Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation und funktionelle Rolle des murinen Transkriptionsfaktors Foxp3 in T-Zellen

The aim of the study was to analyze the function and regulation of the transcription factor Foxp3. In a first step we designed a BAC-transgenic mouse with eYFP under the control of the Foxp3 promoter. For creating these mice we use the ETcloning method. The step of homologous recombination of the target vector into the BAC failed. Because of that, we decided to work in cooperation with the group of Tim Sparwasser from Munich and their BACtransgenic mouse called DEREGmouse. This mouse expresses the coding region of eGFP fused to the diphtheriatoxinreceptor under the control of the Foxp3 promoter. Therefore Foxp3 T cells can be easily detected by eGFP expression and can even be depleted by diphtheriatoxinapplication. We confirmed the coexpression of Foxp3 and eGFP and furthermore tested the functionality of the depletionprocess of Foxp3 T cells by treatment with diphtheriatoxin. In a second study, we analyzed the stability of Foxp3 expressing cells in vivo. Therefore we transferred Foxp3 T cells in syngenic mice and analyzed these cells after 14 days for their Foxp3expression. Furthermore, we tested the induction of Foxp3 expression through TGF-beta and the suppressive activity of these cells. We also analyzed those cells for their methylation pattern, comparing cells, which showed an induction of Foxp3expression after one week of culture with TGF-beta to cells, which received TGF-beta for one week and were then restimulated in the absence of TGF-beta. The stability of Foxp3 expression seems to correlate with the demethylated state of the TSDR (Treg Specific Demethylated Region). To get a closer look on the region called TSDR in the murine foxp3 locus, we decided to analyze this region under different aspects. First, we checked for putative binding sites of transcription factors by database analysis of the TSDR. We also analysed histon modifications, such as acetylation of histon H3 and H4 and trimethylation of lysine 4 at histon3, in this region. Presence of these modifications hinted an epigenetic regulation of Foxp3 involving the TSDR. In a last step, the transcriptional activity of TSDR was tested to delineate whether the TSDR serves as an alternative promoter or acts as a regulative element like an enhancer. Luciferase assays showed that TSDR is a regulative enhancer element, which loses transcriptional activity when methylated. Deletion mutants determined the most important fragment of the TSDR. Schlagworter: Transkriptionsfactor Foxp3; regulatory Tcells ; TSDR = Treg specific demethylated region; epigentic control
Pathway Hunter Tool (PHT) A Platform for Metabolic Network Analysis and Potential Drug Targeting

Metabolic network analysis will play a major role in �Systems Biology� in the future as they represent the backbone of molecular activity within the cell. Recent studies have taken a comparative approach toward interpreting these networks, contrasting networks of different species and molecular types, and under varying conditions. We have developed a robust algorithm to calculate shortest path in the metabolic network using metabolite chemical structure information. A divide and conquer technique using Maximal Common Subgraph (MCS) approach and binary fingerprint was used to map each substrate onto its corresponding product. Then for the calculation of the shortest paths (using modified Breadth First Search algorithm) the two biochemical criteria �local� and �global� structural similarity were used, where �local similarity� is defined as the similarity between two intermediate molecules and �global similarity� is defined as the amount of conserved structure found between the source metabolite and the destination metabolites after a series of reaction steps. The pathway alignment was introduced to find enzyme(s) preference in the pathway of various organisms (a local and global outlook to metabolic networks). This was also used to predict potentially missing enzymes in the pathway. A novel concept called �load points� and �choke points� identifies hot spots in the network. This was used to find important enzymes in the pathogens metabolic network for potential drug targets.
Spatial factors related to mortality and population decline of endangered mountain caribou

Mountain caribou are an endangered ecotype of woodland caribou (Rangifer tarandus caribou) that historically occurred throughout the high snowfall regions of southeast British Columbia and the northwestern United States. The decline in caribou is thought to be due to apparent competition where increases inearly-seral conditionsstimulateanumerical responseinprimaryungulate preyandtheir predators and these incidentally kill an unsustainable number of caribou. Based on the known location of death of 207 radio collared animals, we tested hypotheses pertaining to relationships between landscape composition and predator-specific mortality of mountain caribou at 2 ecologically based spatial scales. Relative to landscape conditions within subpopulation boundaries (level 1) or within home ranges (level 2), caribou were at greater risk of predation at low elevations particularly within otherwise complex terrain (i.e., valleys) with more variation in overstory canopy closure and greater road densities. Caribou vulnerability to bears was also positively related to the variation in overstory age. Cougar predation was not related to roads or terrain complexity but occurred more often in landscapes with warmer aspects and greater proportions of stands of <120 years. Wolf predation occurred primarily at low elevations at the broader scale and in association with roads at the finer scale. Our results indicate that caribou vulnerability to predation was a function of both static (e.g., terrain) and dynamic (e.g., overstory conditions) factors, but we did not find evidence that localized habitat fragmentation due to forest harvest influenced predation on caribou. This result is not inconsistent with the apparent competition hypothesis but suggests that habitat change largely functions at broader spatial scales involving landscapes that can be beyond those occupied by caribou, including the winter ranges of primary ungulate prey. These changes and the season-dependent dispersion of other ungulates and their predators may largely influence mortality risk to mountain caribou. Although roads and forest fragmentation are interrelated, roads may further contribute to caribou predation by increasing the efficiency of movement of some predators and thereby increasing encounter rates with caribou. 2013 The Wildlife Society.
The response regulator RssB, a recognition factor for σS proteolysis in Escherichia coli, can act like an anti‐σS factor

σS (RpoS) is the master regulator of the general stress response in Escherichia coli. Several stresses increase cellular σS levels by inhibiting proteolysis of σS, which under non‐stress conditions is a highly unstable protein. For this ClpXP‐dependent degradation, the response regulator RssB acts as a recognition factor, with RssB affinity for σS being modulated by phosphorylation. Here, we demonstrate that RssB can also act like an anti‐sigma factor for σSin vivo, i.e. RssB can inhibit the expression of σS‐dependent genes in the presence of high σS levels. This becomes apparent when (i) the cellular RssB/σS ratio is at least somewhat elevated and (ii) proteolysis is reduced (for example in stationary phase) or eliminated (for example in a clpP mutant). Two modes of inhibition of σS by RssB can be distinguished. The ‘catalytic’ mode is observed in stationary phase cells with a substoichiometric RssB/σS ratio, requires ClpP and therefore probably corresponds to sequestering of σS to Clp protease (even though σS is not degraded). The ‘stoichiometric’ mode occurs in clpP mutant cells upon overproduction of RssB to levels that are equal to those of σS, and therefore probably involves binary complex formation between RssB and σS. We also show that, under standard laboratory conditions, the cellular level of RssB is more than 20‐fold lower than that of σS and is not significantly controlled by stresses that upregulate σS. We therefore propose that antisigma factor activity of RssB may play a role under not yet identified growth conditions (which may result in RssB induction), or that RssB is a former antisigma factor that during evolution was recruited to serve as a recognition factor for proteolysis.
Simulating Water Flow to a Subsurface Drain in a Layered Soil

The objective of the work presented in this paper was to simulate drain flow into subsurface drainage pipes for a layered soil profile using a finite element based HYDRUS-2D model. Data from the drainage experiment in North Central Ohio were used as input to the model. Studies were conducted to determine the ability of the model to predict drain discharge-water table elevation relationships. The model was also used to evaluate the effect of backfill on drain discharge-water table elevation relationships. HYDRUS-2D underpredicted drain discharge compared to the empirical and Kirkham-Hooghoudt equations for water table elevations above 70 cm. However, HYDRUS-2D predictions were very close to those using empirical and Kirkham-Hooghoudt equations for water table elevations below 70 cm. In the backfill simulation scenario with backfill soil saturated hydraulic conductivity values obtained 40 years after the installation of the drains, the model produced higher drain flow rates than those obtained without simulating backfill when the midspace water table elevation was greater than 70 cm, but still underpredicted drain discharge compared to the empirical and Kirkham-Hooghoudt equations. In conclusion, to predict drain flow into a subsurface drain pipe for a layered soil using HYDRUS-2D, the model may give better results with the hydraulic conductivity values of backfill and the model needs more tests for layered soil conditions.
Forest structure and productivity in Puerto Rico's Luquillo Mountains.

Net aboveground primary production (NPP) at 725 m in elevation in the colorado forest (montane rain forest, sensu Beard; lower montane wet forest, sensu Holdridge) of the Luquillo Mountains of Puerto Rico averaged 7.60 t/ha yr on two 0.4-ha permanent plots and was determined by summing aboveground biomass accrual (0.59 t/ha yr), litterfall (6.80 t/ha yr), and herbivory (0.21 t/ha yr). The total leaf area index (trees, epiphytes, and ground vegetation) was 4.95 m2/i2, the aboveground woody volume and biomass, 220 m3/ha and 130 t/ha, respectively, and standing herbivory and the herbivory rate, 5.1 and 4.0 percent/yr, respectively. The mean standing crop of litter was 680 g/m2, with a turnover rate of 0.78 times per year. Of the structural features studied over a 600-m elevational gradient in the Luquillo Mountains, the number of trees per hectare, basal area, and soil organic matter increased with elevation; whereas, the specific leaf area, canopy height, range of tree diameters, forest volume and biomass, leaf area index, and species richness declined. Of the dynamic features studied, ingrowth and mortality of trees, tree growth (diameter, volume, and biomass growth), litterfall, loose litter, standing herbivory and herbivory rates, litter turnover, aboveground woody NPP, and total NPP all declined with an increase in aboveground elevation. The structural and floristic impoverishment of forests and changes in forest dynamics with ascent in the Luquillo Mountains reflect cooler temperatures, fog, and heavier rainfalls that interact to produce saturated soils and retard the mineralization of organic matter.
FENOLOGIA DA ANDIROBA ( Carapa guianensis, Aubl ., MELIACEAE) NO SUL DO ESTADO DE RORAIMA

O presente estudo foi realizado com o objetivo de estudar o padrao fenologico da especie arborea Carapa guianensis , Aubl. , em floresta natural localizada no sul do estado de Roraima, procurando relacionar a frequencia de ocorrencia das fenofases as condicoes pluviometricas do periodo. Para o levantamento fenologico foram selecionados 20 individuos adultos localizados em uma parcela permanente de 9 ha. As observacoes fenologicas ocorreram quinzenalmente de fevereiro de 2006 a fevereiro de 2009, registrando-se a presenca ou ausencia dos eventos de floracao, frutificacao e mudanca foliar para cada arvore. Para analisar a influencia da precipitacao na fenologia da especie foi utilizado o coeficiente de correlacao de Spearman e, para estimar a sincronia dos eventos fenologico utilizou-se o indice de sincronia da populacao (Z). A floracao da andiroba mostrou-se subanual, sincronica e correlacionada negativamente com precipitacao no periodo do evento fenologico. Foram observados dois ciclos de floracao, sendo um longo com inicio em outubro, estendendo-se para o ano seguinte, por um periodo medio de 9 meses, e um curto com duracao de dois meses (julho a agosto). A frutificacao e anual, longa e sincronica, e correlacionou-se positivamente com a precipitacao. A epoca ideal para a coleta dos frutos maduros no local estudado e durante o periodo chuvoso, que compreende abril a julho. A emissao de folhas ocorreu de forma continua e nao se correlacionou com a precipitacao. Observou-se uma maior proporcao de individuos perdendo folhas, entre os meses de agosto a novembro, que caracterizam um periodo de transicao entre a epoca seca e chuvosa, com sensivel reducao de precipitacao.
POLDISP: A software package for indirect estimation of contemporary pollen dispersal

poldisp 1.0 is a free software package to estimate the distribution of pollen dispersal distances from mother-offspring diploid genotypic data. It requires the spatial coordinates and genotypes of a sample of seed plants and their respective maternal progenies, providing estimates of the average, variance and kurtosis of the pollen dispersal curve. poldisp also estimates the effective reproductive density of pollen donors and the correlation of paternity within and among maternal sibships. poldisp is useful for characterizing the spatial scale of pollen dispersal, for assessing the variation in male fertility and for investigating biological factors affecting correlated paternity in plants.
Two Fractional Model for Evaluating the Activity of Glucoamylase from Aspergillus Niger Under Combined Pressure and Temperature Conditions

The impact of high pressure and temperatures on the conversion reaction of gluco-amylase has been assessed by the kinetic rate constants. Hydrostatic pressure up to 1400 MPa in a temperature range from 40 to 958C has been investigated. A two fractional model is suggested to describe the inactivation behaviour of the enzyme over all tested pT-combinations. It was supposed that the two isoforms of glucoamylase (GA1 and GA2) responded differently to high hydrostatic pressure. The pressure labile form of glucoamylase (GA2) was inactivated quickly at pressures above 850 MPa whereas the stable form (GA1) showed slower inactivation at pressure levels up to 1400 MPa at 508C. A significant stabilization against heat inactivation has been observed at 400 MPa for GA2 and at 550 MPa for GA1. In addition it was observed that high pressure also impedes the enzymatic cleavage of maltose. A reduction of the conversion rate constants with increasing pressures (up to 600 MPa) has been found within the temperature range investigated (40-80°C). For the overall reaction of glucose liberation from maltose monohydrate in ACES buffer at pH 4.5 the optimum was identified at 318 MPa and 84°C for a 30 min process. Compared to the maximum observed at ambient pressure (approximately 62°C) the glucose production was doubled.
English Jurassic dinoflagellate cysts and acritarchs: A reexamination of some type and figured specimens

Abstract As a consequence of advances in knowledge of the morphology and relationships of dinoflagellate cysts and acritarchs and increasing sophistication in optical equipment, earlier descriptions of dinoflagellate cysts and acritarchs are in general obsolete; re‐descriptions are necessary to furnish fuller morphological information. In this paper are given the results of a reexamination of holotypes or figured specimens of 26 species of dinoflagellate cysts and 3 species of acritarchs, all from the Middle to Upper Jurassic (lower Callovian to Kimmeridgian) of England. The new species Gonyaulacysta setcheyensis and the new combination Acanthaulax downiei (Sarjeant) are proposed; two species, Heslertonia teichophera (Sarjeant) and Meiourogonyaulax? acanthosphaera (Sarjeant), are generically reassigned and emended; and the diagnosis of Leptodinium mosaicum (Downie) is emended. It is demonstrated that the genera Netrely‐tron Sarjeant and Paranett‐elytron Sarjeant do indeed possess an endoblast and are thus.
Effect of Aggregation of Laboratory Mice (Mus Musculus) on Food Intake at Different Temperatures

Several authors have studied the effects of aggregati on upon various physiological processes. Most of the previous work has l)een done on invertel)rates avid p)oikilotherluic vertebrates. Only limited stu(lies have l)een made on warml)looded animals, p)articularly on small rodents. The experiments of Vetulani (1931) have demonstrate(l that the postweaning growth of laboratory mice, as indicated by weight increase, is influenced b)v the number of animals in the cage. He found that the weight gain of male mice, kept 2 to 4 per cage, was 17.98 percent higher than the gain of mice kept 1 animal per cage; the weight increase of animals kept 9 to 12 per cage was 8.14 l)ercent more than that of those kept 1 to a cage. These studies were repeated by Retzlaff 1939), who confirmed the findings of Vettulani au(l came to the conclusion that environmental teml)erature is the main factor causing the dlifference in Nveight gain in various population samples. Trhe failure of females to show the same growth response as males, which was observed by both authors, was assigned to pectuliarities in female 1)pvxsiolo-y. (erstell ( 1939) in several experiments has demonstrated that huddling, which tends to conserve body heat, is an important factor in the survival of the bobwhite quail (Colinus virginianus virginiai lits) at low aml)ient temperatures. Sealander (1952) has studied the effect of huddling on the survival of Peromnyscus kept at a low temnperattlre without food and water. He found that the survival time of mice exposed to a mean temnperatutre of -230C was prolonged in groups with 2 to 4 animals per cage, as compared with indivi(lually caged animals. The study of King and Connon (1955) on the effect of social relationships upon mortality in young C57L/ 10 mice has shown that the stirvival of two-week-old animals weighing 7 grams or less (lel)ends significantly on proper thermal con(litions which may he supl)lie(l by other indivi(luals as they huddle together. The relationship between crowding and food consuml)tion has been studied by only a few investicators. It has been demonstrated by Adolph (1931), that crowded tadpoles consumed less food per animal than isolated individuals. Also the growth rate of the crowded animals was decreased. Kalabtuchov (1933, cited by Allee, 1934) has found that individually kept honey-bees eat more T rhis work w-as supported in part by an Institutional Grant from the American Cancer Society, Intc.
A new species of horseshoe bat (Microchiroptera: Rhinolophidae) from south‐central Africa: with comments on its affinities and evolution, and the characterization of rhinolophid species

A new species of horseshoe bat, Rhinolophus sakejiensis, is described from south-central Africa, near the source of the Zambezi River in north-west Zambia. A distinct combination of noseleaf, cranial and baculum characters are diagnostic of the species. It is a member of the ferrumequinum group, and its evolutionary affinities lie closest to R. clivosus Cretzschmar, 1828 and particularly the West African R. hillorum Koopman, 1989. This discovery of a new species of Rhinolophus in the clivosus complex required reappraisal of these and other related taxa. Known only from high forest in West Africa, hillorum is the closest relative of sakejiensis collected in mesic savanna in south-central Africa. Comparisons of this new species with other large Afrotropical Rhinolophus shows that hillorum is specifically distinct from clivosus, and endorses the specific status of deckeni and silvestris. The contemporary taxonomy of Afrotropical Rhinolophus was incapable of accommodating this new taxon, and the latter part of this paper argues for a more objective characterization of rhinolophids as evolutionary species.
Phylogeny and biogeography of water skinks of the genus Tropidophorus (Reptilia: Scincidae): a molecular approach

Phylogenetic relationships of the Oriental semiaquatic lygosomine skinks of the genus Tropidophorus were inferred from 1219 base positions of mitochondrial 12S and 16S rRNA genes. Results of the phylogenetic analyses incorporating data for representatives of other lygosomine genera indicated that the basal phylogenetic split within Tropidophorus separated a clade of continental Indochinese species exclusive of T. cocincinensis and T. microlepis from one comprising T. cocincinensis, T. microlepis and species from Borneo, Sulawesi and the Philippines. Of the latter group, the two continental species form the sister taxon to a clade comprising the island species. Diversification among species in Indochina and among Borneo, the Philippines and Sulawesi was likely concentrated in the Miocene, with no apparent dispersal among these regions during the Pleistocene. The body depression recognized in several Indochinese species is likely to have occurred twice in parallel as an adaptation to saxicolous habitats.
Correlations among various blood parameters at exsanguination and their relationships to pork quality traits

The objectives of this study were to investigate the correlations between various blood parameters compared with cortisol and lactate levels under the standard pre-slaughter procedure and handling conditions and to assess their potential as indicators of pork quality traits. Despite there being no additional pre-slaughter stress treatment, there is considerable variation in blood parameters at exsanguination. Serum cortisol and blood lactate levels, widely used indicators of stress, were positively correlated with blood glucose and electrolytes, such as calcium, potassium and sodium. Moreover, these parameters were significantly correlated with a rapid rate of early postmortem glycolysis and reduced water-holding capacity. In particular, blood lactate and glucose levels significantly differed between porcine quality classes. However, other blood parameters including electrolytes did not significantly differ between quality classes though they significantly correlated with pork quality traits. Therefore, serum cortisol, blood lactate and glucose have potential as indicators of the rate and extent of postmortem metabolism and ultimate pork quality under the standard procedure and handling conditions of pre-slaughter.