Miracle-dz/UniFAR-FTUs huggingface dataset:
The complete mitogenome of Schizopygopsis stoliczkai (Cypriniformes: Cyprinidae) from Western China

Abstract In this study, we firstly sequenced the complete mitochondrial genome of Schizopygopsis stoliczkai (Cypriniformes: Cyprinidae) from the Yarkand River, Xinjiang, China. The mitogenome is 16,833 bp in length, composed of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 non-coding regions (origin of light-strand replication and control region). The gene content and order is in accord with the common vertebrate form. The nucleotide base composition of H-strand is 28.4% A, 27.0% T, 26.1% C, and 18.5% G. The phylogenetic analysis based on the complete mitochondrial sequences showed that S. stoliczkai was clustered into Schizopygopsis clade.
Mineral Type Structures Soil Microbial Communities

ABSTRACT Soil microorganisms living in close contact with minerals play key roles in the biogeochemical cycling of elements, soil formation, and plant nutrition. Yet, the composition of microbial communities inhabiting the mineralosphere (i.e., the soil surrounding minerals) is poorly understood. Here, we explored the composition of soil microbial communities associated with different types of minerals in various soil horizons. To this effect, a field experiment was set up in which mineral specimens of apatite, biotite, and oligoclase were buried in the organic, eluvial, and upper illuvial horizons of a podzol soil. After an incubation period of two years, the soil attached to the mineral surfaces was collected, and microbial communities were analyzed by means of Illumina MiSeq sequencing of the 16S (prokaryotic) and 18S (eukaryotic) ribosomal RNA genes. We found that both composition and diversity of bacterial, archaeal, and fungal communities varied across the different mineral surfaces, and that mineral type had a greater influence on structuring microbial assemblages than soil horizon. Thus, our findings emphasize the importance of mineral surfaces as ecological niches in soils.
MicroRNA-186 and metastatic prostate cancer.

v-vi LIST OF TABLES ix LIST OF FIGURES x-xii CHAPTER I: Introduction, Hypothesis, Specific Aims 1-32 CHAPTER II: Differential Expression of miRNAs in the serum of PCa patients 33-69 Introduction 33-39 Methods 40-50 Results 51-65 Discussion 65-69 CHAPTER III: The Impact of miR-186 on the PCa phenotype In Vitro.70-112 Introduction 70-73 Methods 74-86 Results 87-103 Discussion 104-112
Trailing blackberries : From clear-cuts to your table

Received for publication 22 May 2000. I would like to acknowledge the contributions of Angela Anderson and Rengong Meng, whose MS thesis research at Oregon State Univ. contributed to this paper; Kirsten Wennstrom (USDA–ARS/Oregon State Univ.) for overseeing the maintenance of the plant material and crosses discussed; Hugh Daubeny [Agriculture and Agri-Foods Canada, Agassiz, B.C. (retired)], Rick Harrison (Sweetbriar Inc., Watsonville, Calif.), and Ted Mackey (USDA–ARS) for help in collecting the bulk of the Rubus ursinus; and Jim Luby (University of Minnesota) for his inspiration in the initial conception of the work and help in collection of the plant material. The cost of publishing this paper was defrayed in part by the payment of page charges. Under postal regulations, this paper therefore must be hereby marked advertisement solely to indicate this fact. E-mail address: finnc@bcc.orst. edu The commercial blackberry (Rubus sp.) industry in the United States and Canada can be roughly divided into eastern North America, Oregon, and California components. In the eastern United States, the plantings tend to be fairly small (mostly <0.25 ha, but up to ≈8 ha), geared towards pick-your-own or local sales, with either semierect (e.g., ‘Chester Thornless’) or erect (e.g., ‘Navaho’) cultivars (Clark, 1992). In Oregon, there are ≈2500 ha in production (National Agricultural Statistics Service–Oregon Agricultural Statistics Service, 1999), the crop is primarily machine-harvested for the processing market, and the cultivars are trailing types (e.g., ‘Marion’ and ‘Thornless Evergreen’). The California blackberry industry, while still relatively small, is expanding, using publicly and privately developed trailing, erect, and semierect cultivars that are hand-harvested for wholesale, fresh-market sales. Breeding programs in Florida and Texas have developed blackberry cultivars from indigenous species, but have not accounted for a significant acreage in North America.
Population dynamics and secondary production of juvenile white shrimp (Litopenaeus setiferus) along an estuarine salinity gradient

The views and opinions expressed or implied in this article are those of the author (or authors) and do not necessarily reflect the position of the National Marine Fisheries Service, NOAA. Abstract—We used estimates of shrimp density, growth, mortality, and secondary production during an 84-d sampling period to compare the value of nursery habitat for juvenile white shrimp (Litopenaeus setiferus) among 3 salinity zones (intermediate, brackish, and saline zones) within Sabine Lake, an estuary of the northern Gulf of Mexico. Density, growth, mortality, and secondary production were generally higher in the saline or brackish zones and lowest in the intermediate zone. The saline and brackish zones appeared to provide the most important nursery habitat on a per-area basis, but the intermediate zone also may contribute substantially to total shrimp production; although production in the intermediate zone was modest, this zone encompasses a relatively large portion (26%) of coastal wetlands in Louisiana. The relative value of nursery areas can be dynamic; variation occurs both spatially (e.g., within an estuary and among estuaries) and temporally (e.g., from year to year). We documented within-estuary differences (i.e., differences among salinity zones within the estuary) in the value of nursery habitat for white shrimp in Sabine Lake and expect this value, especially in the intermediate zone, to vary interannually. The dynamic nature of habitats should be considered when assessing the value of estuarine nursery areas. Penaeid shrimps support several valuable commercial fisheries in the United States. Three species, brown shrimp (Farfantepenaeus aztecus), pink shrimp (F. duorarum), and white shrimp (Litopenaeus setiferus), within the family make up most of the landings in terms of weight and economic value (NMFS1). Most white shrimp are landed in the western Gulf of Mexico, specifically in Louisiana and Texas (NMFS1). The white shrimp is an estuarinedependent species that occurs inshore during the early phase of its life history. Spawning takes place offshore from late spring to early fall, postlarvae migrate into estuarine habitat, and juvenile shrimp use this nursery habitat for ~7–16 weeks before returning offshore to complete their life cycle (Muncy, 1984; Baker et al., 2014). The importance of estuarine nursery areas in supporting populations of juvenile penaeid shrimps, such as white shrimp, is
An examination of the potential efficacy of high-intensity fires for reversing woody encroachment in savannas

Summary Frequent fires are often proposed as a way of preventing woody encroachment in savannas, yet few studies have examined whether high-intensity fires can effectively reverse woody encroachment. We applied successive fire treatments to examine the effect of fire intensity on woody vegetation structure. The treatments included early dry season, low-intensity fires; late dry season, higher-intensity fires; and an unburnt control. We used pre- and post-fire airborne LiDAR to compare vegetation structural changes brought about by fires of different intensity. Early dry season fires were of lower intensity (1400–2100 kW m−1) than late dry season fires (2500–4300 kW m−1). The two treatments also differed in terms of fuel consumed, scorch heights and char heights, indicating that clear differences in fire intensity and severity were achieved. After 4 years and two fire applications, relative woody cover increased by between 20 and 110% in different height categories following low-intensity and control treatments and declined by between 3 and 70% following high-intensity fire treatments. Declines were markedly higher following two repeated high-intensity fires than following a high and then a moderate-intensity fire. Because woody shrubs in lower height classes can recover rapidly, repeated high-intensity fires would be needed to maintain lower cover. Tall trees are often assumed to be unaffected by fires. However, we found that the rate of tree loss was directly related to fire intensity, where 36% of trees were lost following repeated high-intensity fires, compared to 22% after a high- and then a moderate-intensity fire and 6% after two low-intensity fires (3% without fire). Synthesis and applications. Using LiDAR data we show that high-intensity fires can, at least in the short term, significantly reduce woody cover in South African savannas. The use of repeated high-intensity fires simultaneously causes both a positive (reduction in cover of short shrubs) and a negative (loss of tall trees) outcome, and managers need to make trade-offs when contemplating the use of fire intensity to achieve specific goals. One potential solution may be to repeatedly apply high-intensity treatments to some areas, and not to others. This could generate a heterogeneous landscape where grasses become dominant and tall trees become scarce in some places, but in others, tall trees persist (or at least decline at slower rates), and shorter woody shrubs increase in dominance. Whether this would be acceptable, or practical, remains to be tested.
Antidote effects of plants of Himalayan sub-origin against arsenic induced toxicity

Arsenic is present in the environment and human all over the world are exposed to small amounts, mostly through food, water, and air. In the developing countries like Bangladesh and India, the high prevalence of contamination, the isolation and poverty of the rural population and the high cost and complexity of arsenic removal systems have imposed a programmatic and policy challenge on an unprecedented scale. Although in India, Arsenic poisoning in ground water in Gangetic basin especially the districts adjoining the river Ganges right from Eastern Uttar Pradesh, Bihar to West Bengal is the major problem of concern. Due to which, major health related problems are arising in the population.To combat the present problem, a pre-clinical study was done on Charles foster rats and sodium arsenite at the dose of 8 mg Kg-1 body weight per day was administered to these rats for 60 days and upon these arsenic pretreated rats, novel plant extracts of Withania somnifera and Pteris longifolia were administered for 45 days to study the antidote effects of these plant extracts. These plants not only eliminated the toxic effects of arsenic but also reversed the normal physiological activity in the animal. Thus, the present study concludes that these novel plants possesses the best bioremedial impact against arsenic induced toxicity.
Bison with benefits: towards integrating wildlife and ranching sectors on a public rangeland in the western USA

Abstract The North American model of wildlife conservation, based on the public trust doctrine, is credited for the recovery of several charismatic wildlife species, including the plains bison Bison bison. In that model, wildlife is a public resource from which the private sector may not profit either individually or collectively. In recent years, however, resilience thinking is driving changes in the traditional state-run wildlife management model to allow for integrated multi-sector approaches at the landscape scale. A free-ranging herd of bison on public land in the Henry Mountains of Utah is used as a case study to consider if and how a community-based conservation programme could be developed for a state-managed wildlife resource to benefit all stakeholders. The Henry Mountains bison, which are disease-free, share the rangeland with cattle that are privately owned by individual ranchers and corporations with various economic goals and environmental values. The ranchers currently derive no benefits from the bison and have concerns regarding competition between bison and cattle. However, a threshold harvesting strategy with community participation could generate revenue to offset these concerns. It could also provide benefits to the local community, increase state revenue, and increase the size of the bison population while securing its long-term genetic viability. Implementation would initially require facilitation by policy specialists, after which we suggest a Henry Mountains bison partnership could serve as a model for bison recovery efforts elsewhere in North America.
Trait variation in response to resource availability and plant diversity modulates functional dissimilarity among species in experimental grasslands

Aims Functional trait differences among species are thought to be a prerequisite for niche differentiation. Plant traits are known to vary plastically in response to environmental conditions and different plant neighbours. However, it is not clear to which extent the direction and magnitude of trait variation differ among species representing different growth forms or varying dominance in different environments and how this trait variation affects community-level trait dissimilarity. Methods In a field experiment, we studied shoot and leaf traits of eight perennial grassland species assigned to two functional groups (grasses vs. forbs) and varying in growth stature (small vs. tall) in monocultures, twoand four-species mixtures that were exposed to two levels of light (shaded vs. full light) and nutrient availability (fertilized vs. non-fertilized) to address this gap of knowledge. Important Findings Fertilization increased leaf greenness and specific leaf area (SLA) as well as tissue nitrogen concentrations. Under shading, changes in morphological and physiological light-acquisition traits as well as increased nitrogen and decreased carbon concentrations in plant tissue indicated larger efforts to acquire light and carbon limitation of plant growth. Similar changes in light-acquisition traits as observed under shading and decreasing shoot biomass also revealed an accelerated carbon limitation at higher species richness (SR) irrespective of the external manipulation of light and nutrient supply. Overall, the direction of trait variation in response to resource availability (shade, fertilization) and SR did not differ between functional groups or growth statures. The magnitude of variation in several traits at different resource availability, however, was larger in grasses than in forbs as well as in small-statured than in tall-statured species. In general, dominant species in terms of aboveground biomass production had taller shoots with higher carbon and lower nitrogen concentrations and allocated less biomass into leaves than subordinates. The expression of leaf traits of dominants (lower SLA and higher leaf greenness than subordinates) indicated their competitive advantage in light acquisition. Shading, as well as fertilization, accentuated trait differences between dominants and subordinates. Fertilization increased community-level dissimilarity in tissue nitrogen concentrations due to differential responses of functional groups and growth statures. However, resource supply did not alter community-level dissimilarity in other traits. Our study shows that a varying extent of trait variation of species belonging to different functional groups or growth statures and varying in their ability to achieve dominance may modulate community-level trait dissimilarity at different resource availability. These results emphasize the importance to consider the context-dependency of traitbased approaches.
Comparison and differentiation of heterotrophic plate count communities in raw and drinking water by eubacterial 16S-rDNA amplicon profiling

The heterotrophic plate count (HPC) is a frequently used approach to monitor microbial water quality in raw and drinking water. It is included in many national legal directives as well as approved by international guidelines. For routine monitoring HPC is investigated in a quantitative way. Nonetheless situations might occur which demand for a qualitative analysis of the HPC community composition and their respective spatial and temporal population changes. In order to provide a fast and efficient approach for HPC community analysis, we adapted a denaturing gradient gel electrophoresis (DGGE) polymerase chain reaction (PCR) based on for the generation of specific 16S-rDNA HPC amplicon profiles. The genetic approach was evaluated and tested on different HPC communities from various ground waters, wells, and drinking water of differing conditions. The results suggests that the presented approach should provide a valuable tool for water management applications such as the analysis of regrowth activities or tracing of bacterial contamination events.
A laboratory environment previously associated with a palatablediet can result in overfeeding in rats

Enriched and non-enriched laboratory environments produce various biological and behavioral effects on laboratory animals. One of the most impacted aspects in this regard is eating behavior. We examined associations between enriched vs. non-enriched environments and palatable vs. non-palatable diets on food intake in rats. Experiment 1 demonstrated that there are no significant differences in palatable food consumption irrespective of whether rats were exposed to enriched or non-enriched environments (P>0.05). In contrast, experiment 2 demonstrated that a combination of exposure to either of these environments and palatable food is enough to produce overfeeding in rats (P less than 0.05). These outcomes in rats may offer significant inferences in regards to the regulation of eating behavior in humans.
Monitoring of reef associated and pelagic fish communities on Australia's first purpose built offshore artificial reef

&NA; Artificial reefs now form part of an integrated approach to enhance fisheries around the world. A responsible approach to artificial reef deployment calls for clear, well defined goals prior to any reef being placed in the field, followed by subsequent monitoring to assess whether these goals are being achieved. In this study, to evaluate if an artificial reef off Sydney was meeting its goal of providing quality fishing opportunities through the establishment of a complex fish assemblage, a 4‐year monitoring program was designed. This program examined the response of reef‐associated and pelagic fishes to the deployment of a purpose built offshore reef, relative to control reefs. Fish were observed immediately following deployment, but the artificial reef fish assemblage remained distinct from the three natural control reefs throughout the monitoring period. Also, the artificial reef displayed inter‐annual variability associated with successional processes, which was not evident on the natural reefs. Fish length data indicated that the artificial reef was providing resources for both juvenile and adults of a number of species. This study demonstrates artificial reefs can provide habitats for a diverse group of fish, but the assemblages are unlikely to mimic those on natural reefs. We have also shown that longer term monitoring periods, covering multiple years are required to gain a robust understanding of the response of fish to reef deployment. This information can be used to understand the benefits and limitations of future artificial reef deployments.
Phylogeographical insight into the Aleutian flora inferred from the historical range shifts of the alpine shrub Therorhodion camtschaticum (Pall.) Small (Ericaceae)

The Aleutian Islands, one of the southern margins of Beringia, were covered with ice caps during the Last Glacial Maximum (LGM). Although insular refugia for animal species have been hypothesized in this region, phylogeographical studies have never explored the biogeographical history of plant species. We aim to assess the population history of the flora of the Aleutian Islands and its biogeographical relevance to East Asia.
Nucleolin Transports Hsp72 to the Plasma Membrane Preparatory to itsRelease into the Microenvironment

Purpose: Our previous studies demonstrated that thermal stress induces the release of Hsp72 from cells by a mechanism independent of the classical protein transport pathway. However, the exact mechanism by which Hsp72, a leaderless protein, gains access to the extracellular milieu remains unknown. Materials and methods: This study is designed to determine the mechanism by which intracellular Hsp72 trafficking and release occurs. The data presented in this study suggests intracellular Hsp72 trafficking using Western blotting and Flow Cytometry. Also, unknown membrane bound proteins were identified doing in-gel digestion and LC-MS/MS. Results: We demonstrate that within 60 minutes after first exposure of cells to heat shock treatment, plasma membrane bound Hsp72 is shed and redistributed into cytosolic compartments. Inhibition of active cell transport by pre-treatment of cells with Cytochalasin B completely abrogated Hsp72 redistribution from the plasma membrane into the cytosol. Cross-linking of plasma membrane bound proteins with Hsp72 followed by Western blot analysis and LC-MS/MS analysis revealed at least seven interacting partners with Hsp72, including nucleolin, Hsp90, gp96, CAP2, TLR2, 4 and 7. Transfection of cells with nucleolin-siRNA completely inhibited baseline and heat shockinduced Hsp72 release. Conclusions: Taken together, this study for the first time demonstrates that the plasma membrane acts as a reservoir for Hsp72 and suggests that nucleolin plays an important role in Hsp72 trafficking and release.
Bioaccessible Iron and Zinc in Native and Fortified Enzyme Hydrolyzed Casein and Soya Protein Matrices

ABSTRACT Casein and soybean are superior quality proteins; however, these are known to inhibit mineral absorption. These investigations were aimed at enzymatic modification of these proteins and to study their effect on mineral bioaccessibility. Casein and soybean proteins were hydrolyzed with alcalase and trypsin individually under optimum conditions. The protein hydrolysates, prepared with different degrees of hydrolysis, were freeze dried, fortified with either iron or zinc and analyzed for bioaccessible minerals in vitro. Proteolytic hydrolysis enhanced the bioaccessibility of iron and zinc in proportion to the degree of hydrolysis. Tryptic hydrolysis enhanced the bioaccessible iron from 1–4% in casein and from 1.3–3.3% in soybean. Alcalase hydrolysis showed a comparatively higher enhancement with both the proteins. Tryptic hydrolysis enhanced zinc bioaccessibity by 3-fold in casein and alcalase hydrolysis enhanced by 2- to 2.5-fold. In soybean, dephytinization showed a synergistic effect. In conclusion, enzymatic hydrolysis of proteins looks promising for enhancing bioaccessibility of minerals in protein matrices.