Miracle-dz/UniFAR-FTUs huggingface dataset:
Changes in feeding behavior and patch use by herbivores in response to the introduction of a new predator

Top-order carnivores are naturally returning, or are being reintroduced, in a number of places where they have previously been extirpated. To explore how prey species adjust their antipredator behavior in response to these predators, we measured giving-up densities (GUDs) in experimental feeding patches and time spent vigilant for greater kudu (Tragelaphus strepsiceros), sable antelope (Hippotragus niger), and warthogs (Phacochoerus africanus) before and after an introduction of wild dogs (Lycaon pictus). Before the introduction, the only predators in the system were cheetahs (Acinonyx jubatus). After the release, none of the prey species changed their microhabitat preference, in that they all preferred open grasslands to mixed tree and bush-clumps and bushclumps. However, kudu and sable fed more intensively (i.e., achieved lower GUDs) and had lower vigilance in open grasslands, while reducing their feeding effort (i.e., higher GUDs) and increasing their vigilance near denser vegetation. When the wild dogs denned in the study site, potentially increasing contact with the prey species, the time kudu spent vigilant and their GUDs increased significantly across all patches, and continued to increase over time. In contrast, sable and warthogs stopped feeding from the experimental patches altogether during this period. The change in feeding intensity and vigilance levels by kudu likely reflected an additive antipredator response to both cheetahs and wild dogs, whereas sable and warthogs only responded to the increased risk from the wild dogs. Our results indicate that the addition of wild dogs influenced the foraging-safety trade-off for the 3 prey species, but that the antipredator behaviors utilized by these species to mitigate predation risk varied within the newly established 2-predator system.
Isolation, Characterization and Identification of Pgpr Isolates from Rhizosphere of Barley Plants (Hordeum Vulgare) in Burdwan

Plant growth promoting rhizobacteria (PGPR) a large group of bacteria that have been occurs in the rhizosphere, in association with roots which can increase plant growth directly or indirectly and crop yield also. In present communication we have isolatd and characterized a PGPR bacterium from the rhizospheric soil of Hordeum vulgare (L.). Among the properties by which PGPR exert beneficial effects on plants are facilitating the uptake of nutrients such as phosphorus via phosphate solubilization, synthesizing stimulatory phytohormones like (IAA) Vessey, J.K. (2003) The PGPR traits of the said bacterium were analysed.IAA production; production of HCN, ammonia, polysaccharide, siderophore, nitrogen fixation etc and the assay of the enzymes like protease, nitrogenase, catalase etc was done. Bioactivities like antifungal and as well as stress tolerance property like heavy metal tolerance and salt tolerance was tested. Molecular identification of the bacterium was done by 16s r-RNA sequencing . Phylogenetic tree was prepared and Phylogenetic analysis of this PGPR bacterium has confirmed that it is Burkholderia fungorum.
Storage strategies and processing of bovine milk samples for pregnancy-associated glycoproteins detection test

ABSTRACT Three experiments were performed to test if the time and storage conditions of milk samples, the preheating of samples in a water bath, as well as the carryover effect in laboratory analysis equipment could affect the pregnancy-associated glycoproteins (PAG) levels, and consequently the results of a pregnancy test. The pregnancy test used in both experiments uses the enzyme-linked immunosorbent assay method to measure the concentrations of PAG and classify the samples as pregnant, nonpregnant or suspicious. As a result, PAG levels showed no variation when the samples were analyzed up to 9 days after collection, whether stored in ambient temperature or refrigerated. The preheating of the samples in a water bath and prior to the analysis of SCC and composition also did not affect the levels of PAG, allowing the same sample used in the quality analysis to be used for the pregnancy test.
The importance of environmental enrichment for explorative animals in captivity - red foxes (Vulpes vulpes) and cyprinid fish as case studies

In captive carnivores, species-specific behaviour is often restricted by inadequate feeding regimens. Feeding live prey is not feasible in most places and food delivery is often highly predictable in space and time which is considerably different from the situation in the wild. As a result, captive carnivores are often inactive, show little behavioural diversity and are prone to behavioural problems such as stereotypic pacing. Using artificial feeding devices to substitute for natural food resources is a way to address these problems. In a group of four red fox (Vulpes vulpes), we compared a conventional feeding method to four different methods through the use of feeding enrichment that were based on natural foraging strategies of opportunistic carnivores. Feeding enrichments consisted of electronic feeders delivering food unpredictable in time which were successively combined with one of three additional treatments: a self-service food box (allowing control over access to food), manually scattering food (unpredictable in space), and an electronic dispenser delivering food unpredictably both in space and time. The aim of administering feeding enrichment in this study was to stimulate appetitive (food searching) behaviour and to increase time spent feeding. Compared to conventional feeding, diversity of behaviour and overall activity were significantly enhanced in the presence of electronic feeders in all four foxes (EF > CON1=CON2, EF+SF > CON1=CON2, EF+MS > CON1 = CON2, EF+ED > CON1=CON2). Behavioural diversity was highest when the foxes had control over access to food (EF+SF), while the manual scattering of food (EF+MS) and the electronic dispenser (EF+ED) enhanced food searching behaviour. These results indicate that in opportunistic carnivores natural foraging and feeding behaviour can be stimulated by simple feeding enrichment strategies, and that foraging behaviour is stimulated most when food delivery is unpredictable both in space and time.
The effects of wood decay type on the growth of bryophyte gametophytes

Deadwood is an important habitat for bryophytes in boreal and subalpine forests. The type of decay in wood (white, brown, and soft rot) caused by fungal colonizers has been revealed to affect bryophyte communities. However, little is known about the effects of decay type on the growth of bryophytes. We tested the effect of wood decay type on gametophyte growth for two common bryophyte species, Scapania bolanderi Austin and Pleurozium schreberi (Brid.) Mitt. , which dominate the logs in subalpine coniferous forest on Mt. Ontake, in central Honshu, Japan. We used pot culture experiments in an open-sky nursery field. After eight months of cultivation, the growth of S. bolanderi was larger on brown rot wood than white rot wood, but the growth of P. schreberi was not. Mixed cultures of the two species also showed greater growth on brown rot wood. However, growth of S. bolanderi was significantly smaller than P. schreberi in mixed culture. These results suggest that brown rot wood enhances growth of S. bolanderi, but growth may be reduced under competition from P. schreberi. The results are in agreement with the field observation that brown rot wood has a positive association with S. bolanderi coverage on deadwood.
A new species in the Skeletocutis subincarnata complex (Polyporales, Basidiomycota) from southwestern China

A new polypore species, Skeletocutis pseudo-odora, was collected on fallen branches of Pinus armandii in Guizhou Province, southwestern China. It is described based on molecular data and morphological characteristics. The species belongs to the Skeletocutis subincarnata complex, and macro-morphologically resembles S. albocream and microscopically is similar to Skeletocutis odora. However, S. albocream can be readily distinguished from S. pseudo-odora by having hyphal pegs and wider basidiospores (4–5 × 1.3–1.7 μm). S. pseudo-odora differs from S. odora in having corky basidiocarps without any odour or taste when fresh, smaller pores (6–8 per mm), thick and entire dissepiments. Phylogeny inferred from the ITS dataset indicates that Skeletocutis under the current concept was not a monophyletic genus and S. pseudo-odora was distinct from other sampled species of Skeletocutis, including S. odora.
Molecular characterisation of the complete nuclear ribosomal DNA sequence of the blacklip abalone Haliotis rubra

ABSTRACT Genes encoded in nuclear ribosomal DNA (nrDNA), which comprise a multi-family of genes with tandem repeat units, play an important role in nucleolus formation. In the present study, we sequenced and analysed the complete rDNA sequence of an economically important shellfish in Australia, Haliotis rubra. The single rDNA unit measured 9881 base pairs (bp) in length and included the following elements in order: 18S rRNA (1858 bp), internal transcribed spacers (ITS, 756 bp), 28S rRNA (3413 bp) and an intergenic spacer (IGS, 3854 bp). The phylogenetic tree was constructed using abalone ITS sequences; here, the relationship revealed that abalone species within the same region and with same chromosome number tended to cluster within a clade. The positions of putative transcription termination and RNA transcription initiation sites were predicted in the IGS region. A comparative sequence complexity analysis and dot plots revealed a high level of variability in the IGS.
Distribution and occupancy of wolverines on tundra, northwestern Alaska

Understanding wildlife distribution and habitat use is needed for effectively balancing resource development, wildlife conservation, and Alaska Native subsistence on the North Slope of Alaska, USA. This region includes the National Petroleum Reserve-Alaska (NPR-A), a 96,000-km remote area of largely undeveloped lands that is important for wildlife, including caribou (Rangifer tarandus), wolves (Canis lupus), and wolverines (Gulo gulo). We focused our study on spring distribution and occupancy of wolverines in the NPR-A because a baseline distribution estimate is required to understand current distribution and track changes over time. We conducted aerial surveys of wolverine tracks in snow during March and April of 2014 and 2015, surveying over 84,400 km using 100-km hexagonal sampling units. We used hierarchical Bayesian occupancy modeling to determine wolverine distribution and estimate probability of occupancy within each hexagon, relative to measured covariates with potential to affect either detection or occupancy. Probability of wolverine occupancy increased as well-drained soils increased, suggesting that wolverines prefer drier areas or habitat features associated with well-drained soils. In addition, as standard deviation of elevation increased, wolverine occupancy also increased, indicating that wolverines may prefer areas with more rugged and variable terrain. Mean elevation was not retained as a covariate in the best-fitting model, supporting the importance of terrain ruggedness rather than elevation on wolverine distribution within the NPR-A. Spatially, areas of highest wolverine occupancy occurred within the southern and northeastern portions of the study area, with lowest occupancy in the northern portion of the study area west of Teshekpuk Lake. Based on the spatial pattern of wolverine probability of occupancy, we proposed 4 potential wolverine management zones with varying priorities for monitoring and managing wolverine populations. 2018 The Wildlife Society.
Crosstalk between autoreactive T cells and alveolar type II epithelial cells in inflammation and tolerance

It is well established, that the lung is an organ with tolerogenic properties to avoid an immunological collapse due to infection and inflammation. However, little is known about the mechanisms underlying peripheral tolerance induction in the lung. To dissect the immunological and molecular mechanisms underlying autoimmune-mediated lung disease, CD4+ T cell reactivity to a lung-specific antigen was studied by transgenic expression of hemagglutinin (HA) in alveolar type II epithelial cells. Concomitant expression of HA and a MHC class II-restricted T cell receptor specific for HA in double transgenic mice resulted in a severe immune-mediated interstitial lung disease. Despite aggressive and rapid progression of inflammation in lung of young mice, the pulmonary inflammation reached a plateau state in elder mice, suggesting the induction of peripheral tolerance mechanisms. Extensive immunological characterization of self-reactive CD4+ T cells isolated from the inflamed lung and global gene expression profiling suggested the induction of functional regulatory T cells in the site of inflammation. Establishing a new protocol to isolate highly pure and vital alveolar type II epithelial cells ex vivo, enabled us to characterize the role of alveolar type II epithelial cells in disease progression and immune regulation. We show that alveolar type II epithelial cells are capable to induce antigen-specific T cell proliferation. Moreover, alveolar type II epithelial cells from diseased mice have a reduced capacity to stimulate naive and pre-activated self-reactive CD4+ T cells and exhibit broad changes in their gene expression profile in comparison to alveolar type II epithelial cells derived from healthy control mice. Furthermore, alveolar type II epithelial cells from diseased mice secrete soluble factors that down modulate T cell proliferation. Data obtained by extensive functional and molecular characterization suggest an important role of alveolar type II epithelial cells for the induction of T cell tolerance and immune regulation in the lung.
Nicotinamide Phosphoribosyltransferase In Smooth Muscle Cells And Aortic Integrity

i Co-authorship iii Acknowledgement iv Table of contents v List of tables xii List of figures xiii List of appendices xvi List of abbreviations xvii CHAPTER 1 GENERAL INTRODUCTION 1 1.1 Vascular system in health and disease 1 1.1.1 Importance of vascular health 1 1.1.2 Vessel morphology 2 1.1.3 The aorta 3 1.1. 4 Aortic diseases 5 1.2 Smooth muscle cell biology, dysfunction, and aging 8 1.2.1 SMC embryological origins 8 1.2.2 Extracellular components of the aorta 11 1.2.2.1 Elastic fibres 11 1.2.2. 2 Collagen 11 1.2.2.3 Proteoglycans 12 1.2.2.4 MMPs/TIMPs 13 1.2.3 SMC senescence 14 1.2.3.1 Mechanisms of cellular senescence 15 1.2.3.2 Markers of senescence 18 1.2.3.3 Vascular cell senescence 19 1.2.3.4 Benefits of cellular senescence 19 1.3 NAD 20 1.3.1 NAD in redox reactions 20
Nitrogen uptake and nitrification in the subarctic North Atlantic Ocean

Nitrification, the oxidation of ammonium to nitrite and then nitrate, is often discounted as a source of nitrate in euphotic zone waters due to photoinhibition of nitrifying microorganisms and/or competition for ammonium with phytoplankton. However, there have also been counterarguments that nitrification represents a significant “regenerated” nitrate source to phytoplankton, augmenting the “new” nitrate supplied via physical processes. If nitrification is an appreciable nitrate source in the euphotic zone, then the assumption of a balance between nitrate uptake and organic matter export will overestimate export production. We investigated the relative importance of nitrification and nitrate uptake in the subarctic North Atlantic in late spring and late summer. The rates and vertical distributions of primary production, nitrogen uptake, and ammonium and nitrite oxidation were determined through isotope tracer experiments and the distributions of the nitrogen and oxygen isotopes of nitrate. In surface waters, ammonium and nitrite oxidation rates were low, representing an average of 5.2% and 2.5% of total euphotic zone nitrate uptake, respectively. The nitrogen and oxygen isotopes of nitrate confirmed that nitrification was not significant within the euphotic zone. Comparison of the rates of nitrogen uptake and primary production showed that while springtime phytoplankton growth could be fully supported by new nitrate and recycled ammonium, up to 50% of summertime productivity was likely fueled by dissolved organic nitrogen (DON). Uptake of DON implies that the fraction of primary production exported from surface waters in the late summer was significantly lower than the measured nitrate and ammonium uptake rates suggest.
Chemical profiling and biological activity analysis of cone, bark and needle of Pinus roxburghii collected from Nepal

Aims: The present study aims to investigate chemical composition and biological activities of Pinus roxburghii collected from Kavre district of Nepal. Material and Methods: Phytochemical screening, antibacterial activities and antioxidant activities were measured. Total phenolic content and total flavonoid content was determined using the spectrophotometric analysis. Chemical composition was carried out using GC-MS analysis. Results: Phytochemical analysis reveals the presence of interesting metabolites like cardiac glycosides, saponin, protein, quinone, sterols, tannin and terpenoids. Highest total phenolic content and total flavonoid content was observed in bark crude methanol extract. Result further revealed that bark methanol extract showed the highest antioxidant activity. Furthermore, methanol and acetone extract of cone, bark and needle showed range of in-vitro antibacterial activity against gram positive and gram negative pathogens. Gas chromatography mass spectroscopy analysis of crude acetone extract of bark revealed the presence of 14 different compounds. The major chemical constituents identified in the bark extract are 1,8 cineole, linalool, beta-thujone, chrysantheone, camphor and terpinen-4-ol. Conclusions: This study showed that among that needle, cone and bark of Pinus roxburghii as a huge source of biological active metabolites. Furthermore, bark extract revealed the presence of diverse chemical constituent.
Imputation of posterior linkage probability relations reveals a significant influence of structural 3D constraints on linkage disequilibrium

Genetic association studies have become increasingly important in unraveling the genetics of diseases or complex traits. Despite their value for modern genetics, conflicting conclusions often arise through the difficulty of confirming and replicating experimental results. We argue that this problem is largely based on the application of statistical relation measures that are not appropriate for genomic data analysis and demonstrate that the standard measures used for Genome-wide association studies or genomics linkage analysis bear a statistic bias. This may come from the violation of underlying assumptions (such as independence or stationarity) as well as from other conceptual limitations in the measures or relations, such as missing invariance with respect to coding or the inability to reflect latent factors. Attempts to introduce unbiased relation measures that avoid these limitations are usually computationally expensive and do not scale for large data sizes being typical for genomics applications. To tackle these problems, we propose a straightforwardly computable relation measure called Linkage Probability (LP). This measure provides the posterior probability of a relation between two categorical data sets and considers potential biases from latent variables. We compare several aspects of popular relation measures through an illustrative example and human genomics data. We demonstrate that the application of LP to the analysis of Single Nucleotide Polymorphisms (SNP) reveals latent 3D steric effects within 1D SNP data, that approximate to chromatin loops captured by high resolution Hi-C maps.
High coverage genome sequencing and identification of genomic variants in Bengal tiger (Panthera tigris tigris)

Bengal tiger (Panthera tigris tigris), one of six extant tiger subspecies, occurs solely in the Indian subcontinent. Although endangered and threatened by various extinction risks, this is the most populous tiger subspecies with the highest genetic diversity and strongest chance of survival in the wild. Availability of high quality genomic information on this animal will help us understand its ability to adapt to different habitats and environmental changes, in addition to comparative studies with other subspecies. Here we report high coverage sequencing of the Bengal tiger genome and its mapping to the Amur tiger genome in order to discover single nucleotide to large structural variants. A total of 345 Gb, roughly equivalent to 144X coverage of the genome, was generated from 1,149,381,669 raw read pairs. Further, 990,060,729 clean read pairs, again equivalent to 115X coverage, were retained from the raw read data and considered for comparative analysis with the Amur tiger genome. This alignment showed that 97.35% of the bases mapped at 5X depth, 97.26% at 10X and 90.44% at 50X depth. We identified a total of 3,601,882 single nucleotide variants, 948 structural variants, 56,649 copy number variants and 1,760,347 simple sequence repeats. We report the first high coverage genome sequence of Bengal tiger with an overview of its genomic variants when compared to the Amur tiger genome. Of the several variants identified, we further have to assess and validate variants potentially associated with the ability of the animal to adapt to environmental changes, disease susceptibility and other important biological phenomena.
Agriculturally relevant microbial community structure in long-term fertilized paddy soils as revealed by phospholipid fatty acid (PLFA) and pyrosequencing analyses

ABSTRACT Evidence linking the direct impact of fertilization on diversity, function and phylogeny of N-fixing and P-solubilizing bacteria in rice ecosystem is lacking. This study using phospholipid fatty acid (PLFA) and 454 pyrosequencing analyses was conducted in long-term fertilized (NP, NK, PK, NPK, compost, NPK + compost) paddy field soil, the objective being to examine the community structure of the functionally important beneficial soil microbial communities. Maximum total PLFAs were observed in organic fertilizer treatments, viz. compost (881.5 ± 11.1 nmol g−1) and NPK + compost (866.5 ± 10.8 nmol g−1). Pyrosequencing revealed that the overall bacterial and eukaryal compositions at phyla level were not significant for all treatments, while the distribution of each phyla differed. Specifically, the major classified bacterial phyla for all treatments were Proteobacteria, Actinobacteria, Cyanobacteria and Firmicutes. Supported by the high throughput sequencing approach we hereby propose that the mechanism of N and P cycling under long-term balanced fertilization in a rice ecosystem is largely governed by microbes, notably by the free living N-fixing and/or P solubilizing heterocystous and/or non-heterocystous cyanobacteria, autotrophic bacteria and heterotrophic bacteria. The current study thus proposes that balanced fertilizers may be used without detrimental effects on rice soils in the long-term.