Miracle-dz/UniFAR-FTUs huggingface dataset:
Studies on HIF hydroxylases

Hypoxia-inducible factor (HIF) is the master regulator of genes involved in adaptation to hypoxia. The stability and transcriptional activity of HIF are regulated by post-translational hydroxylations: prolyl hydroxylation by the prolyl hydroxylase domain-containing enzymes PHD1 – 3 earmarks HIF for proteasomal degradation, whilst asparaginyl hydroxylation by factor inhibiting HIF (FIH) blocks the interaction of HIF with the transcriptional coactivators p300/CBP. The PHDs and FIH hydroxylate HIF directly from molecular oxygen and are therefore oxygen sensors. Recent literature shows that FIH also hydroxylates a number of proteins containing an ankyrin-repeat domain (ARD). Together with reports suggesting that the PHDs are involved in HIF-independent pathways, this suggests that the HIF hydroxylases may have a wide range of non-HIF targets. This thesis describes my investigations into novel substrates of the HIF hydroxylases. This work has characterized the FIH-dependent hydroxylation of the ARD-containing protein Notch1, and defined a consensus sequence for hydroxylation that corresponds to the ankyrin-repeat consensus. Using this consensus potential sites of hydroxylation in a novel ARD FIH substrate, myosin phosphatase targeting subunit 1 (MYPT1), were identified then subsequently confirmed and characterized. Notch1 competes with HIF for FIH hydroxylation. My experiments show that this occurs because Notch1 is a more efficient substrate than HIF, whilst studies on MYPT1 and other proteins indicate that competitive inhibition of FIH may be a general property of ARDs. There are more than 300 ARD proteins in the human genome, and this thesis demonstrates that FIH may hydroxylate a significant percentage of these. In addition to the analysis of ARD hydroxylation a proteomic investigation into novel PHD3 substrates has identified two candidate proteins, suggesting that the PHDs may also have multiple targets. These results have important implications for oxygen sensing, and indicate that post-translational hydroxylation is likely to be a widespread modification in cell biology.
Supercritical fluid extraction of oil from microalga Spirulina (arthrospira) platensis

For the extraction of oil from microalgae, which are recognised as an important renewable source of bioactive lipids, supercritical CO 2 is regarded with interest being safer than hexane and offering a negligible environmental impact, short extraction time and petroleum-free final product. A mathematical model, able to describe the kinetics of a supercritical fluid extraction (SFE) process, was applied to the recovery of oil from the cyanobacterium Spirulina (Arthrospira) platensis, characterised by a particularly high content in γ-linolenic acid (C18:3ω-6). In this paper, we examine the kinetics of the SFE and the effect of operating conditions on extraction yield and fatty acid composition of lipid extracts.
Food Habits of the Swift Fox in Northern Texas

Swift foxes, Vulpes velox velox , are present in many parts of their range where they were once considered to be extinct. Little has been learned about the natural history of swift foxes, probably owing to the scarcity of the species until recent years. Twelve stomachs and 250 scats were obtained at six localities in Hansford County, Texas, and were studied to determine the feeding habits of swift foxes. Most of the land in Hansford County is farmed or overgrazed. Swift foxes and their dens have been found in both cultivated and uncultivated fields (Cutter, 1958). Growers of livestock and poultry are not now (1956) troubled by predators, but perhaps formerly were since government trappers have set “coyote getters” in the past—mechanisms that explode a small bomb in the mouths of investigating coyotes. Two of the 12 stomachs were empty; the 250 scats were gathered near the entrances to dens. The scats and stomachs were collected in late spring, summer and early autumn, with the exception of one stomach and five scats, obtained in winter. Young are in the dens in spring and summer; the scats may be mainly from young animals. Contents of stomachs and scats are discussed separately in the pages that follow. The number of individuals of each species eaten by the swift foxes could not be determined. Rabbits . —Remains of rabbits were found in 55 scats and five stomachs. Remains from two scats and from two stomachs were identified as black-tailed jack rabbit, Lepus californicus , and remains from nine scats and from three stomachs were identified as cottontail rabbit, Sylvilagus sp. (probably S. audubonii ). Rabbits occurred almost as frequently (60 times) as did all other vertebrates (68 times). Many of the rabbit remains were of immature animals; probably most rabbits eaten by swift foxes are …
Development and Parameterization of a Kinetic Framework for Modeling Light- and Phosphorus- Limited Phytoplankton Growth in Cannonsville Reservoir

ABSTRACT A mechanistic framework for simulating phytoplankton growth kinetics in lakes and reservoirs is described. The framework is based on published physiological submodels describing light- and phosphorus-limitation of phytoplankton growth and the relationship between the rates of growth and respiration. The physiological submodels were tested and related kinetic coefficients defined through a program of field measurement and laboratory experimentation. Values for kinetic coefficients were determined using the natural phytoplankton assemblage of Cannonsville Reservoir, a part of the New York City drinking water supply system. The suite of submodels was shown to satisfactorily represent the phytoplankton response to variation in the light and nutrient regime of the reservoir. Efforts to test submodels and determine kinetic coefficients on a site-specific basis are believed to enhance the credibility and reliability of the model framework in its application for water quality management.
Bruton's Tyrosine Kinase Is a Toll/Interleukin-1 Receptor Domain-binding Protein That Participates in Nuclear Factor κB Activation by Toll-like Receptor 4*

In this study we have identified members of the Toll-like receptor (TLR) family (namely, TLRs 4, 6, 8, and 9) as proteins to which the intracellular protein tyrosine kinase, Bruton's tyrosine kinase (Btk), binds. Detailed analysis of the interaction between Btk and TLR8 demonstrates that the presence of both Box 2 and 3 motifs in the Toll/interleukin-1 receptor domain was required for the interaction. Furthermore, co-immunoprecipitation experiments revealed that Btk can also interact with key proteins involved in TLR4 signal transduction, namely, MyD88, Mal (MyD88 adapter-like protein), and interleukin-1 receptor-associated kinase-1, but not TRAF-6. The ability of Btk to interact with TLR4 and Mal suggests a role for Btk in lipopolysaccharide (LPS) signal transduction. Stimulation of the human monocytic cell line THP-1 with LPS resulted in an increase in the level of tyrosine phosphorylation of Btk (indicative of activation). The autokinase activity of Btk was also stimulated after LPS stimulation. In addition, a dominant negative form of Btk inhibited TLR4-mediated activation of a nuclear factor κB (NFκB)-dependent reporter gene in HEK293 cells as well as LPS-induced activation of NFκB in the astrocytoma cell line U373 and the monocytic cell line RAW264.7. Further investigation revealed that the Btk-specific inhibitor, LFM-A13, inhibited the activation of NFκB by LPS in THP-1 cells. Our findings implicate Btk as a Toll/interleukin-1 receptor domain-binding protein that is important for NFκB activation by TLR4.
Effects of dietary carbohydrate:fat ratio on growth and body composition of milk-fed calves

Abstract Growth and body composition measurements were made on young calves after 49 days feeding on one of 12 diets having a range of carbohydrate:fat ratios and where protein intake was either adequate or inadequate for maximum growth. Across Diets 1-6, carbohydrate:fat ratio ranged on an energy basis from 2:1 (56% lactose, 12% fat) to 0.4:1 (31% lactose, 32% fat); resulting daily protein and energy intakes were respectively 244 g and 18.7 MJ (designated low energy-high protein regime). Across Diets 7-12 carbohydrate:fat ratio ranged from 1:1 (54% lactose, 24% fat) to 0.4:1 (34% lactose, 39% fat); daily protein and energy intakes were respectively 194 g and 21.8 MJ (designated high energy-low protein regime). Whereas energy intake restricted growth on the low energy-high protein regime, protein intake restricted growth on the high energy-low protein regime. Calves on the high energy-low protein regime had higher gains of body weight (598 v 569 g/day), fat (114 v 55 g/day), and energy (7.0 v 4.8 MJ/day) .
Geographic structure of human genetic variation: medical and evolutionary implications

The geographic structure of human populations can be summarized by two numbers: 85 and 15, and two keywords: Continuous Genetic Change (CGC), and outliers. Eighty-five and fifteen percent of the global variation represent, on the average, the genetic differences within and between populations, respectively. CGC characterizes most of the differences between groups at different geographic scales; and outlier populations, or genetic isolates, generated by different types of barriers to gene flow, punctuate with peaks the clinal landscape. The presence of this patterning, probably consistent across the genome with some exceptions, has several biomedical and evolutionary implications. However, its origin and evolution is only partially understood, and the geographic distribution of genetic variation at selectively important genes is still poorly investigated. Major efforts in these directions, as well as in the study of potential population outliers, will be of great importance to better define and predict the implications and future evolution of our geographic structure. Keywords: human evolution; population structure; genetic variation; Fst; clines
Variations in prey consumption of centipede predators in forest soils as indicated by molecular gut content analysis

Predation is an important ecological factor driving animal population structures, community assemblages and consequently ecosystem stability and biodiversity. Many environmental factors infl uence direction and intensity of predation, suggesting that trophic linkages between animals vary between diff erent habitats. Th is in consequence has particular relevance in anthropogenically altered habitats such as managed forests, where disturbance regime, tree composition and stand age may change the natural food web structure. We investigated how prey consumption of three common centipede predators ( Lithobius spp., Chilopoda), representing two body sizes varies between four diff erently managed forest types in two regions across Germany. We hypothesized that prey preference of these generalist predators is independent of forest type but rather driven by habitat structure, prey abundance and predator body size. Applying specifi c PCR assays to test for DNA of three abundant prey groups, i.e. Collembola, Diptera and Lumbricidae, in the predators ’ guts, we tracked trophic interactions. Th e results showed that management type indeed has no infl uence on centipede prey consumption but depth of litter layer and soil pH. Trophic interactions varied between the two sampled forests regions mainly due to changes in the detection of Lumbricidae and Diptera. Also, eff ect of litter layer and prey abundance signifi cantly diff ered between the smaller L. crassipes and the larger L. mutabilis , indicating a body size eff ect. Th e results complement food web analyses using fatty acids and stable isotopes by elucidating trophic interactions in soil in unprecedented detail.
Beckwith-Wiedemann Syndrome: a Case Report. -

It is a congenital overgrowth disorder affecting male and female equally with an approximate incidence of one in13, 700-15,000 live births. Most of the cases,>85% are sporadic and <15% are familial. Diagnosis is mainly from clinical pictures, some of the cases are related to partial duplication of chromosome 11 (11p15). Baby conceived through in vitro fertilisation (IVF) have a 3 to 4 fold increased risk to develop this syndrome. Here we report a case of a one day old female baby presented with macrosomia, birth wt 4.210 kg, with feeding difficulty due to large tongue (macroglossia) with hemi hypertrophy of the body.
Habitat overlap of the invasive Impatiens parviflora DC with its native congener I. noli-tangere L.

Small balsam, or Impatiens parviflora, is one of the most invasive herbaceous alien species in European temperate forests, and is increasingly found in the same sites as its native congener I. noli-tangere. The aim of this study was to explore the habitat range of both species and determine whether overlap occurs. Vegetation surveys were conducted in 13 Belgian sites. We performed 139 releves according to the following stratification: pure plots of the invasive balsam, pure plots of the native balsam, mixed plots with both species and plots without either of the two species. Soil characteristics were analyzed (pH, organic matter, C/N ratio and cations) and Ellenberg indicator values were used for light and soil moisture. We assessed species affinities for both Impatiens using indicator species analysis. Discriminant analysis was carried out to assign the sample plots to certain vegetation types. Vegetation and soil characteristics indicated that the species have considerable habitat overlap. This overlap is indicated by similar communities among releves and by the failure of discriminant analysis to correctly assign plots. Populations of both Impatiens species are surrounded by an unsuitable habitat that probably limited their spread. In conclusion, we predicted that the alien balsam could spread rapidly with the help of human disturbance and transport, and could compete with the native congener.
Antibacterial Effects of Monoglycerol Fatty Acid Esters and Sucrose Fatty Acid Esters on Bacillus spp.

Fatty acid esters are food additives with strong antibacterial activity against spore-forming bacteria. The antibacterial activity of monoglycerol fatty acid esters (MGs) and sucrose fatty acid esters (SEs) with various fatty acid chain lengths was systematically investigated on four typical Bacillus species: B. cereus, B. subtilis, B. megaterium, and B. coagulans. Monoglycerol monolaurate (MG12) and monoglycerol monomyristate (MG14) showed relatively strong bactericidal effects on vegetative cells of these species among the MGs tested at both pH 6.0 and pH 8.0. Different SEs showed bactericidal effects on different species at pH 6.0, while the SEs had antibacterial effects only on B. coagulans at pH 8.0. SEs showed antibacterial effects on vegetative cells of these species, as was the case with MGs. In addition, it was found that MGs and SEs showed strong antibacterial effects on both B. cereus and B. subtilis in the logarithmic phase of growth, while the antibacterial activities of MGs persisted longer than those of SEs.
Metabolic changes of cultured DRG neurons induced by adenosine using confocal microscopy imaging

Adenosine exerts multiple effects on pain transmission in the peripheral nervous system. This study was performed to use confocal microscopy to evaluate whether adenosine could affect dorsal root ganglia (DRG) neurons in vitro and test which adenosine receptor mediates the effect of adenosine on DRG neurons. After adding adenosine with different concentration, we compared the metabolic changes by the real time imaging of calcium and mitochondria membrane potential using confocal microscopy. The results showed that the effect of 500 μM adenosine on the metabolic changes of DRG neurons was more significant than others. Furthermore, four different adenosine receptor antagonists were used to study which receptor mediated the influences of adenosine on the cultured DRG neurons. All adenosine receptor antagonists especially A1 receptor antagonist (DPCPX) had effect on the Ca2+ and mitochondria membrane potential dynamics of DRG neurons. The above studies demonstrated that the effect of adenosine which may be involved in the signal transmission on the sensory neurons was dose-dependent, and all the four adenosine receptors especially the A1R may mediate the transmission.
Energy Metabolism During Anoxia and Recovery in Shell Adductor and Foot Muscle of the Gastropod Mollusc Haliotis lamellosa: Formation of the Novel Anaerobic End Product Tauropine

Metabolic responses to experimental anoxia and subsequent recovery, and to exercise were investigated in two different muscular tissues of the ormer, Haliotis lamellosa. The tissues are employed for different tasks by the animal. The foot is mainly responsible for slow gliding movements. The shell adductor muscle pulls down the shell for protection and in righting an animal which has been dislodged from the rocks. Tissue-specific differences in anaerobic energy metabolism occur. During 6 h of experimental anoxia, energy for both muscles was provided by arginine phosphate and co-fermentation of glycogen and aspartate. Glycolysis in the shell adductor muscle led mainly to the formation of the novel end product tauropine; D-lactate production pre-dominated in the foot. This pattern is consistent with observed enzymatic profiles in the two muscles and with the equilibrium constants of the respective enzymes, tauropine and D-lactate dehydrogenase. Recovery from anaerobiosis was characterized by a rapid return .
Some effects of temperature on the embryonic development of the salmon (Salmo salar)

This is a study of the effects of temperature on morphogenesis, and is an attempt to determine whether the order of appearance of anatomical features can be altered within the limits of survival. The time in days (usually from closure of the blastopore) for features to appear was noted, and from this the rates were calculated, being the reciprocals of days × 103. Rate plotted against temperature gives in general a straight line whose slope may be calculated. Some slopes were: hatching, 4.6; digestive system, 6.4; skeleton, 6.5; nervous function, 8.2; external pigment, 9.6; blood vessels, 10.0; fins, 10.3; eye pigment, 12.5. Thus hatching would be expected to appear precociously at low temperatures, and eye pigment at high temperatures.
Mitochondrial DNA reveals high genetic divergence between populations of Chalcides mertensi Klausewitz, 1954 (Reptilia: Scincidae) from Tunisia

Genetic diversity of four populations of Chalcides mertensi (Klausewitz, 1954) from Tunisia was analyzed by means of the Restriction Fragment Length Polymorphism (RFLP) analysis of two fragments of mitochondrial DNA (mtDNA) encompassing NADH dehydrogenase subunits 1 and 2 (ND-1/2) and NADH dehydrogenase subunits 3, 4 and 4L (ND-3/4). Phylogenetic relationships between haplotypes were inferred by analysing the sequence of 396 base pairs at the 5′ end of the mitochondrial gene encoding cytochrome b and a segment of 12S rRNA gene (386 bp). The results of this study highlighted a pronounced genetic divergence between the populations from northern (Ain Soltane and Tabarka) and southern (Kasserine and Sidi Bouzid) Tunisia, that the phylogenetic analysis recovered as two distinct taxonomic entities. These two groups of populations can therefore be ascribed to two distinct taxa, with southern populations probably representing the typical C. mertensi, whereas northern individuals are likely to represent a new species of grass swimming Chalcides. The divergence between these two taxonomic entities can be referred to palaeogeographic and palaeoclimatic events that have affected northwestern Africa during the last 10 Million years. The analysed populations show a low genetic variability that can be related to the past climatic and geologic events and the colonization processes that took place with environmental amelioration, and to the peripheral position of these populations in the distributional range of the species. However, a more exhaustive study, including Algerian and Moroccan skink populations will be necessary in order to clarify these issues.
Banco de sementes do solo em área agrícola sob diferentes sistemas de manejo estabelecida sobre campo natural

Knowledge of the ecology of soil seed banks (SSB) contributes to improving integrated weed SSB management systems in croplands established in natural grassland areas. The aim of this study was to evaluate the effect of different cropping systems, established in a natural grassland field (Depressao Central of Rio Grande do Sul, 30o05´S, 51o40´O, altude 46m, rainfall 1398mm), on the SSB. Three different tillage-crop rotation systems were imposed (no-tillage - NT, reduced tillage - RT, and conventional tillage - CT) in three plots arranged in seven blocks. Two SSB evaluations were carried out in each tillage system, one in May and the other in October/ 2002. The SSB was evaluated by sampling soil cores, which were germinated in a glasshouse, and seedlings were counted and identified. Edaphic variables were registered to relate with collected data. The results indicated that different tillage systems affected the SSB composition, and that certain species responded differently to these influences. The NT system resulted in higher BSS wealth, a lower number of Brachiaria plantaginea seeds, a higher number of Sida rhombifolia seeds, but inverse values were recorded for RT and CT systems. The spatial soil seed bank distribution presented high heterogeneity among cropping systems. Edaphic variables, specially organic matter, pH and phosphorous, showed associations with the variation in SSB composition.
Main factors that affect the economic efficiency of broiler breeder production

This study aimed at identifying the factors that affect the economic efficiency of broiler breeder production using the analysis of stochastic profit frontier function. Data were collected in 48 broiler breeder farms contracted by a commercial company located in southwestern Parana, Brazil. The collected data refer to the last batch of fertile eggs that was delivered to the company, between January, 2008, and July, 2009. The following parameters were evaluated: production of hatching eggs per hen (number of eggs/hen), hatchability (hatch %), feed intake per hatching egg (g feed/ egg), production scale (number of birds/batch), farmer's experience in production activities, and labor type. Factors, such as area of occupied land, electricity costs, and invested capital were also evaluated. Results showed that the cost of electricity, as well as area of occupied land, production scale, and feed intake per hatching egg significantly affect the economic efficiency of the broiler breeder farms in Southwestern Parana, Brazil.