Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for interspecies transmission of small ruminant lentiviruses in sheep and goats in Poland.

A fragment of 394 bp spanning the V1-V2 variable region of small ruminant lentiviruses (SRLV) env gene was amplified by nested-PCR from peripheral blood leukocytes of 27 sheep and seven goats from five Polish flocks. PCR products were then subjected to analysis by the heteroduplex mobility assay. SRLV found in six sheep were more similar to caprine arthritis-encephalitis virus, but no viruses closely related to maedi visna virus were found in the infected goats. However, in one sheep dual infection with SRLV belonging to both A and B group was found. The results showed that interspecies infections of SRLV occur in animals living under natural conditions.
Uptake of algal carbon and the likely synthesis of an "essential" fatty acid by Uvigerina ex. gr. semiornata (Foraminifera) within the Pakistan margin oxygen minimum zone: evidence from fatty acid biomarker and 13 C tracer experiments

Foraminifera are an important component of ben- thic communities in oxygen-depleted settings, where they potentially play a significant role in the processing of organic matter. We tracked the uptake of a 13 C-labelled algal food source into individual fatty acids in the benthic foraminiferal species Uvigerina ex. gr. semiornata from the Arabian Sea oxygen minimum zone (OMZ). The tracer experiments were conducted on the Pakistan margin during the late/post mon- soon period (August-October 2003). A monoculture of the diatom Thalassiosira weisflogii was 13 C-labelled and used to simulate a pulse of phytoplankton in two complementary ex- periments. A lander system was used for in situ incubations at 140 m water depth and for 2.5 days in duration. Shipboard laboratory incubations of cores collected at 140 m incorpo- rated an oxystat system to maintain ambient dissolved oxy- gen concentrations and were terminated after 5 days. Uptake of diatoms was rapid, with a high incorporation of diatom fatty acids into foraminifera after 2 days in both experi- ments. Ingestion of the diatom food source was indicated by the increase over time in the quantity of diatom biomarker fatty acids in the foraminifera and by the high percentage of 13 C in many of the fatty acids present at the endpoint of both in situ and laboratory-based experiments. These results indi- cate that U. ex. gr. semiornata rapidly ingested the diatom food source and that these foraminifera will play an impor- tant role in the short-term cycling of organic matter within this OMZ environment. The presence of 18:1(n-7) in the ex- perimental foraminifera suggested that U. ex. gr. semiornata also consumed non-labelled bacterial food items. In addition, levels of 20:4(n-6), a PUFA only present in low amounts in the diatom food, increased dramatically in the foraminifera during both the in situ and shipboard experiments, possi- bly because it was synthesised de novo. This "essential fatty acid" is often abundant in benthic fauna, yet its origins and
Inhibition of GSK‐3β decreases NF‐κB‐dependent gene expression and impairs the rat liver regeneration

Serine‐threonine protein kinase glycogen synthase kinase (GSK)‐3 is involved in regulation of many cell functions, but its role in regulating liver regeneration is unknown. Here we investigated the effects of GSK‐3β inhibition on liver regeneration after partial hepatectomy in the rat. The potent and selective GSK‐3β inhibitor SB216763 (0.6 mg/kg intravenously) or vehicle (10% dimethyl sulfoxide) was administered 30 min before 70% partial hepatectomy. Liver regeneration was estimated by the cell proliferation, apoptosis, and the related cell signaling and cycling proteins. In 30 min after hepatectomy in the rat, GSK‐3β was found to be translocated to the nucleus, but GSK‐3β inhibitor SB216763 that could phosphorylate residue Ser9 on GSK‐3β did not attenuated the accumulation. Consequently, the inhibition of GSK‐3β decreased the nuclear factor‐κB activity, the NF‐κB‐dependent gene expression, and COX2 expression, but enhanced p21WAF1/Cip1 transcription. Moreover, the injection of SB216763 impaired the proliferation cell nuclear antigen (PCNA) index and increased the apoptosis of liver compared to the vehicle. GSK‐3β plays an important role in rat liver regeneration. We conclude it may partially result from the inhibition of the NF‐κB pathway and enhancement of p21 WAF1/Cip1 expression. J. Cell. Biochem. 102: 1281–1289, 2007. © 2007 Wiley‐Liss, Inc.
Microhabitat factors and the distribution of exotic species across forest edges in temperate deciduous forest of southern Illinois, USA1

Abstract Honu, Y. A. K. and D. J. Gibson (Southern Illinois University at Carbondale, Department of Plant Biology, Center for Ecology, 1125 Lincoln Drive, Carbondale, Illinois 62901-6509, USA). Microhabitat factors and the distribution of exotic species across forest edges in temperate deciduous forest of southern Illinois, USA. J. Torrey Bot. Soc. 133(2): 255–266. 2006. —The study of microhabitat factors has attracted the attention of ecologists for about half a century. We examined crop-forest, access road-forest, and hay field-forest edge types in temperate deciduous forest in Southern Illinois to obtain information that may contribute to the control and management of exotic species. Forest edges have different abiotic factors compared to the interior, a phenomenon known as an edge effect. To investigate microhabitat factors, three 90 m transects were established from the forest boundary into the interior at each of the three edges in July 2002. Twelve 3.14 m2 circular plots at 5 m intervals from each other for the first 20 m and 10 m apart thereafter were established along each transect. A 550 cm3 soil core was extracted from the six cm A-horizon in each plot along the three transects in August 2002 and analyzed for soil texture, pH. , and major soil nutrients. To quantify the edge effect, the Distance of Edge Influence (DEI) was calculated by contrasting the value of microhabitat factors in plots ≤ 50 m from the forest boundary with the value of microhabitat factors in plots > 50 m from the boundary (interior plots) using a permutation approach. The DEI is calculated as the distance where two or more consecutive plots from the forest boundary have values that differ significantly from the expected value of the interior plots. Percent clay and sand generally declined across the crop-forest and access road-forest edges into the interior while the opposite relationship was observed at the hay field-forest edge. Percent silt showed a pattern that was opposite to those exhibited by percent sand and clay at all the three edge types. The DEI of the percent sand, clay, and silt varied between 15 to 50 m at the three edges. Seven exotic species were present in the vegetation and the relationship of the abundance of three of them to 11 microhabitat factors was tested. Lonicera japonica and Allium vineale were absent when canopy openness was < 15 % while the presence of Cardamine hirsuta was independent of canopy openness. Management strategies for the control of the invasive L. japonica and A. vineale should consider canopy closure among other factors. By contrast, management prescriptions for the exotic C. hirsuta may pose a challenge to forest managers and conservation biologists as a result of its insensitiveness to the 11 microhabitat factors including light (canopy openness) measured in this study. For conservation purposes, a buffer strip of 50 m around a conservation area would eliminate most of these microhabitat edge effects.
Habitat associations of a rare South Australian sea star (Parvulastra parvivipara) and a co-occurring chiton (Ischnochiton variegatus): implications for conservation

The sea star Parvulastra parvivipara is a small-range endemic known from only seven granitic headlands in South Australia. Evidence from previous studies suggests that its unstable boulder habitat will experience increased disturbance as sea levels rise. This study investigated distributional and ontogenetic patterns of P. parvivipara across different-sized boulders that vary in physical stability and susceptibility to disturbance. To develop a better understanding of community dynamics in P. parvivipara habitat, patterns were also assessed for a chiton with which the sea star commonly co-occurs (Ischnochiton variegatus), and assemblages of encrusting species were also measured, as these can vary amongst boulder sizes and influence mobile animals. Large boulders had many tubeworms, contributing to a significant boulder-size effect on encrusting species assemblage structure. P. parvivipara was most abundant on the smallest boulders; there was no evidence that abundances were influenced by encrusters. I. variegatus abundances were unaffected by boulder size, but a positive correlation between lengths of individuals and encruster cover occurred on the smallest boulders. Overall, physical habitat features, not encrusting biota, likely caused an association of P. parvivipara with small boulders, while I. variegatus displayed apparent ontogenetic use of encruster-related habitat features. As P. parvivipara uses mostly small boulders that are particularly susceptible to disturbances that are increasing with rising sea levels, future ecological restoration efforts to protect this rare species may be required. Such efforts can be properly informed about necessary habitat requirements from these results.
Assimilation of cholesterol in broth, cream, and butter by probiotic bacteria

High serum cholesterol concentrations are associated with the development of coronary heart disease. It has been reported that some cultures of Lactobacillus spp. actively take up cholesterol from laboratory media. In the present study, the abilities of ten probiotic lactic acid bacteria to assimilate cholesterol in broth medium, cream, and butter were tested and compared. The cholesterol reduction ratios of these human-origin bacteria were determined in MRS-THIO broth supplemented with 150 μg/mL cholesterol. The amount of cholesterol assimilated by the bacteria was measured by gas chromatography. Cholesterol assimilation of these ten bacteria in broth was found to be similar to assimilation in cream. Two of these ten bacteria (Lactobacillus maltaramicus AC 3-16 and L. casei subsp. casei AB16-65) were chosen for making soured butter. The results indicate that the probiotic bacteria applied to cream and butter, as well as to the broth medium, caused a reduction of the cholesterol level of the product's fat content. This study provides some evidence that probiotic cultures have a cholesterol level-reducing effect, and soon we will be able to produce butter without cholesterol via microorganisms.
Studies on taxonomy and ecology of Mysidacea from the EEZ of India

Four species of mysids collected from the Minicoy lagoon are reported. Amsomysis minicoyensis sp. nov. is distinguished from the related species by the shape of the rostrum, the relative length of the antennal scale and the short protuberances on the second segment of the mandibular palp. The other three species recorded are Siriella australiensis, Anisomysis truncata and unidentified species of subfamily Gastrosaccinae.
Predator-mediated interactions between preferred, alternative and incidental prey in the arctic tundra

Apparent competition between prey is hypothesized to occur more frequently in environments with low densities of preferred prey, where predators are forced to forage for multiple prey items. In the arctic tundra, numerical and functional responses of predators to preferred prey (lemmings) aff ect the predation pressure on alternative prey (goose eggs) and predators aggregate in areas of high alternative prey density. Th erefore, we hypothesized that predation risk on incidental prey (shorebird eggs) would increase in patches of high goose nest density when lemmings were scarce. To test this hypothesis, we measured predation risk on artifi cial shorebird nests in quadrats varying in goose nest density on Bylot Island (Nunavut, Canada) across three summers with variable lemming abundance. Predation risk on artifi cial shorebird nests was positively related to goose nest density, and this relationship was strongest at low lemming abundance when predation risk increased by 600% as goose nest density increased from 0 to 12 nests ha � 1 . Camera monitoring showed that activity of arctic foxes, the most important predator, increased with goose nest density. Our data support our incidental prey hypothesis; when preferred prey decrease in abundance, predator mediated apparent competition via aggregative response occurs between the alternative and incidental prey items.
Effets d'amendements carbonatés et organiques sur la culture de deux légumes sur sol contaminé à Lubumbashi (RD Congo)

Face aux risques de contamination des legumes cultives dans les jardins potagers de la ville de Lubumbashi, l’identification de solutions agronomiques pour reduire ces risques a fait l’objet de diverses experimentations. Le choix d’amendements (nature et quantites) appropries et la selection de varietes capables de limiter les transferts des elements traces metalliques (ETM) du sol vers certains organes de la plante font partie des methodes les plus classiques en phytoremediation. Deux especes vegetales, l’amarante verte et la poiree bette, ont ete cultivees en pots selon un dispositif completement randomise avec quatre repetitions, utilisant un sol contamine ayant recu differentes doses d’amendements calcaires et/ou organiques et un sol temoin. Parallelement a la reponse chimique sur les sols, les amendements ont reellement permis de diminuer les transferts du sol vers la plante. Les traitements a base de calcaire ont ete plus efficaces que ceux a base de compost seul. Les teneurs en ETM dans les plantes restent toutefois elevees, quelle que soit l’application d’amendements et laissent entiere la question du risque sanitaire lie a l’ingestion de legumes produits localement.
Amino acids and muscle protein metabolism with aging

Sarcopenia is age-associated loss of skeletal muscle mass and strength which develops slowly over decades and becomes a significant factor to disability among the elderly population. Although several mechanisms of sarcopenia have been proposed, they all seem to affect the balance between muscle protein synthesis and breakdown, resulting in the net muscle loss. In present article, the most recent findings regarding the role of nutritional intake on muscle protein metabolism in the elderly will be reviewed. Particular focus will be given to dietary protein requirement for elderly, acute anabolic response of amino acids and protein intake, age-associated changes in the response of muscle protein to a meal intake, and the role of insulin resistance of muscle protein metabolism among the elderly. Finally, possible benefits and risks of protein and amino acid supplements for the prevention and treatment of sarcopenia will also be reviewed.
Evenness drives consistent diversity effects in intensive grassland systems across 28 European sites

1 Ecological and agronomic research suggests that increased crop diversity in species‐poor intensive systems may improve their provision of ecosystem services. Such general predictions can have critical importance for worldwide food production and agricultural practice but are largely untested at higher levels of diversity. 2 We propose new methodology for the design and analysis of experiments to quantify diversity‐function relationships. Our methodology can quantify the relative strength of inter‐specific interactions that contribute to a functional response, and can disentangle the separate contributions of species richness and relative abundance. 3 Applying our methodology to data from a common experiment at 28 European sites, we show that the above‐ground biomass of four‐species mixtures (two legumes and two grasses) in intensive grassland systems was consistently greater than that expected from monoculture performance, even at high productivity levels. The magnitude of this effect generally resulted in transgressive overyielding. 4 A combined analysis of first‐year results across sites showed that the additional performance of mixtures was driven by the number and strength of pairwise inter‐specific interactions and the evenness of the community. In general, all pairwise interactions contributed equally to the additional performance of mixtures; the grass‐grass and legume‐legume interactions were as strong as those between grasses and legumes. 5 The combined analysis across geographical and temporal scales in our study provides a generality of interpretation of our results that would not have been possible from individual site analyses or experimentation at a single site. 6 Our four‐species agricultural grassland communities have proved a simple yet relevant model system for experimentation and development of methodology in diversity‐function research. Our study establishes that principles derived from biodiversity research in extensive, semi‐natural grassland systems are applicable in intensively managed grasslands with agricultural plant species.
Physiological responses in Nile tilapia exposed to different photoperiod regimes

After conditioning Nile tilapia Oreochromis niloticus for 2 weeks, the photoperiod regime of 12 tanks of fish was changed to a 6L : 6D photoperiod while 12 further tanks were retained on the conditioning photoperiod regime (12L : 12D). Blood samples were collected 3 days (first sampling) and 3 months (second sampling) after changing the photoperiod regime. Blood was collected at 6 h intervals from both photoperiod regimes (1000, 1600, 2200 and 0400 hours). At the first sampling time, fish in the 6L : 6D had significantly higher cortisol both in the light and dark phases than levels in fish in the 12L : 12D photoperiod. At the second sampling time, the levels were significantly higher only in the light phase. The levels of cortisol, glucose and Cl− in fish exposed to the 6L : 6D photoperiod, however, were far lower than those of acute stress-induced levels observed in fish exposed to a stress experiment. Furthermore, there were no significant differences in overall values of all the variables between the photoperiod regimes at the second sampling time. This indicated that the fish exposed to the 6L : 6D photoperiod were not chronically stressed. Significantly higher blood lymphocyte counts were observed in fish exposed to the 6L : 6D compared to those of the 12L : 12D photoperiod during the light phase at the second sampling time. Other variables (glucose, Cl−, haematocrit and neutrophil) did not show a significant difference between the treatments at either sampling time. These results demonstrated that the artificial photoperiod regime did not cause a significant acute or chronic stress response in Nile tilapia.
Crown density changes of Norway spruce and the influence from increased age on permanent monitoring plots in Norway during 1988–1997

Summary On the ‘local county monitoring plots’ located throughout Norway a reduction of crown density has been noted during the period 1988–1997. The aim of this study was to determine whether this change could be attributed to normal effects due to the increased age of trees in the plots. The dataset comprised around 580 plots and 27 000 single trees of Norway spruce (Picea abies), with 10 years of crown density measurements available for each tree. A two-step approach was used, first to search for an expectancy for normal reduction of crown density by age derived from the dataset, and then to compare this with the actual reduction. The interpretation was somewhat complicated as the various results were dependent upon each other. Highly significant correlations were found between crown density and age. The relationship indicated an annual reduction of crown density of around 0.12%. However, the relationship varied both between years and between regions, and it was not possible to definitely determine whether the relationship was best described by linear or nonlinear models. Of major importance here is that the relationship appeared to be influenced by the presence of stresses, whose effects tended to be more severe in old stands. On this basis it seems questionable whether an expectancy for normal ageing can be properly defined. In the present study, however, it could still be definitely determined that the mean crown density change of—0.41% annually was too negative to be attributed to normal ageing, as it was clearly below all the suggested expectancies from the various models. This suggests that the amount of stress in the period under study has been higher than normal, and this encourages the search for causal agents in further studies. Changes in silviculture may have had some influence. The results were valid for most of Norway, with the exception of western and northern regions. Crown density assessments are subjective, which may possibly give erroneous time trends. However, it is argued that this is less likely to be of major importance in the present data.
Field establishment of Aphidius colemani Vier. (Hym., Braconidae, Aphidiinae) in the Czech Republic

Abstract: Aphidius colemani Vier. (a Chilean strain) was introduced and became established in the field between 1992 and 2000 in the Czech Republic. The target aphid species, Aphis spiraephaga Muell. on Spiraea ornamentals, and later the Russian wheat aphid, Diuraphis noxia (Kurdj.) on small grains were found parasitized, but an increasing number of other host aphid species in various urban ecosystems, crops and native communities was also detected. The establishment of A. colemani is classified as positive in supplementing the native parasitoid guilds as well as in contributing to the overall biodiversity of hymenopterous parasitoids in the cultivated landscape.
Effect of Tooth Removal on Recaptures of Raccoons

Abstract Researchers have extensively used mark–recapture techniques to obtain information on demographic parameters of wildlife populations. However, researchers have recognized that a number of factors can influence capture probabilities of wildlife species, which in turn can bias mark–recapture estimates of demographic parameters. Tooth extraction, which is a commonly used technique in studies of mesopredator species to obtain precise age estimates and to monitor the use of vaccine baits, is an aspect of animal handling that clearly might affect the recapture probability of individuals. However, the effect that tooth removal has on the individual recapture probabilities of wildlife species is unknown. During 2005, we trapped and marked 91 raccoons (Procyon lotor) in northern Indiana, USA, as part of a mark–recapture study designed specifically to determine if tooth extractions have an effect on recapture probabilities of individuals. We performed tooth extractions on 50% of the raccoons at the time of capture, and we attempted to balance tooth extractions with respect to sex and age of raccoons. We used logistic regression to model the effects of sex, age, and tooth removal on recapture probabilities, and we used Mann–Whitney U-tests to examine the effect of tooth removal on the number of times we recaptured individuals. The probability of recapture differed between sexes but did not differ as a function of tooth removal or among age classes. In addition, we failed to detect any difference in the mean number of times that we recaptured raccoons between the tooth removed and non–tooth-removed groups. Our results suggest that managers can use tooth extractions as an effective management tool without biasing population estimates or compromising other management objectives.