Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of dietary pea seeds (Pisum sativum L. cv. Tudor) on performance, carcass traits, plasma biochemistry and intestinal microflora in broiler chicks.

The effects of dietary partial replacement of soybean meal (SBM) with peas (cv. Tudor), on performance, carcass traits, plasma biochemistry and intestinal microflora in broiler chicks, was assessed. One-day-old broilers (n=400) divided in 2 groups were fed 2 isocaloric and isonitrogenous diets: control diet (C) based on corn-sorghum-SBM and experimental diet (PT) that contained 200 g/kg peas (cv. Tudor). Results shown that PT addition significantly affect performance, BWG of broilers was higher in starter (13.23%; P<0.0001), finisher (3.21%; P=0.014) and overall period (4.28%; P<0.0001); FI was increased with 7.54% (P=0.005) in starter, 0.89% (P=0.001) in finisher, respectively 1.19% (P=0.043) in overall period vs. C diet. The FCR was decreased in finisher (P=0.024) and total period (P<0.0001) in PT group. Feeding PT did not affect the carcass yields but increased breast yield (P=0.038), and a tendency to increase the legs yield and to decrease the abdominal fat was observed. Plasma total protein content was higher in PT group (P=0.045). Digestive organs weight, length of the intestinal tract and intestinal pH of broilers were not affected by feeding PT diet. No differences were found in the ileal population of Enterobacteriaceae and E. coli among treatments, except the counts of Lactobacillus spp. that increased (5.83%; P<0.0001) in PT group. In conclusion, dietary peas (cv. Tudor), in the amount of 200 g/kg, as partial replacement for SBM, improve performance and carcass traits, has a positive effect on plasma total protein and alter ileal microflora by increasing Lactobacillus spp.
Relationship between early body condition, energetic reserves and fitness in an iteroparous insect

Body condition can be defined as the amount of energetic reserves present within an individual after structural size had been accounted for (i.e. relative amounts of energetic reserves), and estimated by Body Condition indices (BCIs)Several methods have been proposed to calculate BCIs. However, they have traditionally been validated in vertebrate studies and evidence of their power to predict fitness in invertebrates is scarce. Ideally, the use of a particular BCI in an animal population should be validated based on its ability to accurately reflect the relative amount of reserves available to the animal as well as its relationship to fitness.We aimed at increasing the variance in female body condition of Tenebrio molitor beetles by subjecting them to restricted or optimal food conditions at both the larval and/or adult stage. We then explored the predictive power of several BCIs on both the absolute and relative amount of lipids and sugars present in the insect’s body, and their link with adult fitness. Using an iteroparous income breeder allowed us to assess the relative effects of larval vs. adult access to nutritional resources on fecundity along several reproductive events.Simple measurements of phenotypically plastic traits (i.e. mass and volume) correlated well with absolute, but poorly with relative, measures of body reserves. Conversely, we found that BCIs that corrected for the interdependence between phenotypically plastic traits and structural size strongly correlated with relative amounts of body components.We found that even though the adult feeding treatment had a stronger effect, body condition at emergence, but not larval feeding treatment, also affected fecundity. Moreover, while the effect of the adult feeding treatment varied along time (i.e. egg laying rank), the effect of body condition at emergence remained constant.These results show that by carefully using simple morphometric measures and BCIs, it is possible to distinguish between the effects of structural size and body condition on fitness traits in invertebrates, and to show that an iteroparous income breeder can partially rely on its early energetic state for its later fecundity.
Impact of supplemental winter feeding on ruminal microbiota of roe deer Capreolus capreolus

European ungulates such as the roe deer face seasonally varying climatic conditions as well as food availability and quality. In some European countries, including Austria, it is common practice to provide game animals with supplemental feeding in winter. In this study we investigated if supplemental feeding significantly affects the composition of the bacterial rumen community. The rumen microbial composition of eight adult female roe deer was analysed by Illumina MiSeq 16S rRNA gene amplicon sequencing. Animals from a study area with supplemental feeding sites were compared to individuals relying on natural feed. Furthermore, the microbial community composition of different ruminal compartments (liquid phase, solid phase and wall) was compared. Our results revealed a significant qualitative difference between the microbiota composition of the two populations studied. Easily fermentable supplemental feeding promoted the proliferation of phylotypes correlated with conditions of acidosis in domestic ruminants, suggesting a possible similar adaptation and a hypothetical negative effect on health status also in roe deer. The results furthermore confirmed that in roe deer, like in other ruminant species, the most represented phyla are Firmicutes (63.2%) and Bacteroidetes (23.5%), and that the ruminal microenvironments influence the microbial community composition, with the lowest species richness and variation in the epimural microbiota.
Elevated H2AX Phosphorylation Observed with kINPen Plasma Treatment Is Not Caused by ROS-Mediated DNA Damage but Is the Consequence of Apoptosis

Phosphorylated histone 2AX (γH2AX) is a long-standing marker for DNA double-strand breaks (DSBs) from ionizing radiation in the field of radiobiology. This led to the perception of γH2AX being a general marker of direct DNA damage with the treatment of other agents such as low-dose exogenous ROS that unlikely act on cellular DNA directly. Cold physical plasma confers biomedical effects majorly via release of reactive oxygen and nitrogen species (ROS). In vitro, increase of γH2AX has often been observed with plasma treatment, leading to the conclusion that DNA damage is a direct consequence of plasma exposure. However, increase in γH2AX also occurs during apoptosis, which is often observed with plasma treatment as well. Moreover, it must be questioned if plasma-derived ROS can reach into the nucleus and still be reactive enough to damage DNA directly. We investigated γH2AX induction in a lymphocyte cell line upon ROS exposure (plasma, hydrogen peroxide, or hypochlorous acid) or UV-B light. Cytotoxicity and γH2AX induction was abrogated by the use of antioxidants with all types of ROS treatment but not UV radiation. H2AX phosphorylation levels were overall independent of analyzing either all nucleated cells or segmenting γH2AX phosphorylation for each cell cycle phase. SB202190 (p38-MAPK inhibitor) and Z-VAD-FMK (pan-caspase inhibitor) significantly inhibited γH2AX induction upon ROS but not UV treatment. Finally, and despite γH2AX induction, UV but not plasma treatment led to significantly increased micronucleus formation, which is a functional read-out of genotoxic DNA DSBs. We conclude that plasma-mediated and low-ROS γH2AX induction depends on caspase activation and hence is not the cause but consequence of apoptosis induction. Moreover, we could not identify lasting mutagenic effects with plasma treatment despite phosphorylation of H2AX.
Temporal Behavior of Tree Communities in Different Soil Classes

The objective of this work was to evaluate if the soil heterogeneity expressed by the different soil classes would condition tree communities with different dynamic behaviors. The data were collected from 25 plots sized 20 × 20 (400 m2), 10 of them with Inceptisols, 9 with Ultisols, 5 with Entisols B and 1 with Entisols A. All individuals with DBH ≥ 5.0 cm in the plots were sampled in 2000, 2005, 2009 and 2015. Rates of mortality, recruitment, gain, loss and turnover dynamics in number of individuals and basal area were estimated for each soil class. The tree communities present in the soil classes showed no differences in the dynamic behavior to the point of expressing edaphic fragment heterogeneity. The differences are associated with stochastic fluctuations in rates caused by small disturbances, suggesting little influence of the soils on the dynamics of small-scale communities.
Assessing the usage of alternative transcripts in human tissues from RNA-seq and proteomics data

Alternative splicing is an important step in gene expression regulation in eukaryotes, through which a single gene can express different transcript isoforms. We can now use RNA sequencing (RNA-seq) data to identify which isoforms of each gene are being expressed in a specific condition, by quantifying the expression level of each isoform of a gene, even though quantification of isoforms remains a difficult task. In this way, we can better understand how prevalent this process is and how often a gene expresses different isoforms. It can also be evaluated if all isoforms of a gene are about equally expressed or if there is one dominant isoform that is significantly more expressed than the others. Moreover, by applying this analysis to different tissues, it can be assessed if there are changes in splicing between different conditions and if such a change has a biological role. A dataset of 32 normal human tissues was used in this study. The results show that, although alternative splicing can lead to the expression of different transcripts of a gene, many genes have an n-fold dominant transcript – a transcript that is expressed at n times higher level than the second most expressed one [1]. On average, 68% of protein-coding genes expressed in a given tissue have a 2-fold dominant transcript and 47% have a 5-fold dominant transcript. It was observed that the dominant transcript of a gene tends to be the same across tissues, but there are cases where the dominant isoform switches between tissues, these cases are designated switch events. For a given pair of tissues, there are on average around thirty 2-fold switch events and just below four 5-fold switch events. The switching exons often significantly overlap and the most common types of alternative splicing are alternative 3’ selection (24% of the cases) and alternative 5’ selection (21%). To evaluate the conservation of the transcripts, the dominant transcripts were compared to APPRIS principal isoforms. These isoforms are annotated based on their function, protein structure, and cross-species conservation [2]. 69.2% of the 2-fold dominant transcripts and 81.1% of the 5-fold dominant transcripts are APPRIS principal isoforms. It was also observed that in 80% of the switches there are no protein domain changes. Similar results were obtained when the same analysis was done using the GTEx dataset [3], which has a much higher number of samples, containing data from 54 conditions. In
Circadian regulation of muscle growth independent of locomotor activity

Significance A long-standing question, particularly in physiotherapy and sports medicine, is whether time of day affects muscle metabolism and hence growth, either intrinsically or in response to exercise or nutrition. Answers would help to identify the best time of day to exercise, build muscle, and prevent aging- or disease-related sarcopenia. Here, we address this question in live zebrafish myotome in vivo, without interference from other circadian oscillations such as locomotor activity and food intake. We show that active muscle anabolizes more in the day and grows faster, while catabolizing more at night and growing slower. Such day/night differences remain in inactive muscle but disappear after clock disruption. We conclude that muscles display circadian differences in growth independent of activity and feeding. Muscle tissue shows diurnal variations in function, physiology, and metabolism. Whether such variations are dependent on the circadian clock per se or are secondary to circadian differences in physical activity and feeding pattern is unclear. By measuring muscle growth over 12-h periods in live prefeeding larval zebrafish, we show that muscle grows more during day than night. Expression of dominant negative CLOCK (ΔCLK), which inhibits molecular clock function, ablates circadian differences and reduces muscle growth. Inhibition of muscle contraction reduces growth in both day and night, but does not ablate the day/night difference. The circadian clock and physical activity are both required to promote higher muscle protein synthesis during the day compared to night, whereas markers of protein degradation, murf messenger RNAs, are higher at night. Proteasomal inhibitors increase muscle growth at night, irrespective of physical activity, but have no effect during the day. Although physical activity enhances TORC1 activity, and the TORC1 inhibitor rapamycin inhibits clock-driven daytime growth, no effect on muscle growth at night was detected. Importantly, day/night differences in 1) muscle growth, 2) protein synthesis, and 3) murf expression all persist in entrained larvae under free-running constant conditions, indicating circadian drive. Removal of circadian input by exposure to either permanent darkness or light leads to suboptimal muscle growth. We conclude that diurnal variations in muscle growth and metabolism are a circadian property that is independent of, but augmented by, physical activity, at least during development.
Fruit and seed macro- and micromorphologies of the genus Matthiola (Brassicaceae) in Turkey and their taxonomic value

Macroand micromorphological features of fruit and seeds belonging to 12 taxa genera of Matthiola W.T. Aiton were studied via stereomicroscope and scanning electron microscope. In macromorphological studies, the following variables were investigated: the shape, size, and color of fruit and seeds; the length of fruiting pedicel; the structure of the median vein; stigma (horns); and trichome properties and density in fruit. In micromorphological studies, the presence or absence of seed wings, seed coat pattern in disc and wing, and epidermal cell shape in disc and wing were determined. According to our findings, all characters of fruit and seeds are extremely variable and can be used as criteria to distinguish species of the genus.
Morphology and Molecular Analyses of a New Marine Ciliate, Arcuseries minima sp. nov. (Ciliophora: Urostylidae)

A new marine urostylid ciliate, Arcuseries minima sp. nov., was discovered in South Korea. Morphological observations and molecular phylogenetic analyses based on small subunit ribosomal DNA (18S rDNA) sequences were used to describe the new species. Arcuseries minima is most similar to A. scutellum among all Arcuseries species, but differs in the following main characters: number of adoral membranelles (13–16 vs. 17 or 18), cortical granules (yellowish, clustered around cirri and dorsal bristles vs. colorless, irregularly scattered), number of macronuclear nodules (20–27 vs. 42–90), number of midventral cirri (5–10 vs. 12–14), and number f transverse cirri (5 or 6 vs. 8). The new species and A. scutellum differ from A. petzi and A. warreni in having smaller body size (≤80 μm vs. ≥80 μm) and fewer cirri: left marginal (≤ 17 vs. ≥ 18) and transverse (≤ 8 vs. ≥8) cirri. This relationship was supported by the phylogenetic tree, where these two groups were separated into two branches.
The influence of dietary clinoptilolite on blood serum mineral profile in dairy cows

The objectives of this study were to determine whether or not dietary clinoptilolite (CPL) has an influence on the levels of calcium (Ca), magnesium (Mg), phosphorus (P), potassium (K) and sodium (Na) in the blood serum of dairy cows during gravidity and early lactation. The study was conducted on 78 dairy cows of Holstein-Friesian breed. The cows were randomly assigned into two groups: the CPLfed treated group (n = 38) which received 50 g of natural powdered zeolite CPL twice a day from day 180 days before to 60 days after parturition, and the control non-treated group (n = 40). Blood samples were taken on days 180, 90, 60, 30 and 10 before parturition, on the day of calving and on days 5, 12, 19, 26, 33, 40 and 60 following parturition. There were no significant differences in the Ca concentrations between the CPL-fed and the control group. However, after parturition it was noticeable that the Ca concentration was higher in the CPL-fed group, especially on *Corresponding author: Assist. Prof. Ivan Folnožić, PhD, DVM, Clinic for Obstetrics and Reproduction, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia, Phone: +385 1 2390 322; Fax: +385 1 244 1390; E-mail: folnozic@vef.hr DOI: 10.24099/vet.arhiv. 0662
Scorpionflies (Mecoptera: Panorpidae) collected during Project Tiger with the description of three new species from Thailand

Project Tiger was a collaborative effort to study entomological diversity in Thailand in 2007 through 2009 that involved the University of Kentucky, Thai field researchers, and world taxonomic specialists. Three new species of scorpionflies (Mecoptera: Panorpidae) are described from material acquired during Project Tiger and during subsequent collecting by the author. These are: Neopanorpa normpennyin. sp. , a remarkable species with a greatly elongated process on the male 3rd tergum extending caudally nearly to the genital bulb, Neopanorpa arcuatan. sp. , a scorpionfly with unique arched male hypovalves, and the first species of Panorpa from Thailand, Panorpa auripennisn. sp. , with unusual golden yellow wings. Collection data for Mecoptera taken by Project Tiger are presented. Efforts by Project Tiger and follow up collecting bring the number of species of Mecoptera occurring in Thailand to 17, including 15 species of Neopanorpa Weele, 1909, one Panorpa Linnaeus, 1758, and one Bittacus Latreille, 1805, and the number of Mecoptera species known from Indochina to 51, including 44 Neopanorpa, two Panorpa, four Bittacus, and one Bicaubittacus Tan & Hua, 2009.
An unusual dinosaur track assemblage from the Jurassic–Cretaceous boundary, Anning formation, Lufeng Basin, China

ABSTRACT Late Jurassic dinosaur track assemblages from China are much less common than those reported from the Lower and Middle Jurassic which are heavily dominated by well-known theropod ichnogenera such as Grallator, Eubrontes, Kayentapus, and a few sauropodomorph and ornithischian ichnotaxa. We here report two tridactyl dinosaur morphotypes from the Lufeng Basin in southern China that most closely resemble Late Jurassic Dinehichnus from North America, a probable gracile ornithopod morphotype, and an unnamed avian morphotype reported from rare occurrences in North America and Europe, which we here name as Tridentigerpes ichnogen. nov., accommodating two ichnospecies T. huasibanleei ichnosp. nov. from the Lufeng Basin, and T. pinuelai ichnosp nov., from Spain. These ichnites re-orient our understanding of Late Jurassic dinosaur track distributions in the Late Jurassic of China, which was previously based in large part on very poor material of presumed theropod affinity. Given the sparse body fossil record from southern China including very fragmentary sauropod remains, the ichnological record of diverse bipedal dinosaurs, suggestive of avian and non-avian dinosaurs and ornithopods, the Anning Formation represents a type 2b deposit where tracks are more common than skeletal remains and indicative of faunas not represented by the body fossil record.
Widespread herbicide resistance in pigweed species in Ontario carrot production is due to multiple photosystem II mutations

Abstract: The apparent efficacy of linuron to control pigweeds (Amaranthus spp.) has declined in Ontario, Canada, in past decades, possibly due to resistance. Samples were collected in multiple fields across Ontario with reported linuron failure. These were characterized at the whole-plant and molecular levels. Screening with linuron revealed resistance in six out of nine green pigweed (Amaranthus powellii Wats.) populations and 36 out of 38 populations of redroot pigweed (Amaranthus retroflexus L.). Sequencing of the psbA gene showed resistant plants had mutations conferring resistance to photosystem II (PSII) inhibitors. The most commonly seen mutation was coding for a Val219Ile substitution, while other populations had Ala251Val or Phe274Val. Two populations were documented with a double mutation at Val219Ile and Phe274Val. All substitutions endowed plants with low to moderate resistance to linuron, with various levels of cross resistance to other PSII inhibitors. The double mutants were characterized by higher levels of resistance to linuron and diuron compared with each single substitution. The widespread failure of linuron to control pigweed species in many carrot fields in Ontario is due to the selection of PSII mutants. This is the first report of double mutation in psbA in any weed species and the first report of Ala251Val and Phe273Val in pigweed species. The presence of a double mutation is probably the result of continuous selection of plants already resistant due to a single mutation. Our results illustrate the need for diversified weed management strategies in crops where herbicide options are limited.
Somatic Mutation and Evolution in Plants

Somatic mutations are common in plants, and they may accumulate and be passed on to gametes. The determinants of somatic mutation accumulation include the intraorganismal selective effect of mutations, the number of cell divisions that separate the zygote from the formation of gametes, and shoot apical meristem structure and branching. Somatic mutations can promote the evolution of diploidy, polyploidy, sexual recombination, outcrossing, clonality, and separate sexes, and they may contribute genetic variability in many other traits. The amplification of beneficial mutations via intraorganismal selection may relax selection to reduce the genomic mutation rate or to protect the germline in plants. The total rate of somatic mutation, the distribution of selective effects and fates in the plant body, and the degree to which the germline is sheltered from somatic mutations are still poorly understood. Our knowledge can be improved through empirical estimates of mutation rates and effects on cell lineages and whole organisms, such as estimates of the reduction in fitness of progeny produced by within- versus between-flower crosses on the same plant, mutation coalescent studies within the canopy, and incorporation of somatic mutation into theoretical models of plant evolutionary genetics.