Miracle-dz/UniFAR-FTUs huggingface dataset:
The Iberian contribution to cryptic diversity in European bats

ABSTRACT We investigate the contribution of the Iberian bat fauna to the cryptic diversity in Europe using mitochondrial (cytb and ND1) and nuclear (RAG2) DNA sequences. For each of the 28 bat species known for Iberia, samples covering a wide geographic range within Spain were compared to samples from the rest of Europe. In this general screening, almost 20% of the Iberian species showed important mitochondrial discontinuities (K2P distance values > 5%) either within the Iberian or between Iberian and other European samples. Within Eptesicus serotinus and Myotis nattereri, levels of genetic divergence between lineages exceeded 16%, indicating that these taxa represent a complex of several biological species. Other well-differentiated lineages (K2P distances between 5–10%) appeared within Hypsugo savii, Pipistrellus kuhlii and Plecotus auritus, suggesting the existence of further cryptic diversity. Most unsuspected lineages seem restricted to Iberia, although two have crossed the Pyrenees to reach, at least, Switzerland.
Study for the validation of the n-alkane technique to estimate feed intake and digestibility in Alentejano pigs.

The plant epicuticular n-alkanes have been used with success as faecal markers for the estimation of intake and digestibility in ruminants, but few reports have been published with pigs, particularly, “Alentejano” pigs. The aim of this experiment is to validate the n-alkanes technique for the estimation of diet intake and digestibility in pigs of the “Alentejano” breed. An experiment was carried out with eight male “Alentejano” pigs (average LW 58 kg), housed in metabolic cages, in a controlled environment room. The animals were given a diet composed by 3kg of acorns and 400 g of grass per day, distributed into two meals (9:30 am and 5:30 pm). The animals were randomly distributed in two groups of four animals each. Animals in group 1 received one small cake per day containing 100 mg of C32 and 150 mg of C36 and in group 2 received two small cakes per day containing 50 mg of C32 and 75 mg of C36. Faecal samples were collected daily, for ten days, from the first day of alkanes administration, to determine the pattern of excretion of the markers. Also per rectum faecal samples were taken, every four hours, during three days, to determine daily variation of faecal n-alkanes concentration. Moreover, total faecal collection was carried out, for 5 days, to determine faecal n-alkane recoveries. The faecal excretion of the artificial nalkanes stabilized on the fifth day after the first dosing of the alkanes. No daily variation was observed in the faecal concentrations of even-chain and odd chain n-alkanes, therefore indicating that, in similar experimental conditions, intake and digestibility estimates can be based upon only one daily faecal sample collection. The C32 and C36 recoveries were 107% and 110% respectively and those of C27, the C29, the C31 were 75,1% 133,9% and 91,5% respectively. Given the high mean standard error (10,7) obtained, those recoveries were not significantly (P>0,05) different.
Plastics: Modifying the Microclimate for the Production of Vegetable Crops

For centuries horticulturists have attempted to modify the environment in which vegetable crops are grown. A wide variety of techniques, such as glass cloches, hotcaps, cold frames, hotbeds, and various types of glass greenhouses, have been used to extend the production season. The discovery and development of the polyethylene polymer in the late 1930s, and its subsequent introduction in the early 1950s in the form of plastic fi lms, mulches, and drip-irrigation tubing and tape, revolutionized the commercial production of selected vegetable crops and gave rise to a system of production known as plasticulture. Simply defi ned, plasticulture is a system of growing vegetable crops where signifi cant benefi t is derived from using products derived from polyethylene (plastic) polymers. The later discovery of other polymers, such as polyvinyl chloride, polypropylene, and polyesters, and their use in microirrigation systems, pipes, fertigation equipment, fi lters, fi ttings and connectors, containers for growing transplants, picking and packaging containers, and row covers further extended the use of plastic components in this production system. The complete plasticulture system consists of plastic and non-plastic components: plastic mulches, drip-irrigation, fertigation/chemigation, soil sanitation (fumigation and solarization), windbreaks, stand establishment technology, season-extension technology, integrated pest management, cropping strategies, and postharvest handling and marketing. In the plasticulture system, plastic-covered greenhouses, plastic mulches, row covers, high tunnels, and windbreaks both permanent and annual are the major contributors to modifying the cropping environment of vegetable crops, thus enhancing crop growth, yield, and quality. In addition to modifying the soil and air temperatures, there are also the benefi ts of protection from the wind and in some instances rain, insects, diseases, and vertebrate pests.
Development and Optimization of Multiplex PCR for the Identification of Different Strains of Avian Influenza Viruses in Pakistan

The present study was conducted to develop and optimize a multiplex reverse transcriptase-polymerase chain reaction (mRT-PCR) assay for the rapid detection of type A Avian influenza (AI) viruses. The assay simultaneously differentiates avian H5, H7 and H9 hemagglutinin subtypes. Specific primers were used in this assay for H5, H7 and H9 heamagglutinin subtypes. The mRT-PCR DNA products were visualized by gel electrophoresis. The fragments observed were of 362bp, 699bp and 287bp for H5, H7 and H9 hemagglutinin subtypes, respectively. The multiplex PCR is rapid and cost effective compared to other available assays for AI in Pakistan.
Grazing by mesozooplankton and metazoan microplankton on nanophytoplankton in a mesocosm experiment in the northern Baltic

Grazing by two size classes of metazooplankton, mesozooplankton(Meso; >140 um in size) and metazoan microplankton (Micro; 100-140 urn in size), was studied in a mesocosm experiment carried out off the SW coast of Finland, northern Baltic Sea, in late summer. During the 3 week study, the mesocosm was manipulated periodically by the addition of nutrient (ammonium and phosphate) and fish predators (stickleback fry). During the experimental period, the mesocosm was sampled five times to measure metazooplankton grazing, using 5 um pre-filtered and l4C-labelled natural nanoplankton as food. In spite of the presence of fish, Meso biomass increased throughout the experi- mental period. The biomass of Meso was composed mostly of different copepodite stages of Eury- temora affinis and the dadoceran Bosmma longispina maritima, and that of Micro by biomass of copepod nauplii N1II-NVI. Owing to its larger biomass, Meso could exert a greater grazing pressure on the nanophytoplankton than could Micro. The biomass specific clearance rate (BSCR) was gener- ally the same for both groups, occasionally higher in Micro. The BSCR increased during the first half of the study period, after which the clearance rates were depressed, coinciding with a sudden decrease in water temperature. The daily ingestion rate on nanophytoplankton (% of biomass as carbon) varied between 3 and 96% for Meso, and between 4 and 130% for Micro. When integrated over the study period, grazing on nanophytoplankton was estimated to provide about 60% of the carbon require- ments of metazooplankton, respectively, thus, protists were probably important food. The overall gross growth efficiency for the whole metazooplankton community was estimated to be 32%. Meso and Micro grazing was estimated to account for 8 and 2% of primary production, indicating that they were not able to control phytoplankton primary production enriched by nutrient additions.
Avaliação da influência do tempo de exposição de Tradescantia pallida var. purpurea para biomonitoramento da genotoxicidade do ar atmosférico

Tradescantia pallida (Rose) D.R. Hunt var. purpurea Boom is used to assess the genotoxicity of atmospheric air due to the formation of micronuclei (MCN) in meiotic tetrads after acute exposure. We aimed to investigate whether there is a quantitative relationship between MCN formation and the amount of hours of acute air-exposure of branches with flower buds, both in a natural environment and under controlled conditions. In bioassay I, branches with flower buds were exposed to air for 8, 24 or 32 h in Sao Leopoldo city, Southern Brazil, and in a sealed environment, from April 2012 to January 2013 on a quarterly basis. In bioassay II, the exposure of branches with flower buds for 8 hours to the air in Sao Leopoldo and indoor took place from May 2013 to February 2014, on the same basis. The MCN formation showed no relationship with the time of exposure, as no significant difference could be verified between the MCN frequencies in flower buds exposed for 8, 24 or 32 h, neither in Sao Leopoldo (means of 4.8, 4.8 and 4.2) nor in the sealed environment (means of 1.6, 1.5 and 1.3). Flower buds exposed for 8 h showed significantly higher MCN frequencies (1.6 to 7.8) than the ones from the negative control (1.2 to 2.0) in six out of eight exposures, thus evidencing the genotoxicity of the air in Sao Leopoldo. We highlight the importance of the MCN bioassay with T. pallida var. purpurea in environmental diagnoses.
Network Centralities and the Retention of Genes Following Whole Genome Duplication in Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae genome is descendant from a whole genome duplication event approximately 150 million years ago. Following this duplication many genes were lost however, a certain class of genes, termed ohnologs, persist in duplicate. In this thesis we investigate network centrality as it relates to ohnolog retention with the goal of determining why only certain genes were retained. With this in mind, we compare physical and genetic interaction networks and genetic and protein sequence data in order to reveal how network characteristics and post-duplication retention are related. We show that there are two subclasses of ohnologs, those that interact with their duplication sister and those that do not and that these two classes have distinct characteristics that provide insight into the evolutionary mechanisms that affected their retention following whole genome duplication. Namely, a very low ratio of non-synonymous mutations per non-synonymous site for ohnologs that retain an interaction with their duplicate. The opposite observation is seen for ohnologs that have lost their interaction with their duplicate. We interpret this in the following way: ohnologs that have retained their interaction with their duplicate are functionally constrained to buffer for the other ohnolog. For this reason they are retained; ohnologs that have lost their interaction with their duplicate are retained because they are functionally divergent to the point of being individually essential.
ABUNDANCE OF MYCORRHIZAS AND ROOT‐SURFACE MICRO‐ORGANISMS OF PLANTAGO LANCEOLATA IN RELATION TO SOIL AND VEGETATION: A MULTI‐VARIATE APPROACH

Summary At 40 sites in England and South Wales, mostly in grassland, features of the soil and vegetation were measured. Three Plantago lanceolata individuals were collected from each site, nitrogen, phosphorus and potassium concentrations in the leaves were measured, and the abundance of mycorrhizal infection and of fungi and bacteria on the root surface was determined by microscopic examination of stained root segments. The results were subjected to multiple regression analysis. Mycorrhizal abundance was most significantly related to vascular plant cover (negatively) and Plantago leaf length (positively), bacteria to soil organic matter (positively), fungi to cover of non-grasses (positively) and leaf phosphorus concentration (negatively). The ecological interpretation of these relationships is discussed.
Isolation and spread of enteropathogenic Yersinia spp. throughout the pork production chain

s and proceedings Van Damme I. , Habib I. , De Zutter L. (2008) Quantitative and qualitative estimation of the occurrence of pathogenic Yersinia enterocolitica in tonsils from Belgian slaughter pigs. 13 Conference on Food Microbiology, 11-12 September 2008, Ghent, Belgium. Van Damme I. , De Zutter L. (2010). Detection and enumeration of human pathogenic Yersinia enterocolitica: comparison of direct plating and enrichment, VII Congres de la SFM, 2-4 June 2010, Marseille, France. Van Damme I. , De Zutter L. (2010). Comparison of swab and destructive samples for recovery of pathogenic Yersinia enterocolitica from pig tonsils, 22 International ICFMH Symposium (FoodMicro 2010), 30 August – 3 September 2010, Copenhagen, Denmark. Van Damme I. , De Zutter L. (2010). Isolation of pathogenic Yersinia enterocolitica from porcine tonsils: comparison of swabbing and destructive samples, 15 Conference on Food Microbiology, 16-17 September 2010, Ghent, Belgium. Van Damme I. , De Zutter L. (2010). Comparison of swabbing and destructive samples for recovery of pathogenic Yersinia enterocolitica from pig tonsils, 10 International Symposium on Yersinia, 23-27 October 2010, Recife, Brazil. Van Damme I. , De Zutter L. (2011). Occurrence of human enteropathogenic Yersinia spp. in Belgian pigs and contamination of pork carcasses during slaughter, 9 International Conference on the Epidemiology and Control of biological, chemical and physical hazards in pigs and pork (SafePork 2011), 19-22 June 2011, Maastricht, The Netherlands, Proceedings book p 126-129. Van Damme I. , De Zutter L. (2011). Occurrence of human enteropathogenic Yersinia spp. in pigs and contamination of pork carcasses during slaughter, 4 Congress of European Microbiologists (FEMS 2011), 26-30 June 2011, Geneva, Switzerland. Van Damme I. , De Zutter L. (2011). Occurrence of human enteropathogenic Yersinia spp. in pigs and contamination of pork carcasses during slaughter, SfAM Summer Conference 2011, 4 July 2011, Dublin, Ireland. Van Damme I. , De Zutter L. (2011). Occurrence of human enteropathogenic Yersinia spp. in pigs and contamination of pork carcasses during slaughter, 57 International Congress of Meat Science and Technology, 7-12 August 2011, Ghent, Belgium. Van Damme I. , De Zutter L. (2011). Human pathogenic Yersinia enterocolitica and Yersinia pseudotuberculosis in Belgium: prevalence in pigs and contamination of pork carcasses during slaughter, 16 Conference on Food Microbiology, 22-23 September 2011, Brussels, Belgium.
Making Pages That Move Applications of Dynamic HTML in the Biology Laboratory

We are all familiar with the traditional web page containing static text and images. Load the page into your browser window on Friday and you will see the same page that appeared the previous Monday. In most situations, this is satisfactory and occasional updating by the author to bring material up to date is sufficient to keep the page relevant and useful. There may be times, however, when we want the ability to provide dynamic pages to the user, such that the page can be updated continuously. Such pages may display information that is customized to the needs of the individual user, or information that changes as the user manipulates objects on the page (usually by clicking or dragging the mouse). The technology to do this turns out to have useful applications in the biology laboratory. I would like to present a brief overview of the mechanisms used to produce dynamic pages, and a few examples of applications in the laboratory.
Selenium in poultry nutrition and its effect on meat quality

This review focuses on a selected micro mineral, where the highlight is its role in meat quality. Minerals are important for optimising livestock and poultry performance. Initial symptoms of mineral imbalances, subclinical inadequacies, or severe deficiencies include depressed growth, body weight gain, poor feed utilisation efficiency, and reproductive efficiency. Dietary trace elements, particularly selenium, are able to induce physiological changes in muscle tissue, and they can alter meat quality in livestock and poultry. Bearing in mind the role of selenium in the quality of meat produced, the limited research into the association of selenium and skin health has been included in the review.
DIET OF THE NESTLING TREE SWALLOW

Abstract Dietary samples from nestling Tree Swallows (Tachycineta bicolor) in northwestern Minnesota were compared to invertebrate availability as measured by aerial tow nets. The majority of the biomass in the nestlings' diet was adult insects with larval stages of aquatic origin, while absolute numbers of insects of both aquatic and terrestrial origin were similar. Orders of invertebrates in the diet and available were similar in number but not in biomass. Diet showed little variation by time of day, date of sampling or the age of the nestling. The mean number of odonates in the nestling Tree Swallows' diet increased exponentially as the percentage of open water and open water + cattail marsh increased within a 400-m foraging radius. Dieta de los Pichones de Tachycineta bicolor Resumen. Se compararon muestras dietarias de pichones de la golondrina Tachycineta bicolor tomadas en el noroeste de Minnesota con la disponibilidad de invertebrados medida con redes aéreas. La mayor parte de la biomasa en la dieta de los pichones correspondió a insectos adultos con estadíos larvales de origen acuá tico, mientras que los números absolutos de insectos de origen acuático y no acuático fueron similares. Los órdenes de invertebrados presentes en la dieta y disponibles en el ambiente fueron similares en números pero no en biomasa. La dieta mostró poca variación entre horas del día, fechas de muestreo o edad de los pichones. El número promedio de odonatos en la dieta de los pichones de T. bicolor aumentó exponencialmente a medida que se incrementó el porcentaje de agua abierta y de agua abierta + pantanos de espadañas dentro de un radio de forrajeo de 400 m.
Lista con anotaciones de los pteridófitos del estado de México, México

248 pteridophyte species and subspecific taxa are recorded for the state of Mexico, including 60 new state records and two new species. Specific and infraspecific taxa are accompanied by information regarding distribution world-wide and within Mexico and the state of Mexico, as well as life form, habitat, vegetation type, and altitudinal range within the study area.
Use of Sandwich Cultures for the Study of Feeding in the Hexactinellid Sponge Rhabdocalyptus dawsoni (Lambe, 1892)

Wyeth, R. C. , Leys, S. P. & Mackie, G. 0. 1996. Use of sandwich cultures for the study of feeding in the hexactinellid sponge Rhabdocalyptus dawsoni (Lambe, 1892). -Acra Zoologica (Stockholm) 11: 221-232. Fragments of sponge tissue were cultured between glass slides and coverslips, permitting direct observation of cytoplasmic movements and tissue organization in vitro. The cut surfaces healed and the cultures lived for periods of several weeks. Cytoplasmic organization appeared similar to that described from study of sectioned material. Uptake of food particles (Escherichia coli, Isochiysis galbana) and latex beads took place primarily in the region of the flagellated chambers. Cytoplasmic streams were seen throughout the preparation and may serve for distribution of nutrients in these syncytial animals. It is proposed that the sandwich cultures are valid models of the intact sponge. Copyright 0 1996 The Royal Swedish Academy of Sciences. Published by Elsevier Science Ltd.
Functional Implications of Neuroendocrine Differentiated Cells in Prostate Cancer

textabstractThis thesis focuses on NE differentiation in prostate cancer, especially in prostate cancer models. We studied the effects of androgen depletion on the NE differentiated status of in vivo and in vitro prostatic tumor models. Knowledge concerning the function of NE cells in the normal human prostate and in prostate cancer is limited. A number of groups have studied NE differentiation in different epithelial systems. NE cells were found to be present in most prostatic adenocarcinomas (DiSant'Agnese, 1994). There is accumulating evidence that NE cells and tumors with NE cells are related to the androgen independent and poorly differentiated types of prostate cancer. There are indications that at least some secretion products of prostatic NE cells, like GRP and 5-HT, affect both prostate cancer growth and possibly also tumor differentiation. However, the growth modulating effects of neuropeptides and their relation to circulating androgen levels and androgen sensitivity of prostate cancer need to be further assessed. Studies directed towards identifying the role of NE cells in hormonally treated prostate cancer may contribute to the understanding of the transition of androgen dependent to androgen independent prostate cancer. There are still unanswered questions that need to be answered: How is the process of neuroendocrine differentiation regulated and can this process be influenced? Are the NE cells necessary for the regulation of growth and differentiation of the prostate or do they play a role in the maintenance of prostatic homeostasis? Can these cells induce (androgen independent) growth of surrounding cells, for instance by ligand independent activation of the androgen receptor (AR) through neuropeptides secreted by NE cells?
Involvement of calcium ion in elevation of mRNA for γ-glutamylcysteine synthetase (γ-GCS) induced by low-dose γ-rays

Purpose : To investigate the mechanism of the intracellular glutathione elevation induced by low-dose gamma-radiation. Materials and methods : RAW 264.7 cells were irradiated with 1-400 cGy γ-rays. Intracellular total glutathione content was determined by DTNB-recycling assay. Expression of mRNA for intracellular glutathione synthesis-related enzymes with or without treatment with various inhibitors of second messengers of gene expression were examined by Northern blot analysis. Results : Expression of mRNA for γ-glutamylcysteine synthetase (γ-GCS), a rate-limiting enzyme of the de novo glutathione synthesis pathway, was elevated much more than that of glutathione reductase (GR) mRNA after exposure to 50 cGy γ-rays. The low-dose γ-ray-induced γ-GCS mRNA elevation was abolished by inhibitors of protein kinase C and protein tyrosine kinase, as well as by the calcium ion channel blocker, nifedipine. Calcium-related reagents, such BAPTA/AM and EGTA, chelators of intra- and extracellular Ca 2+ respectively, an.