Miracle-dz/UniFAR-FTUs huggingface dataset:
Mode of Action of f-Lactam Antibiotics

Biochemical investigations of the mode of action of p-lactam antibiotics have focused on the interaction of these drugs with sensitive enzymes and penicillin-binding proteins in vitro and on the correlation of these data with physiological responses to the drugs. The classical response is inhibition of growth and cell death followed by lysis; however, the bacteriostatic response to penicillins, which is seen in certain bacterial species such as Streptococcus mutans and in mutants of species such as Streptococcus pneumoniae, is also described. The biochemical data remain consistent with the acyl-D-alanyl-D-alanine donor substrate analogue theory, but multiple targets with differential sensitivity to different /3-lactam antibiotics exist. The relationship of these targets to penicillin-binding proteins and their possible functions in cell growth and division are discussed. Investigations of the mode of action of 3-lactam antibiotics have followed several independent routes that are beginning to converge in a satisfactory but not yet coherent fashion. These investigations have already helped to demonstrate the complexity of the processes of cell division anld cell wall growth in bacteria, and, when integrated, this information should illuminate this major aspect of bacterial physiology. Such knowledge should also help to rationalize structureactivity relationships among 3-lactam antibiotics, thus aiding in rational drug design and partially explaining intrinsic differences in sensitivity among species. In this review I will emphasize the relationship of the biochemical data to the substrate analogue theory of Tipper and Strominger [1], the extent to which data on penicillin-sensitive enzymes can be correlated with data on penicillin-binding proteins, and the major gap remaining in our ability to connect this biochemical information to the physiological consequences of
The effect of buckwheat groats processing on the content of mycotoxins and phenolic compounds

ABSTRACT Two buckwheat groats processing methods were used for production of final commercial product. The first one involved thermal processing (steamed) and then dehulling, and the second one dehulling without thermal treatment (raw). The research evidenced that the raw groats and hulls were several times more contaminated with aflatoxin B1 compared with steamed ones. High concentrations of aflatoxin B1 (75.8 µg kg−1) and T-2 toxin (351.0 µg kg−1) were detected in the raw hull samples. The total phenolics responded more sensitively to thermal treatment than phenolic acids. More than 20 times higher concentrations of quercetin (65.47 ± 6.3 µg g–1) were determined in steamed hulls compared to other raw and steamed samples. Buckwheat groats and hulls, containing the highest concentrations of quercetin and hydroxybenzoic acids, were found to be 10-fold less contaminated with aflatoxin B1 and T-2 toxins; however, the correlations between the phenolics and mycotoxins were statistically insignificant.
Probabilistic models for the identification and interpretation of somatic single nucleotide variants in cancer genomes

Somatic single nucleotide variants (SNVs) are mutations resulting from the substitution of a single nucleotide in the genome of cancer cells. Somatic SNVs are numerous in the genomes of most types of cancers. SNVs can contribute to the malignant phenotype of cancer cells, though many SNVs likely have negligible selective value. Because many SNVs are selectively neutral, their presence in a measurable proportion of cells is likely due to drift or genetic hitchhiking. This makes SNVs an appealing class of genomic aberrations to use as markers of clonal populations and ultimately tumour evolution. Advances in sequencing technology, in particular the development of high throughput sequencing (HTS) technologies, have made it possible to systematically profile SNVs in tumour genomes. We introduce three probabilistic models to solve analytical problems raised by experimental designs that leverage HTS to study cancer biology. The first experimental design we address is paired sequencing of normal and tumour tissue samples to identify somatic SNVs. We develop a probabilistic model to jointly analyse data from both samples, and reduce the number of false positive somatic SNV predictions. The second experimental design we address is the deep sequencing of SNVs to quantify the cellular prevalence of clones harbouring the SNVs. The key challenge we resolve is that allele abundance measured by HTS is not equivalent to cellular prevalence due to the confounding issues of mutational genotype, normal cell contamination and technical noise. We develop a probabilistic model which solves these problems while simultaneously inferring the number of clonal populations in the tissue. The final experimental design we consider is single cell sequencing. Single cell sequencing provides a direct means to measure the genotypes of clonal populations. However, sequence data from a single cell is inherently noisy which confounds accurate measurement of genotypes. To overcome this problem we develop a model to aggregate cells by clonal population in order to pool statistical strength and reduce error. The model jointly infers the assignment of cells to clonal populations, the genotype of the clonal populations, and the number of populations present.
Polychaete fauna of the Aegean Sea : Inventory and new information

Examination of collections from the Aegean Sea and a review of the literature revealed that 592 polychaete species have been recorded from this area. Five of the species identified are reported for the first time from the Mediterranean and the Black Sea, 38 species are new records for the Eastern Mediterranean and 55 are new elements for the Aegean polychaete fauna. Information on the habitat and the geographic distribution of the species newly reported from the Eastern Mediterranean is given. The checklist of the Aegean Polychaeta is presented. Although being located in the vicinity of the Eastern Mediterranean province and the Black Sea which are characterized as faunistically impoverished areas, the Aegean hosts a rich polychaete fauna, second in order in species diversity after the Western Mediterranean. The latter demonstrates the importance of this area in the understanding the patterns of polychaete distribution along the Mediterranean and the Black Sea.
Effects of extracted rice bran supplementation on growth performance, nutrient digestibility, diarrhea score, blood profiles, and fecal microbial shedding in comparison with apramycin (antibiotic growth promoter) in weanling pigs1

Abstract: This study evaluated the efficacy of extracted rice bran (ERB) in weanling piglets. One hundred forty weanling pigs [(Yorkshire × Landrace) × Duroc] with an average BW of 5.70 ± 1.41 kg (21 d of age) were fed in two phases in a 6-wk experiment. Weanling pigs were allotted to diets containing 0 or 0.1 g kg−1 of ERB, and 0 or 165 mg kg−1 of apramycin according to a 2 × 2 factorial arrangement of treatments. Both apramycin and ERB supplementation increased growth efficiency (G:F) during phase 1 and overall, respectively (P < 0.05). The apparent total tract digestibility (ATTD) of dry matter (DM) was increased in response to either ERB or apramycin at wk 2 and 6 (P < 0.05). Supplementation of ERB decreased total cholesterol (TC) and increased high-density lipoprotein cholesterol (HDL-C) in diets lacking ERB at wk 6 (P < 0.05). Pigs receiving diets supplemented with apramycin reduced Escherichia coli at wk 2 and 6, and Salmonella counts at wk 6 (P < 0.05). Supplementation of ERB increased fecal Lactobacillus and reduced Salmonella counts at wk 6 (P < 0.05). In conclusion, results indicated that dietary supplementation of ERB improved performance in weanling pigs.
Scanning electron microscope observations on the morphology of Tylenchorhynchus aduncus

Tylenchorhynchus aduncus De Guiran was described in 1967 and transferred to Tetylenchus Filipjev by Tarjan in 1973. After the suppression of this genus (Sher, 1973; Siddiqi, 1979) the species was replaced in Tylenchorhynchus. Most of the morphological studies of Tylenchorhynchus species have been based on observations with the light microscope. Observations with the scanning electron microscope (SEM) have been made on only five species: T. cylindricus, T. goffarti, T. lamelliferus, T. maximus and T. phaseoli (Sher and Bell, 1975; De Grisse, 1977 and 1979). There is also a lack of biological information on T. aduncus. This note describes characters of this species seen by SEM, and gives information on its distribution in Italy.
Relationship Between Resistance to Boophilus Microplus, Nutritional Status, and Blood Composition in Shorthorn X Hereford Cattle

Relationships between nutrition, blood composition, and tick resistance were studied in three groups of six yearling Shorthorn X Hereford steers. Feeding was ad libitum and group I was offered lucerne hay and safflower seeds, group II lucerne hay only, and group III wheat straw supplemented with molasses. All animals were infested five times with 0·5 g tick larvae during the treatment period of 62 days.
Genetic study and selection in F4 generation of rice (Oryza sativa L.)

An attempt was made to study the variability in 25 F4 generation of T. Aman rice. Highly significant variations were obtained for all the characters studied. The highest mean and range value was observed for grain yield per meter square followed by number of filled grains per panicle, spikelet sterility (%) and 1000-grain weight. Highest genotypic variance was observed for grain yield per meter square followed by plant height, number of filled grains per panicle and spikelet sterility (%) whereas the highest genotypic coefficient of variation was recorded for spikelet sterility (%) followed by grain yield per meter square, panicle weight and plant height. Phenotypic variance was close to the corresponding genotypic variance for all the traits studied except plant height, panicle size, weight and branching habit. On the other hand, all the characters showed close phenotypic and genotypic coefficient of variation except panicle weight and spikelet sterility (%) which indicated additive gene action for expression of the characters. Considering mean, range and all genetic parameters selection could be performed on the basis of number of tillers per hill, number of panicles per hill, panicle length, number of filled grains per panicle, spikelet sterility (%), 1000-grain weight and grain yield per square meter for significantly improvement of rice yield.
Haemoglobinopathies- thalassaemias and abnormal haemoglobins in Eastern Uttar Pradesh and adjoining districts of neighbouring states

The haemoglobinopathies - thalassaemias and abnormal haemoglobins - constitute a major burden of genetic diseases in India. Our study, based on index cases from 120 families detected between May 1999 and May 2003, highlights the ethnic distribution of haemoglobinopathies in regions in and around Varanasi comprising 8-10 districts of eastern Uttar Pradesh and adjoining districts of Bihar, Jharkhand, Chhattisgarh and Madhya Pradesh. Homozygous and heterozygous β-thalassaemia was the most common (66.9%), with thalassaemic haemoglobinopathies HbE-β-thalassaemia (15.9%) and HbS-β-thalasseamia (7.8%) contributing to almost a quarter of the cases. Along with HbSS disease (4.3%), the results indicate a confluence of β-thalassaemia, HbS and HbE in this region. IVS1-5 nt was the most common mutation in the few carriers analysed for mutation detection. The significance of the study lies in the demonstration of wide prevalence of β-thalassaemia across all castes and communities of this region, with migrant population groups of Sindhis and Punjabis comprising only 5.8% of the index cases. Also, HbE seems to have a much higher presence in this region than so far believed and HbS has a significant presence in general castes as well.
Esterase variation in rocky mouse, Apodemus mystacinus (DANFORD and ALSTON, 1877) (Mammalia : Rodentia) in Turkey

The esterase enzyme system (Est) of 44 specimens of the rocky mouse, Apodemus mystacinus, from 10 localities in Turkey was analyzed using polyacrylamide gel electrophoresis. Three loci Est-I, Est-2, and Est-3 were determined. There were two alleles in Est-1 and four alleles in Est-2 and Est-3. The Shannon information index (I) ranged from 0.21 to 0.92. On the basis of genetic relationship of seven A. mystacinus populations based on Nei Genetic Distance of three enzyme loci, seven populations were divided into two main clusters and two subgroups in each cluster; 1: Sebma-Akseki (subgroup 1), Altindere-Akcakoca (subgroup2), 2: BeyŞehir-izaybu (subgroup 1) and Ardanuc (subgroup2).
Epidemiological characterization and risk factors associated with Mycobacterium avium subsp. paratuberculosis infection in dairy goats in the Brazilian semiarid region Caracterização epidemiológica e fatores de risco associados à infecção por Mycobacterium avium subsp. paratuberculosis em caprinos l

The aim of this investigation was to conduct an epidemiological study and identify risk factors associated with the occurrence of paratuberculosis (Johne’s disease) in dairy goats within the semiarid region of Paraiba State. The study was done during the period of March 2009 to July 2011, during which 727 female goats from 86 flocks from the city of Monteiro, Paraiba were investigated. For the serological diagnosis of Mycobacterium avium subsp. paratuberculosis (Map) infection indirect ELISA tests (screening and confirmatory) were performed. Of the 727 animals used six (0.82%) were seropositive at the confirmatory test after screening, and of the 86 flocks six (6.97%) presented at least one seropositive animal. In positive flocks the frequency of reactive animals ranged from 5.26% to 16.60%. Risk factors identified were production system (weaning and reproduction) (odds ratio = 36.0; 95% CI = 2.6 –486.1; p < 0,001) and absence of technical infrastructure (odds ratio = 54.0; 95% CI = 4.5 –642.9; p < 0,001). It was concluded that Mycobacterium avium subsp. paratuberculosis is present in dairy goat flocks in the region; however, its influence on decrease productivity as well as the risk of transmission to humans through animal products must totally evaluated. Based on the analysis of risk factors, improvements are recommended for the technical infrastructure and the management of breeding goats. Palavras-chave: Mycobacterium avium subsp. paratuberculosis, small ruminants, epidemiology, control
Effects of antibiotics on contaminated callus cultures of pyrethrum

Pyrethrum [Tanacetum cinerariifolium (TREVIR.) SCHULTZ-BIP. , Asteraceae] is a source of pyrethrins, natural insecticides that are widely used in agriculture and for domestic purposes. In callus cultures of pyrethrum microbial contaminants were observed routinely, therefore it was necessary to use antibiotics to maintain aseptic cultures. The antibiotics, streptomycin, cephalexin and penicillin-G were used for antibiotic pulse treatment. Their effect on callus growth and microbial elimination was investigated. Callus cultures of two different lines were incubated for 1 or 2 days in liquid medium containing different combinations and concentrations of antibiotics and then cultured for 6 weeks on solid medium without antibiotics. One day of antibiotic treatment had no effect on callus growth. After two days of treatment, however, growth was significantly inhibited. Growth suppression was genotype-dependent and high concentrations of antibiotics were found to be deleterious on callus growth. PCR analysis with eubacterial 16S rDNA primers was done for detecting bacteria, as it enables low, invisible concentrations of bacteria in callus cultures to be traced. Six weeks after antibiotic treatment no bacteria were detected in line L4 incubated for 2 days in medium containing 360 mg/l streptomycin, 160 mg/l cephalexin and 8 mg/l penicillin G. Lower concentrations of antibiotics, however, exhibited no bacteriostatic effect. These results indicate that, although the higher concentrations of antibiotics used in pulse treatment greatly reduce callus growth, they can successfully eliminate bacterial contamination from pyrethrum callus cultures.
MINIREVIEW Lipopolysaccharide Nomenclature-Past, Present, andFuturet

Since their discovery about 100 years ago, bacterial endotoxins have been among the most widely studied of all bacterial components. The interest in endotoxin is based, in large part, on the diversity of biological responses which this molecule elicits both in vitro and in vivo. A second major reason for this interest is that the biologically active moiety of endotoxin, the lipopolysaccharide (LPS), has been identified and biochemically characterized for a variety of enteric organisms. Further, the toxic principle of LPS, lipid A, has been defined and synthesized. Thus, it appears that many of the mysteries still surrounding the mode of action of this unique bacterial constituent will soon be resolved at the molecular level. Most
Susceptibility of vaccinated swine and mice to generalized infection with specific serotypes of Erysipelothrix rhusiopathiae.

: Swine were vaccinated with adsorbate bacterin made from Erysipelothrix rhusiopathiae of serotype 2 and were subsequently allotted to 4 exposure groups, each of which was exposed to 1 of the strains of E rhusiopathiae of serotypes 1, 2, 9, or 10. Mice were vaccinated with the same bacterin and were subsequently allotted to 60 exposure groups which were exposed to 60 strains of E rhusiopathiae, comprising 10 strains each of serotypes 1, 2, 4, 9, 10, and 11. Response to challenge of immunity in swine was determined by the presence of clinical signs of acute generalized erysipelas; response in mice was determined by the quantal (live-dead) method. Vaccinated swine were as susceptible to the strain of serotype 10 as were nonvaccinated control swine, whereas vaccinated swine were immune and control swine were susceptible to the strains of serotypes 1 and 2. The strain of serotype 9 was not sufficiently virulent to induce acute generalized erysipelas, even in control swine. Arthritis was not prevented by vaccination, but its frequency and severity were less in vaccinated swine exposed to strains of serotype 1 or 2 than in those exposed to strains of serotype 9 or 10. Vaccinated mice were significantly (P less than 0.05) more susceptible to the strains of serotype 10 than to those of any other serotype tested.
Proximate Composition and Nutritional Profile of the Black Sea Anchovy (Engraulis encrasicholus) Whole Fish, Fillets, and By-Products

ABSTRACT In this study, the proximate composition and nutritional profile of the Black Sea anchovy and its by-products were investigated. The total yield of by-products from anchovy was about 32% of the whole fish based on wet weight. The protein and fat contents of anchovy by-products were 13.39 and 10.02% for head, 16.47 and 15.50% for frame, and 12.05 and 23.90% for viscera, respectively. Significant differences were detected among the pH and color properties of anchovy whole fish, fillet, and by-products. Profiles of amino acids, fatty acids, and minerals of anchovy by-products showed they are rich sources of lysine (6–7% of total amino acids), leucine (5–6% of total amino acids), and a number of essential amino acid, polyunsaturated fatty acids (about 32–40% of total fatty acids), n-3 fatty acids (about 27–34% of total fatty acids), eicosapentaenoic acid + docosahexaenoic acid (about 26–32% of total fatty acids), and various minerals (P, Fe, Ni, Ca, Mn, Na, and Zn). These results revealed that anchovy by-products can be utilized for the production of value-added products such as protein powder, protein hydrolyzates, fish oils, and mineral supplements.
ALLELOPATHIC INFLUENCE OF CASUARINA EQUISETIFOLIA L. ON GROWTH AND DEVELOPMENT OF RICE (ORYZA SATIVA L.)

Leaf extracts of Casuarina. equisetifolia L. was evaluated for its allelopathic influenced on rice cultivars viz. IR20 and TKM – 9. Leaf extracts was tested at 2.5, 5, 10, 15 and 20% concentration. Seed germination, shoot length, biomass, chl a , chlb, carotenoids, starch, protein and amino acid contents were significantly reduced by leaf extracts and highest inhibition was observed in 20% concentration. But at lower concentration (2.5%), the seedling growth was slightly enhanced than control. The higher degree of germination and growth inhibition was observed in cultivar TKM-9 than IR-20.
Patterns and correlates of claims for brown bear damage on a continental scale

Summary Wildlife damage to human property threatens human–wildlife coexistence. Conflicts arising from wildlife damage in intensively managed landscapes often undermine conservation efforts, making damage mitigation and compensation of special concern for wildlife conservation. However, the mechanisms underlying the occurrence of damage and claims at large scales are still poorly understood. Here, we investigated the patterns of damage caused by brown bears Ursus arctos and its ecological and socio-economic correlates at a continental scale. We compiled information about compensation schemes across 26 countries in Europe in 2005–2012 and analysed the variation in the number of compensated claims in relation to (i) bear abundance, (ii) forest availability, (iii) human land use, (iv) management practices and (v) indicators of economic wealth. Most European countries have a posteriori compensation schemes based on damage verification, which, in many cases, have operated for more than 30 years. On average, over 3200 claims of bear damage were compensated annually in Europe. The majority of claims were for damage to livestock (59%), distributed throughout the bear range, followed by damage to apiaries (21%) and agriculture (17%), mainly in Mediterranean and eastern European countries. The mean number of compensated claims per bear and year ranged from 0·1 in Estonia to 8·5 in Norway. This variation was not only due to the differences in compensation schemes; damage claims were less numerous in areas with supplementary feeding and with a high proportion of agricultural land. However, observed variation in compensated damage was not related to bear abundance. Synthesis and applications. Compensation schemes, management practices and human land use influence the number of claims for brown bear damage, while bear abundance does not. Policies that ignore this complexity and focus on a single factor, such as bear population size, may not be effective in reducing claims. To be effective, policies should be based on integrative schemes that prioritize damage prevention and make it a condition of payment of compensation that preventive measures are applied. Such integrative schemes should focus mitigation efforts in areas or populations where damage claims are more likely to occur. Similar studies using different species and continents might further improve our understanding of conflicts arising from wildlife damage.