Miracle-dz/UniFAR-FTUs huggingface dataset:
Deterioration of enhanced biological phosphorus removal by the domination of microorganisms without polyphosphate accumulation

Enhanced biological phosphorus removal by anaerobic-aerobic operation is not always achieved successfully. In this study, microbial metabolism in the activated sludge of a failed enhanced biological phosphorus removal process was investigated to clarify the cause of the failure. The dominant microorganisms in the sludge consumed carbohydrates in the uptake process of acetate or propionate under anaerobic conditions and accumulated polyhydroxyalkanaate. But significant release of phosphate was not observed because polyphosphate was not utilized. Consumed carbohydrates were found to have been converted to polyhydroxyalkanoate via propionyl-CoA in addition to acetyl-CoA, indicating that the microorganisms had enzymes to convert phosphoenolpyruvate or pyruvate produced in glycolysis to propionyl-CoA. The propionate fermentation was supposed to work as the sink of the reducing power excessively produced in glycolysis; thus while maintaining the redox balance, microorganisms were able to get energy not from polyphosphate but from glycogen. The difference in the metabolic systems between polyphosphate accumulating bacteria and the present microorganisms may give hints to avoid the deterioration of enhanced biological phosphorus removal.
HDAC3 selectively represses CREB3-mediated transcription and migration of metastatic breast cancer cells

We identified CREB3 as a novel HDAC3- interacting protein in a yeast two-hybrid screen for HDAC3-interacting proteins. Among all class I HDACs, CREB3 specifically interacts with HDAC3, in vitro and in vivo. HDAC3 efficiently inhibited CREB3-enhanced NF-jB activation, whereas the other class I HDACs did not alter NF-jB-dependent promoter activities or the expres- sion of NF-jB target genes. Importantly, both knock-down of CREB3 and overexpression of HDAC3 suppressed the transcriptional activation of the novel CREB3-regulated gene, CXCR4. Furthermore, CREB3 was shown to bind to the CRE element in the CXCR4 promoter and to activate the transcription of the CXCR4 gene by causing dissocia- tion of HDAC3 and subsequently increasing histone acetylation. Importantly, both the depletion of HDAC3 and the overexpression of CREB3 substantially increased the migration of MDA-MB-231 metastatic breast cancer cells. Taken together, these findings suggest that HDAC3 selec- tively represses CREB3-mediated transcriptional activation and chemotactic signalling in human metastatic breast cancer cells.
A Study on Genes Information from Microarray Analysis of Cancer

A DNA microarray will track the expression levels of thousands of genes at the same time. Previous analysis has incontestable that this technology is helpful within the classification of cancers. Cancer microarray knowledge ordinarily contains a little range of samples that have an outsized range of organic phenomenon levels as options. To pick out relevant genes concerned in numerous kinds of cancer remains a challenge. So as to extract helpful gene information from cancer microarray knowledge and scale back spatiality, feature selection algorithms were consistently investigated during this study. Employing a correlation-based feature selector combined with machine learning algorithms like call trees and support vector machines, we tend to show that classification performance a minimum of nearly as good as printed results is obtained on cancer of the blood and diffuse massive B-cell cancer microarray data sets. During this paper, we tend to additionally demonstrate that a combined use of various classification and have choice approaches makes it potential to pick out relevant genes with high confidence.
Fusarientoxine und ihre Bedeutung in der Nutztierfütterung: eine übersicht

The contamination of grain with fusarium toxins is a problem worldwide. This paper presents a comparison of the main toxins of the Fusarium species, specially A- and B- trichothecenes, zearalenone, furnonisins and moniliformin. Their toxic effects and characteristic clinical symptoms in domestic animals, as well as their carry over into foods of animal origin, are presented and discussed. Furthermore, their relevance in feeding practice and on animal health is described. The maximum level recommended in Austria for deoxynivalenol in animal feed is 0.5 mg of deoxynivalenol per kg feed (88% DM) for swine. For beef cattle, laying hens, turkey and breeding poultry it is 1 mg/kg and for broilers 2 mg/kg. These recommended levels are presented and discussed. Furthermore, the Austrian levels for zearalenone as 0.05 mg/kg feed (88% DM) for prepubertal female swine, and 0.15 mg/kg for fattening pigs and breeding sows are also given and discussed. There are no maximum values recommended for zearalenone concentration in feed for beef or poultry in Austria. Additionally, the recommended maximum levels of these toxins for animal feed in different countries such as Austria, Germany, Canada and USA are compared and discussed.
Plasmid instability: a report of a meeting of contractants of the Commission of the European Communities (EC)

Compte-rendu du congres de la C.E. sur les facteurs responsables de l'instabilite des plasmides, dans les cellules bacteriennes (principalement, les bacteries gram), de levure, ou vegetales. Consequences sur les applications techniques des organismes recombines et solutions pour l'amelioration de la stabilite des plasmides
Expression and Partial Purification of His-tagged Proteins in a Plant System

[Abstract] Plant protein expression can be a challenging enterprise in any biochemical or molecular biology research project. Several heterologous systems like bacteria, yeast, insect cells and cell free systems have been used to produce plant proteins for in vitro experiments and structural characterization. However, due to particularities of plant proteins, for example the specific type and abundance of post-translational modifications (e.g. glycosylation), a plant system to express plant proteins is extremely desirable. The use of Nicotiana benthamiana (N. benthamiana) plants for protein expression has proven to be quick and reliable. To illustrate the robustness and rapidity of this system, recent efforts to produce the first protein based drug against the Ebola virus was conducted in N. benthamiana protein expression systems (Choi et al., 2015). This protocol describes a simple system for the expression and enrichment (affinity purification) of plant apoplastic proteins in N. benthamiana leaves, which was successfully used in the characterization of the Arabidopsis thaliana pectin acetylesterases, PAE8 and PAE9 (de Souza et al., 2014).
Structure of the VORTEX simulation model for population viability analysis

The structure of the VORTEX computer simulation model for population viability analysis is outlined. The program flow is described here in order to provide a detailed specification of the structure of a widely used population viability analysis model. VORTEX is an individual-based simulation program that models the effects of mean demographic rates, demographic stochasticity, environmental variation in demographic rates, catastrophes, inbreeding depression, harvest and supplementation, and metapop ulation structure on the viability of wildlife populations. The model facilitates analysis of density-dependent reproduction and changing habitat availability, and most demo graphic rates can optionally be specified as flexible functions of density, time, popula tion gene diversity, inbreeding, age, and sex. VORTEX projects changes in population size, age and sex structure, and genetic variation, as well as estimating probabilities and times to extinction and recolonization.
Haematological indices and blood lipid profile of rats administered Trona; a natural food additive.

Trona, a geological mineral is often used as a natural food additive in many parts of Africa. This work was done to evaluate trona for elemental content and ascertain its effect on body weight changes; lipid profile and haematological indices as part of safety assessment. Consequently twenty-four rats were divided into four groups of six rats each. The first group served as the control while the other groups were administered 10, 100, and 1000 mg trona per kg body weight for a period of 28 days. Elemental analysis revealed the presence of high concentrations of sodium and iron. Results revealed dose dependent increase in triacylglycerol levels; however cholesterol, HDL cholesterol, LDL cholesterol, and haematological indices were not significantly affected. Key words: Trona; additive; sodium; triacylglycerol; haematological
Isolation, identification and antibacterial activity of flavonoid compound from vitex aguns castus L. seed

We isolated the flavonoid compound from vitex aguns castus L. seed as red powder at (50 o C). The chemical and physical properties were studied by using thin layer chromatography (TLC), IR-spectrum, ultraviolet-visible spectrum, melting point (m.p) and qualitative testes of it. The Isolated flavonoid compound is shown high antibacterial activity against types of standard strains of bacteria (Staphylococcus aureus NCTC 6571 and Escherichia coli NCTC 5933). The minimum inhibition concentration (MIC) of the isolated flavonoid compound has against gram positive and negative bacteria equal to (1 µgm/ml). We prepared flavonoid complex, where it shows high degree of inhibiting the test organism comparable to the isolated flavonoid compound alone. Keyword: vitex aguns castus L. seed, TLC, flavonoid compound, antibacterial activity, Chemical composition.
Phototrophic Chloroflexus-like bacteria and their role in hypersaline microbial mats

Aims; The aim of this study was to investigate and compare, by 16S rDNA clone library analysis, the community structure of members of the Chloroflexaceae Family from four hypersaline microbial mats from different continents (Chiprana, Spain, Europe; Abu Dhabi, United Arab Emirates, Asia; Guerrero Negro, Mexico, North America; and a mat originating from Chiprana but kept for years in a laboratory based mesocosm system). Methods; The Chloroflexi phylum, which accommodates, among others, filamentous anoxygenic phototrophic bacteria of the Family Chloroflexaceae, roots deeply in the tree of life. Although only few isolates of this Family have been characterized to date, a high diversity of related 16S rDNA sequences has been found in clone libraries of hot spring and hypersaline microbial mats. As the characterized isolates appear metabolically and therefore also likely functionally different, closely related 16S rRNA gene sequences from environmental samples may reflect the occurrence of related functional groups in their natural habitat. Using previously designed specific Chloroflexaceae 16S primers, three clone libraries were constructed from Chiprana, Abu-Dhabi and the Mesocosm mats and phylogenetically compared with the previously described North American one. Results; we observed a number of unique environmental sequences ( homology) in each mat; however, in all four mats clone libraries, the majority of retrieved sequences were most closely related to the previously isolated species ‘Candidatus Chlorothrix halophila’ Main Conclusions: it is concluded that both a relatively high and endemic local diversity is present and that ‘Candidatus Chlorothrix halophila’, a bacteriochlorophyll c-producing species, and/or close relatives are pandemic and dominates the Chloroflexaceae community in hypersaline mats. We hope that this initial comparative study will stimulate further investigations on the biogeography, physiology and phylogeny of this ancient and metabolically diverse group of Chloroflexaceae.
Computational Study of Transcriptional Regulation - From Sequence To Expression

Transcription is the process during which RNA molecules are synthesized based on the DNAs in cells. Transcription leads to gene expression, and it is the first step in the flow of genetic information from DNA to proteins that carry out biological functions. Transcription is tightly regulated both spatially and temporally at multiple levels, so that the amount of mRNAs produced for different genes is controlled across different kinds of cells and tissues, as well as in different developmental stages and in response to different environmental stimulus. In eukaryotes, transcription is a complicated process and its regulation involves both cis-regulatory elements and trans-acting factors. By studying spatiotemporally what genes are regulated by which cis-elements and trans-factors, we can get a better understanding of how we develop, how we react to environmental signals, and the mechanisms behind diseases like cancer that, at least in part, result from failures in proper transcriptional regulation. In this thesis, we present a suite of computational methods and analyses that, combined, provide a solution to problems related to the identification of DNA binding motifs, linking these motifs to the TFs that bind them and the genes that they control, and integrating these motifs and interactions with time series expression data to model dynamic regulatory networks. Specifically, we first develop a novel method for finding discriminative DNA motifs, motifs that are over-represented in a set of positive sequences but depleted in a set of negative sequences. Second, we present a new method of using protein binding microarray data combined with DNase I hypersensitivity and conservation data to predict tissue-specific transcription factor activities and binding sites. Finally, we extend the DREM framework which was previously developed by our group to study dynamic regulatory networks, and we use the improved version to analyze a biological dataset of gene responses in arabidopsis following ethylene treatment. Together, the methods and analyses presented contribute to the studying and understanding of transcriptional regulation.
Functional Analysis of Putative Adenosine Recycling Enzymes in Arabidopsis thaliana

Adenosine (Ado) salvage is essential in plant development. The lack of Ado kinase activity (ADK) in Arabidopsis thaliana adk1 adk2 double mutants results in embryonic lethality; reduction of ADK expression causes a pleiotropic phenotype due to the accumulation of Ado inhibiting transmethylation activities. The phenotype of ADK mutants shows that this enzyme plays a critical role in Ado salvage but the functional significance of the other putative Ado recycling enzymes Ado deaminase (ADA) and Ado nucleosidase (ADN) in Arabidopsis thaliana have yet to be elucidated. ADA catalyzes the irreversible deamination of Ado to inosine. The locus At4g04880 (AtADA) of A. thaliana is annotated as encoding a putative ADA, based on its amino acid sequence similarity and the presence of important, conserved catalytic residues. However, indirect and direct spectrophotometric activity assays of the recombinant enzyme demonstrated that the gene product of this locus does not possess ADA activity; complementation experiments to test for the functionality of the AtADA product in A. thaliana and E. coli confirmed its lack of ADA activity. Instead, phylogenetic analysis revealed that AtADA belongs to the group of ADA-like (ADAL) proteins, a group closely related to ADAs that to date have not been shown to have ADA activity. AtADA is no exception as it also lacks ADA activity based on the in vivo and in vitro experiments outlined in this thesis. Thus, the locus At4g04880 should be re-annotated as ADAL. The question of the function of AtADAL cannot be answered as of yet; in general, the knockout of ADA gene product demonstrated that At4g04880 is not essential for Arabidopsis growth. Since no further ADA-related genes exist in the genome of Arabidopsis it is concluded that ADA activity is not present in this plant. ADN catalyzes the conversion of purine and pyrimidine ribosides to their corresponding bases; although it prefers Ado as a substrate it also acts on cytokinins. The activity of this enzyme has been described in several plant species
Studies on Dormancy and Treatment to Enhance Germination of Champa ( Michelia champaca , Linn.) Seed

Seed of Michelia champaca were treated variously to enhance germination. All coat softening treatments failed to improve germination. Little improvement in germination was observed in seeds prechilled at 5°C. Gibberellic acid was found effective in promoting total germination as well as speed of germination in terms of germination value.
Grenzen und Möglichkeiten der Datenanalyse in der Pflanzenökologie

Possibilities and restrictions of data analysis in vegetation science are dis­ cussed. The analysis of pure vegetation data is of special interest, and five theses are proposed. Aims of classification and ordination approaches are identified. The close relationship of the numerical classification tradition with the BRAUN-BLANQUET school is shown. Data reduction, hypothesis formation, and noise reduction are aims common to all types of data analysis. Two basic assumptions of vegetation analysis are examined: the supposed dominant effect of continous, measurable habitat parameters on the vegetation composition and the taxonomical concept of species. Both cannot be simply assumed in many cases. In addition difficulties in analyzing the correlation between vegeta­ tion data and ecological parameters or artificial indices are discussed. All analyses lead to the recommendation to abandon the concept of vegetation as an analytical tool.
Differential recycling of coral and algal dissolved organic matter via the sponge loop

Corals and macroalgae release large quantities of dissolved organic matter (DOM), one of the largest sources of organic matter produced on coral reefs. By rapidly taking up DOM and transforming it into particulate detritus, coral reef sponges are proposed to play a key role in transferring the energy and nutrients in DOM to higher trophic levels via the recently discovered sponge loop. DOM released by corals and algae differs in quality and composition, but the influence of these different DOM sources on recycling by the sponge loop has not been investigated. Here, we used stable isotope pulse-chase experiments to compare the processing of naturally sourced coral- and algal-derived DOM by three Red Sea coral reef sponge species: Chondrilla sacciformis, Hemimycale arabica and Mycale fistulifera. Incubation experiments were conducted to trace 13C- and 15N-enriched coral- and algal-derived DOM into the sponge tissue and detritus. Incorporation of 13C into specific phospholipid-derived fatty acids (PLFAs) was used to differentiate DOM assimilation within the sponge holobiont (i.e. the sponge host vs. its associated bacteria). All sponges assimilated both coral- and algal-derived DOM, but incorporation rates were significantly higher for algal-derived DOM. The two DOM sources were also processed differently by the sponge holobiont. Algal-derived DOM was incorporated into bacteria-specific PLFAs at a higher rate while coral-derived DOM was more readily incorporated into sponge-specific PLFAs. A substantial fraction of the dissolved organic carbon (C) and nitrogen (N) assimilated by the sponges was subsequently converted into and released as particulate detritus (15–24% C and 27–49% N). However, algal-derived DOM was released as detritus at a higher rate. The higher uptake and transformation rates of algal- compared with coral-derived DOM suggest that reef community phase shifts from coral to algal dominance may stimulate DOM cycling through the sponge loop with potential consequences for coral reef biogeochemical cycles and food webs.
Keanekaragaman jenis dan karakteristik habitat nyamuk Anopheles spp. di Desa Datar Luas, Kabupaten Aceh Jaya, Provinsi Aceh

Malaria merupakan penyakit tular vektor yang masih menjadi masalah kesehatan masyarakat di Indonesia. Upaya pengendalian telah dilakukan program pencegahan dan pengendalian penyakit tular vektor, tetapi belum bisa maksimal. Penyebab belum maksimalnya upaya pengendalian tersebut antara lain karena kurangnya pemahaman mengenai spesies vektor penyakit ini. Penelitian ini bertujuan untuk mempelajari keanekaragaman nyamuk, kepadatan dan perilaku nyamuk Anopheles , dan menganalisis peta karakteristik habitat perkembangbiakan larva Anopheles di Desa Datar Luas, Kecamatan Krueng Sabee, Kabupaten Aceh Jaya. Penangkapan nyamuk dilakukan dengan menggunakan metode human landing collection di dalam dan di luar rumah dari pukul 18:00–06:00 WIB. Selain itu, dilakukan pula pengumpulan larva dan penandaan titik koordinat pada habitat perkembangbiakan potensial. Hasil penelitian menemukan 11 spesies Anopheles yang didominasi oleh spesies An. kochi 45,9%. An. kochi merupakan spesies dominan dengan aktivitas mengisap darah tertinggi dan ditemukan pada pukul 00:00–01:00 WIB. Berdasarkan jenis habitat larva Anopheles , spesies tertentu memiliki kecenderungan terhadap tipe habitat tertentu, sebagai contoh An. letifer banyak ditemukan di kolam, An. barumbrosus dan An. kochi ditemukan di genangan air hujan.
11 Transcription of Vertebrate snRNA Genes and Related Genes

OVERVIEW Small nuclear RNAs (snRNAs) and other RNAs involved in RNA processing (collectively denoted pRNAs) are encoded by a family of genes with structurally related promoters. Yet, some of these genes are transcribed by RNA polymerase II (pol II) and others by RNA polymerase III (pol III). The study of the cis -acting elements and trans -acting factors involved in transcription of pRNA genes has revealed that the TATA-box-binding protein TBP, first thought to be involved only in transcription of mRNA genes by RNA pol II as part of the TFIID complex, also participates in transcription of RNA pol III genes. In addition, RNA pol II transcription complexes can differ in their ability to recognize a termination signal, and these different elongation properties are determined by promoter elements. INTRODUCTION In eukaryotes, transcription is carried out by three different classes of RNA polymerases. Although the large variety of promoter structures found within the class II transcription units always suggested a correspondingly large variety of RNA pol II initiation complexes, these complexes were nevertheless thought to consist of factors specialized for RNA pol II transcription and therefore very different from the factors constituting RNA pol I and RNA pol III initiation complexes. In addition, elongating RNA pol II transcription complexes were thought to be of uniform composition and thus to have similar elongation properties, regardless of which promoter they were derived from. During the past few years, however, several findings have altered these views. First, the genes encoding several RNA polymerase subunits have been.
Complete mitochondrial genome of the stone char Salvelinus kuznetzovi (Salmoniformes, Salmonidae)

Abstract The complete mitochondrial genome was sequenced in two individuals of stone char Salvelinus kuznetzovi. The genome sequences are 16,654 bp in size, and the gene arrangement, composition and size are very similar to the salmonid fish genomes published previously. The low level of sequence divergence detected between the genome of S. kuznetzovi and the GenBank complete mitochondrial genomes of the white char S. albus (KT266870 and KT266871), the Northern Dolly Varden char S. malma (KJ746618) and the Arctic char S. alpinus (AF154851) may likely be due to recent divergence and/or historical hybridization and interspecific replacement of mtDNA.