Miracle-dz/UniFAR-FTUs huggingface dataset:
The importance of bioactive feed additives in feeding pigs and their impact on the digestibility of particular nutrients

In recent years, bioactive additives have become a subject of interest in the field of nutrition of farm animals. Therefore, the application of biosorptive properties of components is an alternative to inorganic mineral compounds and can play an important role in innovative nutritional strategies. The study presents a quantitative measurement of mineral components such as manganese, zinc, copper, and iron by using the scanning electron microscopy with an energy-dispersive X-ray spectroscopy (SEM-EDX). The research material was the feces collected from 39 growing-finishing pigs divided into 3 groups: control one, receiving inorganic mineral compounds, and experimental groups, fed organic mineral mixtures constituting 100% and 125% of the recommended daily intake. Each group of animals consisted of 13 animals (n=13). The results showed a difference in the elemental composition of the pooled samples of all three groups. The highest bioavailability of minerals had the group receiving 100% of the recommended dose of the experimental organic compounds. In the control group, the differences were statistically significant (P<0.05) in the case of manganese, zinc and iron. The study showed that the mineral supplements obtained in the biosorption process showed a high rate of absorption from the gastrointestinal tract and did not require the intake of doses greater than 100% of the daily requirement. The high proportion of trace elements in the second experimental group did not increase their bioavailability and contributed to the reduced digestibility of nutrients.
USE OF FLURESCENT DYES TO MARK THE PATHWAYS OF SALUTE MOVEMENT THROUGH SOILS UNDER LEACHING CONDITIONS: 1. LABORATORY EXPERIMENTS

We offer a technique to identify the pathways of solute movement down columns of sieved soil aggregates using fluorescent dyes and recording their presence by ultraviolet photography. Pyranine was found to be the most useful dye for short-term laboratory experiments because of its high fluorescence and comparatively low adsorption coefficient. The uneven distribution of pyranine across the Horizontal faces of successive soil sections, as shown by ultraviolet photography, indicated that the solute moved preferentially in some parts of the column. The technique was found to be value in checking the uniform packing of columns of soil aggregates and to have potential use under field conditions (Part 2).
Taxonomic and pathogenic characteristics of a new species Aphanomyces trifolii causing root rot of subterranean clover (Trifolium subterraneum) in Western Australia.

Subterranean clover (Trifolium subterraneum) is grown extensively as a pasture legume in agronomic regions with Mediterranean-type climates in parts of Africa, Asia, Australia, Europe, North America and South America. Root diseases of subterranean clover, especially those caused by oomycete pathogens including Aphanomyces, Phytophthora and Pythium, greatly reduce productivity by significantly decreasing germination, seedling establishment, plant survival and seed set. For this reason, experiments were conducted to determine the species of Aphanomyces causing root disease on subterranean clover in the high-rainfall areas of south-west Western Australia. The effects of flooding, temperature and inoculum concentration on the development of root disease on subterranean clover caused by this Aphanomyces sp. were also investigated as was its host range. Morphological and molecular characteristics were used to identify the pathogen as a new species Aphanomyces trifolii sp. nov. (O’Rourke et al.), which forms a distinct clade with its nearest relative being A. cladogamus. A. trifolii caused significant lateral root pruning as well as hypocotyl collapse and tap root disease of subterranean clover. The level of disease was greater in treatments where soil was flooded for 24 h rather than for 6 h or in unflooded treatments. The pathogen caused more disease at 18/13oC than at lower (10/5oC) or higher (25/20oC) temperatures. The pathogen caused more disease at 1% inoculum than at 0.5 or 0.2% (% inoculum : dry weight of soil). In greenhouse trials, A. trifolii also caused root disease on annual medic (M. polymorpha and M. truncatula), dwarf beans (Phaseolus vulgaris) and tomatoes (Solanum lycopersicum). However, the pathogen did not cause disease on peas (Pisum sativum), chickpea (Cicer arietinum), wheat (Triticum aestivum), annual ryegrass (Lolium rigidium) or capsicum (Capsicum annuum). A. trifolii is a serious pathogen in the high-rainfall areas of south-west Western Australia and is likely a significant cause of root disease and subsequent decline in subterranean clover pastures across southern Australia.
Genotypic Differences in Shoot-forming Capacity of Cultured Leaf Explants of Lycopersicon hirsutum

Cultured leaf explants obtained from 36 accessions of the wild tomato species, Lycopersicon hirsutum Humb. and Bonpl. , were evaluated for morphogenic capacity in response to three cytokinins (zeatin, BA, and kinetin) in combination with IAA. Media containing 0.1 μM IAA plus 4.6 or 9.2 μm zeatin were optimal for shoot induction. Cotyledon explants were superior to true leaf explants for obtaining shoot formation
Mosquitoes and West Nile Virus Along a River Corridor from Prairie to Montane Habitats in Eastern Colorado

ABSTRACT: We conducted studies on mosquitoes and West Nile virus (WNV) along a riparian corridor following the South Platte River and Big Thompson River in northeastern Colorado and extending from an elevation of 1,215 m in the prairie landscape of the eastern Colorado plains to 1,840 m in low montane areas at the eastern edge of the Rocky Mountains in the central part of the state. Mosquito collection during June–September 2007 in 20 sites along this riparian corridor yielded a total of 199,833 identifiable mosquitoes of 17 species. The most commonly collected mosquitoes were, in descending order: Aedes vexans, Culex tarsalis, Ae. dorsalis, Ae. trivittatus, Ae. melanimon, Cx. pipiens, and Culiseta inornata. Species richness was higher in the plains than in foothills-montane areas, and abundances of several individual species, including the WNV vectors Cx. tarsalis and Cx. pipiens and the nuisance-biter and potential secondary WNV vector Ae. vexans, decreased dramatically from the plains (1,215–1,487 m) to foothills-montane areas (1,524–1,840 m). Ae. vexans and Cx. tarsalis had a striking pattern of uniformly high abundances between 1,200–1,450 m followed by a gradual decrease in abundance above 1,450 m to reach very low numbers above 1,550 m. Culex species were commonly infected with WNV in the plains portion of the riparian corridor in 2007, with 14 of 16 sites yielding WNV-infected Cx. tarsalis and infection rates for Cx. tarsalis females exceeding 2.0 per 1,000 individuals in ten of the sites. The Vector Index for abundance of WNV-infected Cx. tarsalis females during June–September exceeded 0.5 in six plains sites along the South Platte River but was uniformly low (0–0.1) in plains, foothills and montane sites above 1,500 m along the Big Thompson River. A population genetic analysis of Cx. tarsalis revealed that all collections from the ∼190 km riparian transect in northeastern Colorado were genetically uniform but that these collections were genetically distinct from collections from Delta County on the western slope of the Continental Divide. This suggests that major waterways in the Great Plains serve as important dispersal corridors for Cx. tarsalis but that the Continental Divide is a formidable barrier to this WNV vector.
Comparison of the Attraction Index of Male and Female Drosophila Melanogaster to Varying Odorant Substances

This study aims at investigating the differences if any, in the olfactory discrematory ability of wild type drosophila and mutated Or83b type and also if these differences exists between male and females of both species. Insect and mammalian olfactory systems are strikingly similar. Therefore, Drosophila can be used as a simple model for olfaction. The olfactory system has evolved the capacity to recognize and discriminate an inordinate number of chemically distinct odors that signal the presence of food, predators, or mating partners. Most organisms including humans rely on their olfactory system to detect and analyze olfactory cues in the environment, cues that are subsequently utilized in the context of behavior. Several works have been done on the olfactory system of the insect drosophila, attraction of various strain of drosophila to different odors but no work has been done to investigate sexual differences in this attraction to odorants. In this research we try investigating differences in the sensitivity of the olfactory receptors of male and female drosophila by measuring their attraction index to odors (yeast). O83b mutants and ORR wild type flies were used. By behavioral analysis, using the attraction index as a measure of sensitivity of the olfactory receptors, we were able to show that the female flies have a higher attraction index to odorant than the males but this difference is not significant statistically as indicated by the p value.
Molecular Markers in Plant Breeding-lll: Practical Applications and Difficulties Encountered

Some of the empirical results obtained through the use of RFLP, AFLP, SSR and RAPD markers in the areas of DNA fingerprinting, measurement of genetic distance and heterosis, marker-assisted selections and abiotic stress tolerance are being described. Various difficulties that a user can encounter during the ontogeny of marker's application have also been discussed. Marker mediated varietal fingerprinting and germplasm characterization appeared most common and most pervasive application with AFLP and SSR markers. Being cost effective, easy to handle and devoid of any radioisotope requirement, SSR markers are considered as the most suitable and reliable system for DNA fingerprinting. Capturing heterosis appeared most difficult with very little success due to lack of a facile marker system that could unconditionally identify the heterotic groups, population and progenies. Marker-assisted selections for qualitative traits appeared most successful after DNA fingerprinting while for quantitative characters, major disease resistance genes and genes controlling QTL for abiotic stress tolerance, the success is limited. It is anticipated that application of markers will remain restricted in these areas till the allele-specific markers are available and the cost of marker analysis is reduced significantly.
Molecular evidence for phylogeny and the termite host specificity of exoparasitic fungi, Termitaria spp. (Termitariales: Deuteromycetes), from Japan

Members of the genus Termitaria are entomogenous exoparasitic deuteromycetes growing on the exoskeleton of various species of termites. Distinguished by sporodochial surface color, three types of Termitaria were found from six termite species of four genera from various localities in Japan: Black-type, White-type and Intermediate-type. Molecular phylogenetic analysis focusing on the genetic lineage of Termitaria, using sequences of the nucleotide 18S rRNA gene, suggested that these three types were actually different species. The resultant phylogenetic tree of Termitaria did not show any contradiction to the topology known in the host phylogeny. This suggests that there is a parallel cladogenesis between the hosts and fungi, and that there has been scarcely any detectable horizontal transmission of fungi between the host species. The only exception was found in Yakushima Is. , where Black-type may have changed its host from Hodotermopsis japonica to Reticulitermes speratus.
Anti‐inflammatory effects of a synthetic peptide derived from pigment epithelium‐derived factor on H2O2‐induced corneal injury in vitro

Background The common pathological characteristics of corneal injury include inflammatory factors activation, vascular endothelial cells or inflammatory cells infiltration into lesions, corneal edema, corneal neovascularization (CNV), and scar formation. PEDF‐34 is the functional fragment of pigment epithelium‐derived factor (PEDF) that has anti‐angiogenic and anti‐inflammatory properties and contains an N‐terminal 34‐amino acid peptide. This study was to investigate the antiinflammatory effects of PEDF‐34 on H2O2‐induced corneal injury in vitro. Methods After cultured in H2O2 (0.1 mmol/L) for 2 hours, human corneal fibroblasts (HCFs) and human umbilical vein endothelial cells (HUVECs) were treated with PEDF‐34‐nanoparticles (NPs) at different concentrations (0.1, 0.5, 1.0, 2.0 &mgr;g/ml) or 2.0 &mgr;g/ml control‐NPs for 24 hours. The viable cells were quantified using the MTT assay. Western blotting or ELISA analysis was performed for measuring the human vascular endothelial growth factor (VEGF) and intercellular adhesion molecule‐1 (ICAM‐1) expression of both HCFs and HUVECs. VEGF and nuclear factor &kgr;B (NF‐&kgr;B) mRNA levels of HCFs were semi‐quantified by RT‐PCR. Results The survival rates of HCFs or HUVECs stimulated by H2O2 did not decrease significantly (P >0.05) compared to those in the normal conditions. As compared to control‐NP group, PEDF‐34‐NPs had dose‐dependent inhibitive effect on HUVECs with the MTT assay, but not HCFs. Western blotting analysis showed that the VEGF and ICAM‐1 levels in the HCFs and HUVECs stimulated by H2O2 were significantly higher than those in the normal conditions, which were decreased dramatically in those treated with PEDF‐34‐NPs. RT‐PCR analysis revealed that the VEGF mRNA and NF‐&kgr;B mRNA levels increased in H2O2‐stimulated HCFs, while both of them decreased in PEDF‐34‐NP groups dose dependently. Conclusions PEDF‐34‐NPs may play an important role in regulating the NF‐&kgr;B pathway, inhibiting inflammatory activity. PEDF‐34‐NPs may be a potential new drug for treating corneal injury in the future.
Duchenne muscular dystrophy : mutation profiling in view of the emerging gene-based therapies

Duchenne Muscular Dystrophy (DMD) is a lethal, X-linked, recessive muscle-wasting disorder affecting 1 in 3 500 live male births worldwide, for which only palliative care is available to date. Large exonic deletions or duplications are found in approximately 70% of DMD patients, for which diagnostic testing is available. The remaining 30% carry point utations, which go largely undetected, as no testing is currently offered due to the great s revealed 10 small/point athogenic changes, 39 polymorphisms and 4 changes of uncertain significance. No mutation arrying patients in the cohort and skipping exons 45 55 could benefit a further 12,5%, ion detection in the DMD gene, to help find “family mutations”, us facilitating genetic counselling and ultimate determination of eligibility for mutationased therapy in the future. m size of the DMD gene and the logistical challenges involved. Positive outcomes of research into gene-based therapies necessitate availability of protocols which will extend the scope of testing to detection of point mutations. In this study, the DNA samples of 24 patients previously tested negative for exonic deletions with the mPCR method, were subjected to a complete mutation screen of the coding region of the DMD gene using the MLPA and hrMCA. Four deletions and 2 duplications were revealed by the initial screen with the MLPA. The DNA of the remaining 18 patients was then subjected to mutation scanning with hrMCA on the RotorGeneTM6000, of 96 PCR fragments encompassing the entire coding region of the DMD gene, amplified using M13-tailed primers, and subsequent sequencing of variant fragments. The analysi p pathogenic mutations were found in 8 patients of the cohort. The 10 disease-causing changes identified, consisted of 3 nonsense, 4 frameshifts, 1 splicesite, 1 compound mutation (a GGTG duplication and a missense), 1 missense, and 1 point substitution in the Dp427promoter/exon1 region of the DMD gene. The deleterious nature of the mutations detected was inferred by their nature and by the output of bioinformatic analyses with regard to the effect on splicing, amino acid changes and regulatory sequences. Also, the results of family studies showed that the pathogenic mutations were familial in their origins and that they tracked with the disease within the families. Predictions of future therapeutic options revealed that by virtue of cohort selection none of the patients would benefit from AON-induced skipping of exon 51, which is currently undergoing clinical trials. However, multiexon skipping of exons 6 – 8 could benefit ~30% of the c emphasizing the potential therapeutic impact of the multiexon skipping approach. The study findings suggested that hrMCA could be successfully incorporated into the diagnostic protocol for mutat th b
Structural basis of surface antigen glycoprotein mediated virulence in Toxoplasma gondii

Supervisory Committee Dr. Martin J. Boulanger, Assistant Professor, Department of Biochemistry and Microbiology Supervisor Dr. Caroline Cameron, Associate Professor, Department of Biochemistry and Microbiology Departmental Member Dr. Fraser Hof, Assistant Professor, Department of Chemistry Outside Member Toxoplasma gondii is a eukaryotic, intracellular parasite capable of infecting any vertebrate animal and establishing a life-long latent infection. Despite the prevalence of T. gondii infections, the molecular mechanisms by which these parasites gain access to the host cell remain largely unknown. Recent knockout studies have implicated a select group of T. gondii surface proteins, termed SRSs (Surface Antigen Glycoprotein Related Sequences), in directing parasite attachment and persistence. Follow-up structural studies with the prototypical SRS antigen, SAG1, revealed a novel fold, termed the SRS fold, and a dimeric structure with a topologically defined basic groove predicted to play a role in ligand binding. While these initial results were very exciting, follow-up work has failed to identify a host cell ligand for SAG1, and no other members out of more than 160 members of the SRS superfamily have been structurally characterized. As a result, conservation of the SRS fold and, more specifically, structural determinants of molecular recognition remain elusive. While sequence alignments of the SRS superfamily suggested conservation of the SRS fold, several insertions and deletions presented the possibility of localized structural elements that may be essential in molecular recognition. To characterize how these insertions/deletions are represented at the structural level, the X-ray crystal structures of two members of the SRS superfamily, BSR4 and SRS2, were solved. Structural analysis revealed an unexpected degree of diversity in the SRS fold. Divergent connectivity of the beta-strands in studied proteins indicates that the SRS superfamily may be more structurally diverse than previously thought, while structural variations in the beta-strands iv and the loops of D1 domain suggests a possible mechanism to recognize diverse host cell ligands, such as heparan sulfate proteoglycans (HSPGs). To probe HSPGs binding and determine the role of homodimerization, the dimer constructs of SRS2 and BSR4 were engineered, produced and tested in a carbohydrate binding macro-array. Selective binding of the SRS2 dimer to heparin was detected during screening and validated using heparinagarose pull-down and native gel shift assays. Possible molecular mechanism for SRSHPGS interaction and the implications in T. gondii virulence are also discussed.
Analysis of signal transduction pathways linking L-plastin Ser5 phosphorylation to breast cancer cell invasion

Deregulated cell migration and invasion are hallmarks of metastatic cancer cells. Phosphorylation on residue Ser5 of the actin-bundling protein L-plastin activates L-plastin and has been reported to be crucial for invasion and metastasis. Here, we investigate signal transduction leading to L-plastin Ser5 phosphorylation using 4 human breast cancer cell lines. Whole-genomemicroarray analysis comparing cell lines with different invasive capacities and corresponding variations in L-plastin Ser5 phosphorylation level revealed that genes of the ERK/ MAPK pathway are differentially expressed. It is noteworthy that in vitro kinase assays showed that ERK/MAPK pathway downstream ribosomal protein S6 kinases a-1 (RSK1) and a-3 (RSK2) are able to directly phosphorylate L-plastin on Ser5. Small interfering RNAor short hairpin RNA-mediated knockdown and activation/inhibition studies followed by immunoblot analysis and computationalmodelingconfirmed that ribosomal S6kinase (RSK) is an essential activator ofL-plastin.Migration and invasion assays showed that RSKknockdown led to a decrease of up to 30% of migration and invasion of MDA-MB-435S cells. Although the presence of L-plastin was not necessary for migration/invasion of these cells, immunofluorescence assays illustrated RSK-dependent recruitment of Ser5phosphorylated L-plastin to migratory structures. Altogether, we provide evidence that the ERK/MAPK pathway is involved in L-plastin Ser5 phosphorylation in breast cancer cells with RSK1 and RSK2 kinases able to directly phosphorylate L-plastin residue Ser5. —Lommel, M. J., Trairatphisan, P., Gäbler, K. , Laurini, C. , Muller, A. , Kaoma, T. , Vallar, L. , Sauter, T. , Schaffner-Reckinger, E. L-plastin Ser5 phosphorylation in breast cancer cells and in vitro is mediated by RSK downstream of the ERK/MAPK pathway. FASEB J. 30, 000–000 (2016). www.fasebj. org
Hepatoblastoma

Hepatoblastoma (HB) is the most common primary malignant neoplasm of the liver in children below the age of 5 years. This is a heterogeneous tumor composed of various epithelial and mesenchymal elements. Based on these various elements HBs are classified into 4 epithelial subtypes and 2 mixed subtypes. Although a rare tumor, the incidence has increased in the last decades, a period of time that corresponds to increased survival of premature infants of low birth weight. Most tumors are sporadic. Patients with congenital syndromes such as familial adenomatous polyposis and Beckwith–Wiedemann syndrome have a significantly by increased risk for the development of HBs. These disorders have provided an insight into the molecular pathophysiology of HBs, pointing to an up-regulated Wnt signaling pathway by defects in beta-catenin degradation. New understanding of the underlying molecular mechanisms may provide new therapeutic tools in the treatment of these tumors. Recent improvements in chemotherapy have increased the number of resectable tumors, therefore improving survival.
GIBBS SAMPLER FOR IDENTIFICATION OF SYMMETRICALLY STRUCTURED, SPACED DNA MOTIFS WITH IMPROVED ESTIMATION OF THE SIGNAL LENGTH AND ITS VALIDATION ON THE ArcA BINDING SITES

1 State Scientific Centre “GosNIIGenetica”, 1st Dorozhny pr. , Moscow, 117545, Russia; 2 Institute for Problems of Information Transmission, Russian Academy of Sciences, Bolshoi Karetny per. 19, Moscow 127994, Russia; 3 Dept of Bioengineering and Bioinformatics, Moscow State University, Lab. Bldg B, Vorobiovy Gory 1-37, Moscow 119992, Russia; 4 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow 119991, Russia * Corresponding author: e-mail: favorov@sensi.org