Comparative epigenetic and genetic spatial structure in Mediterranean mountain plants: a multispecies study.

Changes in epigenetic states can allow individuals to cope with environmental changes. If such changes are heritable, this may lead to epigenetic adaptation. Thus, it is likely that in sessile organisms such as plants, part of the spatial epigenetic variation found across individuals will reflect the environmental heterogeneity within populations. The departure of the spatial epigenetic structure from the baseline genetic variation can help in understanding the value of epigenetic regulation in species with different breadth of optimal environmental requirements. Here, we hypothesise that in plants with narrow environmental requirements, epigenetic variability should be less structured in space given the lower variability in suitable environmental conditions. We performed a multispecies study that considered seven pairs of congeneric plant species, each encompassing a narrow endemic with habitat specialisation and a widespread species. In three populations per species we used AFLP and methylation-sensitive AFLP markers to characterise the spatial genetic and epigenetic structures. Narrow endemics showed a significantly lower epigenetic than genetic differentiation between populations. Within populations, epigenetic variation was less spatially structured than genetic variation, mainly in narrow endemics. In these species, structural equation models revealed that such pattern was associated to a lack of correlation between epigenetic and genetic information. Altogether, these results show a greater decoupling of the spatial epigenetic variation from the baseline spatial genetic pattern in endemic species. These findings highlight the value of studying genetic and epigenetic spatial variation to better understand habitat specialisation in plants.

The chloroplast protein HCF164 is predicted to be associated with Coffea SH9 resistance factor against Hemileia vastatrix.

To explore the connection between chloroplast and coffee resistance factors, designated as SH1 to SH9, whole genomic DNA of 42 coffee genotypes was sequenced, and entire chloroplast genomes were de novo assembled. The chloroplast phylogenetic haplotype network clustered individuals per species instead of SH factors. However, for the first time, it allowed the molecular validation of Coffea arabica as the maternal parent of the spontaneous hybrid "Híbrido de Timor". Individual reads were also aligned on the C. arabica reference genome to relate SH factors with chloroplast metabolism, and an in-silico analysis of selected nuclear-encoded chloroplast proteins (132 proteins) was performed. The nuclear-encoded thioredoxin-like membrane protein HCF164 enabled the discrimination of individuals with and without the SH9 factor, due to specific DNA variants linked to chromosome 7c (from C. canephora-derived sub-genome). The absence of both the thioredoxin domain and redox-active disulphide center in the HCF164 protein, observed in SH9 individuals, raises the possibility of potential implications on redox regulation. For the first time, the identification of specific DNA variants of chloroplast proteins allows discriminating individuals according to the SH profile. This study introduces an unexplored strategy for identifying protein/genes associated with SH factors and candidate targets of H. vastatrix effectors, thereby creating new perspectives for coffee breeding programs.

Body mass decline in a Mediterranean community of solitary bees supports the size shrinking effect of climatic warming.

The long-known, widely documented inverse relationship between body size and environmental temperature ("temperature-size rule") has recently led to predictions of body size decline following current climatic warming ("size shrinking effect"). For keystone pollinators such as wild bees, body shrinking in response to warming can have significant effects on pollination processes but there is still little direct evidence of the phenomenon because adequate tests require controlling for confounding factors linked to climate change (e.g., habitat change). This paper assesses the shrinking effect in a community of solitary bees from well-preserved habitats in the core of a large nature reserve experiencing climatic warming without disturbances or habitat changes. Long-term variation in mean body mass was evaluated using data from 1704 individual bees (137 species, 27 genera, 6 families) sampled over 1990-2023. Climate warmed at a fast rate during this period, annual mean of daily maximum temperature increasing 0.069°C/year on average during 2000-2020. Changes in bee body mass verified expectations from the size shrinking effect. The mean individual body mass of the community of solitary bees declined significantly, irrespective of whether the analysis referred to the full species sample or only to the subset of species that were sampled in both the old (1990-1997) and recent (2022-2023) periods. On average, body mass declined ~0.7%·year-1 , or an estimated average cumulative reduction of ~20 mg per individual bee from 1990 to 2023. Proportional size reduction was greatest among large-bodied species, ranging from around -0.6%·year-1 for the smallest species to -0.9%·year-1 for the largest ones. Declining rate was steeper for cavity-nesting than ground-nesting species. The pollination and mating systems of bee-pollinated plants in the study region are probably undergoing significant alterations as a consequence of supra-annual decline in bee body mass.

BEHACOM - a dataset modelling users' behaviour in computers.

This paper details the methodology and approach conducted to monitor the behaviour of twelve users interacting with their computers for fifty-five consecutive days without preestablished indications or restrictions. The generated dataset, called BEHACOM, contains for each user a set of features that models, in one-minute time windows, the usage of computer resources such as CPU or memory, as well as the activities registered by applications, mouse and keyboard. It has to be stated that the collected data have been treated in a privacy-preserving way during each phase of the collection and analysis. Together with the features and their explanation, we also detail the software used to gather and process the data. Finally, this article describes the data distribution of the BEHACOM dataset.

Pollination effectiveness in a generalist plant: adding the genetic component.

The pollination effectiveness of a flower visitor has traditionally been measured as the product of a quantity component that depends on the frequency of interaction and a quality component that measures the per-visit effects on plant reproduction. We propose that this could be complemented with a genetic component informing about each pollinator's contribution to the genetic diversity and composition of the plant progeny. We measured the quantity and quality components of effectiveness of most pollinator functional groups of the generalist herb Erysimum mediohispanicum. We used 10 microsatellite markers to calculate the genetic component as the diversity of sires among siblings and included it into the calculation of the pollination effectiveness. Functional groups varied in the quantity and quality components, which were shown to be decoupled. Functional groups also differed in the genetic component. This component changed the estimates of pollination effectiveness, increasing the differences between some functional groups and modifying the pollination effectiveness landscape. We demonstrate that including the genetic component in the calculation of the pollination effectiveness may allow a more complete quantification of the contribution of each pollinator to the reproductive success of a plant, providing information on its mating patterns and long-term fitness.

Potential of RP-UHPLC-DAD-MS for the qualitative and quantitative analysis of sofosbuvir in film coated tablets and profiling degradants.

Sofosbuvir is one of the new direct-acting antiviral drugs against hepatitis C virus (HCV) infection. This drug has recently been launched into the market, and generic versions of the medication are expected to be produced by local drug producers in some countries. Therefore, new methods are required to control sofosbuvir in pharmaceuticals. In the present study, a new method based on reversed phase (RP)-ultra-high performance liquid chromatography (UHPLC) coupled to diode array detection (DAD) and mass spectrometry (MS) was developed to facilitate the qualitative and quantitative analysis of sofosbuvir in film coated tablets. A wavelength of 260 nm was selected to perform a cost-effective quantification and the method showed adequate linearity, with an R2 value of 0.9998, and acceptable values of accuracy (75%-102%) and precision (residual standard deviation <5%). The detection and quantification limits were 0.07 µg/mL and 0.36 µg/mL, respectively. Furthermore, the use of high-resolution MS enabled us to ensure the specificity, check impurities and better sensitivity. Therefore, this methodology promises to be suitable not only for the routine analysis of sofosbuvir in pharmaceutical dosage forms, but also for potential degradants.

Potential of RP-UHPLC-DAD-MS for the qualitative and quantitative analysis of sofosbuvir in film coated tablets and profiling degradants / 药物分析学报

Sofosbuvir is one of the new direct-acting antiviral drugs against hepatitis C virus (HCV) infection. This drug has recently been launched into the market, and generic versions of the medication are expected to be produced by local drug producers in some countries. Therefore, new methods are required to control sofosbuvir in pharmaceuticals. In the present study, a new method based on reversed phase (RP)-ultra-high performance liquid chromatography (UHPLC) coupled to diode array detection (DAD) and mass spectrometry (MS) was developed to facilitate the qualitative and quantitative analysis of sofosbuvir in film coated tablets. A wavelength of 260 nm was selected to perform a cost-effective quantification and the method showed adequate linearity, with an R2 value of 0.9998, and acceptable values of accuracy (75%–102%) and precision (residual standard deviation < 5%). The detection and quantification limits were 0.07 μg/mL and 0.36 μg/mL, respectively. Furthermore, the use of high-resolution MS enabled us to ensure the specificity, check impurities and better sensitivity. Therefore, this methodology promises to be suitable not only for the routine analysis of sofosbuvir in pharmaceutical dosage forms, but also for potential degradants.

Inter-annual maintenance of the fine-scale genetic structure in a biennial plant.

Within plant populations, space-restricted gene movement, together with environmental heterogeneity, can result in a spatial variation in gene frequencies. In biennial plants, inter-annual flowering migrants can homogenize gene frequencies between consecutive cohorts. However, the actual impact of these migrants on spatial genetic variation remains unexplored. Here, we used 10 nuclear microsatellite and one plastid genetic marker to characterize the spatial genetic structure within two consecutive cohorts in a population of the biennial plant Erysimum mediohispanicum (Brassicaceae). We explored the maintenance of this structure between consecutive flowering cohorts at different levels of complexity, and investigated landscape effects on gene flow. We found that cohorts were not genetically differentiated and showed a spatial genetic structure defined by a negative genetic-spatial correlation at fine scale that varied in intensity with compass directions. This spatial genetic structure was maintained when comparing plants from different cohorts. Additionally, genotypes were consistently associated with environmental factors such as light availability and soil composition, but to a lesser extent compared with the spatial autocorrelation. We conclude that inter-annual migrants, in combination with limited seed dispersal and environmental heterogeneity, play a major role in shaping and maintaining the spatial genetic structure among cohorts in this biennial plant.

Photophysics of a Live-Cell-Marker, Red Silicon-Substituted Xanthene Dye.

Dyes with near-red emission are of great interest because of their undoubted advantages for use as probes in living cells. In-depth knowledge of their photophysics is essential for employment of such dyes. In this article, the photophysical behavior of a new silicon-substituted xanthene, 7-hydroxy-5,5-dimethyl-10-(o-tolyl)dibenzo[b,e]silin-3(5H)-one (2-Me TM), was explored by means absorption, steady-state, and time-resolved fluorescence. First, the near-neutral pH, ground-state acidity constant of the dye, pKN-A, was determined by absorbance and steady-state fluorescence at very low buffer concentrations. Next, we determined whether the addition of phosphate buffer promoted the excited-state proton-transfer (ESPT) reaction among the neutral and anion form of 2-Me TM in aqueous solutions at near-neutral pH. For this analysis, both the steady-state fluorescence method and time-resolved emission spectroscopy (TRES) were employed. The TRES experiments demonstrated a remarkably favored conversion of the neutral form to the anion form. Then, the values of the excited-state rate constants were determined by global analysis of the fluorescence decay traces recorded as a function of pH, and buffer concentration. The revealed kinetic parameters were consistent with the TRES results, exhibiting a higher rate constant for deprotonation than for protonation, which implies an unusual low value of the excited-state acidity constant pK*N-A and therefore an enhanced photoacid behavior of the neutral form. Finally, we determined whether 2-Me TM could be used as a sensor inside live cells by measuring the intensity profile of the probe in different cellular compartments of HeLa 229 cells.

Evolution of pollination niches in a generalist plant clade.

It is widely assumed that floral diversification occurs by adaptive shifts between pollination niches. In contrast to specialized flowers, identifying pollination niches of generalist flowers is a challenge. Consequently, how generalist pollination niches evolve is largely unknown. We apply tools from network theory and comparative methods to investigate the evolution of pollination niches among generalist species belonging to the genus Erysimum. These species have similar flowers. We found that the studied species may be grouped in several multidimensional niches separated not by a shift of pollinators, but instead by quantitative variation in the relative abundance of pollinator functional groups. These pollination niches did not vary in generalization degree; we did not find any evolutionary trend toward specialization within the studied clade. Furthermore, the evolution of pollination niche fitted to a Brownian motion model without phylogenetic signal, and was characterized by frequent events of niche convergences and divergences. We presume that the evolution of Erysimum pollination niches has occurred mostly by recurrent shifts between slightly different generalized pollinator assemblages varying spatially as a mosaic and without any change in specialization degree. Most changes in pollination niches do not prompt floral divergence, a reason why adaptation to pollinators is uncommon in generalist plants.

The occurrence and bioactivity of polyphenols in Tunisian olive products and by-products: a review.

Polyphenols have become a subject of intense research because of their perceived beneficial effects on health due to their anticarcinogenic, antiatherogenic, anti-inflammatory, and antimicrobial activities. It is well known that olives and their derivatives are rich in phenolic substances with pharmaceutical properties, some of which exert important antioxidant effects. The characterization and quantification of their polyphenol composition is one of the first steps to be taken in any evaluation of the putative contribution of the olive to human health. This review is concerned with polyphenols in Tunisian olive (Olea europaea L.) products (fruit and oil) and some by-products (leaves and olive-mill wastewater) with an emphasis on the analytical methods used, as well as the biological activities described in recent years.