Miracle-dz/UniFAR-FTUs huggingface dataset:
The Effects of Growth Hormone and Insulin-Like Growth Factor-1 Treatments on Hepatic Gene Expression in Obese and Diabetic Mice with Nonalcoholic Fatty Liver Disease

Nonalcoholic fatty liver disease (NAFLD), defined as hepatic steatosis with less than 20 g of daily alcohol intake, is the most prevalent liver disease in the world because of its close association with obesity and metabolic disorders. Currently, the only available treatment for NAFLD is diet and exercise. Our lab has found that treatment with growth hormone (GH) or insulin-like growth factor-1 (IGF-1) significantly reduces liver triglyceride content in diet-induced obese and diabetic mice exhibiting NAFLD. The goal of this study was to characterize the molecular mechanisms at the mRNA level of these novel treatments using One-color Agilent 4x44K Whole Mouse Genome Arrays. Two major treatment regimens were used. In treatment regimen #1, mice were subjected to 16 weeks of low-fat (LF) or high-fat (LF) diet, which induces obesity, diabetes, and NAFLD, followed by three weeks (21 days) of twice daily injections. The LF and HF controls received phosphate-buffered saline (PBS). The 3 experimental treatments were GH, IGF-1, and a combination of GH/IGF-1 (Combo). The GH and Combo treatments lowered fat mass and liver triglyceride content, and increased lean mass, plasma IGF-1, and glucose tolerance. The IGF-1 treatment lowered liver triglyceride content and increased lean mass. A subset of four mice from the LF and HF controls and the GH and IGF-1 treated groups were selected for microarray experiment #1 (LF, HF, GH21 & IGF21, respectively). A total of 910, 372, and 256 genes were differentially expressed when comparing HF versus LF, GH21 versus HF, and IGF21 versus HF, respectively.
Evolutionary relationship among three native and two crossbreed sheep breeds of Turkey: preliminary results

SUMMARY The Turkish native sheep breeds, possibly being the neighbours of the earliest domesticated sheep populations, might be harbouring important genetic characteristics to be employed in the future for the improvement of sheep breeds. In order to design a conservation strategy, their genetic diversities must be determined. In the present study, based on three microsatellite loci, the genetic diversity of the Kivircik, Awassi, Akkaraman breeds (native) of Turkey as well as two of their crossbreeds Turkgeldi and Konya Merino were studied comparatively. It was observed that their heterozygoties are all high (0.6673-0.7822) compared to previously studied breeds, as expected for populations close to the center of domestication. Neighbour Joining (NJ) tree based on allele sharing distances indicated that the inertia of the breeds are not high. Yet, the genetic differentiations between the breeds based on pairwise FST (inbreeding coefficient) values are all significant. Furthermore, the three microsatellite loci could distinguish three groups of native breeds and their crossbreeds; 1) Awassi, 2) KivircikTurkgeldi and 3) Akkaraman-Konya Merino.
Development and application of new molecular markers for analysis of genetic diversity in Verticillium dahliae populations

The aim of this study was to develop new polymorphic markers for analysis of genetic diversity in the fungal soilborne plant pathogen Verticillium dahliae. Twelve polymorphic markers (five microsatellites and seven polymorphic sequences) were developed from a genomic library enriched for microsatellites. Screening of polymorphic loci was done using a collection of 25 V. dahliae isolates of diverse geographic origins, host sources and vegetative compatibility groups (VCGs). Three methods were used to score alleles: polyacrylamide gel electrophoresis (PAGE), sequencing of PCR-amplified loci, and capillary electrophoresis. The new markers were used to assess genetic differentiation between isolates associated with different host plants. Two collections of isolates were analysed, obtained from artichoke (30 isolates) and potato (20 isolates) from crops grown in rotationlocatedinthesameareaineastern-centralSpain.Theresolutionofgeneticdifferentiationbetweenthesetwocollections using the new markers was compared to that provided by other often-used markers (SCARs and VCGs). Sequence analysis of the alleles proved to be the most unambiguous technique for scoring microsatellite data. The relatively high genetic differentiation observed between isolates from different crops (genetic differentiation coefficient, GST =0 AE24) and their high genotypic diversity suggest a divergence between V. dahliae from artichoke and potato. It is hypothesized that evolution of V. dahliae fromthelocalresidentpopulationinassociationwiththetwohostcropshasoccurred.Thenewmarkersareusefulforresolving populationstructurewithinV.dahliaeandmaycontributetoabetterunderstandingofthepopulationbiologyofthisfungus.
Main determinants of forest soil respiration along an elevation/temperature gradient in the Italian Alps

The main determinants of soil respiration were investigated in 11 forest types distributed along an altitudinal and thermal gradient in the southern Italian Alps (altitudinal range 1520 m, range in mean annual temperature 7.8°C). Soil respiration, soil carbon content and principal stand characteristics were measured with standardized methods. Soil CO2 fluxes were measured at each site every 15–20 days with a closed dynamic system (LI‐COR 6400) using soil collars from spring 2000 to spring 2002. At the same time, soil temperature at a depth of 10 cm and soil water content (m3 m−3) were measured at each collar. Soil samples were collected to a depth of 30 cm and stones, root content and bulk density were determined in order to obtain reliable estimates of carbon content per unit area (kg C m−2). Soil respiration and temperature data were fitted with a simple logistic model separately for each site, so that base respiration rates and mean annual soil respiration were estimated. Then the same regression model was applied to all sites simultaneously, with each model parameter being expressed as a linear function of site variables. The general model explained about 86% of the intersite variability of soil respiration. In particular, soil mean annual temperature explained the most of the variance of the model (0.41), followed by soil temperature interquartlile range (0.24), soil carbon content (0.16) and soil water content (0.05).
Genetic relationships and population structure within taxa of the endemic Sideritis pusilla (Lamiaceae) assessed using RAPDs

RAPD analysis has been performed for 15 plant populations, covering eight different infraspecific taxa ofSideritis pusilla(Lange) Pau, member of the Lamiaceae endemic to southeastern Spain, and their putative parental speciesSideritis hirsutaL. andSideritis leucanthaCav. Genetic distances, together with the presence of numerous fixed molecular markers differentiatingS. pusillafrom its putative ancestors, indicate that it should be considered as a true species. Cladistic and populational analysis led to the allocation ofS. pusillapopulations into three major groups—osteoxylla, flavovirensandpusilla/almeriensis—which include taxa previously described as ranging from the varietal to the specific level. Low genetic differentiation among groups revealed by a reduced number of specific molecular markers justify their assignment under the infraspecific range. Moreover, the existence of both morphological and biogeographical differences, supports a status for these groups as subspecies ofS. pusilla.Highly significant (P<0.002) variance partitioning data (AMOVA) extracted from the analysis of individuals withinS. pusillapopulations show that, of the total genetic diversity, 68.8% was attributable to individual differences within populations, 19.9% to populational differences within groups, and only 11.3% to divergence between groups. This distribution is in agreement with the outcrossing nature of these plants. Comparative analysis of variance within populations reveals a reduced genetic variation for theosteoxyllagroup, thus supporting its previous consideration as an endangered taxon.
On assumptions behind estimates of abundance from counts at multiple sites

Count data of animals observed from multiple sites are commonly used to study variation in abundance across space and time. Because some individuals typically go undetected in such surveys, count data alone have traditionally been thought to not contain information about absolute abundance. In a recent paper, we showed that estimates of absolute abundance using single‐visit methods with covariates (Sólymos, et al. Environmetrics, 2012, 23, 197 ) can be biased arbitrarily low if the link function used for detection probability is mis‐specified. Sólymos & Lele (Methods in Ecology and Evolution, 2015, in press) argue that this is not a relevant issue in practice. We discuss the implications of the assumptions necessary for estimating abundance from the single‐visit model and clarify and extend results in Knape & Korner‐Nievergelt (Methods in Ecology and Evolution, 2015, 6, 298). We also discuss assumptions of the Dail‐Madsen model. We show that for the single‐visit model a partially scaled link function which covers the full range from 0 to 1 leads to the same scaling issue as the scaled link function used in Knape & Korner‐Nievergelt (2015) which only covers a restricted range. We argue that there is essentially no information about absolute abundance contained in single‐visit count data. Additional more direct data on detection probabilities is required to robustly estimate absolute abundances.
Molecular and morphological systematics of hypogean schizomids (Schizomida : Hubbardiidae) in semiarid Australia

We used molecular and morphological techniques to study troglobitic schizomids inhabiting a variety of subterranean landforms in semiarid Western Australia. The study was designed to explore the taxonomic and phylogenetic status of newly discovered populations of subterranean schizomids. Molecular sequences of the mitochondrial DNA (mtDNA) cytochrome oxidase subunit 1 (COI) and small subunit rRNA (12S) were obtained from a total of 73 schizomid specimens. Populations sampled from boreholes within mesa landforms in the Robe Valley were highly genetically distinct from species of Draculoides Harvey, 1992 found elsewhere in the Pilbara (Cape Range and Barrow Island). Pronounced genetic structuring was also evident at a fine spatial scale within the Robe Valley, with populations from each of the mesas examined exhibiting unique and highly divergent mtDNA lineages. These molecular data were generally supported by small but significant morphological features, usually in the secondary male structures, but some species were represented only by female specimens that possessed more conservative morphologies. The molecular data defined two major in-group clades, which were supported by morphological differences. One clade was widespread and included the type species of Draculoides, D. vinei (Harvey), along with D. bramstokeri Harvey & Humphreys, D. brooksi Harvey, D. julianneae Harvey, D. mesozeirus, sp. nov. and D. neoanthropus, sp. nov. The second clade was restricted to the Robe Valley and deemed to represent a new genus, Paradraculoides, which included four new species P. anachoretus, sp. nov., P. bythius, sp. nov., P. gnophicola, sp. nov. and P. kryptus, sp. nov. (type species).
Relations between polyphenols content and antioxidant activity in vine grapes and leaves

The occurrence and content of some polyphenols and the antioxidant activity of compounds present in grape berries, stems and leaves of Vitis vinifera L. were evaluated. Three white and three blue varieties of grapevine were investigated. The contents were determined of trans-resveratrol, trans-piceid, caftaric acid, tryptophan, catechin, epicatechin, total polyphenols, and flavanols, both in healthy material and in the samples of the plant material infested with microorganisms (Botryotinia fuckeliana Whetzel anamorph Botrytis cinerea Pers.; Uncinula necator (Schw.) Burr; Plasmopara viticola (Berk. & M.A. Curtis) Berl & De Toni). The antioxidant activity of the extracts obtained was determined by different methods: FRAP (Ferric Reducing Antioxidant Power), DPPH (2,2-diphenyl-1-picrylhydrazyl radical) and TAC-PCL (Total Antioxidant Capacity of Photochemiluminescence). The content of trans-resveratrol varied between 0.3-2.3 mg/kg and 0.7-12.1 mg/kg in non-infested and infested grape berries, respectively. The content of trans-piceid between 0.6-2.9 mg/kg and 1.5-6.3 mg/kg in non-infested and infested grape berries, respectively. The content of trans-resveratrol varied between 2.5-10.3 mg/kg and 3.7-20.9 mg/kg in healthy and in infected leaves, respectively. The content trans-piceid varied between 11.3-58.4 mg/kg and 18.5-60.9 mg/kg in the healthy and in the infected leaves, respectively. The highest content of trans-resveratrol was found in stems (16.3-276.3 mg/kg). In young lateral shoots, the highest levels of trans-piceid (12.6-99.7 mg/kg) and caftaric acid (474-2257 mg/kg) were determined. The infested grape berries showed a higher antioxidant activity, which was most closely correlated with the content of total polyphenols (correlation coefficient = 0.8336-0.9952).
Assessing effects of laser point density, ground sampling intensity, and field sample plot size on biophysical stand properties derived from airborne laser scanner data

Canopy height distributions were created from small-footprint airborne laser scanner data with an average sampling density of 1.13 points·m–2 collected over 132 sample plots and 61 forest stands. Field measurements of each plot were carried out within two concentric circles corresponding to fixed areas of 200 m2 and 300 or 400 m2. The laser point clouds were thinned to approximately 0.25, 0.13, and 0.06 point·m–2. For all comparisons, the maximum values of the first as well as last return canopy height distributions differed significantly between the full density and the thinned data. The combined effects of number of field plots, field plot sizes, and point densities on the accuracy of mean tree height, stand basal area, and stand volume predicted at stand level using a two-stage procedure combining field training data and laser data, were assessed using Monte Carlo simulation randomly selecting 75% and 50% of the field plots. The average standard deviation showed only a minor increase by decreasing poin.
Comparative effects of probiotic, prebiotic and synbiotic supplements on performance, jejunal morphology, serum lipid profile and antibody response of broiler chicks

A 42-d trial was conducted to compare the effects of probiotic, prebiotic and synbiotic supplements on growth performance, morphology of the jejunum, serum lipid profile and antibody response of broiler chickens. A total of 400 one-d-old male broiler chicks were randomly divided into four treatment groups of four replicates (25 birds per replicate) and fed corn-soybean meal diets. The dietary treatments consisted of a basal diet without any feed additive (control diet), a basal diet with added probiotics (diet Pro), a basal diet with added prebiotics (diet Pre), and a basal diet with added synbiotics (diet Syn). The birds fed diet Syn exhibited higher body weight gain (BWG) and better feed conversion ratio (FCR) than those fed the control diet during the entire experimental period (P<0.05). Feeding diets Pro, Pre and Syn significantly increased the villus height and villus height:crypt length ratio in the jejunum of broilers at 42 d of age (P<0.05). The birds fed any of the experimental diets, exhibited lower levels of serum total cholesterol and low-density lipoprotein cho- lesterol (LDL-C) than those fed the control diet at 28 and 42 days of age (P<0.05). At 41 d of age, the total antibody titer against sheep red blood cell (SRBC) in the birds fed diets Pro, Pre and Syn were higher than in the birds fed the control diet, with the birds fed diet Syn having the highest antibody titer (P<0.05). None of the diets affected feed intake, crypt depth in the jejunum, serum triglyceride level and primary antibody response against SRBC. The results suggested that diets supplemented with probiotics, prebiotics and synbiotics could improve growth performance and health benefits of the broiler chicks by improving intestinal morphology, fat metabolism and immune function. Keywords: broilers, immunity, intestinal morphology, non-antibiotic supplements, serum lipids
Oedemognathus exodon and Sternarchogiton nattereri (Apteronotidae, Gymnotiformes): the Case for Sexual Dimorphism and Conspecificity

ABSTRACT. Oedemognathus exodon, a monotypic genus and species of Amazonian apteronotid electric fishes, is based on a single specimen with uniquely externalized jaw teeth projecting from a bulbous snout. Recently, many additional specimens of Oedemognathus, all mature males, have been collected in the Amazon by trawling in channels and seining in floating vegetation mats. These new specimens were collected with many monomorphic female, male and immature specimens of Sternarchogiton nattereri, a related and similar species. On this basis we suggested a hypothesis of sexual dimorphism and conspecificity for O. exodon and S. nattereri. Although this idea has been taxonomically accepted by recent authors with treatment of O. exodon as a junior synonym of S. nattereri, the evidentiary basis for this remains unpublished. Herein we present that evidence. In addition to being associated at sexual maturity during breeding season, S. nattereri and O. exodon are closely similar in external and internal morphology, pigmentation, and mitochondrial cytochrome b sequences. Furthermore, we observe that the striking dentition, jaw and snout morphology of Oedemognathus has its developmental origin in mature males that are equal, or nearly so, in size to non-dimorphic S. nattereri.
The application of single-strand conformation polymorphism (SSCP) technique for the analysis of molecular heterogeneity of grapevine virus A

The results of the analysis of grapevine virus A (GVA) isolates by single-strand conformation polymorphism (SSCP) confirm that this technique is very helpful in rapid and relatively low cost preliminary analysis of molecular heterogeneity of viruses. The results clearly show that the reliability of SSCP analysis of GVA depends on oligonucleotide primers for successful RT-PCR amplification of the highest possible number of molecular variants of the virus. Among 7 pairs of GVA-specific primers designed in different laboratories only two, those from Canada (117038 and C7273) and Switzerland (MP and CPdt), allowed positive RT-PCR amplification of all our isolates of the virus mechanically transmitted from various grapevines to Nicotiana benthamiana . With SSCP analysis of 238 bp DNA fragments complementary to part of ORF5 of GVA, produced by RT-PCR using the first pair of primers, we were able to detect 1-35 nt differences between GVA isolates. The DNA fragments, about 986 bp, complementary to part of ORF3 and ORF4, ORF5 and 3'UTR of GVA, produced by RT-PCR using the second pair of primers, were useful for SSCP analysis only after their digestion with the restriction enzyme Dde I. The results strongly suggest that SSCP analysis of 238 nt fragment of ORF5 of GVA along with Dde I/SSCP analysis of about 986 nt 3'terminal fragment of the virus allow rapid and reliable determination of the number of dominant nt sequence variants of GVA present in a single N. benthamiana or grapevine plant.
In vitro evaluation of biocontrol agents and botanicals against Wilt incidence of watermelon, tomato and marigold.

Efficacy of saprophytically competitive bioagents and some plants leaf extract against Fusarium spp. were studied in vitro. Six bioagents viz., Trichoderma viride, Gliocladium virens, T. harzianum, T. hamatum, Aspergillus niger, Psuedomonas fluorescens and five plant extracts viz., Azadirachta indica, Pongamia pinnata, Parthenium hysterophorus, Calotropis gigantia and Annona squamosa were assessed for their efficacy against Fusarium spp. by using dual culture technique. The suppression of the growth of the pathogen was significantly higher with T. viride, T. harzianum, T. hamatum, Aspergillus niger, A. flavus which were at per among themselves. The minimum inhibition was seen with Psuedomonas fluorescens. In case of plants leaf extracts, the growth of pathogen was significantly lowest on Azadirachta indica followed by Pongamia pinnata, Parthenium hysterophoras, Calotropis gigantia and Annona squamosa leaf extracts. It was concluded that all the bioagents reduced the wilt incidence improving seed germination, shoot length and root length over control. Seed treatment with Trichoderma viride and T.harzianum gave significantly better results in respect to seed germination, shoot length, root length, and wilt incidence. The growth of pathogen was significantly lowest on Azadirachta indica followed by Pongamia pinnata, Parthenium hysterophorus, Calotropis gigantia and Annona squamosa leaf extracts.
Enterococcus avium nom. rev., comb. nov.; E. casseliflavus nom. rev., comb. nov.; E. durans nom. rev., comb. nov.; E. gallinarum comb. nov.; and E. malodoratus sp. nov.

Biochemical, chemical, and genetic data indicate that strains labeled Streptococcus avium (Nowlan and Deibel), "Streptococcus casseliflavus" (Vaughn, Riggsby and Mundt), "Streptococcus durans" (Sherman and Wing), "Streptococcus faecalis subsp. malodoratus" (Pette), and Streptococcus gallinarum (Bridge and Sneath) are closely related to members of the genus Enterococcus Schleifer and Kilpper-Balz. We propose that these taxa be classified as members of the genus Enterococcus, as Enterococcus avium nom. rev., comb. nov., Enterococcus casseliflavus nom. rev., comb. nov., Enterococcus durans nom. rev., comb. nov., Enterococcus malodoratus sp. nov., and Enterococcus gallinarum comb. nov., respectively.
Relationships between crown architecture and available irradiance in two cerrado species with different leaf phenologies

Structural differences between cerrado species with different leaf phenologies are linked to crown architecture, leaf production, and biomass allocation to shoots and leaves. The present study characterized crown structures and the patterns of biomass allocation to leaves and shoots in two woody cerrado species with contrasting leaf phenologies and quantified the irradiance reaching their leaves to determine the best period during the day for photosynthetic activity. The shoots and leaves of five individuals of both Annona coriacea (deciduous) and Hymenaea stigonocarpa (evergreen) were collected along a 50 m transect in a cerrado fragment within the urban perimeter of Catalao - GO, to determine their patterns of biomass allocation in their crowns. The evergreen H. stigonocarpa had significantly higher mean values of shoot inclination (SI), petiole length (PL), leaf area (LA), leaf display index (LDI), and individual leaf area per shoot (ILA), while the deciduous species A. coriacea had significantly higher leaf numbers (LN). The more complex crown of H. stigonocarpa had shoots in more erect positions (orthotropic), with intense self-shading within shoots; A. coriacea, on the other hand, had slanting (plagiotropic) shoots in the crown, allowing similar irradiance levels to all leaf surfaces. The production of plagiotropic shoots by the deciduous species (A. coriacea) is a strategy that enables its use of incident sunlight early in the morning and preventing excessive water loss or excessive irradiance. Hymenaea stigonocarpa (an evergreen), by contrast, had orthotropic shoots and uses intense self-shading as a strategy to avoid excessive irradiance, especially at midday. Differences in crown architectures between evergreen and deciduous species of cerrado sensu stricto can therefore be viewed as adaptations to the environmental light regime.