Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcription of a Rhizobium ieguminosarum biovar phaseoli gene needed for melanin synthesis is activated by nifA of Rhizobium and Klebsiella pneumoniae

The Rhizobium leguminosarum biovar phaseoli symbiotic plasmid pRP2JI carries a gene, melA, specifying the enzyme tyrosinase, which is responsible for the production of the pigment melanin in these bacteria. Transcription of melA is activated by the nifA gene of Rhizobium and, when the cloned melA gene is transferred to Escherichia coli, melA is expressed if the recipients contain nifA gene of Klebsiella pneumoniae. This nifA‐dependent activation was temperature sensitive and required the ntrA gene. The cloned nifA gene of K. pneumoniae, when transferred to a nifA mutant of Rhizobium phaseoli biovar phaseoli, corrected the Mer− but not the Fix− phenotype. nifA of R. leguminosarum biovar phaseoli activated melA at higher levels in cells grown in low concentrations of oxygen. Also, nifA of fl. leguminosarum biovar phaseoli activated nifH of K. pneumoniae in Escherichia coli cells grown In low‐oxygen concentrations.
IDENTIFICATION OF YEAST ISOLATED FROM SOTOL (Dasylirion spp .) NATURAL FERMENTATION

The fermentation of sotol juice is mainly a process traditionally carried out by indigenous microorganisms, and knowledge about them allows establishing control parameters during the process. The aim of this study was identified several yeast that participated as starter of stool natural fermentation. Specie identification was performed by 18S rDNA sequencing. Two different yeasts were identified, which had similar 18S rDNA sequences. The two sequences correspond to Kluyveromyces marxianus. The yeasts identified in this study are different from those found in the database.
RECOMBINANT TECHNOLOGY AND PROBIOTICS

Recombinant technology has led the way to monumental advances in the development of useful molecules, including the development of safe probiotics. The development of novel approaches using recombinant technology and probiotics that allow accurate targeting of therapeutics to the mucosa is an interesting area of research. The creation and use of recombinant probiotics expressing recombinant ovalbumin, recombinant ovalbumin mutants and yet-to-be-designed recombinant hypo/non-allergenic molecules offer the opportunity to further investigate their effects for food, nutrition, environment and health. This review highlights advances in native probiotics and recombinant probiotics expressing native and recombinant molecules for food, nutrition, environment and health.
Comparison of methods to quantify respirational carbon loss of coarse woody debris

Carbon (C) loss from coarse woody debris (CWD) may be important in forest ecosystem C budgets, yet there are no standard methods of quantifying it. Here we assessed respirational C loss of log segments of European beech (Fagus sylvatica L.) and Norway spruce (Picea abies (L.) Karst. ), to compare the two main measurement approaches (the static and dynamic methods using soda lime and an infrared gas analyser, IRGA) with three different measurement options for CWD logs. These included (i) incubation of the whole log segment, (ii) the use of small in situ chambers on the curved log surface, and (iii) extracted wedges of wood. On average, significantly higher amounts of CO2 were measured with the IRGA (125%) compared with soda lime. In addition, the soda lime method requires careful calibration of incubation length and amounts of soda lime used. Regardless of the measurement method and tree species, substantially higher amounts of CO2 were measured for whole log segments than for the other two options. Measuri.
Isolation and Expression of a cDNA Encoding a Male-specific Rat Sulfotransferase That Catalyzes Activation

A cDNA (STlC1 cDNA) encoding a N-hydroxyarylamine sulfotransferase (HAST-I) was isolated from a liver cDNA library of a male adult rat and was expressed in COS-1 cells. STlCl cDNA (1363 base pairs) encoded a protein of 304 amino acids with a molecular mass of 35,768 daltons, which shared 50.7 and 46.1% sequence identity with rat aryl (STlA1 (PST-1)) and estrogen (rOST) sulfotransferases, respectively. N-terminal amino acid sequences of three digested polypeptide fragments of HAST-I were completely identical with two portions of the STlCl amino acid sequence. The profile of age- and sex-related expression of STlCl mRNA was quite consistent with changes in the sulfating activity of N-hydroxyarylamine and HAST contents in rat livers. STlCl expressed in COS-1 cells catalyzed a sulfation of N-hydroxy-2acetylaminofluorene (N-OH-AAF) at a rate of 4.98 nmol/mg of protein/min and mediated PAPS (3”phosphoadenosine-5’-phosphosulfate)-dependent DNA binding of N-OH-AAF. Although ASTIV was believed to be responsible for the activation of N-OH-AAF, STlAl encoding an arylsulfotransferase ASTIV, showed only a marginal activity in a sulfation and covalent binding of N-OH-AAF. These data clearly indicate that STlCl cDNA codes a new form of a maledominant sulfotransferase (HAST) responsible for the bioactivation of N-hydroxyarylamines in rat livers.
Increased temperature and altered summer precipitation have differential effects on biological soil crusts in a dryland ecosystem

Biological soil crusts (biocrusts) are common and ecologically important members of dryland ecosystems worldwide, where they stabilize soil surfaces and contribute newly fixed C and N to soils. To test the impacts of predicted climate change scenarios on biocrusts in a dryland ecosystem, the effects of a 2–3 °C increase in soil temperature and an increased frequency of smaller summer precipitation events were examined in a large, replicated field study conducted in the cold desert of the Colorado Plateau, USA. Surface soil biomass (DNA concentration), photosynthetically active cyanobacterial biomass (chlorophyll a concentration), cyanobacterial abundance (quantitative PCR assay), and bacterial community composition (16S rRNA gene sequencing) were monitored seasonally over 2 years. Soil microbial biomass and bacterial community composition were highly stratified between the 0–2 cm depth biocrusts and 5–10 cm depth soil beneath the biocrusts. The increase in temperature did not have a detectable effect on any of the measured parameters over 2 years. However, after the second summer of altered summer precipitation pattern, significant declines occurred in the surface soil biomass (avg. DNA concentration declined 38%), photosynthetic cyanobacterial biomass (avg. chlorophyll a concentration declined 78%), cyanobacterial abundance (avg. gene copies g−1 soil declined 95%), and proportion of Cyanobacteria in the biocrust bacterial community (avg. representation in sequence libraries declined 85%). Biocrusts are important contributors to soil stability, soil C and N stores, and plant performance, and the loss or reduction of biocrusts under an altered precipitation pattern associated with climate change could contribute significantly to lower soil fertility and increased erosion and dust production in dryland ecosystems at a regional scale.
Contaminant release from sediments: a mass flux approach

Door de voorspelde klimaatverandering is de kans groot dat we vaker te maken krijgen met overstromingen, zowel door rivieren als door zee. Tijdens overstromingen zullen sedimenten die normaal op de bodem van het waterlichaam liggen, of in de uiterwaarden, worden opgewerveld en als suspensie worden meegenomen door het water. Als deze sedimenten verontreinigd zijn, kunnen de verontreinigende stoffen uit de sedimentdeeltjes vrijkomen en in het water worden opgelost. Ook onder normale, rustiger stromingscondities kunnen verontreinigingen vrijkomen, zij het minder snel dan tijdens overstromingen. Het vrijkomen van verontreinigingen uit sedimenten is de eerste stap in een serie van mogelijke processen, zoals afbraak of opname in de voedselketen. De snelheid waarmee de verontreinigende stoffen vrijkomen is onderzocht met een reactor die wij speciaal voor dit doel hebben ontwikkeld. In deze reactor –de SPEED reactor– kunnen mengintensiteit en stromingssnelheid of verdunningssnelheid worden ingesteld zodat verschillende stromingscondities kunnen worden nagebootst. Ook is het met deze reactor mogelijk om zeer lage concentraties van verontreinigingen in het water te meten. In dit proefschrift is voornamelijk gewerkt met dieldrin, een persistente organische stof die in het verleden gebruikt is als insectenverdelger.With the predicted climate change it is expected that the chances of flooding increase. During flood events sediments will suspend and if sediments are polluted, contaminants can be released to water. Also under gentle flow regimes, when sediments are settled and form a sediment bed, transfer of contaminants to water is possible. The release of contaminants from the sediment –particles and bed– to the aqueous phase is the first step in a sequence of processes. When this step is the rate limiting process we speak of mass transfer limitation. In this thesis the release of (mainly) dieldrin from field aged sediment was studied using the SPEED reactor we developed for this purpose. In this reactor parameters like mixing intensity and water flow –or dilution– rate can be controlled and low aqueous concentrations of contaminants can be quantified. Dieldrin release from the sediments was assessed for different situations: simulating a flood event and simulating more gentle flow conditions. In line with the variable discharge rates in rivers, we performed experiments with different flow rates and assessed the release of dieldrin in time.
Isolation of a Bacillus thuringiensis strain from South African soils and the characterization of its cry gene sequence.

2 DECLARATION 3 ACKNOWLEDGEMENTS 4 TABLE OF CONTENTS 5 LIST OF FIGURES 8 LIST OF TABLES 10 LIST OF ABBREVIATIONS 11 A LITERATURE REVIEW 12 1.1 BACILLUS THURINGIENSIS: NATURE’S DESIGN FOR AN INDUSTRIAL POWERHOUSE 12 1.2 BACILLUS THURINGIENSIS IN NATURE 14 1.3 THE ∆-ENDOTOXIN MODE OF ACTION 19 1.4 THE INSECTICIDAL CRYSTAL PROTEINS (ICP) 21 1.5 THE CRY GENE FAMILY 29 1.6 THE CRY1 GENES 29 1.7 COMMERCIAL APPLICATION OF CRY PROTEINS FOR THE CONTROL OF PEST INSECTS AND CROP PROTECTION 30 1.8 THE DEVELOPMENT OF CRY BASED PESTICIDES 32 1.9 THE USE OF CRY GENES IN GENETICALLY MODIFIED CROPS 32 MOTIVATION FOR RESEARCH 34 AIMS AND OBJECTIVES 34 ISOLATION OF BACILLUS THURINGIENSIS FROM SOUTH AFRICAN SOIL 35 2.
Light and Electron Microscopic Study of Rickettsia-Like Organisms Causing Systemic Granulomas in Farmed Sea Bass (Dicentrarchus labrax)

Systemic granulomas caused by rickettsia-like organisms in farmed sea bass (Dicentrarchus labrax) are described. In general, infected fish were anorexic and lethargic, and mortality was high. Affected fish (150-250 g) had skin lesions ranging from small patches to shallow hemorrhagic ulcers and abdominal dropsy. One or two pathogenic gram-negative bacteria were cultured from the liver, kidney, or spleen of affected fish, following incubation at 22oC for 72 h. The bacteria, Vibrio spp. and motile aeromonads, were isolated and identified as secondary fish pathogens. A parasite, Lernanthropus kroyeri, was also present in the gills. Internally, most of the affected fish exhibited white to yellow multifocal nodules on the kidney and spleen. Blood smears, stained with May Grunwald-Giemsa, showed that most peripheral blood monocytes contained a few to many basophilic rickettsia-like organisms within the cytoplasm. Histological sections (5-µm), stained with hematoxylen & eosin, tissue gram, Ziehl-Nielson, and periodic acid-Schiff, showed multifocal necrogranulomatous inflammation in the liver, spleen, kidney, and skeletal muscle. Pericarditis, epicarditis, and myocarditis were present in the heart, in addition to epithelial cell hyperplasia in the gills, hyperemia in brain tissue, and mild inflammation in the pancreas and adipose tissue. Granulomatous lesions contained coccoid bacteria that were gram and acidfast negative. Ultrathin sections of blood samples were examined under transmission electron microscopy. Rickettsia-like organisms (0.1-0.5 µm) were most frequently observed within the cytoplasm of phagocyctic blood
Behavioural ecology at sea of Atlantic salmon (Salmo salar L.) kelts from a Newfoundland (Canada) river

For migratory fishes such as Atlantic salmon, temporal variation in the utilization of thermal and depth habitats in the marine environment is likely to occur at both broad and fine scales, reflecting both ecological and metabolic factors. To test this, we implanted 26 Atlantic salmon kelts (i.e., post-spawners) descending Campbellton River, Newfoundland, with data storage tags that recorded date/time, internal and external temperatures, pressure, and light. The salmon that returned to Campbellton River after an average of 62 days at sea were consecutive spawning kelt. Detailed data were recovered from eight of these fish and revealed distinct patterns in their utilization of thermal and depth habitats. Water temperatures experienced over the period at sea showed a wide range for all fish (from <0 to nearly 20°C); however, there were two clear frequency modes; one at 6–7°C and the other at 11–12°C. The cooler mode was indicative of daytime profiles and the warmer mode of night-time profiles. This corresponded with the depth profiles, which indicated that salmon dove more frequently below 5 m (mean ± SD = 23 ± 0.9 dives per day) and spent less time (approximately 18%) near the sea surface (<1 m) during the day than during the night (4 ± 0.4 dives per night; approximately 45% time <1 m). The diurnal pattern may be indicative of a reliance on vision for feeding at depth and the short duration of dives (<10 min) may be a strategy that allows salmon a metabolic advantage (e.g., swimming capacity) over their prey living constantly at depth in cool waters.
Solitary Hymenoptera Aculeata Inhabiting Trap-Nests in Lithuania: Nesting Cavity Choice and Niche Overlap

The study has been carried out during the years 1989-2002 in five localities of Lithuania, using bundles of 25-35 internode fragments of Phragmites australis stems as trap-nests. We obtained 3237 nests of 33 identified solitary wasp and bee species. The dominant species were as follows: Symmorphus allobrogus (2030 nests), Ancistrocerus antilope (260), S. murarius (222), Discoelius zonalis (139), S. bifasciatus (115), Trypoxylon figulus (99), S. debilitatus (52), A. trifasciatus (40), T. clavicerum (39 nests), T. minus (36), S. crassicornis (36), and S. gracilis (33). The other 21 wasp and bee species built less than 30 nests each. We appraised the differences in the species preference for the inner diameter of the trap-nest, height above the ground, orientation of the wall, on which the trap-nest was situated, and the nest entrance direction. The studied species formed groups with median nesting cavity diameter of 2.5-4.0 mm (Chelostoma maxillosum, Hylaeus communis, Passaloecus corniger, S. bifasciatus, S. debilitatus, T. clavicerum, T. minus), 4.6-5.2 mm (A. trifasciatus, D. dufourii, S. allobrogus, S. gracilis, T. figulus), and 5.5-6.5 mm (A. antilope, A. nigricornis, D. zonalis, S. crassicornis, S. murarius, Osmia rufa), possibly having synusial dependence on exit holes of particular xylophagous beetles. Most wasp species had wide range of the used nesting cavity diameter and considerable niche overlap. However, some congeneric species seem to avoid competition by different nesting cavity diameter preferences, as D. dufourii and D. zonalis, or S. allobrogus and S. bifasciatus. On the other hand, some other congeneric species that use the same nesting cavity diameter (S. allobrogus and S. gracilis, S. bifasciatus and S. debilitatus, S. crassicornis and S. murarius) coexist in the same habitat due to other niche differences, as different prey.
PHYLOGEOGRAPHY AND SYSTEMATICS OF Lacerta agilis BASED ON MITOCHONDRIAL CYTOCHROME B GENE SEQUENCES: FIRST RESULTS

The phylogeny and phylogeography of Lacerta agilis was inferred from the nucleotide sequences of the mitochondrial cytochrome b gene. Lacerta agilis (Sauria: Lacertidae) is a widespread species composed of several described subspecies. Fifty specimens of Lacerta agilis were studied from different locations throughout the distribution range. Two species, Lacerta media and Lacerta praticola were used as outgroup taxa. Within Lacerta agilis three genetically distinct groups were found. The first monophyletic group (morphologically treated as L. a. brevicaudata and L. a. exigua subspecies) includes specimens from a large part of European Russia, Caucasus, and Kazakhstan. The second monophyletic group comprises two subgroups of L. a. agilis specimens from Denmark, Germany, Czech Republic and L. a. chersonensis from Northwest Russia. Specimens of L. a. boemica from Northern Caucasus form the separate group, which appears to be genetically distinct from other groups of Lacerta agilis. Some hypotheses on the history of the distribution of Lacerta agilis are proposed considering the molecular data.
B.13 In Vitro/In Vivo Correlation for Drug-Drug Interactions

Over the last 15 years, drug–drug interactions (DDIs) have become one of the emerging topics of the clinical drug development. For drugs with narrow therapeutic indices, the increase or decrease of plasma concentrations can lead to adverse effects or loss of efficacy, respectively. The increase of exposure caused by DDIs can be substantial (e.g., ketoconazole and midazolam with an interaction ratio of 16-fold for AUC is a well-known example) in particular with CYP3A4 (> Fig. B.13-1). Indeed, health authorities released dedicated guidelines in the late 1990s, some of them recently updated (FDAGuidance for Industry 2006). In this context, simulations or predictions of DDI, bridging the gap between in vitro outcomes and clinical situation are challenging for the pharmaceutical industry, fueled by recent growth of knowledge in molecular biology, computer-based simulation/predictions, and a better understanding of the inhibition and induction mechanisms. From an industrial point of view, a drug can be considered as a perpetrator and/or a victim. Victims are those drugs whose clearance is affected by a perpetrator. This last category are those drugs (or other environmental factors) that inhibit or induce the proteins (i.e., enzymes, transporters) responsible for clearing a victim drug. A pharmacokinetic drug interaction implies that a perpetrator causes a change in the clearance of the victim, in turn either decreasing or increasing concentrations of the victim drug in plasma and presumably at the site of action. Most of the proteins (but certainly not all! ) to which drugs may bind are commercially available or readily produced in house, their role in pharmacokinetics may be dissected and assessed. Such tests include in vitro investigations to characterize a drug as a victim or a perpetrator toward drug-metabolizing enzymes, transporters, or plasma proteins. Quantitativemetrics describing the interaction of the drug with the protein, such as binding constants, inhibition constants, induction potential are part of this assessment and allow qualifying a drug as a potential victim and/or perpetrator toward a given enzyme/protein.
FODRIN IS LOCALIZED IN THE CYTOPLASM OF KERATINOCYTES CULTURED IN LOW CALCIUM MEDIUM : IMMUNOELECTRON MICROSCOPIC STUDY

Distribution of fodrin in a mouse keratinocyte cell line, Pam 212, was studied by two novel techniques of immunogold electron microscopy. Firstly, by utilizing ultra-small (1 nm) gold-conjugated antibody and silver enhancement in the preembedding procedure, the difference of fodrin distribution in three culture conditions was shown in a semiquantitative manner. Fodrin was observed throughout the cytoplasm in cells cultured in low calcium (LC: 0.06 mM) medium, but it was concentrated beneath the plasma membrane in cells in standard calcium (SC: 1.87 mM); when cells in LC medium were treated with 10ng/ml 12-o-tetradecanoylphorbol-13-acetate (TPA) for two hr, the protein became dense near the plasma membrane. Secondly, by treating the immunogold-labeled sample by the dry-blowing method (Araki, N. and Ogawa, K.: Acta histochem. cytochem. 19; 31-37, 1986), fodrin was observed along actin-like microfilaments in Pam 212 cells in LC medium. After treatment with 30 μM cytochalasin B for one hr, the labeling became confined to an amorphous substance which is likely to be composed of depolymerized actin.The present study showed the distributional change of fodrin at the ultrastructural level: in LC cells fodrin was mostly in the cytoplasm and at least some were associated with actin filaments; ‘calcium switch’ produced its redistribution to the plasma membrane. In addition, since TPA was revealed to cause a similar result as ‘calcium switch’, phosphorylation of fodrin molecule might be causally related to the rearrangement.
Revision of Isoparorchis Southwell, 1913 (Digenea, Hemiuroidea, Isoparorchiidae), Parasites of the Air Bladder of Freshwater Catfishes: a Molecular and Morphological Study

Isoparorchis Southwell, 1913 (Digenea, Hemiuroidea, Isoparorchiidae), parasites of the air bladder of freshwater catfishes (Osteichthyes, Siluriformes) from East, Southeast and South Asia and Australia, is revised based on a molecular and morphological study. Materials, including syntypes where available, were examined from Russia (Primorskiy Kray), Japan, Vietnam, Cam- bodia, Bangladesh, India and Australia. The entire second internal transcribed spacer region of the ribosomal DNA (ITS2 rDNA) was sequenced for 18 distinct samples. Four of the five previously described species are considered to be valid: Isoparorchis trisimilitubis Southwell, 1913 (type spe- cies) from India, I. hypselobagri (Billet, 1898) from Vietnam, I. eurytremum (Kobayashi, 1915) from Japan and Russia and I. tandani Johnston, 1927 from Australia. Isoparorchis pakistani Bilqees and Khatoon, 1972 from Pakistan is regarded as a species inquirenda. Not only syntypes of I. trisimilitubis but also other materials from India and Bangladesh consisted of specimens of two morphologically distinct species. One is identified as I. trisimilitubis, and the other remains an undescribed species, Isoparorchis sp. 3. Distinctions in the ITS2 sequences obtained for samples from India support the interpretation that there are two species there. One sequence is related to I. trisimilitubis, but it remains undetermined whether the other sequence (Isoparorchis sp. 1) relates to Isoparorchis sp. 3. Some materials from East, Southeast and South Asia require further critical studying for definitive species identification. Each species is described and figured with a summa- rized life cycle where known. Molecular data are given. A key to the species is presented.