Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA-protein interactions : a practical approach

Expression Systems Gel electrophoresis and bending in cisplatin-modified linear DNA Use of DNA microcircles in protein-DNA binding studies Use of topology to measure protein-induced DNA bend and unwinding angles Bandshift, gel retardation, or electrophoretic mobility shift assays Practical aspects of Fluorescence Resonance Energy Transfer (FRET) and its applications in nucleic acid biochemistry Determination of DNA-ligand interactions by fluorescence correlation spectroscopy DNA wrapping in E. Coli RNA polymerase open promotor complexes revealed by scanning force microscopy Microcalorimetry of protein-DNA interactions DNA-protein cross-linking by formaldehyde: a probe for RNAP-open promoter complex structure Solid-phase DNAse I footprinting Hydroxyl radical footprinting Radiolytic cleavage of DNA: Mapping of the Protein Interaction Sites UV - Laser photoreactivity of nucleoprotein complexes in vitro In vivo UV-laser footprinting Digitization and quantitative analysis of footprinting gels Mapping histone positions in chromatin by protein-directed DNA cross-linking and cleavage Kinetics of DNA-protein interactions Kinetics of DNA interactions studied by surface plasmon resonance spectroscopy Quantitative DNase I Kinetics Footprinting Real time fluorescence anisotropy for studying protein-DNA interactions Analysis of protein-DNA interactions in complex nucleoprotein assemblies Site-specific protein-DNA photocrosslinking Visualization of protein-DNA complexes by cryo em and on grids Characterization of T7 RNA polymerase protein-DNA interactions during the initiation and elongation phases
Identify and classify concepts and components of intellectual capital in the organizations

Introduction: Measurement and evaluation of intellectual capital which aimed to improve management and increase competitive advantage requires a comprehensive review of concepts and providing components and dimensions that will cover all aspects of intellectual capital. The aim of the study is to identify, and classify concepts and components of intellectual capital in organizations in the literature. Materials & Methods: In this review study, articles which were published between the years of 1991 and 2015 were reviewed. PubMed, Scopus, Sciences Direct, and Google Scholar English data bases as well as SID and Magian among the Persian databases were searched. In both databases, keywords such as intellectual capital, components of intellectual capital, concept of intellectual capital and organization were used (in Persian database keywords were translated to the respected language). In the initial stage, a total number of 383 articles were found and irrelevant articles were eliminated. This resulted in, 86 final articles which were consistent with the objectives of the research and included in the research. Findings: The review indicate that, there is no single precise agreed definition for intellectual capital and its dimensions. Most scholars defined three or four dimensions of the concept and named them differently. The most common popular names for dimensions were “human capital”, “structural capital”, and “relational capital”. In each dimension several components were named. The main components of the human capital skills, experience and knowledge, the most important structural capital components were organizational culture, processes and information systems and the most important relational capital component were customer relationship, customer loyalty and customer satisfaction. Conclusion: Gathering existing definitions of intellectual capital, and suggestions on its components and dimensions in this study creates a more holistic view of this concept and thus more efficient use of intellectual capital in organizations. Using these components to develop an instrument is suggested.
Phytotoxic, antialgal, and antifungal activity of constituents from selected plants of Kazakhstan

Ninety two extracts representing 23 species of plants endemic to Kazakhstan have been investigated for their phytotoxic, antialgal, and antifungal activities. Twenty extracts were found to have antifungal activity against one or more of the pathogenic fungi Colletotrichum accutatum, C. fragariae, and C. gloeosporioides. Two extracts of Verbascum songoricum demonstrated good activity against the cyanobacterium Oscillatoria perornata. Bioactivity-guided fractionation of the water extract of V. songaricum afforded aucubin as the active algaecidal compound. Extracts prepared from Artemisia terrae-albae, Geranium collinum, Haplophyllum sieversii, and Tamarix arceuthoides were phytotoxic to bentgrass, but not to lettuce seedlings. Analysis of the extract from of Nepeta pannonica obtained by supercritical fluid extraction resulted in the identification of the major components 1,8-cineole and cis,cis-nepetalactone.
Reinvestigation into the mechanisms of Campylobacter jejuni invasion of intestinal epithelial cells

Background: Campylobacter jejuni is an important foodborne pathogen and the leading cause of bacterial gastroenteritis. Despite the importance of C. jejuni infection and decades of research, the mechanisms for colonisation of the human intestinal tract by C. jejuni and how this causes diarrhoeal disease remain unclear, with a significant number of conflicting reports in the literature creating controversy in this area. Methods: The effect of different inhibitors of host cell pathways on the ability of the C. jejuni 81-176 wild-type strain to interact with and invade intestinal epithelial cells (IECs) was investigated. Defined isogenic C. jejuni 81-176 & 11168H ciaB, cadF and flpA mutants were constructed and characterised for the ability to interact with and invade host cells. Results: Disruption of microfilaments with Cytochalasin D increased C. jejuni invasion. Disruption of caveolae-mediated endocytosis with Methyl-beta-cyclodextrin, disruption of microtubules with Colchicine, disruption of clathrin-mediated endocytosis with Monodansylcadaverine, inhibition of phosphatidylinositol 3-kinase with Wortmannin all decreased C. jejuni invasion. Infection of the Galleria mellonella insect model with ciaB, cadF and flpA mutants resulted in a significantly reduced cytotoxic effect on the larvae. The ability of ciaB, cadF and flpA mutants to interact with and invade Caco-2 and T84 IECs was significantly reduced. The ciaB, cadF and flpA mutants exhibited a more significant decrease in the number of invasive bacteria when co-cultured with IECs in the Vertical Diffusion Chamber model. Pre-treatment of Caco-2 IECs with OMVs isolated from the ciaB, cadF and flpA mutants reduced interactions and invasion of these IECs by live C. jejuni. Conclusion: C. jejuni invasion of IECs involves modulation of many host cell pathways. CiaB, CadF and FlpA all play an important role in C. jejuni interactions with IECs leading to bacterial invasion. Further studies are still required to elucidate the exact roles that these important C. jejuni virulence factors play during interactions with and invasion of host cells.
Estimating the variance of male fecundity from genotypes of progeny arrays: evaluation of the Bayesian forward approach

1. Characterizing fine scale mating patterns in plant populations makes it possible to investigate genetic drift, gene flow and selection gradients at a contemporary time scale. Molecular markers are valuable tools for this type of analysis, and numerous statistical methods have been developed to make the best of the information they can provide. In particular, we recently proposed a Bayesian approach based on a paternity analysis wherein we estimate jointly the variance in male fecundity and the pollen dispersal kernel.
Studies on maturity stages and spawning periodicity of Crassostrea madrasensis (Preston) at Tuticorin bay

Studies undertaken during 1976 on the gonadal maturity of the backwater oyster Crassostrea madtasensis at Tuticorin revealed a biannual spawning periodicity. March-April and August-September were found to be the peak periods of spawning. A broad correlation has been observed between diurnal temperature difference and spawning of oyster
Morphologie et germination in vitro du pollen de Dacryodes edulis (Burseraceae)

L'etude de la morphologie du pollen de Dacryodes edulis a montre qu'il est: isopolaire, tricolpore, longiaxe et possede une exine epaisse qui le predispose a une conservation a long terme. La germination in vitro est optimale sur le milieu de Brewbaker et Kwack additionne de 15 ou 20% de saccharose a pH 5,3. L'incubation se faisant a l'obscurite et a 30°C, la germination est rapide, pres de 60% des pollens germent apres une heure d'incubation, mais un temps superieur a trois heures est necessaire pour avoir une germination optimale et une elongation maximale du tube pollinique. Le pouvoir germinatif est de 8% apres 24 mois de stockage a—20°C. A study of the morphology of pollen of Dacryodes edulis has shown that it is: isopolar, tricolporate, prolate. The structural characteristics of the exine show the possibility for long‐term pollen storage. In vitro germination is optimal on Brewbaker & Kwack medium containing 15 or 20% sucrose at pH 5,3. Incubation is carried out at 30°C in the dark. Germination is v.
Molecular Cloning and Sequencing of cDNA Encoding Goat Pre α-Lactalbumin

In poly(A)+RNA extracted from a lactating goat mammary gland, mRNA of about 750 nucleotides was shown to encode pre alpha-lactalbumin by using in vitro translation and immunoprecipitation. From the total poly(A)+RNA, the cDNA library was constructed using the Escherichia coli plasmid pUC18; it was screened with the oligodeoxyribonucleotide probe corresponding to the amino acid sequence of Trp60-Gln65 of goat alpha-lactalbumin. A plasmid containing almost full-length cDNA of goat pre alpha-lactalbumin, pGLA-1, was identified. The cDNA insert of pGLA-1 comprises 727 base pairs and contains the signal peptide and mature protein sequence.
Análise de sobrevivência de cadela com tumores mamários após mastectomia: aspectos epidemiológicos, clínicos e morfológicos

Mammary gland tumors are the most common type of tumors in bitches but research on survival time after diagnosis is scarce. The purpose of this study was to investigate the relationship between survival time after mastectomy and a number of clinical and morphological variables. Data was collected retrospectively on bitches with mammary tumors seen at the Small Animal Surgery Clinic Service at the University of Brasilia. All subjects had undergone mastectomy. Survival analysis was conducted using Cox's proportional hazard method. Of the 139 subjects analyzed, 68 died and 71 survived until the end of the study (64 months). Mean age was 11.76 years (SD=2.71), 53.84% were small dogs. 76.92% of the tumors were malignant, and 65.73% had both thoracic and inguinal glands affected. Survival time in months was associated with age (hazard rate ratios [HRR] =1.23, p-value =1.4x10-4), animal size (HRR between giant and small animals =2.61, p-value =0.02), nodule size (HRR =1.09, p-value =0.03), histological type (HRR between solid carcinoma and carcinoma in a mixed tumor =2.40, p-value =0.02), time between diagnosis and surgery (TDS, with HRR =1.21, p-value =2.7x10-15), and the interaction TDS*follow-up time (HRR =0.98, p-value =1.6x10-11). The present study is one of the few on the subject matter. Several important covariates were evaluated and age, animal size, nodule size, histological type, TDS and TDS*follow up time were identified as significantly associated to survival time.
Genotypic and endosymbiont-mediated variation in parasitoid susceptibility and other fitness traits of the potato aphid, Macrosiphum euphorbiae

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The evolution of host specificity in the vertebrate gut symbiont Lactobacillus reuteri

Although vertebrates harbor bacterial populations in their gastrointestinal tract whose composition is host specific and, to some degree, phylogenetically conserved, little is known on how specific bacterial lineages become acquired. We have recently shown that the vertebrate gut symbiont Lactobacillus reuteri evolved to be host specific. The goal of this study was to gain insight into the mechanisms that mediate host specific colonization of Lactobacillus reuteri in the murine gut. Experiments with mono-associated mice revealed that the ability of L. reuteri strains to form biofilms in the mouse forestomach, but not colonization per se, is strictly dependent on the origin of the strain. To unravel the molecular basis for this host-specific biofilm formation, we applied a combination of transcriptome analysis and comparative genomics to identify genes of L. reuteri 100-23 whose transcription was differentially expressed during textitin vitrop biofilm formation and/or that were predicted to be important in biofilm formation. Eleven candidate genes were selected and their ecological significance and transcriptional expression during in vivo biofilm formation were determined. The findings revealed that several genes involved in epithelial adherence, cell aggregation, environmental sensing, and cell lysis were important for biofilm formation and overexpressed during gut colonization. These findings provided a first insight into the molecular processes that underlie biofilm formation of L. reuteri, which are likely to constitute a key mechanism by which a vertebrate symbiont becomes specifically associated with its host.
Seed selection for grassland restoration: competitive effect of a dominant grass is mediated by seed source and nutrient availability

Cultivars are selected for advantageous traits, which may enable them to have a greater competitive effect (CE), particularly under high nutrient conditions. Sites with high nutrient availability may favor the development of dominant grasses rather than subordinate species, especially in nutrient‐limited systems, such as calcareous grasslands. The aim of this experiment was to determine whether seed source influences the CE of a dominant grass on a subordinate species, and whether this relationship is mediated by nutrient availability. A greenhouse experiment with three nutrient levels was established; Dianthus carthusianorum was chosen as the subordinate “phytometer” to detect variation in the CE of different Festuca rubra seed sources. The grass species was sourced from 13 cultivar and 12 commercially propagated, but not selected, wild sources. When CE was calculated from biomass, propagated wild seed sources of F. rubra had a greater CE on the subordinate species than cultivars for medium and high nutrient levels. Based on phytometer height, propagated wild seed sources of F. rubra had a greater CE under all three nutrient levels. Our findings do not support the general notion that cultivars are more competitive than wild genotypes. Thus, the cultivar F. rubra may facilitate the establishment of other species during grassland restoration, particularly under elevated nutrient conditions.
Mixoploidy and cytotypes: a study of possible vegetative species differentiation in stapeliads (Asclepiadaceae)

Mixoploidy is common in proembryos and embryos as well as in meristems of radicles, primary, secondary and adventitious roots and in innovation shoots of stapeliad species (Asclepiadaceae). The proportion of polyploid cells in the meristem of single adventitious roots is significantly higher than in meristems of primary and secondary roots. This may lead to a complete polyploidisation of adventitious roots. Innovation shoots display a low percentage of polyploid cells, comparable to the condition found in primary and secondary roots. Nevertheless cells of different euploid levels are frequently found. During field studies, however, individuals of a given population were always found to have the same chromosome number: infraspecific polyploidy was found in only three out of 305 investigated stapeliad species. Genera with an orthotropic growth form were found to be diploid throughout, whereas the genera of which the members spread vegetatively by means of innovation shoots, comprise di-, tetra- and polyploid species. This phenomenon can be ascribed to ecological rather than morphological factors. The often proposed hypothesis that new cytotypes can have a vegetative origin is not found to be acceptable.
The Role Of Soil Microorganisms In The Resistance Of Giant Ragweed, Horseweed, And Common Lambsquarters To Glyphosate

Schafer-Bugg, Jessica R. Ph.D., Purdue University, December 2013. The Role of Soil Microorganisms in the Resistance of Giant Ragweed, Horseweed, and Common Lambsquarters to Glyphosate. Major Professors: Steven G. Hallett and William G. Johnson. Continuous glyphosate use has contributed to an increasing number of problematic glyphosate-resistant (GR) weeds. The mechanism of resistance in many GR weeds is poorly understood, in part, due to a poor understanding of how exactly glyphosate kills a plant. In previous research, the efficacy of glyphosate was demonstrated to be strongly influenced by root invading soil-borne microorganisms. However, this interaction among plants, glyphosate, and soil microorganisms has only been studied in a number of crop plants, but not in weed species. This is surprising since the soil biotic environment has a strong impact on the activity of this important herbicide. Gaining a better understanding of these interactions may shed more light on the performance of glyphosate in the field and the evolution of glyphosate resistance. The objective of this research was to determine the role of soil microbes in the resistance to glyphosate of three problematic weeds of the midwestern United States: giant ragweed (Ambrosia trifida L.), horseweed [(Conyza canadensis (L.) Cronq. ], and common lambsquarters (Chenopodium album L.). Through a series of greenhouse and lab experiments we determined that root colonization by soil microorganisms increased the activity of glyphosate in glyphosate-resistant (GR)
Connexin-built channels as modulators of lung inflammation

L'epithelium respiratoire est expose au milieu exterieur etant ainsi en contact avec de nombreux pathogenes. Suite a une infection, des cellules inflammatoires comme le neutrophile transmigrent vers le tissue pulmonaire en traversant la barriere alveolo-capillaire. Parmi les differents types d'interactions cellulaires, la communication intercellulaire directe via les jonctions communicantes pourrait participer aux reponses inflammatoires du poumon. Les jonctions communicantes, formees par l'apposition de deux hemicanaux membranaires, permettent le passage d'ions et de petites molecules entre les cellules en contact. Chaque hemicanal est constitue par l'association de six connexines. Les hemicanaux peuvent former des jonctions communicantes ou peuvent rester libres a la membrane des cellules. Peu est connu sur l'implication des connexines dans le recrutement des leucocytes, leur adhesion et leur transmigration a travers la barriere alveolo-capillaire. L'objectif de mon travail de these est de determiner le role des connexines et des jonctions communicantes dans les interactions cellulaires entre le neutrophile et la barriere alveolo-capillaire.
Growth and Welfare under Endogenous Lifetime

We study the role of endogenous healthcare choices by households to extend their expected lifetimes on economic growth and welfare in a decentralized overlapping generations economy with the realistic feature that households’ savings are held in annuities. We characterize healthcare spending in the decentralized market equilibrium and its effects on economic growth. We identify the moral-hazard effect in healthcare investments when annuity rates are conditioned on average mortality and explain the conditions under which this leads to over-investment in healthcare. Moreover, we specify the general equilibrium effects and macroeconomic repercussions associated with this moral-hazard effect. In a numerical simulation of our model with OECD data, we find that the moral-hazard effect may be substantial and implies sizeable welfare losses of approximately 1.5%. At a more general level, our study suggests that welfare improvements from longevity increases may be lower than suggested when considered in planner economies.
MOLECULAR MARKERS OF DIFFERENT TOMATO GENOTYPES

The present study aimed to identify the molecular markers as well as the effects of genotype, explant and hormone balance on the ability of shoot regeneration in vitro tomato propagation. Six commercial cultivars (SM, UC97-3, CR, SQ, SSB and RS) and four hybrids (SM×CR, SSB×CR, RS×CR and SQ×CR) were used as different genotypes. Two explant types (shoot tip, eypocotyl) and three media composition [M1 (MS + BA 2 mg/l + Kin1 mg/l.), M2 (MS + BA 0.5mg/l + Kin0.5mg/l.), and M3 (MS + BA1 mg/l + Kin2 mg/l.)] affected shoot regeneration in all the tested genotypes. The three types of media promoted the shoot tip explant to produce shoots. Only M1 medium promoted the eypocotyl explant to produce shoots. Three criteria were measured on all produced plantlets (leaf number, plant height and number of shoots/ explant). Three genotype(SM, UC97-3, CR and RS) showed the highest number of shoots, number of leaves and plant height, respectively as a response to the culture medium M1 (2mg/l BA +1mg/l kin) So, they are good combiners for the production of hybrids. The hybrid (SM×CR) possessed high number of shoots.Ten ISSR primers were individually amplified to allow the differentiation of the materials under study. All ten primers generated 98 DNA bands, with an average of 9.8 per primer and 78 being polymorphic, The profiles generated by primer 17898 B (CA) 6GT contained the highest number of polymorphic bands (12 bands). All primers detected unique bands except HB13and HB10 primers. The two varieties (SM) and UC97-3 possessed highly shoot regeneration than the other genotypes and they had unique bands may be used as molecular markers for highly shoot regeneration. These molecular markers were 917 bp by primer 17899 A (CA) 6 AG, 365 bp, 333 bp and 291 bp by 17898 A(CA) 6AC and 515 bp and 343 bp by primer 17898 B (CA) 6GT. The evaluation of the dendrogram showed 79% similarity between SSB and UC97-3 cultivars and they are located in a separate group, and 82% similarity between CR, SQ, RS, SM cultivars. From the results obtained in this study, ISSR markers have a high efficiency to differentiate the tomato cultivars. Three primers i.e., 17899 A (CA) 6 AG, 17898 A(CA) 6AC and 17898 B (CA) 6GT consider as a specific primers in tomato genotypes for discovery of molecular markers to high ability shoot regeneration genotypes.
Asteroid polarimetry : validation run on the CAPS polarimeter

Polarimetric study of atmospherless bodies is a powerful tool to determine their physical properties (albedo, diameter) [1]. The “Calern Asteroids Polarimetric Survey” polarimeter has been designed for this purpose. It is a “single shot” CCD polarimeter based on a “double-Wollaston” configuration [3, 4]. This allows to measure simultaneously the three Stokes parametersI, Q andU without any moving parts. This instrument has been designed for the F/ 12.5 Cassegrain focus of the1 meter West telescope of the “Centre Pédagogique Planète et Univers” facility (C2PU, Observatoire de la Côte d’Azur, Plateau de Calern, France). We present in this talk the first calibration and measurements made with CAPS. The results show that the instrument remained stable with a precision of 10−4 during the whole observing campaign (two months). We also present the very first polarimetric measurements on30 main belt asteroids, in good agreement with previously published results.