Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of individual assignment methods and factors affecting assignment success in cattle breeds using microsatellites

Abstract Comparisons of seven different individual assignment methods based on likelihood and distances were carried out with four different sets of data, which varied both in number of populations and genetic divergence. Based on 27 microsatellites genotyped in eight cattle breeds (Icelandic and seven Norwegian), 28 hybrid populations were simulated. Factors affecting individual assignment success, such as number and divergence of populations, sample size and number of loci, were assessed from actual and simulated data. The Bayesian, frequency and Nei-minimum methods performed more or less similarly. Individual assignment success depended mainly on population number and divergence (FST). Higher success was observed at high level of divergence among populations and at low number of source populations considered. With eight pure breeds and 27 loci considered the assignment success rate ranged from 55 to 70%. Generally, assignment success increased with increasing number of loci and/or sample size.
Nonsynchronous Spatial Overlap of Lizards in Patchy Habitats

Sympatric native Anolis species with similar structural habitats but contrasting climatic habitats are closer in head and body size on species—rich than on depauperate islands. In two localities, sympatric Anolis species with differential occurrences in sun or shade sought lower, more shaded perches during midday, resulting in partly nonsynchronous utilization of the vegetation by the two species. The second observation may be related to the first in the following way: nonsynchronous spatial overlap could dictate relatively great resource overlap for species coinhabiting patchy or edge areas, requiring great differences between the species in prey size in addition to those in climatic habitat. The extent of such overlap on small depauperate islands could be greater if these contained a greater proportion of patchy or edge habitats (with respect to insolation), or if climatic preferences were broader and more overlapping than on large, species—rich islands. In each locality, the relatively more shade—inhab.
Physiological Responses of Rats to High Fiber Bread Diets Containing Several Sources of Hulls or Bran

Fiber-supplemented breads, prepared by replacing 7.5% of the hard wheat flour with field pea, flax or sunflower hulls, wheat bran or microcrystalline cellulose, were evaluated for breadmaking characteristics and physiological effects on rats. Cellulose-supplemented dough and bread resembled the straight-grade wheat bread while pea hull and wheat bran breads were similar to whole wheat bread. Flax and sunflower hulls had adverse effects on dough mixograph properties, loaf volume and crumb characteristics while sunflower hulls also contributed grittiness and aftertaste in taste panel evaluations. The fiber-supplemented breads, when fed to weanling rats, gave similar feed consumptions, weight gains and serum cholesterol levels as rats fed the whole wheat bread. Pea hulls increased daily fecal weight and, with coarse sunflower hulls, decreased dry matter digestibility. Fine wheat bran and fine sunflower hulls in the bread diets were associated with low fecal weight, low fecal volume, high fecal density and high digestibility of dry matter.
Bioconcentration kinetics of hydrophobic chemicals in different densities of Chlorella pyrenoidosa

Algal density‐dependent bioconcentration factors and rate constants were determined for a series of hydrophobic compounds in Chlorella pyrenoidosa. The apparent uptake rate constants of the hydrophobic compounds in algae varied between 200 and 710,000 L/kg/d, slightly increased with hydrophobicity within an experiment, were relatively constant for each algal density, and fitted fairly within existing allometric relationships. The bioavailability of the hydrophobic test compounds was significantly reduced by sorption by algal exudates. The sorption coefficients of the hydrophobic compounds to the algal exudates were between 80 and 1,200 L/kg, and were for most algal densities in the same order of magnitude as the apparent bioconcentration factors to the algae, that is, between 80 and 60,200 L/kg. In typical field situations, however, no significant reduction in bioavailability due to exudates is expected. The apparent elimination rate constants of the hydrophobic compounds were high and fairly constant for each algal density and varied between 2 and 190/d. Because the apparent elimination rate constants were higher than the growth rate constant, and were independent of hydrophobicity, we speculated that other factors dominate excretion, such as exudate excretion‐enhanced elimination. Bioconcentration factors increased less than proportional with hydrophobicity, i.e., the octanol–water partition coefficient [Kow]. The role of algal composition in bioconcentration is evaluated. Bioconcentrations (kinetics) of hydrophobic compounds that are determined at high algal densities should be applied with caution to field situations.
Palaeoecology and Palaeoethology of the Plio-Pleistocene Genus Cervalces (Cervidae, Mammalia) in Eurasia

Abstract The paleoecology and palaeoethology of the Eurasian species of the extinct genus Cervalces are inferred by morpho-functional comparison with its living relative Alces alces. Most of the characters that differentiate A. alces from all other deer are shared by Cervalces: the peculiar morphology of the cheek teeth; the shape of the premaxillary tips; the long legs; the peculiar morphology of the femur; the extreme fusion of the tarsal elements; the peculiar articular surface of the third phalanx. The most important morpho-skeletal differences between the two genera are: the long nasal bones contiguous with the short premaxillary bones in Cervalces (whereas Alces has very short nasal bones not contiguous with the extremely long premaxillary bones); the stronger and more backward inclined ascending ramus of the mandible in Cervalces; the much wider span of antlers in Cervalces because of its longer beams; the different shape of the antler palmation; the stronger proximal ulna/radius connection in Cervalces. The close similarity between the morphological features of the dentition and postcranial skeleton of Alces and Cervalces suggests that they could have chewed the same kind of food and moved in the same way. However, their quite different facial skeleton and antler shape, should have played some ecological role, even if interpretation of such a role is difficult. Such wide antlers may possibly have served as display organs in open ground. Nevertheless, the common idea that Cervalces should have lived in more open environments than living moose is probably an oversimplification.
Plasmid‐encoded mercury resistance in a Pseudomonas stutzeri strain that degrades o‐xylene

A Pseudomonas stutzeri strain, previously isolated for its ability to utilize o-xylene, bears a plasmid, pPB, of about 80 kbp. pPB was found to encode resistance to mercuric chloride and organomercury compounds. Loss of the plasmid resulted in a simultaneous loss of the metal resistance, but not of the ability to degrade o-xylene. Transfer of the Hgr phenotype to an Hgs strain was achieved by mobilizing pPB with RP4. Mercury reductase activity was induced by mercuric chloride and by phenylmercuric acetate and Thimerosal. pPB may be considered a broad spectrum resistance plasmid.
Chapter 8: Phylogeography and Adaptive Plumage Evolution in Central American Subspecies of the Slate-Throated Redstart (Myioborus Miniatus)

Abstract The Slate-throated Redstart (Myioborus miniatus) is a common warbler of montane forests from northern Mexico to Argentina. We examined phylogenetic structure and plumage pattern in relation to subspecific taxonomy across the broad geographic range of this species. Phylogenetic analysis of two complete mitochondrial protein-coding genes (subunits 2 and 3 of NADH dehydrogenase) from 36 individuals, representing 10 of the 12 subspecies, revealed four clades, three of which showed general concordance with subspecific classification. However, in a Central American clade, four subspecies (hellmayri, connectens, comptus, and aurantiacus) could not be resolved by the molecular phylogenetic analysis, even though populations of hellmayri and connectens are currently geographically isolated from those of comptus and aurantiacus by the Nicaraguan lowlands. The genetic homogeneity within this clade suggests a late Pleistocene range expansion at a time when today's montane forest types existed at lower elevati.
Improvement of the Aluminum Borate Whisker-Mediated Method of DNA Delivery into Rice Callus

Abstract We improved the aluminum borate whisker-mediated method of DNA delivery into rice callus (Oryza sativa L., cv. Notohikari). The following factors were examined: amount of whiskers, the kind of apparatus for agitation, the type of whiskers, duration of agitation, and agitation speed. Twenty callused scutellar tissues were agitated in a 1.5 ml microtube containing aluminum borate whiskers (ABW), liquid medium, and the plasmid pAct1-F carrying the β-glucuronidase (GUS) gene. After the agitation, the scutellar tissues were subjected to transient GUS expression assay, which visualizes GUS-expressing cells as blue spots. Efficiencies of DNA delivery were evaluated as the number of blue spots resulting from the assay. In the present study, we succeeded in improving the efficiency of DNA delivery by changing the apparatus for agitation from rotary (Vortex Genie 2) to multidirectional (MT-360), and the type of ABW from Alborex Y to an aminosilane-coated Alborex (Alborex YS3A).
Characterization of microbial communities in pest colonized books by molecular biology tools

This work presents the identification of bacteria and fungi colonies in insect infesting books, by cultural-independent methodologies based on molecular biology techniques. Microbial genomic DNA extraction, in vitro amplification of specific target sequences by polymerase chain reactions (PCR), sequencing and sequence analysis were performed. These procedures minimized the samples amount, optimized the diagnostic studies on bacteria and fungi colonization and allowed the identification of many species also in complex microbial consortia. The molecular techniques for sure accomplish and integrate the microbiological standard methods ( in vitro culture) and morphological analyses (OM, SEM, CLSM), in order to understand the role of microorganisms in bio-deterioration of cultural assets. This monitoring is also indispensable to shed light on the risk for visitors and/or professionals to contract potential illnesses within indoor environments.
Pond drying and hatching date shape the tradeoff between age and size at emergence in a damselfly

The trade off between age and size at emergence, which plays a central role in life history theory, is hypothesized to be more pronounced under stressful conditions, especially when these conditions are combined. Empirical evidence for this is equivocal. We tested the hypothesis by imposing combinations of two types of time stress (pond drying and late hatching date) in larvae of the damselfly Lestes viridis. Larvae from a temporary pond and a permanent pond population were reared in outdoor tubs from egg hatching until emergence. Unexpectedly, larvae did not accelerate their life history in response to simulation of pond drying. Instead, larvae reared in temporary tubs generally had a slower development and growth than larvae reared in permanent tubs. Probably deteriorating growth conditions in temporary tubs associated with higher densities and lower food levels caused this pattern. In agreement with a higher time stress in late hatched larvae, they generally had faster development and growth than larvae that hatched early in the season. Drying regime and hatching date shaped the covariation pattern between age and size at emergence, but the tradeoff was only apparent when time stress was relaxed. The tradeoff between age and size at emergence was only present in early hatched larvae, especially in permanent tubs (lowest time stress). Conversely, in late hatched larvae there was a strongly negative relationship between age and size at emergence, especially in temporary tubs (highest time stress). Our results support an alternative hypothesis that deteriorating growth conditions (i.e. pond drying) may decouple the tradeoff under time stress. The absence of a tradeoff in more time-stressed late hatched larvae can be explained by their higher intrinsic growth rates, independent of deteriorating growth conditions. We hypothesize that the pattern of less clear tradeoffs under the imposed types of time stress may be general.
Flying Squirrel Demography Varies between Island Communities with and without Red Squirrels

Abstract Recent studies in Southeast Alaska suggest the ecology of Glaucomys sabrinus differs from populations in the Pacific Northwest. In Southeast Alaska, densities were the highest reported for the species, populations were not as closely linked to old-forest attributes, and individuals had a more diverse diet that was less dependent on mycophagy. Pacific Northwest communities are comprised of several arboreal rodents; Southeast Alaska has a depauperate mammal fauna. I hypothesized that Southeast Alaska populations had a broader realized niche because of competitive release. The red squirrel (Tamiasciurus hudsonicus) is the only other arboreal squirrel and it is absent from the southern outer islands of Southeast Alaska's Alexander Archipelago. I compared demography and body mass of G. sabrinus on Prince of Wales Island to a population in sympatry with T. hudsonicus on a separate island (Mitkof). Home ranges were larger and population density, breeding female density, and juvenile recruitment of G. sabrinus were all lower in sympatry with T. hudsonicus. In a companion study, G. sabrinus on Prince of Wales Island used cavities for denning relatively more frequently than in sympatry with T. hudsonicus on Mitkof Island. Female G. sabrinus depend on cavities for natal dens, and breeding female and population densities are positively correlated with large snag or tree density. The presence of T. hudsonicus may influence G. sabrinus populations by limiting availability of cavities. Furthermore, variation in vertebrate assemblages among islands may influence realized niches of resident species, which manifest unique demographic profiles compared to populations of different ecological communities.
Current and potential U.S. corn stover supplies.

Agricultural residues such as corn (Zea mays L.) stover are a potential feedstock for bioenergy and bio-based products that could reduceU.S. dependence on foreign oil. Collection of such residues must take into account concerns that residue removal could increase erosion, reduce crop productivity, and deplete soil carbon and nutrients. This article estimates where and how much corn stover can be collected sustainably in the USA using existing commercial equipment and estimates costs of that collection. Erosion constraints to collection were considered explicitly, and crop productivity and soil nutrient constraints were considered implicitly, by recognizing the value of residues for maintaining soil moisture and including the cost of fertilizer to replace nutrients removed. Possible soil carbon loss was not considered in the analysis. With an annual production of 196 million Mg of corn grain (about9.2 billion bushels), the USA produces 196 million Mg of stover. Under current rotation and tillage practices, about 30% of this stover could be collected for less than $33 per Mg, taking into consideration erosion and soil moisture concerns and nutrient replacement costs. Wind erosion is a major constraint to stover collection. Analysis suggests three regions of the country (central Illinois, northern Iowa/southern Minnesota, and along themore » Platte River in Nebraska) produce sufficient stover to support large biorefineries with one million Mg per year feedstock demands and that if farmers converted to universal no-till production of corn, then over 100 million Mg of stover could be collected annually without causing erosion to exceed the tolerable soil loss. « less
sRNAbench: profiling of small RNAs and its sequence variants in single or multi-species high-throughput experiments

The availability of high-throughput sequencing (HTS) technologies plays now a pivotal role in the expression profiling of known small RNAs and the discovery of novel classes of non-coding RNA [1]. Over the last decade, in both plants and animals a notable number of novel small RNA classes have been described [2, 3]. It became apparent that the biogenesis of microRNAs and other small RNA classes, their contribution to gene regulation mechanisms and the cellular control of their expression are more complex than previously envisioned. Therefore, apart from microRNA profiling and detection, the analysis of other small RNAs became an important task. In plants, small interfering RNAs (siRNA), trans-acting RNAs (ta-RNA) and heterochromatic siRNAs have been shown to regulate gene expression and being responsible for the deposition of repressive chromatin marks (DNA methylation and histone marks) [4]. In animals, apart from microRNAs and piRNAs, other putatively important processed small RNA fragments do exist, including yRNA, tRNA and snoRNA fragments [5, 6]. Furthermore, microRNAs are reproducibly diversified at the sequence level in both animals and plants, including posttranscriptional modifications such as adenylation [7–9]. Many tools have been developed to analyze HTS small RNA data covering many crucial aspects, such as quality control, expression profiling, prediction of novel microRNAs, snoRNAs, tRNAs, piRNAs or ta-siRNAs, identification of siRNAs or piRNAs clusters and isomiR quantification. In order of appearance: small RNA toolkit Abstract: MicroRNAs and other small RNAs are known to play important functions in gene regulation. Over the last years, it became also apparent that many virus genomes encode microRNAs and that those strongly interact with the host transcriptome. Important functions include the evasion of the immune response and the regulation of the switch to lytic infection. Since the advent of deep sequencing protocols for small RNAs, expression profiles can be routinely determined. However, currently the tools developed for the data analysis of small RNA deep sequencing experiments are limited to the analysis of only one species at a time. In order to facilitate the analysis of experimental setups that include genetic material from several species, we developed sRNAbench. It maintains the main features implemented in its predecessor program, miRanalyzer, and includes new functionalities such as full isomiR support including statistical test on differential frequency, improved prediction of novel microRNAs, extended summary files and data visualization support. Both a standalone program and a webserver are available at: http://bioinfo5.ugr. es/sRNAbench/. Research Article Open Access
Germination of two warm-temperate oaks, Quercusemoryi and Quercusarizonica

Quercusemoryi Torr. (emory oak) and Quercusarizonica Sarg. (Arizona white oak) are the dominant trees in many of the oak savannas and woodlands of Arizona and northern Mexico. The objectives of this study were (i) to evaluate germination on two media as influenced by storage and stratification and (ii) to determine the effects of oak canopy and depth of burial on acorn viability and germination. Germination was higher (P 0.10) but exceeded germination at the surface (17%). These results represent the first reported germination of either species and indicate that recruitment into mature oak woodlands is not limited by germination.
A Synopsis of Bryoerythrophyllum and Morinia (Pottiaceae) in the New World1

Taxa in Bryoerythrophyllum Chen & Morinia Card. (Pottiaceae) in the New World are B. bolivianum (C.Muell.) comb. nov., B. columbianum (Herm. & Lawt.) comb. nov., B. ferruginascens (Stirt.) Giac. , B. jamesonii (Tayl.) Crum, B. recurvifolium (Tayl.) Zander, B. recurvirostrum (Hedw.) Chen var. recurvirostrum, B. recurvirostrum var. aeneum (C.Muell.) Zander, B. re- curvum (Griff.) K.Saito, M. crassicuspis (H.Robins.) comb. nov., M. ehrenber- giana (C.Muell.) Thir. var. ehrenbergiana and M. ehrenbergiana var. elongata (Wils. in Mitt.) comb. & stat. nov. The previously poorly understood species B. bolivianum, B. ferruginascens, B. jamesonii and B. recurvum are rede- scribed and illustrated. Sporophytes of B. ferruginascens are described for the first time. Bryoerythrophyllum jamesonii is considered a polymorphic complex with many synonyms. Notes on relationships, infraspecific variation, geo- graphic distribution and nomenclature are given for other taxa. Globulina C.Muell. , hom. illeg. , is a valid name and is a synonym of Bryoerythrophyllum, but Seligeria sect. Globulina C.Muell. is a synonym of Globulinella Steere. Barbula andreaeoides Kindb. is a good species, not a synonym of Bryoeryth- rophyllum ferruginascens. Tortula herzogii is a nom. nov. for T. angustifolium (Herz.) Herz. , hom. illeg. Species of four genera of New World Pottiaceae, Bryoerythrophyllum Chen, Erythrophyllopsis Broth. in Herz. , Morinia Card. and Rhexophyllum Herz. , are oc- casionally confused in the herbarium. Gametophytically, the species are similar: red- dish plants, stems with central strand, leaves usually lanceolate, usually reflexed above a differentiated leaf base, costa usually with papillose ventral epidermal cells (these often similar to the laminal cells), upper laminal cells mostly quadrate with thin to evenly thickened cell walls and laminal papillae apparently scattered over the lumens, often crowded, hollow (o- to c-shaped in optical section) to solid, low and granular, bi- to multifid. Rhexophyllum and Erythrophyllopsis are both monotypic. These are illustrated, the former by Grout (1938) and the latter under synonyms by Sullivant (1860) and Herzog (1916). I have previously discussed synonymy and mor- phological variation in both Rhexophyllum subnigrum (Mitt.) Ther. ex Hilp. (Zander,
Prescribed fire effects on mixed conifer forest structure at Crater Lake, Oregon

Prescribed fire was applied to a mixed conifer forest in southern Oregon, part of which was selectively logged in the 1930's. Structural effects were measured over a 4-year postfire period. Initial tree mortality was concentrated in small diameter and height classes of Abiesconcolor (Gord. and Glend) Lindl. , Pinuslambertiana Dougl. , and Pinusponderosa Dougl. Most mortality in all three species after the 1st year was associated with bark beetles. Mortality after 1 year for Abiesconcolor remained primarily in smaller tree classes, while both small and large pines were killed. Implications for restoring natural conditions in these ecosystems include recognizing structural as well as process goals, while reintroducing fire, and recognizing the significance of available prescription variables in the prediction of fire effects.
Cytogenetic and Molecular Reevaluation the Relationships of Species Belonging to the Two Genera Brassica and Sinapis

Two genera, Brassica and sinapis, belong to the family Cruciferae (Brassicaceae). It had been suggested that they had have 1 ancestor and 2 different lineages. Detailed cytogenetical study had been carried out on 6 species belonging to them. These are: B. nigra, B. rapa ( campestris) and B. tournefortii from genus Brassica and S. alba, S. allionii and S. turgida from genus Sinapis. Data obtained by the present study support this suggestion. Karyomorphological analysis for 4 species reveals that B. nigra is the most primitive and it was similar to S. turgida and S. allionii. Also meiotic analysis and electrophoretic seed protein profiles confirm the karyomorphological results. Moreover, seed protein electrophoresis indicates that these 2 genera had a characteristic protein composition which is of taxonomic importance. So, the present resulted information could be considered a reliable data which aid in reevaluation the evolutionary relationships of the 2 genera. Moreover, these present data prove that they are highly paraphylogeny.