Miracle-dz/UniFAR-FTUs huggingface dataset:
Food choice of an Algerian population of the spur‐thighed tortoise, Testudo graeca

Abstract The diet of an Algerian population of spur‐thighed tortoise (Testudo graeca) was studied with the aims of exploring: (i) the variation in diet among males, females and juveniles, (ii) the relationships between consumption and relative availability of the plant species, and (iii) which plant tissues, vegetative or reproductive, are eaten by tortoises. We recorded more than forty plant species at the study area, with monocot species (n = 7) having a greater percent cover than that of dicot species (n = 31 species) or Gymnospermae (n = 2). Tortoise diet was studied by categorising 4422 plant and animal fragments in faecal pellets of 20 males, 16 females and eight juveniles. Tortoises ate a wide variety of plant species, including 13 dicots and three monocots, and occasionally invertebrates. The number of fragments for a plant species was correlated with plant species cover, and plant vegetative tissues exceeded plant reproductive tissues in the faeces. Dicots (Fabaceae, Composeae, Primulaceae, and Caryophyllaceae) accounted for over 70% of the diet (faecal fragments). The high dietary (niche) overlap, and null model analysis (RA3 algorithm with 30,000 Monte Carlo simulations), indicate that males, females and juveniles did not partition food resources; all three groups ate the same plant species.
SCAR Markers for Practical Application of Marker-assisted Selection in Persimmon (Diospyros kaki Thunb.) Breeding

In previous studies, we have developed molecular markers linked to the AST locus that controls fruit astringency type in persimmon; however, these markers are not feasible for practical application to breeding programs since they are not fully effective for discriminating the pollination constant and non-astringent (PCNA) genotype from the non-PCNA genotype in a progeny derived from ‘Kurokuma’. Here we developed new sequence characterized amplified region (SCAR) markers that enable easy and reliable selection of the PCNA genotype from breeding populations. Genomic regions adjacent to probe 5R, which showed polymorphic fragments between PCNA and non-PCNA genotypes in restriction fragment length polymorphism (RFLP) analysis, were isolated from the genomic libraries of ‘Nishimura-wase’, ‘Jiro’, and ‘Kurokuma’-derived offspring. The isolated genomic regions were characterized and 3 insertion/deletion mutations were observed between ast- and AST-linked regions. Several primers were designed in the flanking region of Indel-3 and, in multiplex PCR, it was shown that using 2 forward primers, AST-F and PCNA-F and a reverse primer, 5R3R, is the most useful and reliable primer set. The AST-linked 220-bp fragment proved to be a common marker of ‘Kurokuma’-, ‘Nisimura-wase’- and ‘Aizumishirazu’-derived progenies. This multiplex PCR is considered the most practical tool for marker-assisted selection (MAS) and can enhance and accelerate progress in persimmon breeding.
Inverse density dependent parasitism in a patchy environment: a laboratory system

Abstract. 1. Two species of parasitoids (Anisopteromalus calandrae (Howard) and Heterospilus prosopidis Vier) attacking the bruchid beetle, Callosobruchus chinensis (L.), show marked inverse density dependent relationships between per cent parasitism and host density per patch.
Measuring shape variation of two-dimensional outlines

-An image-analytic technique that automatically determines the outlines for simple silhouettes is described. These outlines are numerically characterized using elliptic Fourier decomposition. Since the resulting Fourier coefficients can be normalized so that they are invariant to changes in magnification and rotation as well as other such transformations of the original silhouette, they quantify shape per se, and can be used as variables in multivariate analysis of form. In an application, discriminant analysis distinguishes between electrophoretically distinct populations of the mussel Mytilus edulis. While the technique was able to demonstrate an association between genotype and morphdlogy, it was not able to identify reliably the population from which each specimen was collected. [Automatic identification; pattern recognition; feature extraction; elliptic Fourier description; Mytilus edulis; shape analysis; species discrimination. ] For many years there has been interest in the possibility of using the computer to view directly, via a television camera and a digitizer, a series of biological specimens, determine the most informative characters, and then construct a rule that could be applied by the computer to separate automatically a collection of specimens into two or more taxonomic groups. Once a suite of characters has been recorded, there are many methods for determining rules for identifying specimens to minimize the expected number of misclassifications. Many statistical techniques are described, for example, in the general text by Hand (1981). The main difficulties for automatic recognition by computer are those of image segmentation (isolating the image of the desired object from its background) and feature extraction (the definition and actual measurement of a suite of characters from the image). Rohlf and Ferson (1983) gave a general review of these problems. In the present paper, we report the successful practical application of these techniques to a set of biological images. Shells of the mussel Mytilus edulis are easily distinguished from image background, and their form is simple enough to be described by fitting mathematical functions with few parameters. Koehn et al. (1984) characterized the population genetics of two putative mussel species, presently recognized as Mytilus edulis, in eastern North America. The mussels studied here were collected near Sunnyside and Bellevue, Newfoundland, in areas of spatial interdigitation between two electrophoretically distinct groups. Genotypes at the phosphoglucomutase (EC 2.7.5.1; Pgm) and glucosephosphate isomerase (EC 5.3.1.9; Gpi) loci indicate membership in one of two groups. Figure 1 displays the outlines of 194 mussels divided into two groups based a priori on genotype at these loci. We carried out this shape analysis to test the impression (based on another sample) that the shapes of shells from mussels from the first group were more recurved, less ovoid in shape, than those from the second group.
Adaptation Patterns and Yield Stability of Durum Wheat Landraces to Highland Cold Rainfed Areas of Iran

Because of unpredictable conditions in Mediterranean environments, successful crop production requires improved adaptation and yield stability to mitigate major abiotic stresses such as drought and cold. In this study 380 durum wheat (Triticum turgidum L.) landraces with worldwide origins and four checks were evaluated in four rainfed research stations for 3 yr (2008–2011). The main objective was to investigate yield stability and adaptation patterns of the landraces to highland rainfed cold regions of Iran, where drought and cold are limiting factors. The experimental design was an unreplicated trial at each environment. Best linear unbiased predictions (BLUPs) data were used to analyze landrace × environment interactions using multivariate statistical methods. Considerable variability in yield, adaptation, and stability was observed for the landraces, which could be exploited for crop improvement. The landrace and environment groups allowed characterization of origins on the basis of similar performance of landrace within particular environments. Grouping of environments was not repeatable among the years. Many of the durum landraces exhibited a high combination of yield and stability for both drought and cold stresses, comparable to cold- and/or drought-tolerant checks. Most landraces originating from Europe and the United States could be considered as a genetic resource for specific adaptation, while the landraces from Asia may enhance genetic potential of yield stability. In conclusion, current durum wheat selection may lead to yield stability and specific adaptation, which provides opportunities for this collection to be useful for genetic improvement of both drought and cold tolerance in durum wheat
Changes in Chloride Fluxes and Cytosolic pH Induced by Abscisic Acid in Elodea densa Leaves

The effects of ABA on intracellular pH, net H+ extrusion, Cl− fluxes and Em values were studied in Elodea densa leaves, and the possible relationships between the ABA-induced changes of cytosolic pH and of Cl− and H+ fluxes were investigated. Cytosolic and vacuolar pH were calculated by the weak acid and weak base distribution method. The data show that, also in this material (a water plant without stomata), ABA induces a decrease in both net H+ extrusion and intracellular pH, and strongly inhibits Cl− efflux. No significant effect of ABA is detectable on Em values, either at short or long intervals in the presence or absence of K+. Cl− efflux is apparently independent of the activity of the plasmalemma H+ pump and of the Em values. Conversely, it strongly depends on the value of cytosolic pH, a larger efflux occurring for the lower pH values both in the presence and in the absence of ABA. These results indicate that the ABA-induced cytosolic acidification cannot be the cause but, possibly, a consequence of the decrease in Cl− efflux, and are consistent with the hypothesis of a primary role of ABA in regulating Cl− efflux, presumably by directly affecting a class of Cl−-permeable channels.
Suitability of the biomass crop Miscanthus sinensis as a host for the aphids Rhopalosiphum padi (L.) and Rhopalosiphum maidis (F.), and its susceptibility to the plant luteovirus Barley Yellow Dwarf Virus

1 The reproductive performance of two aphid pest species, Rhopalosiphum padi and Rhopalosiphum maidis, was investigated on two seedling growth stages of Miscanthus sinensis, rhizomatous M. sinensis‘Giganteus’ and barley. Rhopalosiphum padi was unable to complete its development on Miscanthus. Rhopalosiphum maidis was most fecund on rhizomatous plants compared with seedling stages.
A turbulent channel flow apparatus for the determination of the adhesion strength of microfouling organisms

The development of novel, fouling‐release surfaces has led to the need for better test methods to evaluate their performance. A water channel has been designed to measure the adhesion strength of microfouling organisms to test surfaces. The apparatus allows six replicate microscope slides to be mounted in a fully‐developed, turbulent channel flow. Wall shear stress in the test section can be varied from 0.9–30 Pa over a Reynolds number range of 2,800 to 27,000 based on the bulk mean velocity and channel height. Calibration of the device indicates that the accuracy and repeatability in the wall shear stress is within 4% throughout the range. Experiments using the fouling diatom Amphora settled on acid‐washed glass slides are presented. The results show significant differences in the shear stress required to remove Amphora cells with settlement time. No significant differences among the replicate slides were observed, indicating flow uniformity in the test section.
αvβ6integrin promotes invasion of squamous carcinoma cells through up‐regulation of matrix metalloproteinase‐9

The integrin αvβ6 is a fibronectin receptor, which is not detectable on normal epithelium but is neo‐expressed in oral epithelial dysplasia and oral squamous‐cell carcinoma (SCC), suggesting a role in promoting malignant behaviour and tumour progression. We used transfection and retroviral infection to create a panel of SCC cell lines expressing various levels of αvβ6 to examine this possibility. We found that increased expression of αvβ6 in malignant keratinocytes up‐regulates MMP‐9 and MMP‐2 expression and promotes invasion in an MMP‐9‐dependent manner. Our results suggest a possible mechanism for the involvement of αvβ6 in squamous carcinoma in vivo. © 2001 Wiley‐Liss, Inc.
Unique aperture stratification in Carex (Cyperaceae) pollen

Abstract Mature pollen usually has a conspicuously thick intine in the aperture regions, whereas in the interapertural area(s) the intine is thin. In Carex (and in other Cyperaceae with pseudomonads), usually five to six circular or elongated apertures (poroids) are present, one situated distally and the others equatorially. In the species studied here the situation is opposite: the apertures (poroids) are characterised by a very thin intine, whereas in the interapertural area(s) the intine is conspicuously thickened. A similar condition is only known for Vinca (Apocynaceae). A second unusual sporoderm feature in Carex relates to the foot layer. In the interapertural area(s) the foot layer is thin and discontinuous. The equatorial poroids exhibit a compact, thick and homogeneous foot layer, whereas the distal poroid is distinguished by an elaborated foot layer, structurally similar to a transfer-cell wall labyrinth. This unique elaborated foot layer in the distal poroid probably functions as a nutrimental passage between the tapetum and the maturing pollen. The pseudomonads are usually pear-shaped, sometimes spherical. Ornamenting elements are microechini, granules, and perforations, all sometimes placed on verrucae.
Distribution and ultrastructure of taste buds in the oropharyngeal cavity of the rainbow trout, Salmo gairdneri Richardson

The distribution, external surface morphology and ultrastructure of taste buds in the oropharyngeal cavity of the rainbow trout, Salmo gairdneri Richardson, were studied using scanning and transmission electron microscopes (SEM and TEM). The SEM revealed three taste bud types, varying only in their degree of elevation from the general level of the epithelium. Types I and II were located on elevated papillae associated with teeth on the dentary, maxilla, palate, tongue and pharyngeal pads while the unelevated Type III were mainly found in the anterior (branchial) pharynx. Each taste bud was composed of four cell types: basal, dark, intermediate and light cells, the apical processes of the last three filling the taste pores. The intermediate and light cells appeared similar in ultrastructure, varying only in the amount and organization of smooth endoplasmic reticulum (SER) in their cytoplasm. In addition to its contacts with the processes of intragemmal nerves distally, the basal cells established independent contacts with processes of extragemmal nerves basally. It is suggested that the distribution of the taste buds and their close association with teeth are adaptations to the predatory feeding habit of the rainbow trout. Age differences may account for the existence of two types of gustatory cells and the manner of innervation of the taste bud suggests the existence of two pathways for the transmission of gustatory sensation to the central nervous system (CNS).
Current status of prevalence of yeast-like fungi in the environment of horses bred in Poland / Aktualny status występowania grzybów drożdżopodobnych w środowisku hodowlanym koni w Polsce

Abstract This study presents an analysis of the yeast-like fungi population in the healthy horses’ living environment. The study material was sampled from various elements and equipment of a stable. We compared the yeast-like fungi population from the breeding environment of five groups of horses (English Thoroughbred horses, Arabian horses, Polish Half-Bred horses, cold-blooded horses, and Hucul horses and Highland ponies). The samples were collected in the summer and winter period. The laboratory examination involved 260 samples and resulted in identification of yeast-like fungi belonging to 13 species. Over 50% of the samples collected from the horse environment in wintertime and fewer than 18% of the summer samples displayed fungal growth. The largest amounts of yeast fungi were isolated from samples collected from water and feed troughs. The laboratory analysis demonstrated qualitative diversity of the yeast-like fungi population depending on the breeding environment of the individual horse groups. Quantitative differences of isolates were additionally related to the season of the year. Streszczenie Niniejsza praca przedstawia analizę występowania grzybów drożdżopodobnych w środowisku życia zdrowych koni. Materiał do badań pobrano z różnych elementów stajni i wyposażenia. W pracy porównano częstość izolacji grzybów z próbek pochodzących ze środowiska hodowlanego 5 grup koni (pełnej krwi angielskiej, czystej krwi arabskiej, małopolskich i zimnokrwistych oraz koni rasy huculskiej i Highland ponies). Próby pobierano w okresach letnim i zimowym. Łącznie przebadano laboratoryjnie 260 prób, z których wyhodowano i zidentyfikowano grzyby drożdżopodobne należące do 13 gatunków. Wykazano zróżnicowanie częstości izolacji różnych gatunków w zależności od środowiska hodowlanego poszczególnych grup koni. Różnice te związane były ponadto z porą roku. Z prób pobranych ze środowiska koni w okresie zimowym w ponad połowie przypadków wystąpił wzrost grzybów, natomiast w okresie letnim - w niespełna 18%. Najwięcej drożdżaków wyizolowano z prób pobranych z poideł i żłobów.
Cross-generation effects due to cold exposure in Drosophila serrata

Summary 1 Environmental variation experienced in the parental and grandparental generation can affect progeny phenotype, performance and response to selection. Here the effects of parental and grandparental exposure to a non-lethal cold shock are considered in Drosophila serrata Malloch. Development time, viability and early age productivity were measured in flies originating from border and central locations in the distribution of this species that had been held under two separate laboratory maintenance schedules. 2 Cross-generation effects were detected for several traits. Development time usually decreased following maternal and/or grandmaternal cold exposure. Parental cold exposure negatively influenced viability while grandparental effects on viability were negligible. Early female productivity showed opposing responses depending on generation; maternal cold exposure increased progeny productivity while grandmaternal exposure decreased it. Male parental and grandparental exposure to cold shock decreased male productivity, although this pattern may have been partly confounded by size effects. 3 Population effects, reflecting geographical origin, were limited to development time, while selective background effects were demonstrated for most traits. The influence these factors had on the expression of cross-generation effects was negligible, given interactions with treatment were not evident. These responses suggest that environmental variation experienced in preceding generations can influence progeny phenotype in a manner that is complex and difficult to predict.
Evaluation of Glycine Germplasm for Nulls of the Immunodominant Allergen P34/Gly m Bd 30k

Soybean [Glycine max (L.) Merr. ] seed contains an immunodominant human allergen P34 or Gly m Bd 30k (mentioned as P34) of the cysteine protease family. Of approximately 16266 accessions from USDA soybean germplasm screened, 12 P34 null lines were identified among soybean (G. max), wild annual (Glycine soja Sieb. and Zucc.), and wild perennial Glycine spp. Glycine soja were low P34 expressers, while G. max and wild perennial species had nondetectable levels of the allergenic protein. Further investigation of G. max nulls by 2DIEF/SDS PAGE showed all primary seed proteins present indicating that the loss of P34 was not due to large scale restructuring of protein content. Southern and northern analysis showed no large insertions or deletions to render the gene nonfunctional. The cDNA of both G. max nulls each showed the same six point mutations indicating the two nulls have a single origin. Of these six single nucleotide changes, four are predicted to result in an amino acid alteration. One such alteration resultsinaserinebeingreplacedbyacysteineresidue. Theintroductionof a cysteine residue might produce a mismatched disulfide bond formation producing an unstable P34 protein in the null soybean accessions. The isolation and introgression of soybean lines with low allergen levels will provide the basis for developing a low allergen line incorporated with other agronomically desirable traits in a breeding program.
Structural basis of the interaction between IgG and fcγ receptors

Abstract The binding of multivalent antigen-antibody complexes to receptors for the Fc portion of IgG (FcγR) induces the clustering of the FcγR and triggers cell activation leading to defence reactions against pathogens. The Fc portion of IgG consists of two identical polypeptide chains which are related to each other by a 2-fold axis and are folded in two structural domains, the CH2 domain, near the flexible hinge region of the IgG molecule, and the CH3 domain. We studied the interaction in solution between the Fc fragment of mouse IgG2b and the extracellular region of mouse FcγRII. We find that one Fc molecule binds one FcγRII molecule only. Using NMR spectroscopy, we show that FcγRII binds to a negatively charged area of the CH2 domain, corresponding to the lower hinge region, and that the binding of FcγRII onto one of the two symmetrically related sites on the Fc induces a conformational change in the other site. We therefore propose a model that explains why IgG molecules are unable to trigger FcγR-mediated cellular responses spontaneously in the absence of crosslinking by multivalent antigens.
Functional properties of dietary fibre enriched extrudates from barley.

Abstract Products with new functional and nutritional properties are a precondition for a higher acceptance of barley in human nutrition. Amylose can be partly converted into enzyme-resistant starch (RS) by technological treatments. Optimal conditions for generation of RS from barley using a single-screw laboratory extruder were the following: feed moisture approximately 20%, mass temperature approximately 150 °C, screw speed approximately 200 rev/min and a relatively wide die. Extrusion followed by freeze-storage resulted in formation of RS up to 6%. Under these conditions, the macromolecular state of β-glucan was preserved. Functional and physico-chemical properties of extruded preparations and of their extracts were determined and compared to an autoclaved product. In extracts, high viscosities and a pseudoplastic behaviour were found. Viscosity and flow behaviour were temperature- but not pH-dependent. Water binding properties and the acid-extract viscosity were influenced by process parameters during extrusion. The molecular weights of β-glucans isolated from extrudates were between 80 000 and 125 000. Extruded products interacted with glycoconjugated bile acids (pH 5·0–6·5). During in vitro fermentation of pancreatin-digested extruded or autoclaved products with human faeces flora, the production of short-chain fatty acids and the molar portion of butyrate were more increased compared with pancreatin-digested barley meal.