Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic polymorphism of KRT 1.2, kap 1.3 and THH gene in magra sheep

Physical traits of wool like fibre diameter, medullation, length and lustre are important in textile industry. Magra sheep has been recognised to possess good quality lustrous wool, which has high demand in the Indian carpet industry. The gene responsible for lustre wool in Magra sheep is not known. The present study was aimed to detect polymorphisms at three loci in candidate genes for wool quality viz., KRT 1.2, KAP 1.3 and THH in Magra sheep. KRT 1.2 and KAP1.3 loci were found polymorphic with three genotypes each viz., MM, MN and NN for the former and XX, XY and YY for the latter. Two genotypes (AAand AB) were observed in THH gene locus with genotype frequency of 0.97 and 0.03, respectively. The predominant genotypes were: MM for KRT 1.2, YY for KAP 1.3 and AA for THH locus. Sequence analysis of THH revealed that some repeats (intron) are missing in Magra sheep as compared to Merino sheep. Phylogenetic analysis with THH sequences of other domestic species revealed separate clustering of THH gene sequences in this study. This could be because of two novel SNPs in Magra sheep which have not been reported in any of the analysed species.
Molecular genetics analysis of milk protein gene polymorphism of dairy cows and breeding bulls in Latvia

Milk protein is the most valuable component of milk from a dietary point of view. whey proteins S1 S2 casein, casein). The object of the research was the genetic polymorphisms of milk protein genes in populations of cows and breeding bulls of milk producing breeds in Latvia. The aim was to promote cow breeding in Latvia by developing and testing molecular genetics analyses for future based on the research of genes encoding milk protein polymorphism. In methodology the molecular markers were chosen which would be suitable for characterization of polymorphism of five milk protein genes in the population of dairy cows reared in Latvia. As a genetic method chosen the Restriction Fragment Length Polymorphism (RFLP) method and most analysed alleles of milk proteins. Using data of through six SNP of five milk protein genes: CSN1S1 c. 175A > G, CSN2 c.4451A > C, CSN3 c.11625C > T and c.11661A > C, LAA c.15A > G and LGB c.3106T > C. The results of PCRRFLP analysis showed, as it was expected, that all genotypes were found in the populations.
Two new plasmid post-segregational killing mechanisms for the implementation of synthetic gene networks in E. coli

Plasmids are the workhorse of both industrial biotechnology and synthetic biology, but ensuring they remain in bacterial cells is a challenge. Antibiotic selection, commonly used in the laboratory, cannot be used to stabilise plasmids in most real-world applications, and inserting dynamical gene networks into the genome is difficult. Plasmids have evolved several mechanisms for stability, one of which, post-segregational killing (PSK), ensures that plasmid-free cells do not grow or survive. Here we demonstrate the plasmid-stabilising capabilities of the axe/txe two component system and the microcin-V system in the probiotic bacteria Escherichia coli Nissle 1917 and show they can outperform the hok/sok system commonly used in biotechnological applications. Using plasmid stability assays, automated flow cytometry analysis, mathematical models and Bayesian statistics we quantified plasmid stability in vitro. Further, we used an in vivo mouse cancer model to demonstrate plasmid stability in a real-world therapeutic setting. These new PSK systems, plus the developed Bayesian methodology, will have wide applicability in clinical and industrial biotechnology.
Molecular characterisation of a gene trap integration into the Aminopeptidase O (ApO) gene

The protease aminopeptidase O (ApO) was isolated during a gene trap screen designed to identify novel developmentally regulated genes involved in cardiovascular development. The aims of this thesis were to characterise the gene trap integration, determine the full-length open reading frame (ORF) and to investigate any functional domains that the gene contained. Additionally, germline transmission of the gene trap demonstrated expression in the vasculature of mice. Work was undertaken to investigate if there was a phenotype in the homozygous gene trap mice with particular emphasis on whether this gene was involved in the process of new blood vessel formation (angiogenesis). Initially, 5' RACE (Rapid Amplification of cDNA Ends) generated a 206 bp sequence that aligned with expressed sequence tag data to build a contig with a partial ORF of 177 amino acids. Additional rounds of 5'RACE generated a full length open reading frame of 823 amino acids. The nucleotide and protein sequence are highly conserved between mouse, rat and human. The gene encodes a catalytic domain characteristic of the Ml family of aminopeptidases and contains a C-terminal armadillo repeat sequence and a putative nuclear localisation signal (NLS). The NLS was experimentally confirmed by transfection of eGFP-ApO constructs demonstrating that the signal localised the fusion protein to the nucleoli. The gene trap ES cells were injected into blastocysts and transmitted through the germline. Generation of homozygous animals resulted in normal, healthy, viable mice with no apparent phenotype. Expression analysis by lacZ staining and RNA in situ indicated that ApO expression was restricted to the cardiovasculature of embryos and adult tissues. The possibility that the ApO may be involved in the process of angiogenesis was investigated using the aortic ring assay. Northern blot analysis has shown that there are tissue specific isoforms and RT-PCR analysis has revealed that the catalytic domain and nuclear localisation signal can be removed by alternative splicing. An antibody was raised against purified full length murine APO protein and the immunopurified antibody tested by Western blot, immunoprecipitation and immunohistochemistry. Table of contents Chapter 1:
Intestinal Pichia burtonii associated with Qiweibaizhusan

Qiweibaizhusan is a millennium ancient prescription of traditional medicine and is commonly used to treat pediatric diarrhea. Qiweibaizhusan has shown to enhance the growth of fungi, but which fungi species are associated with Qiweibaizhusan treatment remains unknown. Here we isolated a yeast strain Y1 from mouse’s intestine whose growth was enhanced by Qiweibaizhusan and identified the strain by morphologic, biochemistry and molecular biological methods. The yeast colonies were milky white, homogeneous texture. The strain could form pseudohyphae, budding breed in multiterminal buddings. It could ferment glucose and D-xylose but not form amyloid substance, assimilate glucose, sucrose, D-xylose, fructose and sorbitol. It couldn’t use potassium nitrate and urea for nitrogen source. A phylogenetic tree constructed by comparing with the published 18SrDNA and 26SrDNA sequences of relative yeast species suggested that the yeast Y1 strain was the closest relative to Pichia burtonii with more than 99% sequence similarity. So the yeast Y1 strain was Pichia burtonii. It was the first report that yeast strain in mouse intestine associated with the Traditional Chinese medicine, Qiweibaizhusan.
Herbaceous Perennial Seed Germination and Seedling Growth in Biochar-amended Propagation Substrates

The ﬁrst objective of this study was to assess the effects of coconut shell biochar in propagation substrate on seed germination and seedling growth of Coreopsis grandiﬂora (Hogg ex Sweet) ‘Early Sunrise’, Leucanthemum 3 superbum (Bergman ex J. Ingram) ‘Silver Princess’, and Eschscholzia californica (Cham.). Cornell seed germination mix was amended with the biochar (0%, 5%, 10%, 20%, or 40%, v/v). Seed germination and seedling growth were determined during a 21-day period in two germination rooms. This particular biochar amendment did not affect ﬁnal germination percentage for any of the species. All three species had seedling shoot and primary root length growth with low to moderate positive correlation ( r = 0.33–0.54) with coconut shell biochar amendment volume. Coreopsis seedling dry weight was signiﬁcantly higher with 40% biochar than the control ( P £ 0.05). The second objective of the study was to compare digitally collected data with manually collected data. Two-dimensional scans of Coreopsis and Leucanthemum seedlings were collected. Seedling dry weight (mg) and seedling length (mm) predicted seedling two-dimensional area for Coreopsis ( R 2 = 0.73, P < 0.001) and Leucanthemum ( R 2 = 0.87, P < 0.001). Digitally traced shoot and root lengths were strongly positively correlated ( r = 0.99–0.97)
Materials and methods for the efficient production of Pasteuria

(57) Abstract: The present invention provides a new advantageous method for growing bacteria. The method of the present invention is particularly useful for growing parasitic bacteria in vitro in the absence of a host tissue. In one aspect of the present invention, root-knot nematode and (rootknot nematode) Arena rear Meloidogyne Pasteuria spores as infect (Meloidogyne arenaria) or other host nematodes are grown in vitro. Pasteuria Because can grow even in the absence of nematode organization process of the present invention is extremely beneficial.
Neighboring Tree Effects and Soil Nutrient Associations with Surviving Green Ash (Fraxinus pennsylvanica) in an Emerald Ash Borer (Agrilus planipennis) Infested Floodplain Forest

Few ash trees (Fraxinus spp.) have survived the initial devastation that emerald ash borer beetle (EAB) (Agrilus planipennis) has caused in natural populations. We studied green ash (Fraxinus pennsylvanica) trees in a floodplain population after >90% of ash had died from EAB infestation. We examined the relationship among the canopy health classes of surviving ash trees and their nearest neighboring trees (within 6 m) and available soil nutrients. A subset of focal ash trees was randomly selected within health classes ranging from healthy to recently deceased. Focal trees with the healthiest canopy class had significantly fewer ash neighbors compared to declining health classes. Other species of tree neighbors did not have a significant impact on surviving ash tree canopy health. Nutrients in soils immediately surrounding focal trees were compared among health classes. Samples from treeless areas were also used for comparison. There was a significantly greater amount of sulfur (ppm) and phosphorus (mg/kg) in ash tree soil compared to treeless area soil. The relationships between these soil nutrient differences may be from nutrient effects on trees, tree effects on nutrients, or microsite variation in flooded areas. Our data do not directly assess whether these ash trees with healthier canopies have increased resistance to EAB but do indicate that at neighborhood scales in EAB aftermath forests, the surviving ash trees have healthier canopies when separated at least 6 m from other ash trees. This research highlights scale-dependent neighborhood composition drivers of tree susceptibility to pests and suggests that drivers during initial infestation differ from drivers in aftermath forests.
Nontarget effects on songbirds from habitat manipulation for Greater Sage-Grouse: Implications for the umbrella species concept

ABSTRACT The “umbrella species” concept is a conservation strategy in which creating and managing reserve areas to meet the needs of one species is thought to benefit other species indirectly. Broad-scale habitat protections on behalf of an umbrella species are assumed to benefit co-occurring taxa, but targeted management actions to improve local habitat suitability for the umbrella species may produce unintended effects on other species. Our objective was to quantify the effects of a common habitat treatment (mowing of big sagebrush [Artemisia tridentata]) intended to benefit a high-profile umbrella species (Greater Sage-Grouse [Centrocercus urophasianus]) on 3 sympatric songbird species of concern. We used a before–after control-impact experimental design spanning 3 yr in Wyoming, USA, to quantify the effect of mowing on the abundance, nest-site selection, nestling condition, and nest survival of 2 sagebrush-obligate songbirds (Brewer's Sparrow [Spizella breweri] and Sage Thrasher [Oreoscoptes montanus]) and one open-habitat generalist songbird (Vesper Sparrow [Pooecetes gramineus]). Mowing was associated with lower abundance of Brewer's Sparrows and Sage Thrashers but higher abundance of Vesper Sparrows. We found no Brewer's Sparrows or Sage Thrashers nesting in the mowed footprint posttreatment, which suggests complete loss of nesting habitat for these species. Mowing was associated with higher nestling condition and nest survival for Vesper Sparrows but not for the sagebrush-obligate species. Management prescriptions that remove woody biomass within a mosaic of intact habitat may be tolerated by sagebrush-obligate songbirds but are likely more beneficial for open-habitat generalist species. By definition, umbrella species conservation entails habitat protections at broad spatial scales. We caution that habitat manipulations to benefit Greater Sage-Grouse could negatively affect nontarget species of conservation concern if implemented across large spatial extents.
Dorper × Santa Ines F1 crossbred lambs under different grazing times and supplement levels in tropical regions: performance and macromineral requirements

Abstract The objective of this study was to evaluate the performance and net requirements for calcium (Ca), phosphorus (P), magnesium (Mg), potassium (K) and sodium (Na) in Dorper × Santa Ines F1 crossbred lambs under different grazing times and supplement levels. We used 36 uncastrated male lambs with initial body weights (BW) of 15.5 ± 1.9 kg. Twelve animals were used as a reference group, and the remaining 24 animals were divided into three treatments according to grazing time and supplement level: 9 h × 1.2% BW, 6 h × 0.84% BW and 3 h × 0.48% BW. There were increases in the final BW, average daily gain (ADG) and dry matter intake (DMI) of pasture (p < .05) in lambs that grazed longer (9 h × 1.2% BW). Feed efficiency (G/F ratio) was similar between the 9 h × 1.2% BW and 6 h × 0.84% BW groups and both the groups were greater than the 3 h × 0.48% BW. However, there was a reduction in the DMI of concentrate, total DMI, and Ca, P, Mg and K intake (p < .05) for lambs that grazed longer. However, pasture DMI and sodium intake increased (p < .05) in animals that grazed for less time (3 h). The chemical composition of the empty bodies in DM, fat, ash, Ca and P showed the greatest values (p < .05) in groups with animals grazing 9 h with a supplement level of 1.2% BW. Net maintenance requirements were 0.101–0.202 g Ca/day, 0.204–0.408 g P/day, 0.053–0.105 g Mg/day, 0.386–0.771 g K/day and 0.105–0.211 g Na/day for crossbred lambs between 15 and 30 kg BW. For the same group, net requirements to gain 100/200 g/day BW were 1.171/2.341–1.667/3.333 g Ca/day, 0.694/1.398–0.998/1.995 g P/day, 0.027/0.054–0.032/0.063 g Mg/day, 0.098/0.195–0.091/0.182 g K/day and 0.315/0.629–0.311/0.621 g Na/day. Lambs grazing longer (9 h × 1.2% BW) displayed increased ADG and concentrate intake and reduced forage intake, which increased intake and body retention of Ca, P, Mg and K.
Multiple Pleistocene refugia and repeated phylogeographic breaks in the southern Caspian Sea region: Insights from the freshwater crab Potamon ibericum

Phylogeographic studies on a number of Western Palaearctic taxa imply that the southern Caspian Sea region served as a refugium during the Last Glacial Maximum (LGM). Nevertheless, the LGM biogeography of the terrestrial and freshwater organisms in this region is poorly understood. By studying phylogeography of a species of freshwater crab, we unravel the location of probable local refugia and colonization patterns across this topographically complex landscape.
Stream community richness predicts apex predator occupancy dynamics in riparian systems

high species richness of fish families preferred by river otter also had increased river otter persistence. Mink occupied sites with increased fish richness, muskrat presence and mussel community index. Taken together, our results show occupancy of both mink and river otter were predicted by aspects of prey diversity and presence, indicating the importance of community composition in occupancy dynamics of riparian predators. Ultimately, these relationships suggest that habitat heterogeneity and system stability are important to apex predator site use. However, the relative role of bottom–up and top–down forcing in stream systems remains to be resolved.
Effects of Perch Location on Wintering Raptor Use of Artificial Perches in a California Vineyard

Abstract Most raptor species rely on perches for hunting, resting, preening, and roosting, and in many agricultural areas the availability of adequate perches can limit raptor abundance and diversity. This has negative implications for both raptor conservation and for the provisioning of natural pest control services for farmers. Installing artificial perches on agricultural lands can therefore benefit both raptors and farmers, but perches must be installed in optimal locations to maximize raptor use and minimize unnecessary costs to farmers. We monitored raptor use of artificial perches in a California vineyard over winter using remote photography to compare two sets of perch types: perches at the top versus perches at the bottom of a steep hill, and perches located among trees versus perches located in an open area. We found that raptors preferred perches on hilltops over perches at the base of hills, and that raptors seem to prefer perches in open habitat over perches located adjacent to trees, although a small sample size for this comparison limited our analysis.
Are soils under monodominant Gilbertiodendron dewevrei and under adjacent mixed forests similar? A case study in the Democratic Republic of Congo

Abstract: Soil has been proposed as a driver explaining the development of monodominant forests in the tropics, for example, Gilbertiodendron dewevrei forests (GDF) in central Africa. The aim of this study was to compare the physical and chemical properties of soils under GDF with those under an adjacent mixed forest (AMF), while controlling for topography. To this end, we set up sixteen 0.25-ha plots according to forest type and topography (plateau vs. bottomland), in the Yoko forest reserve, Democratic Republic of Congo. In each plot, we measured litter thickness and collected a total of 80 soil samples at depths of 0–5, 5–10, 10–20, 20–40 and 120–150 cm, for standard physical and chemical analyses. When controlling for topography and soil texture, we found that most of the chemical properties of soils under GDF did not differ from those of soils under AMF, particularly acidity, cation concentration, total N and the C:N ratio. The litter layer was 2.3 times thicker under GDF than under AMF stands, and, for a given texture, soils under GDF had a slightly higher organic C concentration in the 0–5 cm soil layer. This study suggests that G. dewevrei stands modify organic matter dynamics, which may be important in maintaining its monodominance.
Genetic Diversity Analysis for Salinity Tolerance in Indian Mustard [Brassica juncea (L.)] Using SSR Markers

Brassica juncea commonly known as Indian mustard is an amphidiploid species that originated through the interspecific hybridization of Brassica rapa and Brassica nigra (U., 1935). It is utilized as an oilseed, a condiment, vegetable, green manure, forage and cultivated primarily in tropical and subtropical countries (Gangapur et al., 2010). Brassica oilseed crops have a very significant role in agriculture because almost each part of plant is consumed either by human beings or animals depending upon the crop and its growth stage.
Evaluating population viability and efficacy of conservation management using integrated population models

1. Predicting population responses to environmental conditions or management scenarios is a fundamental challenge for conservation. Proper consideration of demographic, environmental and parameter uncertainties is essential for projecting population trends and optimal conservation strategies. 2. We developed a coupled integrated population model-Bayesian population viability analysis to assess the (1) impact of demographic rates (survival, fecundity, immigration) on past population dynamics; (2) population viability 10 years into the future; and (3) efficacy of possible management strategies for the federally endangered Great Lakes piping plover Charadrius melodus population. 3. Our model synthesizes long-term population survey, nest monitoring and mark–resight data, while accounting for multiple sources of uncertainty. We incorporated latent abundance of eastern North American merlins Falco columbarius , a primary predator of adult plovers, as a covariate
Neuronal Differentiation of P19 Embryonal Cells in Polyhydroxybutyrate Scaffold as a Model for Nerve Tissue Engineering

To promote long-term nerve repair, conduits made of biodegradable polymers have greatly attracted attention of tissue engineers. In this study we fabricated PHB scaffolds by two methods and compared their properties. Methods contain micro-molding (using mould), salt leaching (using sodium chloride as salt leach). The properties of fabricated scaffolds were investigated and compared using scanning electron microscopy (SEM) for morphology study, dynamic mechanical thermal analysis (DMTA). Results show that scaffolds made of salt leach method have connectivity between porous and scaffolds made of micro-molding method have better mechanical properties without porous connectivity. For in – vitro evaluation the P19 mouse embryonal carcinoma cell line was used as a suitable model system of neuronal differentiation. P19 cells differentiated into neurons and astrocytes on scaffold as indicated by optical photomicrographs method. Results notice that cells attached and differentiated on the scaffold. In – vitro assay show that it is a suitable model for use as a platform for neural tissue engineering applications.