Miracle-dz/UniFAR-FTUs huggingface dataset:
Enzymological aspects of phytoalexin accumulation in Phaseolus vulgaris

In wounded cotyledons of Phaseolus vulgaris the accumulation of the 5-hydroxy isoflavonoids 2'-hydroxygenistein and kievitone preceded the major increases in the levels of the 5-deoxy compounds coumestrol and phaseollin. Increased phytoalexin (kievitone and phaseollin) levels were preceded by transient increases in the extractable activities of L-phenylalanine ammonia-lyase (EC 4,3.1.5), chalcone synthase and chalcone isomerase (EC 5.5.1.6). ^^C-NMR analysis of kievitone and phaseollin produced after feeding [l,2-^^C2] acetate to wounded cotyledons demonstrated the incorporation of intact acetate units into the aromatic A-rings. Phaseollin showed a specific folding of the polyketide chain whereas kievitone exhibited a randomisation of the label in keeping with the intermediacy of a 2',4*,6'-trihydroxychalcone during its formation. The biosynthetic routes to these 5-hydroxy and 5-deoxy isoflavonoids thus diverge prior to chalcone formation. The results suggest the involvement of a 6'-deoxy chalcone synthase in the biosynthesis of 5-deoxy isoflavonoid compounds. However, efforts to locate the activity of such an enzyme were unsuccessful. 6'-Hydroxy chalcone synthase and chalcone isomerase were purified from cell suspension cultures of P. vulgaris. Chalcone synthase showed many similarities to the enzyme purified from Petroselinum hortense but was much less stable, had significantly different apparent values for the two substrates and produced different in vitro release products following purification. With malonyl CoA as variable substrate, double reciprocal plots for naringenin formation were sigmoidal suggesting positive cooperativity which may favour the formation of chalcones in vivo. Only a single form of chalcone isomerase was found; however, the enzyme catalysed the isomérisation of both 6'-hydroxy and 6'-deoxy chalcones to the corresponding flavanones. Kievitone strongly inhibited the activity of both enzymes whilst coumestrol was a potent inhibitor of chalcone isomerase A range of other 5-hydroxy and 5-deoxy isoflavonoid compounds tested had little or no effect on the activity of the two enzymes. The possible relevance of the inhibitory effects of such compounds is discussed in relation to the role of both enzymes in the induced accumulation of isoflavonoid phytoalexins in P. vulgaris.
Biocompatibility and zinc release testing of a zinc-containing vaginal gel.

OBJECTIVE To test the biocompatibility of a zinc-containing vaginal gel, evaluate its ability to release zinc, and to assess the transepithelial permeability of zinc on human vaginal epithelium. METHODS The release and membrane diffusion of zinc from the vaginal gel was tested by a vertical Franz-diffusion cell system. The biocompatibility of the gel was tested on HaCaT cells and reconstructed human vaginal epithelium. MTT assay was used to detect cell viability. Lactate dehydrogenase (LDH) assay was used to access cytotoxicity. The permeability of zinc was tested on the reconstructed human vaginal epithelium. The integrity of the reconstructed human vaginal epithelium after the permeability experiments was measured by transepithelial electric resistance. Zinc levels were determined by inductively coupled plasma optical emission spectrometry. RESULTS 20 μM zinc sulfate did not decrease cell viability during the 24 and 72-hour treatment. Similarly, cell viability did not decrease significantly after 60 minutes of incubation with the gel and no toxic compound released from the vaginal gel during the 120 minutes diffusion experiment. A total of 72-hour exposure to the zinc-containing vaginal gel showed no cytotoxicity using LDH assay. Using cellulose-acetate membranes, 24.6% of the zinc content of the gel was released and appeared in the acceptor phase after 15 minutes. Zinc had high permeability (2.2 ± 0.8 × 10 cm/s) from the vaginal gel on reconstructed human vaginal epithelium. CONCLUSIONS The zinc-containing (20 μM) vaginal gel was not toxic. The release of zinc is rapid from the vaginal gel. Zinc permeated rapidly through the vaginal epithelial cell layers.
Habitat Indicators of a Federally Listed Glacial Relict Plant Species Restricted to Cliffs in the Northern United States

ABSTRACT: Conservation of global biodiversity requires studies of rare taxa at high risk for extinction due to anthropogenic impacts. Rhodiola integrifolia subsp. leedyi (Leedy's roseroot, Crassulaceae) is a rare cliff-dwelling subspecies federally listed as threatened in the United States. Thought to be glacial relicts, all seven known populations of Leedy's roseroot are endemic to cliffs, likely in large part due to the specific environmental factors at these cliffs. This study took place at Glenora Cliffs, New York, the location of the largest population of this subspecies in the world. We identified habitat factors associated with Leedy's roseroot occurrence by comparing areas where Leedy's roseroot was present to adjacent areas where Leedy's roseroot was absent. Leedy's roseroot occurrence was associated with increased light, lower height on the cliff, geologic features of the cliff including greater degree of water seeping from crevices, higher plant species richness, and higher mean temperatures, with temperature trends varying over the growing season. Leedy's roseroot stem length was correlated with decreased light and temperature, and cliff features. Analysis of the Glenora Cliffs plant species community suggested seepage and cliff features structure the community. Leedy's roseroot co-occurred with other cliff-dwelling species that may serve as indicators of Leedy's roseroot habitat. Our characterization of habitat factors associated with Leedy's roseroot supports its glacial relict status, suggests global climate change may impact it differently than most plant species, and informs management and potential ex situ conservation of this rare subspecies.
Identification of deregulated transcription factors involved in subtypes of cancers

We propose a methodology for the identification of transcription factors involved in the deregulation of genes in tumoral cells. This strategy is based on the inference of a reference gene regulatory network that connects transcription factors to their downstream targets using gene expression data. The behavior of genes in tumor samples is then carefully compared to this network of reference to detect deregulated target genes. A linear model is finally used to measure the ability of each transcription factor to explain those deregulations. We assess the performance of our method by numerical experiments on a breast cancer data set. We show that the information about deregulation is complementary to the expression data as the combination of the two improves the supervised classification performance of samples into cancer subtypes.
Historical biogeography of Melicope (Rutaceae) and its close relatives with a special emphasis on Pacific dispersals

The genus Melicope (Rutaceae) occurs on most Pacific archipelagos and is perfectly suited to study Pacific biogeography. The main goal was to infer the age, geographic origin and colonization patterns of Melicope and its relatives. We sequenced three nuclear and two plastid markers for 332 specimens that represent 164 species in 16 genera of Rutaceae. Phylogenetic reconstruction, molecular dating, ancestral area reconstruction and diversification analyses were carried out. The two main clades (Acronychia‐Melicope and Euodia) originated in Australasia and their crown ages are dated to the Miocene. Diversification rates differed among the subclades and were lowest in the Euodia lineage and highest in the Hawaiian Melicope lineage. The Malagasy and Mascarene species form a clade, which split from its SE Asian relatives in the Pliocene/Pleistocene. At least eight colonizations to the Pacific islands occurred. The timing of all colonizations except for the Hawaiian group is congruent with age of the island ages. Australia, New Guinea and New Caledonia have been the source of colonizations into the Pacific islands in the Melicope clade. Melicope shows high dispersability and has colonized remote archipelagos such as the Austral and Marquesas Islands each twice. Colonization of islands of the Hawaiian‐Emperor seamount chain likely predates the ages of the current main islands, and the initial colonization to Kaua'i occurred after the splitting of the Hawaiian lineage into two subclades. Wider ecological niches and adaptations to bird‐dispersal likely account for the much higher species richness in the Acronychia‐Melicope clade compared to the Euodia clade.
Meso-Carnivore Niche Expansion in Response to an Apex Predator's Reintroduction - a Stable Isotope Approach

Apex predators can have considerable impacts on meso-carnivore diets, through competition or facilitation. Facilitation occurs when smaller predators consume carrion created by larger predators, especially large-bodied prey species normally inaccessible to meso-carnivores. In contrast, apex predators can also negatively affect meso-carnivore consumption of important resources through competitive interactions. Thus, predicting meso-carnivore responses to trophic structure changes (i.e. apex predator extirpation or reintroduction) is often difficult. We investigated stable carbon and nitrogen isotope niche breadths of black-backed jackal (Canis mesomelas) in response to the reintroduction of an apex predator, the African lion (Panthera leo), to the Karoo National Park, South Africa. Jackal faecal isotopic niche widths were larger in post-lion than pre-lion samples, indicating a niche expansion to include pure C3- and C4-based food sources when lions were present. Most prey items of this nature in the study area are large-bodied ungulates. Our results agree with results of traditional scat analysis, which showed that prey species >92 kg were consumed more often after the lion reintroduction. Stable isotope data from carnivore faeces are effective for tracking responses of wildlife to changing ecological conditions, providing an alternative source of information about changes in community structure brought about by management interventions.
USP11 promotes tumorigenesis and enhances MRI detection in breast cancer

Background: Ubiquitin-specific protease 11 (USP11) is a member of the deubiquitylating enzyme families. It usually works as an oncogene in some types of cancer such as colorectal and pancreatic cancers. But whether USP11 has a role in mediating tumorigenesis in breast cancer, the evidence is rare. Methods: In order to evaluate the role of USP11 in breast cancer, qRT-PCR, western blot, cell growth assay, transwell assay and in vivo MRI assay was used. Co-immunoprecipitation assay and GST pull down assay revealed that the mechanism of USP11 contributes to the breast cancer progression in vivo and in vitro . Results: The higher expression of USP11 was observed in the 120 breast cancer samples as well as the breast cancer cell lines compared with the normal breast tissues or normal breast mammary epithelial cell line. Furthermore, the higher expression of USP11 indicated a poorer overall 5-year survivals and worse prognosis. We identified USP11 played a critical role in the breast cancer cells proliferation, invasion and in vivo magnetic resonance imaging detection through counterbalanced Enhancer of zeste homologue 2 (EZH2) ubiquitination and stabilized it in MCF-7 cells and MDA-MB-231 cells. Conclusions: Taken together, our study suggested that USP11 promoted breast cancer cell tumorigenesis and might work as a new biomarker and novel therapeutic target.
Genome-wide sampling suggests island divergence accompanied by cryptic epigenetic plasticity in Canada lynx

ABSTRACT Determining the molecular signatures of adaptive differentiation is a fundamental component of evolutionary biology. A key challenge remains for identifying such signatures in wild organisms, particularly between populations of highly mobile species that undergo substantial gene flow. The Canada lynx (Lynx canadensis) is one species where mainland populations appear largely undifferentiated at traditional genetic markers, despite inhabiting diverse environments and displaying phenotypic variation. Here, we used high-throughput sequencing to investigate both neutral genetic structure and epigenetic differentiation across the distributional range of Canada lynx. Using a customized bioinformatics pipeline we scored both neutral SNPs and methylated nucleotides across the lynx genome. Newfoundland lynx were identified as the most differentiated population at neutral genetic markers, with diffusion approximations of allele frequencies indicating that divergence from the panmictic mainland occurred at the end of the last glaciation, with minimal contemporary admixture. In contrast, epigenetic structure revealed hidden levels of differentiation across the range coincident with environmental determinants including winter conditions, particularly in the peripheral Newfoundland and Alaskan populations. Several biological pathways related to morphology were differentially methylated between populations, with Newfoundland being disproportionately methylated for genes that could explain the observed island dwarfism. Our results indicate that epigenetic modifications, specifically DNA methylation, are powerful markers to investigate population differentiation and functional plasticity in wild and non-model systems. SIGNIFICANCE Populations experiencing high rates of gene flow often appear undifferentiated at neutral genetic markers, despite often extensive environmental and phenotypic variation. We examined genome-wide genetic differentiation and DNA methylation between three interconnected regions and one insular population of Canada lynx (Lynx canadensis) to determine if epigenetic modifications characterized climatic associations and functional molecular plasticity. Demographic approximations indicated divergence of Newfoundland during the last glaciation, while cryptic epigenetic structure identified putatively functional differentiation that might explain island dwarfism. Our study suggests that DNA methylation is a useful marker for differentiating wild populations, particularly when faced with functional plasticity and low genetic differentiation.
Increasing bacterial affinity and cytocompatibility with four-arm star glycopolymers and antimicrobial α-polylysine

A series of four-arm star copolymers, incorporating glycopolymer and antimicrobial polypeptide domains, was developed in the design of forthcoming anti-infective agents. Mannose, glucose, and galactose-based glycopolymers with a variety of well-defined chain lengths were prepared via atom transfer radical polymerization, whereas linear α-polylysine was prepared via ring-opening polymerization of N-carboxyanhydride monomers. Copper-catalyzed azide–alkyne cycloaddition was employed for ‘click’ conjugation of the glycopolymer arms and the polypeptide chains. The glycopolymer–polypeptide conjugates were non-hemolytic and exhibited higher cytocompatibility than the linear α-polylysine. The conjugates with shorter chains of mannose-based glycopolymer arms showed an enhanced bactericidal efficacy against Gram-negative and Gram-positive bacteria, with a therapeutic selectivity half of that of the linear α-polylysine. The pendant mannose moieties of the conjugates increased microbial targeting due to their specific affinity for bacterial surfaces, and binding competition with free mannopyranoside was demonstrated. Therefore, the molecular combination of glycopolymers and polypeptides without loss of their respective activities provides an interesting concept in the design of antimicrobial agents to combat infectious disease.
Enzymatic synthesis of structured lipids from liquid and fully hydrogenated high oleic sunflower oil

ABSTRACT Structured lipids (SL) were synthesized via enzymatic (EI) and chemical interesterification of high oleic sunflower oil (SO) and fully hydrogenated high oleic SO with Lipozyme TL IM (Thermomyces lanuginose) for 3 h at 70°C, 300 rpm. Reaction showed changes in the triacylglycerols (TAGs) composition, solid fat content (SFC), thermal behavior, regiospecific distribution, microstructure, and polymorphism. Results revealed that the EI caused considerable rearrangement of the TAG species with lower levels of tri-saturated and tri-unsaturated TAG and higher levels of monoun- and diunsaturated TAG. The interesterified blends showed reduced SFC between 20 and 35°C, lowering the melting point. After 3-h incubation, EI produced acyl migration to some extent. The SL showed the required characteristics for application as bakery fats and as additives for lipid crystallization in the food industry.
Pigments, Polyphenols and Antioxidant Activity of Leaf Extracts from Four Wild Rose Species Grown in Sicily

Leaf methanolic extracts of four wild Rose species ( Rosa canina L., R. corymbifera Borkh., R. micrantha Borrer ex Sm and R. sempervirens L.) grown in Sicily were analysed in order to evaluate differences among indigenous roses which could be used such as source of bioactive compounds and natural antioxidants. Leaves were harvested during two different periods (June and October) and their morphological characteristics were described. Leaf content of chlorophylls, total anthocyanins, total flavonoids, total polyphenols (Folin-Ciocalteu method) and antioxidant activity (DPPH method) were determined. Results showed that the contents of chlorophylls and carotenoids were higher in leaves of all species harvested in June than in those harvested in October. On the contrary, total anthocyanins of R. micrantha and R. corymbifera leaves were higher in October. Total polyphenol content was higher in leaves of all species were harvested in October. No difference in total flavonoids content was recorded between the two harvest periods but only among the four species. Antioxidant activity was generally high in leaf extracts of all species in both periods and, particularly, in R. micrantha leaves harvested in June. These outcomes seem to support the assessment that leaves harvested from some Sicilian wild roses may be used as promising source of healthy compounds and that their content varies with the species and harvest period.
Parameter study of particle collisions to avoid particle clustering in ISPH

Incompressible Smoothed Particle Hydrodynamics (ISPH) is a particle method to simulate complex flows, which is suited to flows with large deformation and violent free surface. A regular or even particle distribution is a crux for the stability and accuracy of ISPH. Particle clustering is a common phenomenon in particle methods, in particular when simulating unsteady flows. In the past, several remedies to prevent particle clustering were presented, for example the Particle Shifting Technique (PST) based on a diffusive term first introduced by Xu et al. [1] and the particle collision model described by Kruisbrink et al. [2].
Nest-Site Characteristics and Nesting Success of the Chestnut Thrush

Abstract Nest-site characteristics may affect the daily survival rate of avian nests. We monitored the nests of Chestnut Thrush Turdus rubrocanus breeding in an agricultural landscape near the Lianhuashan Natural Reserve (central China) during the breeding seasons of 2013 and 2014. We describe the Chestnut Thrush's breeding ecology and used logistic-exposure methods and an information theoretic approach to assess the factors influencing daily survival rates of nests. Results from model averaging indicated that daily survival rates of nests consistently decreased from habitat edge to interior, contradicting the classic edge effect hypothesis describing predation of avian nests. Concealment of nests from below was positively correlated with nest daily survival rates, whereas concealment from the side and from above were not. These results suggest that determining the various effects of vertical and/or horizontal concealment on nest survival rates may help us assess the variation in the ability of local predators to detect nests.
Multivariate autoregressive modelling and conditional simulation for temporal uncertainty propagation in urban water systems

Abstract. Uncertainty is often ignored in urban water systems modelling. Commercial software used in engineering practice often ignores uncertainties of input variables and their propagation because of a lack of user-friendly implementations. This can have serious consequences, such as the wrong dimensioning of urban drainage systems (UDS) and the inaccurate estimation of pollution released to the environment. This paper introduces an uncertainty analysis framework in urban drainage modelling and applies it to a case study in the Haute-Sûre catchment in Luxembourg. The framework makes use of the EmiStatR model which simulates the volume and substance flows in UDS using simplified representations of the drainage system and processes. A Monte Carlo uncertainty propagation analysis showed that uncertainties in chemical oxygen demand (COD) and ammonium (NH4) loads and concentrations can be large and have a high temporal variability. Further, a stochastic sensitivity analysis that assesses the uncertainty contributions of input variables to the model output response showed that precipitation has the largest contribution to output uncertainty related with water quantity variables, such as volume in the chamber, overflow volume and flow. Regarding the water quality variables, the input variable related to COD in the wastewater has an important contribution to the uncertainty for COD load (66 %) and COD concentration (62 %). Similarly, the input variable related to NH4 in the wastewater plays an important role in the contribution of total uncertainty for NH4 load (34 %) and NH4 concentration (35 %). The Monte Carlo simulation procedure used to propagate input uncertainty showed that among the water quantity output variables, the overflow flow is the most uncertain output variable with a coefficient of variation (cv) of 1.59. Among water quality variables, the annual average spill COD oncentration and the average spill NH4 concentration were the most uncertain model outputs (coefficients of variation of 0.99 and 0.82, respectively). Also, low standard errors for the coefficient of variation were obtained for all seven outputs. These were never greater than 0.05, which indicates that the selected MC replication size (1,500 simulations) was sufficient. We also evaluated how uncertainty propagation can explain more comprehensively the impact of water quality indicators for the receiving river. While the mean model water quality outputs for COD and NH4 concentrations were slightly above the threshold, the 0.95 quantile was 2.7 times above the mean value for COD concentration, and 2.4 times above the mean value for NH4. This implies that there is a considerable probability that these concentrations in the spilled CSO are substantially larger than the threshold. However, COD and NH4 concentration levels of the river water will likely stay below the water quality threshold, due to rapid dilution after CSO spill enters the river.