Miracle-dz/UniFAR-FTUs huggingface dataset:
Construction of Ortholog/Paralog Group Table for PTS

The identi cation of the functions for all proteins in the genome is important to understand the features of the organism. With the increasing amount of complete genome sequences, the approaches based on comparative genomics have become particularly useful. There are attempts to automatically construct the ortholog table containing orthologous relations of genes in di erent organisms, but the complexity of organisms often requires manual e orts to add or remove speci c cases and to improve the quality of data. In order to facilitate the process of constructing ortholog tables we have been focusing on speci c aspects of protein functions [1, 2] rather than trying to cover the entire spectrum. Here we present a new addition of the ortholog/paralog group table for PTS. The phosphoenolpyruvate:carbohydorete phosphotransferase systes (PTSs) are both transport and sensing systems in gram-negative and gram-positive bacteria. They take in and phosphorylate a large number of carbohydrates, and play as signal transducers to move to these carbon sources. In general they have unique gene structures in the genome. The PTS comprises 5 or 6 components (EI, HPr, EIIA, EIIB, EIIC, EIID) where EI and HPr are common components and there are multiple components (paralogs) of EIIs depending on substrates. The EII components often form gene clusters in the genome and some of them (EIIA, EIIB, EIIC) sometimes fuse into one protein. There are many variations in the order of the components and the fusion protein in the gene cluster. In contrast to the bacterial ABC transport system [1], the PTS contains a large number of \fusion of components" that makes it di cult to cluster genes for functional grouping and to perform multiple alignment for identifying functional residue. In order to cope with this di culty, the fusion proteins were divided into the components by the homology search against our collection of known components.
Inactivation of Norovirus Surrogates after Exposure to Atmospheric Ozone

Human norovirus is the leading cause of epidemic gastroenteritis, especially in semiclosed settings such as daycares, nursing homes, hospitals, schools and on cruise ships. Outbreaks are often accompanied by contamination of environmental surfaces and commonly handled items. Surface disinfection of norovirus surrogates, feline calicivirus and murine norovirus, by 20 parts per million atmospheric ozone in a chamber maintaining 80% relative humidity was investigated. After treatment, neither virus could be detected on glass surfaces, but >5 log infectious virus was recovered from untreated controls. Ozone chambers used to decontaminate small, hand-contact items could be an important tool for controlling norovirus outbreaks.
Simplified Sample Preparation for HPLC Analysis of Ergovaline in Tall Fescue

Increased interest in the endophytic fungus, Acremonium coenophialum Morgan-Jones & Gams, and its symbiotic inhabitance of tall fescue, Festuca arundinacea Schreb. , has created the need for rapid and reliable ergovaline analysis in research and in extension service (for diagnosis). A simplified sample preparation method provides faster and more reproducible results for ergovaline quantitation in tall fescue (.)
Climate-induced mountain tree-line evolution in southern Siberia

Abstract The elevational tree-line change within the transitional zone between boreal forest and Mongolian steppes was quantified for the last millennium. The basic approach included studies along transects and measurements of tree-line positions to identify current, historical, refugee and regeneration tree lines. Tree mortality and natality were determined based on dendrochronology analysis. Tree mortality in the sixteenth to eighteenth centuries coincided with the Little Ice Age, while tree establishment was stimulated by warming at the end of nineteenth century. Downward shifts in tree line varied by an order of magnitude. The current tree-line position reoccupied the historical tree line in some transects, and was below or above the historical line in others. The regeneration line surpassed the historical tree line by 91±46 m (mean± SD). Such a heterogeneous response was attributed to local topoclimatic conditions and sapling recruitment efficiency. A mean annual 1°C increase in temperature was associated with an upward shift of the tree line by about 70 m. The upward migration rate of the current tree line was about 0.8 m year−1 during the last century. The regeneration migration rate was about 2.3 m year−1 over the past three decades. Finally, the transformation of krummholz forms of larch and Siberian pine into arborescent form was documented.
Habitat Selection by the Stream Mayfly Paraleptophlebia guttata

The causes and consequences of habitat distribution of larvae of the mayfly Paraleptophlebia guttata were analyzed in a 2nd-order stream in west-central Kentucky. Among macrohabitats, larvae were typically significantly more dense in runs and riffles than in pools. Densities were positively related to the percentage of coarse substrata in macrohabitats, but were not correlated with current velocity, predatory fish densities, or the quantity of fine particulate organic matter (food) in macrohabitats. This relationship between density and substratum coarseness was further evidenced in an in-situ colonization experiment in which larvae selected gravel and pebble substrata over sand. Among microhabitats, larvae were more abundant in leaf litter and in gravel/pebble than in silt/sand. Laboratory manipulations showed that predation rates by fish were significantly lower on mayflies in leaf litter and gravel than in fine substrata. The combined effects of substratum particle size and fish predation determine habitat distributions of larvae. Larger larvae were more abundant in runs than in riffles, but larval growth rates in artificial stream channels were similar between current velocities simulating those in riffles and runs. These results, coupled with data from drift samples, suggest that larvae shifted macrohabitats with size. Size-related differences in macrohabitat use may reflect size-related changes in microhabitat use; larvae were significantly larger in leaf litter than in other microhabitats, and leaf litter amounts were greater in runs than in riffles.
A successful application of the embryo rescue technique as a model for studying crosses between Salix viminalis and Populus species

Embryos and plants from the crosses Salix viminalis L. as the female parent and Populus alba L. , P. violascens Dode or P. tremula L. as the male parent were obtained by in vitro embryo rescue technique. F1 intergeneric progeny were obtained by overcoming post-zygotic barriers caused by the deficiency of endosperm as nutritive tissue during the first stage of embryo development. Ovules containing immature heart-stage embryos as well as early cotyledonary embryos were isolated and rescued in modified 1/2 MS medium supplemented with 3% sucrose to ensure maturity. Seedlings were cultured under in vitro conditions in 1/2 MS medium that contained 0.2 mg l–1 naphtaleneacetic acid and plantlets after rooting were transferred first into pots and subsequently to the experimental field in the Botanical Garden in Poznan, Poland. After 2 years, the putative hybrid nature of the plants was checked by analysing morphological characters and molecular markers. Scanning electron microscopy, flow cytometry and random amplification of polymorphic DNA screening of individuals confirmed the hybrid nature of the S. viminalis × P. alba and S. viminalis × P. violascens progeny and of 25% of the analysed plants from the cross S. viminalis × P. tremula. This study showed the feasibility of overcoming pre- and post-fertilisation barriers to achieve intergeneric hybrids between species from two genera of Salicaceae. The in vitro system to produce hybrids with characters of both parents could be of great importance for increasing biomass production. This study also opens new opportunities to improve other traits in trees, such as resistance to pathogens inherited from one parent.
Nest-Site Selection by Wood Turtles (Glyptemys insculpta) in a Thermally Limited Environment

Abstract In oviparous species that lack parental care, fitness of the mother depends on the selection of a high-quality nest site, as mothers do not compensate for poor incubation environment post-hatching. Near the northern range limit of Glyptemys insculpta (Wood Turtle), short summers and cool temperatures may be factors that limit population persistence because potential nest sites may not provide adequate conditions for successful egg incubation in some years. We quantified nest-site selection by examining soil temperature and substrate composition of real Wood Turtle nests (n = 5) and constructed false nests. False nests comprised two treatments: negative-test false nests (n = 5) constructed on beaches not used by females, and positive-test false nests (n = 5) constructed on beaches used by females but in microsites not chosen by females. Temperature was measured as total thermal units and mean temperature during the diel cycle. Soil composition was quantified using moisture content, organic content, and grain-size distribution. Soil temperature was the most important factor in nest-site selection. Temperatures and total thermal units were significantly higher and more variable in real nests than in false nests, except during the night. Soil composition was not significantly different among treatments. Grain sizes ranged from fine to gravel, and real nests contained mainly (58% to 96%) medium sand or larger grains. There was little variation in soil moisture among real nests, suggesting that females were choosing specific humidity conditions for nesting. Our findings can be directly applied to protecting nesting beaches for Wood Turtles, which are considered a species at risk.
Proteomics: present and future in fish, shellfish and seafood

The aim of proteomics is to simultaneously resolve all potential proteins expressed by a cell, tissue or organism in a specific physiological condition. It will allow scientists to build and test better hypotheses, with the ultimate goal to find better solutions to challenges in agricultural sciences, medicine and environmental management. Recent and very promising applications of proteomics have also been provided in the field of aquaculture, such as the search for antigenic proteins, the detection of differentially regulated proteins and the characterization of biologically active proteins primarily to investigate the physiology, development biology and impact of contaminants in aquatic organisms. Thus, a brief overview of present classical proteomics methodology (electrophoresis and mass spectrometry) is presented, and the proteome technique will be focused in the context of applications beneficial to the field of fish, shellfish and seafood ⁄seafood product. In addition, the future potential application and challenge of proteomics in aquaculture will also be discussed.
Clonal Diversity in Alpine Populations of Polygonum viviparum (Polygonaceae)

Asexual reproduction is extremely common among arctic and alpine species, and successful sexual reproduction may be rare. In asexual populations, the absence of segregation and recombination predicts reduced levels of genetic variation. Thus, genetic diversity within arctic and alpine plant populations may be quite low. Allozyme analysis of three alpine populations of Polygonum viviparum, a common herbaceous perennial with no observed sexual reproduction, revealed surprising levels of genetic diversity. There were 23 unique clones within a sample of 150 ramets. Few clones were large or distributed among all three sample populations; the majority of clones was rare (n ≤ 5) and unique to a single population. Genotypic diversity differed among the three sample populations. The number of clones and measures of diversity and evenness were much lower in the fell-field population than in wet meadow and dry meadow populations. Overall, genotypic diversity and structure of alpine P. viviparum are similar to other clonal species in which sexual reproduction is rare, and they are similar to the average for clonal species in general.
Influence of post-harvest residue management and cultivar on tiller dynamics and seed yield in timothy

Timothy (Phleum pratense L.) is a bunch-type cool season perennial grass species grown in Manitoba primarily for seed production. The objectives of this study were to determine the effect of post-harvest residue management (straw removal-SR, straw and stubble removal-SSR and fall burning-Burn) on tiller production, yield components and seed yield of five timothy cultivars (Basho, Climax, Goliath, Hokuo and Salvo), and to better understand the association between yield components and final seed yield in timothy crops grown in the dry subhumid region of the Canadian prairies. Two experiments were conducted over four production seasons at Arborg, MB and one production season at St. Claude, MB. Tiller number per m2 in spring (TS) and at harvest (THV) were measured in 1990 at St. Claude and in 1990 and 1991 at Arborg. Residue management (RM) treatment ranking for TS was Burn < SR < SSR, but tiller senescence and compensatory mechanisms resulted in equivalent THV values across all RM treatments. The number of s.
Characterization of calpastatin gene in purebred and crossbred Turkish Grey steppe cattle.

Calpastatin (CAST) is a specific inhibitor of calcium-dependent neutral protease μ-calpain found in mammalian tissues. The genetic variants in the bovine CAST gene were analysed by using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The animal material of the study consisted of 132 bulls and heifers in Turkish Grey steppe cattle and Turkish Grey steppe x Brown Swiss crossbreds. C and G alleles are characterized by CAST/RsaI polymorphism were detected in the sample of animals were studied. Allele frequency C was significantly frequent in the crossbred group compared to the pure Turkish Grey steppe animals (P<0.05). In the total samples of animals, the average allele frequency C was 56.1%. Genotypic frequencies were estimated as 0.257, 0.499 and 0.243 in the purebred Turkish Grey steppe, and 0.388, 0.470 and 0.142 in the Turkish Grey steppe x Brown Swiss crossbred population for genotypes CC, CG and GG, respectively. As a result, genotypic distributions were equilibrium in both pure and crossbred examples of Turkish Grey steppe cattle.
Review of STANDSIM model for yield projection of natural ash eucalypt forests

Summary Data from the permanent plots in natural regrowth forests of mountain ash (Eucalyptus regnans F. Muell.) and alpine ash (E. delegatensis R.T. Bak.) in Victoria were used to evaluate the accuracy of projection by the growth model, STANDSIM. In general, where the stand ages used to initiate STANDSIM's projection were 15 yr or more, the errors (biases) for one-year projections would be expected to be within ±1% of the observed values for the projected future stand densities, ±0.5% of the observed values for the projected stand basal areas, and within ±1% of the observed values for the projected total product volumes. These resultant error estimates indicated that the accuracy of the future yields projected from STANDSIM model was generally in an acceptable range, if the projection intervals were less than 50 yr and projections were initiated at a stand age of 15 yr or older. However, the projected yields from this model would have a lower precision if the projections were initiated at stand ages of less than 15 yr. As indicated by a previous researcher, the small-diameter trees were under-represented in the projected diameter distributions. This problem may indicate that the STANDSIM model overestimates the competition-induced mortality of natural ash eucalypt forests. However, our investigation did not indicate that this would result in a direct underestimation of pulpwood and overestimation of sawlog yield.
A comparison of three bacterial phosphonoacetate hydrolases from different environmental sources

Cleavage of the carbon–phosphorus bond of the xenobiotic phosphonoacetate by phosphonoacetate hydrolase represents a novel route for the microbial metabolism of organophosphonates, and is unique in that it is substrate‐inducible and its expression is independent of the phosphate status of the cell. The enzyme has previously only been demonstrated in cell extracts of Pseudomonas fluorescens 23F. Phosphonoacetate hydrolase activity is now reported in extracts of environmental Curtobacterium sp. and Pseudomonas sp. isolates capable of the phosphate‐insensitive mineralization of phosphonoacetate as the sole source of carbon, energy and phosphorus at concentrations up to 40 mmol l−1 and 100 mmol l−1, respectively. The enzymes in both strains were similarly inducible by phosphonoacetate and had a unique specificity for this substrate. However, they differed significantly from each other, and from the previously described Ps. fluorescens 23F enzyme, in respect of their apparent molecular masses, temperature optima, thermostability, sensitivity to inhibition by chelating agents and by structural analogues of phosphonoacetate, and in their affinities for the substrate.
ANTIOXIDANT ACTIVITY OF DIFFERENT SOLVENT EXTRACTS OF RICE BRAN AT ACCELERATED STORAGE OF SUNFLOWER OIL

The antioxidant activity of different extracts of rice bran (var. Super Kernel) prepared using a number of solvents (100% methanol, 80% methanol, 100% acetone and 80% acetone) were evaluated in sunflower oil (SFO) under accelerated storage conditions. The crude concentrated extracts of rice bran were added at 600 mg/kg into refined, bleached and deodorized SFO samples and stored under accelerated (65C) conditions for 24 days. Analyses were done every 4 days, and the extent of oxidative deterioration was followed by measurement of activity index, peroxide, p-anisidine, and conjugated diene and triene values. The overall order of antioxidant efficacy of rice bran extracts as determined by various antioxidant assays was 80% methanolic extract, >100% methanolic extract, >80% acetone extract and >100% acetone extract. The antioxidant activity of rice bran extracts might be attributed to the presence of phenolics and high contents of tocopherol. The results of the present comprehensive analysis demonstrated that extracts of the rice bran of Super Kernel, an indigenous cultivar of Pakistan, are a viable source of natural antioxidants and might be exploited for functional foods and nutraceutical applications.
Asian Tapirs Are No Elephants When It Comes To Seed Dispersal

The elimination of the largest herbivores (elephants and rhinoceroses) from many forests in tropical East Asia may have severe consequences for plant species that depend on them for seed dispersal. We assessed the capacity of Malayan tapirs Tapirus indicus—the next largest nonruminant herbivore in the region—as a substitute for the lost megafauna in this role by studying their ability to disperse the seeds of nine fleshy‐fruited plants with seeds 5–97 mm in length. We combined information from feeding trials, germination tests, and field telemetry to assess the effect of tapir consumption on seed viability and to estimate how far the seeds would be dispersed. The tapirs (N=8) ingested few seeds. Seed survival through gut passage was moderately high for small‐seeded plants (e.g., 36.9% for Dillenia indica) but very low for medium‐ (e.g., 7.6% for Tamarindus indica) and large‐seeded (e.g., 2.8% for Artocarpus integer) plants. Mean seed gut passage times were long (63–236 h) and only the smallest seeds germinated afterwards. Using movement data from four wild tapirs in Peninsular Malaysia we estimated mean dispersal distances of 917–1287 m (range=22–3289 m) for small‐seeded plants. Malayan tapirs effectively dispersed small‐seeded plants but acted as seed predators for the large‐seeded plants included in our study, suggesting that they cannot replace larger herbivores in seed dispersal. With the absence of elephants and rhinos many megafaunal‐syndrome plants in tropical East Asia are expected to face severe dispersal limitation problems.
Two new species of marine algae from Stewart Island, New Zealand, Medeiothamnion norrisii and Ptilothamnion rupicolum (Ceramiaceae, Rhodophyta)*

Abstract Medeiothamnion norrisii sp. nov. and Ptilothamnion rupicolum sp. nov. are newly described from Stewart Island, New Zealand. M. norrisii differs from its closest relative, Medeiothamnion lyallii (Harvey) Gordon, by its low stature, tufted habit and comparatively small cells. Reproductive development is typical of the genus except for the development of two small-celled involucral filaments from the hypogenous cell of the female fertile axis in addition to the single large-celled involucral filament found on most species of Medeiothamnion. One such small-celled filament is also reported in this paper for M. lyallii. P. rupicolum is distinct in the genus Ptilothamnion by its lithophytic habit in contrast to the epiphytic nature of the other species, and by the production of only two pericentral cells on the subapical cell of the female fertile axis instead of three as is typical for the genus. These features extend the generic limits of Ptilothamnion.
GENETIC DIVERSITY AND POPULATION STRUCTURE IN TRADESCANTIA HIRSUTICAULIS (COMMELINACEAE)

Tradescantia hirsuticaulis, the hairy-stemmed spiderwort, is an insect-pollinated perennial plant species found primarily on rock outcrops in Georgia, South Carolina, and Alabama. Although populations of T. hirsuticaulis are rare and scattered, local populations are frequently large. Levels of genetic variation were assessed for 13 populations representing the species' range in these three states. Despite the disjunct distribution of this habitat specialist and apparent lack of specialized seed and pollen dispersal mechanisms, exceptionally high levels of genetic variation are maintained within the species, with a moderate level of variation (18%) found among populations. Twenty-nine of the 33 loci resolved (88%) were polymorphic within the species; the mean number of loci polymorphic within populations was 54%. The mean number of alleles per polymorphic locus was 3.24 across all populations and averaged 2.37 within populations. Genetic diversity was 0.206 for the species, whereas mean population genetic diversity was 0.157, both much higher than the average for other short-lived herbaceous perennials. Estimated levels of gene flow were moderate (Nm = 0.95), and a significant association between geographic distance and genetic distance between populations was found (r = 0.68; P < 0.0001). Habitat destruction is the major threat to this genetically diverse species. Since gene flow among its highly dispersed populations is limited, diminution or extinction of local populations could jeopardize the long-term evolutionary potential of this species.