Miracle-dz/UniFAR-FTUs huggingface dataset:
Single-nucleotide polymorphisms reveal distribution and migration of Chinook salmon (Oncorhynchus tshawytscha) in the Bering Sea and North Pacific Ocean

We genotyped Chinook salmon (Oncorhynchus tshawytscha) from the Bering Sea and North Pacific Ocean for 43 single-nucleotide polymorphisms (SNPs) to investigate seasonal distribution and migration patterns. We analyzed 3563 immature fish from 22 spatiotemporal strata; composition analyses were performed using genotype data from spawning stocks spanning the species range. Substantial variation in stock composition existed among spatial and seasonal strata. We inferred patterns of seasonal migration based upon these data along with data from previous tag, scale, and parasite studies. We found that stocks from western Alaska and Yukon River overwinter on the Alaska continental shelf then travel to the middle and western Bering Sea during spring–fall. Stocks from California to Southeast Alaska were distributed in Gulf of Alaska year-round, with a substantial portion of this group migrating northward to the eastern Bering Sea during spring–fall. Proportions of Russian stocks increase when moving east to west in.
High-level mupirocin resistance in a Staphylococcus pseudintermedius strain from canine origin.

Mupirocin is an important antibacterial agent used in both humans and animals topically, especially against nasal carriage and decolonization of methicillin-resistant Staphylococcus pseudintermedius. In this report, a S. pseudintermedius strain was isolated from a dog with pyoderma. Molecular identification of this strain was performed by digestion of pta gene with MboI enzyme. High-level mupirocin resistance was determined by agar dilution method and amplification of ileS-2 gene. Sequence analysis of 16S rRNA and ileS-2 gene of S. pseudintermedius was also performed and both sequences were accessed in GenBank. This is the first report of a highlevel mupirocin resistant S. pseudintermedius strain from a dog with pyoderma in Turkey.
Eastern Spotted Skunk (Spilogale putorius) Survival and Cause-specific Mortality in the Ouachita Mountains, Arkansas

Abstract Survival and cause-specific mortality of eastern spotted skunks (Spilogale putorius) was assessed for a radio-monitored population in the Ouachita Mountains of westcentral Arkansas, USA. We monitored 33 eastern spotted skunks over a 23 mo period. Mean annual survival was 0.354 (0.339–0.368, 95% CI), and survival estimates were similar across age and sex categories. Survival increased for males as measures of body condition index increased. This pattern was reversed for females, although interpretation of the patterns is potentially confounded by female reproductive status. Of 19 mortality events, 63% (12) were caused by avian predators, most likely great horned owls (Bubo virginianus), 26% (5) were caused by mammalian predators, and 11% (2) were due to unknown causes. Although eastern spotted skunks are known to avoid open areas and forested areas where the understory is less dense and the canopy more open, 11 of 12 avian-caused deaths occurred in mature shortleaf pine stands with an open canopy and herbaceous understory.
The use of dyes to mark populations of beneficial insects in the field

Dyes and dusts have been used to mark insects internally and externally for decades, the majority of examples coming from laboratory-reared pest species used in mark-release-recapture studies. Using dyes or dusts to mark populations of pests and beneficial insects simultaneously in the field has received less attention. We evaluated a water-soluble fluorescent dye and a resin-based fluorescent pigment sprayed on crops to mark beneficial and pest insects, and monitored the dispersal of marked insects. Our results show that resin-based dyes provide an effective mark on several species of insects among several orders. The resin-based dye is also relatively inexpensive, non-toxic, UV-stable and water resistant, unlike a water-soluble dye. Using the resin-based dye in a broccoli production system, we were able to monitor simultaneously the movement of field populations of the parasitoids, Diadegma semiclausum (Hellén) (Hymenoptera: Ichneumonidae), and Apanteles ippeus (Nixon) (Hymenoptera: Braconidae) and the adult stage of the host, diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae). Resin-based dye applied on a crop is an effective way to mark and monitor the dispersal of populations of beneficial and pest insects in relation to agricultural practices, integrated pest management and conservation biological control.
"Untersuchungen zur Optimierung pharmakologischer Studien an hepatischen Zellen in 2D- und 3D-Kulturen"

IV INTRODUCTION . 5 METHODS . 6 Cells . 6 2D culture of hepatic cells . 6 Bioreactor and perfusion system . 6 Metabolic parameters . 7 Immune histochemistry . 7 Gene array analysis . 8 Statistics . 8 RESULTS . 9 Suitability oftheHepaRG cell line as an alternative cell source to primary human hepatocytes . 9 Morphology and distribution of HepaRG cells in comparison to pHH . 9 Comparison of metabolic activities . 9 CYP activity assay in HepaRG cells and primary human hepatocytes . 10 CYP activity and induction in pHH and HepaRG, compared to otherhepatic cells . 10 Intrinsic clearance of reference drugs . 10 Serum-free 3D-culture of primary human hepatocytes in a new miniaturized version of the bioreactor system for pharmacological in vitro studies . 10 Downscalingof the bioreactor from clinical scale to laboratory scale . 10 Adaptation of perfusion and gas flow rates . 11 Optimization of the CYP activity assay and adaptation to the 3D culture system. 11 Comparison of metabolic activities in serum-containing and serum-free bioreactor cultures . 12 Immune histochemcal characterization of bioreactor cultures . 12 Gene expression analysis of bioreactor cultures under serum-containing or serum-free culture conditions . 13 DISCUSSION . 13 REFERENCES . 17
EEG beta band sources modulated by gait cycle during robot-assisted walking

Figure 1: a) Significant (corrected p<0.05) spectral changes (gait vs. rest) in each subjects individual beta frequency peak. Activity illustrated in blue indicates spectral decrease; activity in red spectral increase. The voxels with significant spectral decrease in the sensorimotor foot areas were clustered and used for analyzing time courses of brain activities in these regions. b) Individual beta peak frequencies (max. spectral decrease gait vs. rest) and correlation coefficients r between 0-50% and 50-100% of the gait cycle. c) Time course (mean±std over subjects) of spectral magnitudes in the sensorimotor foot areas.
Prioritising species for research, conservation and management: a case study of exploited fish species

Studies that categorise species according to their conservation status often fall short in their implementation by not having taken into account the impacts on, or the response from, those that either benefit from, or exploit, the resource under consideration. This is especially true in multispecies fisheries where personnel and funding limitations often create the dilemma over which species should be the first to receive management and research attention. This study uses a multicriteria decision analysis approach to prioritise 176 South African linefish species on the basis of a number of criteria indicating conservation and socio-economic, including fishery sector, importance. For each species, conservation criteria were: abundance trend, level of knowledge, vulnerability, range, and relative exploitation throughout that range. Sectoral criteria were: total catch, degree of targeting, the number of participants and the economic value of each species. The scores given to each species on the basis of each of these criteria were summed to allow an examination of each fish's importance from the points of view of (i) conservation, (ii) each fishery sector separately and combined, and (iii) the overall combined conservation and sectoral importance. Different weight sets were used in the weighted summation of the scores, and results were examined for sensitivity. The results were reasonably insensitive to these changes in weights. Relative scores within each of the fishery sectors were dominated by two or three species. Consequently, the scores separating the remaining species from each other were small. This meant that, in many cases, even when the rank of species changed by a number of places with a different weight set, the differences in score were slight. On the whole, the top fish included the most important species in each sector and biogeographical region and in terms of conservation. The separate and overall rankings should assist in the development of broadly acceptable management strategies for different fish species.
Seasonal variations in phytoplankton composition and biomass in a small lowland river-lake system (Melen River, Turkey)

A series of studies were carried out to determine the succession and phytoplankton community of the Melen River in the Western Black Sea region of Turkey. The study was conducted at 6 stations at monthly intervals between May 2003 and April 2004. It was observed that the abundance and biovolume of phytoplankton were low in winter, though higher values were recorded in late spring and summer. Among the values noted, the spring peak was 534.38 × 105 ind. L-1 and 7384.8 mm3 L-1 belonging to Peridinium sp. The most common diatom, Cyclostephanos dubius, was favoured by low discharge at stations 1 and 2 in the early summer (214.29 × 105 ind. L-1 and 9.84 × 105 ind. L-1), respectively. Chlorophyll-a concentrations were between 0.86 and 64.2 mg L-1. A total of 135 taxa belonging to Cyanophyta, Bacillariophyta, Chlorophyta, Dinophyta, Euglenophyta, Heterokontophyta, Streptophyta, and Xanthophyta were identified. The total biomass of the stations 1 and 2 was mainly characterised by Dinophyta and at other stations by Bacillariophyta. Five major genera (Peridinium, Ceratium, Phacus, Cyclostephanos, and Melosira) accounted for over 70% of the total phytoplankton abundance. Phytoplankton abundance was significant and positively correlated with Chl-a and temperature (r = 0.57 and r = 0.78, respectively P < 0.05). Species richness and diversity indices increased gradually throughout the course of the river.
Powdery Mildew Resistance Genes in 127 Northwest European Spring Barley Varieties

One hundred and twenty-seven spring barley varieties grown in Denmark since 1979 were characterized for resistance genes using 30 powdery mildew isolates. The resistance genes are traced in the pedigrees to verify the results. Eleven named genes, 12 tentatively named genes/resistances and six unknown resistances were found. Resistance in many varieties was based on combinations of either known genes or of known and new factors. The following five new or relatively new resistance genes more or less effective against the present powdery mildew populations were detected: the ‘Mlo’ resistance conferred by the recessive mlo gene with the characteristic infection type 0/(4), ‘Ricardo’ and ‘Turkish’ sources having gene Mla3 in common and ‘Turkish’ with Ml(Tu2) in addition. In three varieties the new resistance Ml(IM9) was found in combination with different Mia alleles. Variety ‘Jarek’ has two new unidentified resistances.
Role of extracellular matrix and mitochondria related genes in determining cardiac defects in Down syndrome

Mitochondrial dysfunction, which is consistently observed in Down syndrome (DS), is suspected to worsen mental retardation and congenital cardiopathies in DS subjects, as well as to determine other phenotypic abnormalities, such as Alzheimer's disease, type 2 diabetes, obesity, and hypertrophic cardiopathy. As the heart is one of the main targets of DS, we have analyzed gene expression of DS fetal hearts demonstrating a global downregulation of nuclear encoded mitochondrial genes (NEMGs) together with the upregulation of clusters of extracellular matrix proteins (ECMs). A mitochondrial dysfunction was found associated with NEMG downregulation in DS fetal fibroblasts (DS-HFFs). Based on these previous results, this doctorate thesis was aimed: - to identify Hsa21 genes responsible for either NEMG downregulation or ECM upregulation; - to develop strategies to counteract the negative effects triggered by NEMG dysregulation in DS; - to investigate how NEMG downregulation or ECM upregulation might affect cardiac phenotype. Performing a meta-analysis on public expression data we identified two genes mapping to chromosome 21 (Hsa21), namely NRIP1/ RIP140 (nuclear receptor interacting protein 1) and RUNX1 (Runt related transcription factor 1), as good candidates for NEMG downregulation and ECM upregulation, respectively. These genes are overexpressed in DS cells and in heart tissue. NRIP1 negatively regulates PGC-1α, a master regulator of the mitochondrial function. We attenuated by siRNA NRIP1 expression in a cell model of DS demonstrating an inverse correlation between NRIP1 and PGC-1α expression, together with an improvement of mitochondrial function in silenced cells. We therefore developed a strategy to correct mitochondrial alterations in DS by pharmacologically stimulating the activity of the NRIP1 targets PGC-1α and PPARs. To this aim we supplemented cultures of DS-HFFs with drugs affecting PGC-1α, namely Metformin and Pioglitazone, to evaluate their modulatory impact on mitochondrial function. We found both strategies effective on rescuing mitochondrial function in terms of oxigen consumption, ATP production and mitochondrial biogenesis.
Epidemiological situation of Citrus tristeza virus in mainland Portugal.

This study was conducted to update the occurrence and molecular variability of Citrus tristeza virus (CTV) isolates recently obtained from surveys in different orchards in mainland Portugal. The asymmetric PCRELISA typing method based on the coat protein (CP) gene was used to characterize CTV isolates. Most isolates of the virus found in the Algarve region, where major citrus producing zones exist, belonged to the mild phylogenetic group (GpM). The prevalence of haplotypes from this group suggests that the aphid vector Toxoptera citricidus, which is present in the northern region of the country associated to diverse severe strains, has not yet reached the Algarve. Although most of the isolates harbour haplotypes from group M, haplotypes from the remaining phylogenetic groups were also identified and characterized.
Beastly Bondage: The Costs of Amplexus in Cane Toads (Bufo marinus)

Abstract Reproductive activities can impose fitness costs as well as benefits. In most anuran species, males clasp females for prolonged periods prior to gamete release, and intuition suggests that the male's presence may impair the female's ability to move about and to feed. We tested the prediction that female locomotion and feeding would be reduced during amplexus in laboratory experiments with Cane Toads, Bufo marinus. Amplexus reduced the female's locomotor (sprint and swim) performance, with the degree of locomotor impairment (speed and distance per hop) dependent upon the body size of the amplectant male for trials of terrestrial locomotion, but not for aquatic locomotion. Amplexus also reduced feeding rates in females; amplectant males did not feed at all. Overall, our data confirm that amplexus imposes locomotor and feeding costs to female Cane Toads, and suggest that this distinctive posture may generate sexual conflict in at least some anuran species.
Arabidopsis thaliana thylakoid lumen 18.3 protein (TLP 18.3) gene regulate developmental process

Arabidopsis thaliana thylakoid lumen 18.3 kDa protein (TLP18.3) gene (At1g54780) has a domain of unknown function, which is a family of uncharacterized protein. To examine the developmental regulation of this gene, Arabidopsis thaliana TLP18.3 T-DNA insertion mutant (SALK_109618) and wild type plant were observed for the effect of ABA, NaCl and mannitol on the germination of seeds. Â 50 mM NaCl inhibit more germination rate in mutant plants than wild type plants followed by 0.1 ÂµM ABA and 20 mM mannitol. But in control condition also mutant plants have less (54%) germination rate than the wild type plant which having germination (77%). Arabidopsis thaliana TLP18.3 T-DNA insertion mutant plants (SALK_109618) Â have shown 6-9 days of flowering delay but after Â Agrobacterium mediated transformation of Arabidopsis thaliana TLP18.3 T-DNA insertion mutant with pPZP200GB-TLP18.3 construct rescued the flowering delay and germination. The translational analysis have shown that the TLP18.3 protein accumulation wild type plant of Arabidopsis thaliana and it was not detected in western blot analysis of Arabidopsis thaliana TLP18.3 T-DNA insertion mutant demonstrated that this protein was absent in mutant plants. For the subcellular localization of Arabidopsis thaliana TLP18.3, the protoplast of transformed Arabidopsis thaliana TLP18.3 T-DNA insertion mutant after Agrobacterium mediated transformation with pPZP200GB-TLP18.3 construct which is having GFP green fluorescence image, which was completely overlapped with red autoflorescence of chloroplast image clearly showed the chloroplast localization of TLP18.3.
Effect of a Geographic Barrier on Adaptation in the Dwarf Sunflower (Helianthus pumilus Nutt.)

Premise of research. Geographic isolation promotes local adaptation but may also prevent the movement of advantageous gene complexes throughout a species distribution. We identify a geographic barrier that inhibits gene flow and adaptation across the disjunct species range of the Rocky Mountain endemic sunflower Helianthus pumilus. Methodology. Habitat suitability modeling and least-cost path analysis were used to characterize environmental preferences across the species range and to identify barriers to gene flow. Simple sequence repeat data were used to assess genetic structure and estimate recent levels of gene flow across the distributional disjunction. A common garden was used to study phenotypic differentiation and local adaptation. Controlled crosses tested for intrinsic barriers to reproduction. Pivotal results. Despite significant differences in available habitat, individuals in northern and southern regions occupy similar sites, suggesting limited adaptive differentiation in environmental preference. A region of low-suitability habitat separates the two regions. Northern and southern plants are genetically distinct. There has been little recent gene flow. Southern plants had higher fitness (measured as seed set) in the northern region than northern plants. A suite of morphological characters, present in half of southern plants, conveyed a twofold fitness advantage in the north, but this adaptive phenotype is virtually nonexistent in the northern range. Between-region crosses were equal to or more productive than within-region crosses. Conclusions. The Pikes Peak massif, a high-altitude eastward projection of the Rocky Mountains, forms a geographic barrier to gene flow in H. pumilus, a lowland foothills species. No intrinsic barriers to gene exchange between regions have yet evolved. Therefore, the geographic barrier appears to impede the movement of the adaptive phenotype found in the southern region, resulting in a northern group that is less fit than it might be, contrary to the expectation of local adaptation.
Genetic variation in rural and urban populations of Epipactis helleborine (L.) Crantz. (Orchidaceae) in Britain

Abstract Genetic variation in Epipactis helleborine in the British Isles was assessed using starch gel electrophoresis of isozymes; 273 individuals were sampled from 13 populations and examined for genetic variation using eight enzyme systems encoded for by 13 loci. Overall, 46% of the loci examined were polymorphic, with an average of 1.69 alleles per locus. Within populations, a mean of 33% of the loci were polymorphic, with a mean number of 1.46 alleles per locus. Levels of genetic variation were compared between urban and well established rural populations to assess the genetic consequences of colonization of the urban sites. The average levels of genetic variation detected in urban populations were lower than that found in rural populations, although there was a much greater range of variation among the urban populations. Large urban populations actually have patterns of variation similar to rural populations and show evidence of multiple founders. This indicates that the high dispersibility of Epipactis seeds can in some cases overcome the predicted loss of genetic variation associated with founder effects during colonization. Small urban populations, however, show significantly lower levels of genetic variation compared with these large urban populations and the rural populations, and it seems likely that this is attributable to single founding events and/or genetic drift.
Les amoebophryidae (Syndiniales) parasitoïdes de dinoflagellés : cycle de vie, dynamique et spécificité in situ

Les Syndiniales sont des parasitoides marins capables d'infecter un tres grand nombre d'organismes planctoniques, des dinoflagelles jusqu'aux larves de poissons. Parmi ces pathogenes, les Amoebophryidae infectent tout particulierement les dinoflagelles. En riviere de Penze (Bretagne Nord, France), ces parasitoides infectent toutes les especes presentes, y compris l'espece toxique Alexandrium minutum qui produit des toxines paralysantes. La specificite de ces interactions est grande : une espece hote est infectee par un parasitoide genetiquement distinct, le meme pathogene infectant la meme espece d'une annee sur l'autre (entre 2004 et 2006). Ces pathogenes semblent capables de reguler les populations hotes, la specificite d'interaction entrainant une succession rapide des especes de dinoflagelles. Dans cette etude, ce controle a ete simule en reprenant le modele d'Anderson-May et en l'incluant dans un reseau trophique microbien integrant la predation. Une souche d'un parasitoide infectant le dinoflagelle non toxique Scrippsiella trochoidea a ete isolee. La presence du pathogene induit la production de kystes de resistance de l'hote, issus de la reproduction sexuee. Cependant, un faible pourcentage de ces kystes est infecte. Apres deux mois de dormance, la germination a pu etre observee, aussi bien pour l'hote que pour le parasitoide, et de nouveaux cycles d'infection ont egalement ete observes. Cette interaction physique entre l'hote et son pathogene induit donc un couplage tres fort entre les deux partenaires, ce qui permet d'expliquer la recurrence des infections d'une annee sur l'autre en baie de Penze. Nous avons emis l'hypothese que le nombre croissant de marees rouges (ou efflorescences de dinoflagelles) pouvait etre une consequence du decouplage entre le dinoflagelle hote et son pathogene naturel. Cette hypothese permet de mieux comprendre l'historique de certaines efflorescences toxiques recurrentes entre la fin des annees 1980 et 2001, mais qui aujourd'hui apparait parfaitement regule par ces pathogenes naturels. Cette hypothese a ete egalement confirmee dans l'etang de Thau (mer Mediterranee), ou Alexandrium catenella, invasives depuis la fin des annees 1990, etait la seule espece de dinoflagelles a ne pas etre infectee par des Amoebophryidae durant les efflorescences toxiques printanieres et automnales de 2007.