: Neuroinflammatory and oxidative/nitrosative pathways in neuropsychiatric and neurological diseases and their possible neuropharmacological regulation, Volume II

Departamento de BiologíaMolecular, Centro de BiologíaMolecular “SeveroOchoa” (UAM-CSIC), Madrid, Spain, Instituto Universitario de Biología Molecular, IUBM, Universidad Autónoma de Madrid, Madrid, Spain, Departamento de Farmacología y Toxicología, Facultad deMedicina, Universidad Complutense de Madrid (UCM), Instituto de Investigación Sanitaria Hospital 12 de Octubre (Imas12), Instituto Universitario de Investigación Neuroquímica (IUIN-UCM), Madrid, Spain, Centro de Investigación Biomédica en Red de Salud Mental, Instituto de Salud Carlos III (CIBERSAM, ISCIII), Madrid, Spain
Comparative and Evolutionary Studies of Vertebrate Arylsulfatase B,Arylsulfatase I and Arylsulfatase J Genes and Proteins: Evidence for anARSB-like Sub-family

Multiple sulfatase genes have been reported on the human genome, including Arylsulfatase B (ARSB), Arylsulfatase I (ARSI) and Arylsulfatase J (ARSJ). ARSB is localized in lysosomes and catalyses the hydrolysis of chondroitin and dermatan sulfate groups. Bioinformatic analyses of vertebrate genomes were undertaken using known human ARSB, ARSI and ARSJ amino acid sequences to study the relatedness and evolution of these genes and proteins. Several domain regions and key residues were conserved including signal peptides, active site residues, metal (Ca2+) and substrate binding sequences, disulfide linkages and N-glycosylation sites. The genes were widely expressed in human tissues with highest levels in esophagus (ARSB), lung (ARSI) and fibroblast cells (ARSB). Human ARSB was larger in size (>200 kb) and contained 8 coding exons, whereas ARSI and ARSJ contained only 2 coding exons among all vertebrate genomes examined. CpG islands were located within the 5’ region of the human ARSB, ARSI and ARSJ genes. In addition, six and seven miR-binding sites were observed within the 3’-UTR of human ARSB and ARSJ genes, respectively. Phylogenetic analyses describe a proposal for a primordial invertebrate SUL-3 gene serving as an ancestor for unequal cross over events generating these three genes in vertebrate genomes.
Exploring the metabolic and physiological roles of HQT in S. lycopersicum by gene editing

The most abundant phenolic compound in Solanaceous plants is chlorogenic acid (CGA), which possesses protective properties such as antimicrobial and antioxidant activities. These properties are particularly relevant when plants are under adverse conditions, such as pathogen attack, excess light, or extreme temperatures that cause oxidative stress. Additionally, CGA has been shown to absorb UV-B light. In tomato and potato, CGA is mainly produced through the HQT pathway mediated by the enzyme hydroxycinnamoyl-CoA:quinate hydroxycinnamoyl transferase. However, the absence of natural or induced mutants of this gene has made it unclear whether other pathways contribute to CGA production and accumulation. To address this question, we used CRISPR technology to generate multiple knock-out mutant lines in the tomato HQT gene. The resulting slhqt plants did not accumulate CGA or other caffeoylquinic acids (CQAs) in various parts of the plant, indicating that CQA biosynthesis depends almost entirely on the HQT pathway in tomato and, likely, other Solanaceous crops. We also found that the lack of CGA in slhqt plants led to higher levels of hydroxycinnamoyl-glucose and flavonoids compared to wild-type plants. Gene expression analysis revealed that this metabolic reorganization was partly due to flux redirection, but also involved modulation of important transcription factor genes that regulate secondary metabolism and sense environmental conditions. Finally, we investigated the physiological role of CGA in tomato and found that it accumulates in the upper epidermis where it acts as a protector against UV-B irradiation.
The amphibians of Isalo Massif, southern-central Madagascar: high frog diversity in an apparently hostile dry habitat

We provide a list of the amphibians from the Isalo Massif, southern-central Madagascar, with data on their ecology and acoustics. Although this area is constituted by a xeric sandstone massif crossed by canyons and extended savannah-like grasslands, the number of discovered frog species turned out to be high (21). This is the highest number of amphibian species ever found at a western locality of Madagascar. The number of species known to be endemic from this area is at least five (Mantella expectata, Gephyromantis azzurrae, G. corvus, Mantidactylus noralottae ,a nd Scaphiophryne gottlebei), with some other taxa (Boophis occidentalis, B. cf. periegetes, Mantidactylus sp. aff. ulcerosus), that are possibly Isalo-endemic too. This high endemicity level indicates the refuge effect played by the massif during repeated climatic changes, and the specialisation of these species to the peculiar canyon-habitat. Two sympatric species of Gephyromantis (G. azzurrae and G. corvus) evolved independently, likely for adaptation to two different aspects of the canyons (narrow or open). Part of the massif is currently managed as a national park, which is the most visited protected area of Madagascar. The remaining part of the massif is still unprotected and is threatened by the repeated fires and by the ongoing exploitation for sapphire mining. Two species, Mantella expectata and Scaphiophryne gottlebei, are captured for pet-trade, and considerations are provided regarding their conservation status.
Nest and nest characteristics of common kingfisher (Alcedo atthis) and white-throated kingfisher (Halcyon smyrnensis) in Bangladesh

This study was on nest and its site, measurement and building time of Common Kingfisher ( Alcedo atthis ) and White-throated Kingfisher ( Halcyon smyrnensis ) in Bangladesh. After pair formation, both species chose nearly 900 sloppy sandy-loam areas for nesting. The nests were tunnel-like, the length of which were 31 to 48 cm (median 36.5 cm, n = 8) for Common Kingfisher and 44 to 86 cm (median 59.25 cm, n = 10) for White-throated Kingfisher. The horizontal diameter of the outer opening of the hole of White-throated Kingfisher was almost double (6.5 to 14 cm, median 9.5 cm, n = 10) than Common Kingfisher (3.8 to 5 cm, median 4.25 cm, n = 8), whereas the vertical diameter was almost same (Common: 7.7 to 10 cm, median 4.25 cm, n = 8; and White-throated: 7.5 to 12 cm, median 10.5 cm, n = 10). The average horizontal and vertical diameters of ovalshaped egg chamber of Common Kingfisher were, 11 to 15 cm, respectively (median 12.7 cm, n = 8) and 11 to 13 cm (median 11.6 cm, n = 8) and Whitethroated Kingfisher 11 to 21 cm (median 17 cm, n = 10) and 10 to 16 cm (median 12 cm, n = 10). Both species reused old nests through cleaning (37.5% in Common Kingfisher and 50% in White-throated Kingfisher) and the nest building periods were 12 to 20 days (16.1 ± 2.5 days, n = 8) and 8 to 18 days (13.2 ± 3.5 days, n = 10), respectively. Bangladesh J. Zool. 44 (1): 99-109, 2016