Miracle-dz/UniFAR-FTUs huggingface dataset:
Selective inhibition and mechanistic studies of the human O2 sensor, Prolyl Hydroxylase Domain 2 (PHD2)

Prolyl Hydroxylase Domain 2 (PHD2) has been identified as a key oxygen sensor in humans along with Factor Inhibiting Hypoxia Inducible Factor (FIH). As such PHD2 and FIH play critical roles in myriad pathways of medical relevance by hydroxylation of their target substrate hypoxia inducible factor (HIF), a transcription factor responsible for the regulation of over 100+ genes. With such critical roles in human physiology the ability to selectively regulate these two enzymes could potentially lead the way for novel therapeutic treatments of a vast array of disease states from cancer to myocardial infarction. We report on three classes of iron chelators which show promise for independent regulation of the HIF hydroxylases. Compounds representing the pyrones/pyridinones, pyridines and catechols were tested and found to have differential impacts on PHD2 and FIH under the same experimental conditions. The mode of inhibition is the result of binding to the active site iron and is supported by UV-visible and electroparamagnetic resonance spectroscopy. PHD2 at the current time does not have a well resolved mechanistic understanding regarding its catalytic cycle and subsequent rate determining steps. We have employed pH, solvent isotope, and X-ray absorption studies in an effort to gain further understanding regarding PHD2's overall mechanism. Our data support that dissociation of an iron(II)-OH2 bond centered about the active site contributes to a portion of the overall rate determining steps in the catalytic reaction of PHD2 that activates oxygen and ends with the production of hydroxylated substrate.
Determinants of Bilateral Trade Between BRICs and South Africa What the Gravity Model Tells Us

This study examines the fundamental determinants of bilateral trade flows between South Africa and BRIC countries. This is done by exploring the magnitude of exports among these countries. The Gravity model approach is used as the preferred theoretical framework in explaining and evaluating successfully the bilateral trade flows between South Africa and BRIC countries. The empirical part of this study uses panel data methodology covering the time period 2000-2013 and incorporates the five BRICS economies in the sample. The results of the regressions are subject to panel diagnostic test procedures. The study reveals that, on the one hand, there are positive and significant relationships between South African export flows with the BRICs GDP, the South Africa GDP, the population of south Africa, The distance, the language dummy, and South Africa and the BRIC openness . On the other hand, the BRICs’ population the real exchange rate, are found to be negatively related to export flows.
Characterization of a β‐N‐acetylhexosaminidase and a β‐N‐acetylglucosaminidase/β‐glucosidase from Cellulomonas fimi

The Gram‐positive soil bacterium Cellulomonas fimi is shown to produce at least two intracellular β‐N‐acetylglucosaminidases, a family 20 β‐N‐acetylhexosaminidase (Hex20), and a novel family 3‐β‐N‐acetylglucosaminidase/β‐glucosidase (Nag3), through screening of a genomic expression library, cloning of genes and analysis of their sequences. Nag3 exhibits broad substrate specificity for substituents at the C2 position of the glycone: kcat/Km values at 25 °C were 0.066 s−1·mm−1 and 0.076 s−1·mm−1 for 4′‐nitrophenyl β‐N‐acetyl‐d‐glucosaminide and 4′‐nitrophenyl β‐d‐glucoside, respectively. The first glycosidase with this broad specificity to be described, Nag3, suggests an interesting evolutionary link between β‐N‐acetylglucosaminidases and β‐glucosidases of family 3. Reaction by a double‐displacement mechanism was confirmed for Nag3 through the identification of a glycosyl–enzyme species trapped with the slow substrate 2′,4′‐dinitrophenyl 2‐deoxy‐2‐fluoro‐β‐d‐glucopyranoside. Hex20 requires the acetamido group at C2 of the substrate, being unable to cleave β‐glucosides, since its mechanism involves an oxazolinium ion intermediate. However, it is broad in its specificity for the d‐glucosyl/d‐galactosyl configuration of the glycone: Km and kcat values were 53 µm and 482.3 s−1 for 4′‐nitrophenyl β‐N‐acetyl‐d‐glucosaminide and 66 µm and 129.1 s−1 for 4′‐nitrophenyl β‐N‐acetyl‐d‐galactosaminide.
The effects of Insulin-nutrient supply interactions on ewe lactation

Six lactating abomasally cannulated ewes were subjected to a hyperinsulinemic euglycemic clamp with or without casein supplementation in a two period crossover design experiment. There was a significant response in milk (1169 ± 46 g/d vs 952 ± 46 g/d, P<0.001) and milk protein (66.4 g/d ± 2.7 g/d vs 54.2 g/d ± 2.7 g/d P<0.006), yield from casein supplemented ewes. There w as no overall effect of the clamp on milk and milk protein yield, while the interaction was also non-significant. However, there was a significant reduction in feed intake (P<0.001) as the clamp continued, which may have compromised milk and milk protein respons e. There was also a significant period effect across all the measured parameters, which could also be a stage of lactation effect, due to th rapid decline of milk production during ewe lactation. In this study, in contrast to concentrate-fed cows, the utilisation of this technique did not increase milk protein yield in pasture fed lactating ewes.
Marine Natural Products. XIX. : Pervicosides A, B, and C, Lanostane-Type Triterpene-Oligoglycoside Sulfates from the Sea Cucumber Holothuria pervicax

Triterpene-oligoglycoside constituents, contained in the body walls and the Cuvierian tubules f the sea cucumber Holothuria pervicax (torafu-namako in Japanese), were investigated and purified in their desulfated forms. These desulfated lanostane-type triterpene tetraglycosides, designated DS-pervicoside A (7), DS-pervicoside B (8), and DS-pervicoside C (9), have antifungal activity, and their structures were determined on the basis of chemical and physicochemical evidence. The parent oligoglycosides of these desulfated tetraglycosides, named pervicosides A (10), B (11), and C (12), were shown to be the 4'-sulfates of DS-pervicosides A (7), B (8), and C (9), respectively.
Testing for the relative contribution of patch neighborhood, patch internal structure, and presence of predators and competitor species in determining distribution patterns of rodents in a fragmented landscape

Factors affecting the distribution of species in fragmented landscapes, and their relative importance, are often unclear. Few studies have deliberately compared various hypotheses in relatively controlled conditions. Moreover, most studies to date have not incorporated false absences in their modeling. Following a multiple hypotheses testing framework, we tested the relative role of landscape structure, patch and neighborhood configuration, patch internal structure, presence or absence of predators, and presence or absence and abundance of potential competitor species on the occupancy patterns of three rodent species (Myodes glareolus (Schreber, 1780), Apodemus flavicollis (Melchior, 1834), Apodemus sylvaticus (L., 1758)) in a highly fragmented landscape in Tuscany, central Italy. Distribution patterns and occupancy dynamics of the three rodent species were affected by patch and patch neighborhood characteristics, as well as the vicinity of other patches occupied by the species. However, we found no relev.
Ecological Correlates of a Neotropical Mutualism: Ant Assemblages at Costus extrafloral Nectaries

The species richness and composition of ant assemblages at the extrafloral nectaries of four Costus spp. (Zingiberaceae) in Panama were quantified to determine (1) the relative specificity of these ant—plant mutualisms, and (2) the ecological factors that influence ant assemblages. Although inflorescences of Costus spp. commonly produce extrafloral nectar for several months (species means 1—2 mo, range to 4 mo), there was little turnover in ant—species composition on individual inflorescences. A total of 34 ant species in five subfamilies were observed, but plant species varied significantly in ant species richness. The number of ant species expected from equal sampling (40 inflorescences per Costus sp.) was 9 for C. pulverulentus, 13 for C. scaber, 15 for C. allenii, and 20 for C. laevis. Among—species differences in ant species richness were not a function of plant distribution, the volume or composition of extrafloral nectar, or the duration of nectar flow. The number of ant species was positively correlated with inflorescence height, which varied from 0.6 to 2.0 m. The differences in ant species richness with inflorescence height were due primarily to the addition of arboreal ants, which increased from 3 species representing 3% of all ant species observations on the shortest plant, C. pulverulentus, to 12 species representing 62% of all ant observations on the tallest plant, C. laevis. The number of terrestrial ant species varied only from six to eight. Cumulative ant—species curves as a function of number of inflorescences sampled (N = 41—80) did not plateau for any Costus sp. , indicating that a large number of ant species can utilize extrafloral nectar in this system. The high ant species richness and the similarity in nectar characteristics among Costus spp. suggest these are relatively generalized mutualisms with limited coevolution between the plants and their attendant ants. The brief period of extrafloral nectar production (° = 36—55 d), coupled with spatial variation in ant species distributions, probably limit the degree of specialization among mutualists. This is in contrast to more specialized ant—plant mutualisms where plants are relatively predictable sources of food and/or nest sites for ants.
DNA-damage-mediated remodeling of normal and tumor microenvironments modulates cell survival

While numerous cell-intrinsic processes are known to play decisive roles in chemotherapeutic response, relatively little is known about the impact of the tumor microenvironment on therapeutic outcome. Here, we use a wellestablished mouse model of Burkitt's lymphoma to show that paracrine factors in the tumor microenvironment modulate lymphoma cell survival following the administration of genotoxic chemotherapy. Specifically, IL-6 and Timp-1 are released in the thymus in response to DNA damage, creating a "chemo-resistant niche" that promotes the survival of a minimal residual tumor burden and serves as a reservoir for eventual tumor relapse. Notably, IL-6 is released acutely from thymic endothelial cells in a p38-dependent manner following genotoxic stress,
The effects of plant structure on the spatial and microspatial distribution of a bromeliad‐living jumping spider (Salticidae)

Summary 1 In several regions of South America, the neotropical jumping spider Psecas chapoda inhabits and reproduces strictly on the bromeliad Bromelia balansae. Previous studies reported that this spider is more frequent on bromeliads in grasslands than on those growing in forests, and on larger plants, but only when the bromeliads are without inflorescence. Upon blooming, B. balansae fold their leaves back, thereby changing the plant architecture from a tri-dimensional to a bi-dimensional flattened shape, and our hypothesis is that this alteration affects the spider's habitat-selection decisions. 2 In the present study, we examined experimentally the effects of inflorescence, plant size and blockade of the axil of the leaves (spider shelters) of forest bromeliads on the colonization of a bromeliad by P. chapoda. By using sticky traps, we also compared prey availability in grassland and forest. 3 Plants with simulated inflorescence were colonized at a lower frequency than those without inflorescence simulation. Grassland bromeliads in which the rosettes were blocked with dry leaves were colonized less frequently than open bromeliads, whereas forest bromeliads from which dry leaves had been removed were not colonized. Spiders generally abandoned bromeliads in which three-quarters of the length of the leaves had been removed, although females with eggsacs remained on these plants. Prey availability (biomass and number) was up to 18 fold higher in the grassland than in the forest. These results suggest that microhabitat structure and prey availability shape the spatial distribution of P. chapoda populations. 4 Our findings suggest that Psecas chapoda can evaluate, in fine detail, the physical state of its microhabitat, and this unusual spider–plant association is readily destabilized by changes in the microhabitat (i.e., it is strictly dependent on the size and morphology of the host plant). This study is one of the few to report a strict association between a spider species and its host plant, and also one of the few to examine the effects of habitat and microhabitat structure on the spatial distribution of active hunters on plants.
Two new species of Pratinus Attems, with taxonomic notes on the genus and a redescription of its type-species (Diplopoda, Polydesmida)

Recently, in my paper on the Paradoxosomatidae of Borneo (JEEKEL, 1963), I discussed the taxonomy of the genus Pratinus Attems, 1937, and showed that the species of this genus in the wide sense as conceived by ATTEMS (1937, 1953) in majority belong to three other genera, viz., Orthomorpha Bollman, 1893, Leiozonius Jeekel, 1963, and Gigantomorpha Jeekel, 1963. Pratinus itself was restricted to a concept largely conforming to the idea held by POCOCK when he established this genus under the preoccupied name of Prionopeltis in 1895. Furthermore, attention was drawn to the fact that the two species of Euphyodesmus Attems, 1931, described from Ceylon, for which CHAMBERLIN (1941) created a separate subgenus Ceylonesmus, actually belong to Pratinus. In recapitulation, Pratinus was emended to embrace the following species: P. planatus (Poc., 1895), P. taurinus (Poc., 1895), P. cervinus (Poc., 1895), P. greeni (Att., 1936), and P. vector (Chamb., 1941). A re-examination of the type-species of the genus, P. cervinus, the study of the two new species described in the present paper, and a review of the pertinent literature now has convinced me that the concept of Pratinus must still undergo a slight alteration to the effect that the Indochinese species which ATTEMS (1937, 1953) described in the genus Centrodesmus Pocock, 1894, should be reallocated in Pratinus. The type-species of Centrodesmus, C. typicus Pocock, 1894, from Sumatra is known only in the female sex. The other Sumatran species, C. discrepans Silvestri, 1895, also was based on a female. As regards the development of the lateral keels, these species bear a certain resemblance to some species of Pratinus and some of the Indochinese species which ATTEMS referred to Centrodesmus. However, such a similarity might as well be a case of evolutionary parallelism and not necessarily signifies congenerity. Moreover, POCOCK already considered the species of Pratinus generically distinct from Centrodesmus, and since he is probably still the only one who has seen the type-species of both genera, it seems better to follow tentatively his usually sound opinion. At any rate, the species referred to Centrodesmus by ATTEMS, on account of their gonopod structure cannot be kept separate from Pratinus.
A Study on the Mechanism of Nodding Initiation of the Flower Stalk in a Poppy, Papaver Rhoeas L.

A study was made to find whether the nodding of the flower stalk in a poppy, Papaver Rhoeas L. , immediately after its formation was triggered by the weight of its flower bud or by positive georeaction and the following results were obtained. (1) The direction of the nodding was mostly toward the inclined side of the stalk, which was opposite the leaf, for apical flower buds. (2) If the weight of the flower bud at stage 1 was cancelled by applying a load equivalent to the bud weight, the nodding of the stalk was not initiated. (3) The stalk at stages 1 and 2 and the upper part of the stalk (bending zone), as compared with the basal part, at later stages were highly deformable according to measurements by the bending method. (4) The cell wall of highly deformable stalks was rich in hemicelluloses and that of the basal part was abundant in pectic substances. From these results, we concluded that the initiation of the nodding in the flower stalk was caused by the weight of the flower bud and positive geotropic reaction was probably not involved.
Comparisons of macrofungi in plantations of Sitka spruce (Picea sitchensis) in its native range (British Columbia, Canada) versus non-native range (Ireland and Britain) show similar richness but different species composition

In the absence of native forests, non-native plantation forests have been identified as having an important function in conserving native biodiversity world-wide, including fungal biodiversity. The non-native tree species Sitka spruce (Picea sitchensis (Bong.) Carriere) is now the most abundant tree species in forests in Ireland and Britain, and these forests have been the focus of recent research into their ability to conserve native biodiversity. We conducted an analysis using data from macrofungal surveys from Sitka spruce forests in its native (Vancouver Island, Canada) and non-native (Ireland and Britain) range. Also included in all analyses were data for macrofungal diversity from other native tree species forests in each of the three regions. A total of 630 macrofungal species from seven forest types were analyzed, including 122, 247, and 70 species from Irish, British, and Vancouver Island Sitka spruce forests, respectively. In all three regions, notwithstanding differences in the ages of the site.
Mitochondrial and Nuclear DNA Sequence Data Provide Resolution to Sister-Group Relationships within Pteronotus (Chiroptera: Mormoopidae)

Whereas it is generally agreed that the Neotropical bat family Mormoopidae, as well as the two mormoopid genera (Mormoops and Pteronotus) are each monophyletic, relationships among the six extant species of Pteronotus remain unresolved. The purpose of this study was to evaluate phylogenetic relationships within Pteronotus using DNA sequence data from the mitochondrial ribosomal and cytochrome b genes and the nuclear Recombination Activating Gene-2 based on likelihood inferential techniques (maximum likelihood and Bayesian phylogenetics). Results of this study present, for the first time, a fully resolved and strongly supported phylogeny for all relationships within Pteronotus. These data strongly support: sister-group relationships between davyi and gymnonotus (subgenus pteronotus), between macleayii and quadridens (subgenus chilonycteris), and between the subgenera pteronotus and chilonycteris. Pteronotus personatus is sister to this clade and P. parnellii is the most basal lineage of Pteronotus. Although this is the first study to provide a fullyresolved and strongly supported hypothesis for the phylogenetic relationships among species of Pteronotus, future work must focus on phylogeographic surveys within each species because previous studies have suggested that parnellii and personatus may contain undescribed species.
TGF-β Suppresses IFN-γ-STAT1-Dependent Gene Transcription by Enhancing STAT1-PIAS1 Interactions in Epithelia but Not Monocytes/Macrophages1

IFN-γ and TGF-β are important regulators of mucosal immunity, typically functioning in opposition to each other. In this study, we assessed whether TGF-β could modulate IFN-γ-induced STAT1 signaling. Model epithelial cell lines (HEp-2, HT-29, and T84) or monocytes/macrophages (THP-1 cell line, human blood mononuclear cells) were pretreated with TGF-β (1 ng/ml; 5–60 min), followed by IFN-γ exposure (20 ng/ml; 30 min), and then STAT1 transcriptional activity, DNA-binding activity, phosphorylation, and methylation were assessed. Some epithelia were transfected with an expression plasmid encoding SMAD7 to block TGF-β-SMAD signaling. Epithelia, but not macrophages, pretreated with TGF-β were hyporesponsive to IFN-γ stimulation as indicated by reduced expression of four STAT1-regulated genes and reduced STAT1 DNA binding on EMSA. However, STAT1 Tyr701-, Ser727 phosphorylation, and nuclear recruitment of STAT1 were not significantly different in IFN-γ with or without TGF-β-treated cells, indicating that the effects of TGF-β are downstream of IFN-γR-JAK-STAT1 interaction. The TGF-β effect was not dependent on ERK1/2, p38, or JNK activation but was prevented by overexpression of the inhibitory SMAD7 protein. Additional studies suggest that TGF-β blockade of IFN-γ activity in epithelia is via enhanced sequestering of STAT1 by pre-existing protein inhibitor of activated STAT1. These results demonstrate that TGF-β rapidly suppresses IFN-γ-driven STAT1 signaling by reducing DNA binding via promotion of STAT1-protein inhibitor of activated STAT1 interactions and not inhibition of STAT1 activation; an event that may be specific to epithelia and represent a novel mode of action of TGF-β.
Cytological, genetic, and biochemical characteristics of an unusual non‐Chlorella photobiont of Stentor polymorphus collected from an artificial pond close to the shore of Lake Biwa, Japan

Stentor polymorphus (Müller) Ehrenberg (Heterotrichea, Ciliophora) is a trumpet‐form ciliate with endosymbiotic green algae (photobionts). Previous reports have indicated that this photobiont has a form typical of Chlorella Beijerinck (Trebouxiophyceae), with one chloroplast and a distinct pyrenoid. We collected S. polymorphus from an artificial pond on the shore of Lake Biwa in Japan. Microscopic examination demonstrated that there was no pyrenoid in the photobiont, and thus we analyzed the cytological, genetic, and biochemical characteristics of these algal cells. Cultured photobionts were smaller than those in hospite. Phylogenetic analyses placed the photobiont within the genus Mychonastes Simpson and Van Valkenburg, a chlorophycean alga occurring in fresh/brackish waters that lacks pyrenoids. Mychonastes provided little photosynthate to its host; the quantity of carbohydrate amounted to only 2% of that provided to Paramecium bursaria (Ehrenberg) Focker by its photobiont.
Utilization of 1BL/1RS translocation in wheat breeding in China

In total, 179 predominant cultivars in recent 30 years and new breeder's lines from main ecological zones of China were examined by SDS PAGE and SCAR for the presence of 1BL/1RS. On average, 38% of Chinese wheats released since 1980 contained 1BL/1RS, however, its frequency differed in different ecological zones, which was 59% for Northern Winter Wheat Zone, 42% for Yellow Huai River Valley Winter Wheat Zone and 20% for both Middle and Low Valley of Yangtze River Winter Wheat Zone and Southwest Winter Wheat Zone. No 1BL/1RS cultivars were found in Northeast Spring Wheat Zone. The cultivars with high dough elasticity were generally not 1BL/1RS translocations. High molecular weight glutenin subunits (HMW GS) may have some complementary effects on the quality defects caused by 1BL/1RS. From breeding point of view, 1BL/1RS parents are generally not recommended in breeding for medium to high dough elasticity, or one of the parents at least should not be 1BL/1RS. Good combination of HMW GS should be presented when 1BL/RS parent is used. The quality defects of 1BL/1RS should also be considered in soft wheat breeding.