Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutagenic Properties of 3-(Deoxyguanosin-N2-yl)-2-acetylaminofluorene, a Persistent Acetylaminofluorene-Derived DNA Adduct in Mammalian Cells†

The carcinogen 2-acetylaminofluorene is metabolically activated in cells and reacts with DNA to form N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (dG-C8-AAF), N-(deoxyguanosin-8-yl)-2-aminofluorene (dG-C8-AF), and 3-(deoxyguanosin-N(2)()-yl)-2-acetylaminofluorene (dG-N(2)-AAF) DNA adducts. The dG-N(2)-AAF adduct is the least abundant of the three isomers, but it persists in the tissues of animals treated with this carcinogen. The miscoding and mutagenic properties of dG-C8-AAF and dG-C8-AF have been established; these adducts are readily excised by DNA repair enzymes engaged in nucleotide excision repair. In the present study, oligodeoxynucleotides modified site-specifically with dG-N(2)-AAF were used as DNA templates in primer extension reactions catalyzed by mammalian DNA polymerases. Reactions catalyzed by pol alpha were strongly blocked at a position one base before dG-N(2)-AAF and also opposite this lesion. In contrast, during translesion synthesis catalyzed by pol eta or pol kappa nucleotides were incorporated opposite the lesion. Both pol eta and pol kappa incorporated dCMP, the correct base, opposite dG-N(2)-AAF. In reactions catalyzed by pol eta, small amounts of dAMP misincorporation and one-base deletions were detected at the lesion site. With pol kappa, significant dTMP misincorporation was observed opposite the lesion. Steady-state kinetic analysis confirmed the results obtained from primer extension studies. Single-stranded shuttle vectors containing (5)(')TCCTCCTCXCCTCTC (X = dG-N(2)-AAF, dG-C8-AAF, or dG) were used to establish the frequency and specificity of dG-N(2)-AAF-induced mutations in simian kidney (COS-7) cells. Both lesions promote G --> T transversions overall, with dG-N(2)-AAF being less mutagenic than dG-C8-AAF (3.4% vs 12.5%). We conclude from this study that dG-N(2)-AAF, by virtue of its persistence in tissues, contributes significantly to the mutational spectra observed in AAF-induced mutagenesis and that pol eta, but not pol kappa, may play a role in this process.
Characterization of Pyoverdinpss, the Fluorescent Siderophore Produced by Pseudomonas syringae pv. syringae

Pseudomonas syringae pv. syringae B301D produces a yellow-green, fluorescent siderophore, pyoverdinpss, in large quantities under iron-limited growth conditions. Maximum yields of pyoverdinpss of approximately 50 μg/ml occurred after 24 h of incubation in a deferrated synthetic medium. Increasing increments of Fe(III) coordinately repressed siderophore production until repression was complete at concentrations of ≥ 10 μM. Pyoverdinpss was isolated, chemically characterized, and found to resemble previously characterized pyoverdins in spectral traits (absorbance maxima of 365 and 410 nm for pyoverdinpss and its ferric chelate, respectively), size (1,175 molecular weight), and amino acid composition. Nevertheless, pyoverdinpss was structurally unique since amino acid analysis of reductive hydrolysates yielded β-hydroxyaspartic acid, serine, threonine, and lysine in a 2:2:2:1 ratio. Pyoverdinpss exhibited a relatively high affinity constant for Fe(III), with values of 1025 at pH 7.0 and 1032 at pH 10.0. Iron uptake assays with [55Fe]pyoverdinpss demonstrated rapid active uptake of 55Fe(III) by P. syringae pv. syringae B301D, while no uptake was observed for a mutant strain unable to acquire Fe(III) from ferric pyoverdinpss. The chemical and biological properties of pyoverdinpss are discussed in relation to virulence and iron uptake during plant pathogenesis.
Gene-centromere mapping of 312 loci in pink salmon by half-tetrad analysis

We estimated recombination rates between 312 loci and their centromeres in gynogenetic diploid pink salmon (Oncorhynchus gorbuscha ) that we produced by initiating development with irradiated sperm and blocking the maternal second meiotic division. Amplified fragment length polymorphisms (AFLPs) were significantly more centromeric than loci identified by three other techniques (allozymes, microsatellites, and PCR using primer sequences from interspersed nuclear elements). The near absence of AFLPs in distal regions could limit their utility in construct - ing linkage maps. A large proportion of loci had frequency of second division segregation (y) values approaching 1.0, indicating near complete crossover interference on many chromosome arms. As predicted from models of chromosomal evolution in salmonids based upon results with allozyme loci, all duplicated microsatellite loci that shared alleles (isoloci) had y values of nearly 1.0.
The subfamilial and tribal classification of the family Asclepiadaceae

Abstract A modified classification of the family Asclepiadaceae R. Br. s.s . into three tribes — Secamoneae, Asclepiadeae s.l . and Stapelieae s.l . — is proposed. The position of attachment of the caudicles to the pollinia is suggested as a criterion for defining the erect and pendulous stature of the pollinaria. The concept of the transverse stature of pollinaria has been abandoned. In addition to the stature of the pollinaria, the morphology of the anther sacs (whether or not embedded in the tissue of the anther wings) and the position of anther wings with respect to the anther sacs are suggested as supplementary characters for tribal classification of the family. The characters of the gynoecium, particularly the presence or absence of true styles and the sharp constriction between stigma-head and ovaries (i.e. clavuncular morphology) have also been suggested as useful in differentiating Asclepiadeae s.l . and Stapelieae s.l . , along with the stature of the pollinaria. The circumscription of Asclepiadeae is emended to accommodate taxa of the former tribe Gonolobeae as a subtribe. The circumscription of Stapelieae has been retained in a wider sense, as suggested by Decaisne (1844). The tribes Fockeeae Kunze, Liede & Meve (1994), Marsdenieae Benth. (1876), Ceropegieae Benth. (1876), and Stapelieae s.s . sensu Benth. (1876; non Decne., 1844) have been relegated to subtribe status in the tribe Stapelieae Decne. (1844). Homology of the different parts of the gynoecium in the Asclepiadeae ( s.l .) with those in the Stapelieae ( s.l .) has been drawn. Segments of the style have been distinguished into ‘true style’ and ‘pseudostyle’, the former as parts of the ovary segment in development, the latter as stigma segment in development. The genus Tylophora R. Br. which was formerly treated under Stapelieae Decne. has been transferred to Asclepiadeae based on the morphology of the pollinaria, gynoecium and seed coat architecture.
Effects of Decompression and Puncturing the Gas Bladder on Survival of Tagged Yellow Perch

Abstract Overinflation of the gas bladder following rapid depressurization is relatively common in fishes caught in deep water and brought to the surface. Currently, the most commonly used method to reduce mortality caused by overinflation is to puncture the gas bladder with a hypodermic needle. Although the method is widely used, few studies have been conducted to determine its effectiveness. We conducted a series of experiments on yellow perch Perca flavescens collected at 10 and 15 m depths in Lake Michigan. Fish were either measured for length (control), measured and tagged, or measured, tagged, and punctured. The fish were then taken to an enclosed hatchery facility. Fish brought to the surface in stages (decompressed) had higher survival than nondecompressed fish; this effect was greater for fish caught at 10 than 15 m. Unpunctured fish floated for up to 72 h before regaining neutral buoyancy; less than 2% of the punctured fish floated on the first day. Puncturing the swim bladder had a significant,.
Possibility of improving the quality characteristics of olive‐pomace oil and enhancing its differentiation from refined olive‐pomace oil

An investigation was carried out to evaluate the oxidative and hydrolytic degradation of 37 olive-pomace oils marketed in southern Italy and to compare the results with those obtained from 10 deodorised olive-pomace oils representative of large stocks of oil obtained after the final step of refining. One aim of the research was to ascertain the quality characteristics of commercial olive-pomace oils; another was to verify whether the legally prescribed addition of virgin olive oil to refined pomace oil, so that the final product may be classified commercially as olive-pomace oil, was actually sufficient to justify upgrading. The analytical methods used were silica gel column chromatography and high-performance size exclusion chromatography. The data obtained showed that the final retail olive-pomace oils had a lower degree of oxidative degradation than the refined oils, as indicated by the lower values obtained when summing the proportions of triglyceride oligopolymers and oxidised triglycerides. Conversely, hydrolytic degradation, which was evaluated by determining diglycerides, proved to be the same in the two categories of oil. The proportions of virgin olive oil added are small, as indicated by the statistically indistinguishable values of triglyceride oligopolymers and free fatty acids obtained. The possibility of setting a limit to the amount of triglyceride oligopolymers present in the commercial category of olive-pomace oil has been considered. This limit would ensure standardisation of the level of oxidation and, consequently, of the quality of marketed oils and would enhance differentiation between olive-pomace oil and refined olive-pomace oil. © 2000 Society of Chemical Industry
Health aspects of thermoxidized oils and fats.

Early studies used extremely overheated fats which were toxic if fed to animals. Later fats and oils were heated in equipments for deep-fat frying under the conditions of good commercial practice. Such heated fats showed no detrimental effects even if fed in long-term feeding trials. The results are reported and critically evaluated. However, certain fractions of the heated fats, e.g. the so called Total Polar Materials caused clearly noticeable effects in the feeding studies: growth retardation, increased liver and kidney weights, and disorders of the enzyme system but only if fed in high doses. In the last years several research groups specialized in the use of cell cultures and enzymo-logical methods and gained insight into resorption and metabolism. Model compounds or compound mixtures have been synthesized. Their structure and/or composition deviated more or less from the genuine compounds or fractions of the heated fats and the results of these studies must not be generalized. New analytical procedures allow to isolate well-defined fractions, and quantitative data about their contents in heated fats are obtained: (a) harmless mono- and diglycerides and free fatty acids, (b) dimeric and polymeric triglycerides and dimeric fatty acids, harmless as well because of very low resorption rates and (c) oxidized triglyceride monomers. Their saponification and degradation products are oxidized monomeric and dimeric acids, oxidized cyclic fatty acids, and other polar compounds. These low molecular oxidized compounds are nutritionally suspect. Since 60 years and with considerable effort more or less systematic investigations have been performed in many countries to answer the question, if heated fats are detrimental to health.
Studies on replicating patterns of bovine sex chromosomes using 5‐bromo‐deoxyuridine (BrdU)

Contents: The replicating patterns of bovine sex chromosomes were examined using the method of the alternate administration of BrdU and dT throughout the DNA synthesis of the cell cycle. It was clear that two X chromosomes of the female complement behaved in a different replicating patterns and that these differences were markedly shown in the last stage of the S period. The X chromosome of the male behaved in a similar replicating pattern to one of the two female X chromosomes. It was suggested that at the beginning of the S period, the X chromosomes replicated the DNA at the end of the short arm, in the central region, and at the distal region of the long arm. It was clear that the entire Y chromosome replicated in the last S period. Inhalt: Untersuchungen zum Reproduktionsmuster der Geschlechtschromosomen des Rindes mit Hilfe von 5-Bromodeoxyuridin (BrdU) II. Das Reproduktionsmuster des spaten X-Chromosoms, des fruhen X-Chromosoms und des Y-Chromosoms wahrend der DNA Synthese Das Reproduktionsmuster der Geschlechtschromosomen des Rindes wurde wahrend der DNA Synthese eines Zellzyklus unter alternierender Behandlung mit BrdU und dT untersucht. Die beiden weiblichen X-Chromosomen wiesen ein unterschiedliches Reproduktionsmuster auf. Diese Unterschiede reigten sich deutlich in der letzten Phase der S-Periode. Das mannliche X-Chromosom zeigte ein ahnliches Reproduktionsmuster wie eines der beiden weiblichen X-Chromosomen. Dies ist ein Hinweis, daβ die X-Chromosomen am Anfang der S-Periode die DNA am Ende des kurzen Armes, im zentralen Bereich und im distalen Bereich des langen Armes reproduzieren. Dabei war sichergestellt, daβ das ganze Y-Chromosom in der letzten Phase der S-Periode reproduzierte.
Autoimmunity to the Mr 32,000 subunit of replication protein A in breast cancer

Purpose: We sought to identify autoantigens recognized by antibodies in breast cancer patient sera with potential diagnostic or prognostic significance. Experimental Design: Serum from a female breast cancer patient exhibiting a high titer antinuclear antibody was used to screen a HeLa cDNA expression library, leading to the cloning of a cDNA for the M r 32,000 subunit of replication protein A (RPA32). RPA32 expression and localization were assayed in autologous tumor by monoclonal antibody staining. A specific ELISA using recombinant protein was used to screen sera from 801 breast cancer patients and 65 controls. Results: A relationship between anti-replication protein A (RPA) antibodies and the ductal breast carcinoma of the proband was suggested by overexpression and aberrant localization of RPA32 in tumor cells as compared with surrounding normal ductal tissue and by the presence of anti-RPA32 antibodies before the diagnosis. The prevalence of anti-RPA32 antibodies was significantly higher ( P in situ carcinoma. No associations were found between anti-RPA antibodies and survival, occurrence of a second tumor, metastases, or antibodies to p53. Reactivity to RPA32 also was detected in sera from 3 of 47 patients with other cancers. Conclusions: In view of the central role of RPA in DNA replication, recombination, and repair, we suggest that autoimmunity to RPA32 may reflect molecular changes involved in the process of tumorigenesis. The finding of antibodies to RPA32 before diagnosis and their prevalence in in situ carcinoma suggest that they are potentially useful markers of early disease.
Desempenho produtivo de vacas da raça Gir leiteira em confinamento alimentadas com níveis de concentrado e proteína bruta nas dietas

The objective of this work was to evaluate the effect of increasing levels of concentrate and crude protein in the diets, in which intakes of dry matter and nutrients, coefficients of digestibility, milk production and composition and efficiency of food use were evaluated. Twenty cows in lactation were distributed in a random block design, with five replicates per diet, defined according to milk production. The experimental diets were constituted of sorghum silage as roughage and concentrate at the following levels: 11.7; 23.3; 35.2 and 46.8% with four levels of crude protein (CP) (11.0; 12.0; 14.0 and 16.0%) on diet dry matter basis. Increases in the levels of concentrate and crude protein caused a greater increase in the total dry matter intake. The coefficient of digestibility of crude protein was influenced by greater levels of concentrate and crude protein in the diet. Milk production was greater for cows fed diets with greater levels of concentrate and crude protein but it did not differ among cows fed other diets. For cows of milking Gyr breed kept in the conditions of this research, levels of 23.3% concentrate and 12% of crude protein in the diet present the best productive response.
Generation Mean Analysis Technique for Determining Genetic Parameters for some Quantitative Traits in Two Maize Hybrids (Zea mays L.)

This experiment was conducted at the Maize Researches Department, General Commission for Scientific Agriculture Researches (G.C.S.A.R.) Damascus, Syria during the summer growing seasons of 2010, 2011 to 2012. Treatments were arranged in a Randomized Complete Blocks Design with three replications. This research aimed to evaluate genetic parameters for days to 50% silking, plant and ear height, ear length, ear diameter, number of rows per ear, number of kernels per row, 100 kernel weight and grain yield per plant using generations means analysis of two yellow maize hybrids (IL.292-06 × IL.565-06, IL.459-06 × IL.362-06) to detect epistasis and estimates of m, d, h, i, j and l parameters. Results showed that the additive - dominance model was adequate to demonstrate the genetic variation and its importance in the inheritance of most studied traits. Non-allelic gene interaction was operating in the control of genetic variation in most studied traits. The signs of [h] and [l] were opposite in most studied traits for the two crosses. Also, the inheritance of all studied traits was controlled by additive and non-additive genetic effects, but dominance gene effects play the major role in controlling the genetic variation of the most studied traits. Suggesting that the improvement of those characters need intensive selection through later generations. High phenotypic variations were composed of high genotypic variations and less of environmental variations, indicating the presence of high genetic variability for different traits and less influence of environment. Highly significant heterosis relative to mid and better parents, respectively was found for all characters, correlated that with inbreeding depression for all traits. Narrow sense heritability and genetic advance were low in most cases due to the dominance of non-additive gene action in controlling the genetic variation of the most studied traits.
EFFECTS OF HIGH REARING DENSITIES AND LOADING RATES ON THE GROWTH AND STRESS RESPONSES OF JUVENILE RAINBOW TROUT

Abstract Growth and changes in serum concentrations of cortisol, glucose, and chloride in response to acute stress challenge tests were compared in juvenile rainbow trout Oncorhynchus mykiss (143–190 mm TL) reared at density indices of 2.8–9.3 g/(L · cm) and loading rates of 0.5 and 0.75 kg/(L · min). In experiment 1, there were no differences in growth or measures of physiological stress in fish reared for 4 weeks at loading rates of 0.5 or 0.75 kg/(L · min). Fish reared at density indices of 5.6 and 8.4 g/(L · cm) gained significantly less weight than fish at a density index of 2.8 g/(L · cm), and fish reared at 2.8 and 5.6 g/(L · cm) had better food conversion rates (weight of food fed/weight gained) than those at 8.4 g/(L · cm). Changes in the serum concentrations of cortisol, glucose, and chloride, however, suggested that the reduced growth at elevated densities was not due to physiological stress. In experiment 2, cortisol levels were higher in fish 3 d after transfer to net-pens than in fish 10 or .
PML‐RARA fusion transcripts in irradiated and normal hematopoietic cells

It is believed that two important factors in the genesis of reciprocal chromosomal translocations in malignant cells are the physical proximity of the involved regions and local structural features of the chromatin fiber that make them more susceptible to breakage and rearrangement. In this work we sought to investigate whether PML‐RARA fusion transcripts, characteristic of acute promyelocytic leukemia (APL), could be induced by a clastogenic agent in cells known to have, a priori, a favorable spatial distribution of these genes. A lymphoid‐cell line, lacking the t(15;17) but having the PML and RARA genes in close proximity in specific phases of the cell cycle, was irradiated with 10 Gy of 60Co, and the incidence of PML‐RARA transcripts was analyzed by a highly sensitive PCR assay. Despite gene proximity, typical PML‐RARA transcripts were only rarely detected in irradiated cells. The same phenomenon was observed at similar frequency in control non‐irradiated cells. These findings made us investigate whether such transcripts could also be detected in peripheral blood cells from normal individuals. PML‐RARA transcripts were observed at low frequencies in isolated lymphoid and granulocytic cell populations, with similar incidence in both cell types. The data thus indicate that the PML and RARA genes are not particularly susceptible to the clastogenic effects of γ‐irradiation, and that, similar to what has been reported for other chromosomal translocations, transcriptionally active PML‐RARA rearrangements can be generated in normal hematopoietic cells of different lineages without apparent oncogenic consequences. © 2000 Wiley‐Liss, Inc.
A systematic revision of Neotropical lizards in the clade Hoplocercinae (Squamata: Iguania)

The clade Hoplocercinae includes 13 species assigned to three taxa traditionally ranked as genera—Enyalioides, Hoplocercus, and Morunasaurus—, and distributed on both sides of the Andes from Panama to Brazil. We provide a revised taxonomy of Hoplocercinae including synonymies, diagnoses, standardized descriptions, distributions, notes on color and natural history, and a key for species identification. We also propose vernacular names in English and Spanish for all species.
Improvements to Power-On Base Pressure Prediction for the Aeroprediction Code

New technology has been developed and added to the power-on base drag prediction model in the aeroprediction code. The new technology showed improvement over the January 2009 release of the code comparedwith experiment for all cases considered.Of particular note is the capability to predict base pressure for power-off conditions andat all values of power-on including base bleed and values of thrust coefficient belowwhere theminimumvalue of power-on base pressure occurs. To the authors’ knowledge, this is the first theoretical method available to predict power-on base pressure at any value of thrust coefficient.
Path to Facilitate the Prediction of Functional Amino Acid Substitutions in Red Blood Cell Disorders – A Computational Approach

Background: A major area of effort in current genomics is to distinguish mutations that are functionally neutral from those that contribute to disease. Single Nucleotide Polymorphisms (SNPs) are amino acid substitutions that currently account for approximately half of the known gene lesions responsible for human inherited diseases. As a result, the prediction of nonsynonymous SNPs (nsSNPs) that affect protein functions and relate to disease is an important task. Principal Findings: In this study, we performed a comprehensive analysis of deleterious SNPs at both functional and structural level in the respective genes associated with red blood cell metabolism disorders using bioinformatics tools. We analyzed the variants in Glucose-6-phosphate dehydrogenase (G6PD) and isoforms of Pyruvate Kinase (PKLR & PKM2) genes responsible for major red blood cell disorders. Deleterious nsSNPs were categorized based on empirical rule and support vector machine based methods to predict the impact on protein functions. Furthermore, we modeled mutant proteins and compared them with the native protein for evaluation of protein structure stability. Significance: We argue here that bioinformatics tools can play an important role in addressing the complexity of the underlying genetic basis of Red Blood Cell disorders. Based on our investigation, we report here the potential candidate SNPs, for future studies in human Red Blood Cell disorders. Current study also demonstrates the presence of other deleterious mutations and also endorses with in vivo experimental studies. Our approach will present the application of computational tools in understanding functional variation from the perspective of structure, expression, evolution and phenotype.