Spatial and temporal variation in population dynamics of Andean frogs: Effects of forest disturbance and evidence for declines

AbstractBiodiversity loss is a global phenomenon that can result in the collapse of food webs and critical ecosystem services. Amphibian population decline over the last century is a notable case of species loss because amphibians survived the last four major extinction events in global history, their current rate of extinction is unprecedented, and their rate of extinction is greater than that for most other taxonomic groups. Despite the severity of this conservation problem and its relevance to the study of global biodiversity loss, major knowledge gaps remain for many of the most threatened species and regions in the world. Rigorous estimates of population parameters are lacking for many amphibian species in the Neotropics. The goal of our study was to determine how the demography of seven species of the genus Pristimantis varied over time and space in two cloud forests in the Ecuadorian Andes. We completed a long term capture–mark–recapture study to estimate abundance, survival, and population growth rates in two cloud forests in the Ecuadorian Andes; from 2002 to 2009 at Yanayacu in the Eastern Cordillera and from 2002 to 2003 at Cashca Totoras in the Western Cordillera. Our results showed seasonal and annual variation in population parameters by species and sex. P. bicantus experienced significant reductions in abundance over the course of our study. Abundance, apparent survival, and population growth rates were lower in disturbed than in primary or mature secondary forest. The results of our study raise concerns for the population status of understudied amphibian groups and provide insights into the population dynamics of Neotropical amphibians

Herbage Intake, Methane Emissions and Animal Performance of Steers Grazing Dwarf Elephant Grass with or without Access to \u3cem\u3eArachis pintoi\u3c/em\u3e Pastures

The inclusion of legumes in diets based on grass has nutritional benefits due to ingestive and digestive interactions (Niderkorn and Baumont 2009). Moreover, it is speculated that tropical legumes can contribute to reducing the emission of greenhouse gases (GHG) compared to diets exclusively composed of grasses (Archimède et al. 2011). However, under grazing conditions, these advantages are not always possible to obtain. This occurs when the spatial distribution of sward grasses impose limitations on access to legumes by grazing animals (Solomon et al. 2011). This can be the case, for example, when legumes are overlapped by the leaves of a tufted tall grass, as dwarf elephant grass (Crestani et al. 2013). Considering that management strategies for increasing legumes in the diet of grazing animals should be better studied and data on enteric methane emitted by ruminants eating tropical forages are scarce, the aim of this work was to evaluate the effect of access to an exclusive area of peanuts (Arachis pintoi cv. Amarillo) for cattle grazing dwarf elephant grass (Pennisetum purpureum cv. BRS Kurumi) on herbage intake, animal performance and enteric methane emission

Modeling methylation data as an additional genetic variance component

High-throughput platforms allow the characterization of thousands of previously known methylation sites. These platforms have great potential for investigating the epigenetic effects that are partially responsible for gene expression control. Methylation sites provide a bridge for the investigation of real-time environmental contributions on genomic events by the alteration of methylation status of those sites. Using the data provided by GAW20’s organization committee, we calculated the heritability estimates of each cytosine-phosphate-guanine (CpG) island before and after the use of fenofibrate, a lipid-control drug. Surprisingly, we detected substantially high heritability estimates before drug usage. This somewhat unexpected high sample correlation was corrected by the use of principal components and the distributions of heritability estimates before and after fenofibrate treatment, which made the distributions comparable. The methylation sites located near a gene were collected and a genetic relationship matrix estimated to represent the overall correlation between samples. We implemented a randomeffect association test to screen genes whose methylation patterns partially explain the observable high-density lipoprotein (HDL) heritability. Our leading association was observed for the TMEM52 gene that encodes a transmembrane protein, and is largely expressed in the liver, had not been previously associated with HDL until this manuscript. Using a variance component decomposition framework with the linear mixed model allows the integration of data from different sources, such as methylation, gene expression, metabolomics, and proteomics. The decomposition of the genetic variance component decomposition provides a flexible analytical approach for the challenges of this new omics era

Modeling methylation data as an additional genetic variance component

High-throughput platforms allow the characterization of thousands of previously known methylation sites. These platforms have great potential for investigating the epigenetic effects that are partially responsible for gene expression control. Methylation sites provide a bridge for the investigation of real-time environmental contributions on genomic events by the alteration of methylation status of those sites. Using the data provided by GAW20’s organization committee, we calculated the heritability estimates of each cytosine-phosphate-guanine (CpG) island before and after the use of fenofibrate, a lipid-control drug. Surprisingly, we detected substantially high heritability estimates before drug usage. This somewhat unexpected high sample correlation was corrected by the use of principal components and the distributions of heritability estimates before and after fenofibrate treatment, which made the distributions comparable. The methylation sites located near a gene were collected and a genetic relationship matrix estimated to represent the overall correlation between samples. We implemented a randomeffect association test to screen genes whose methylation patterns partially explain the observable high-density lipoprotein (HDL) heritability. Our leading association was observed for the TMEM52 gene that encodes a transmembrane protein, and is largely expressed in the liver, had not been previously associated with HDL until this manuscript. Using a variance component decomposition framework with the linear mixed model allows the integration of data from different sources, such as methylation, gene expression, metabolomics, and proteomics. The decomposition of the genetic variance component decomposition provides a flexible analytical approach for the challenges of this new omics era

Semiclassical approach to fidelity amplitude

The fidelity amplitude is a quantity of paramount importance in echo type experiments. We use semiclassical theory to study the average fidelity amplitude for quantum chaotic systems under external perturbation. We explain analytically two extreme cases: the random dynamics limit --attained approximately by strongly chaotic systems-- and the random perturbation limit, which shows a Lyapunov decay. Numerical simulations help us bridge the gap between both extreme cases.Comment: 10 pages, 9 figures. Version closest to published versio

Rice F-bZIP transcription factors regulate the zinc deficiency response

The F-bZIP transcription factors bZIP19 and bZIP23 are the central regulators of the zinc deficiency response in Arabidopsis, and phylogenetic analysis of F-bZIP homologs across land plants indicates that the regulatory mechanism of the zinc deficiency response may be conserved. Here, we identified the rice F-bZIP homologs and investigated their function. OsbZIP48 and OsbZIP50, but not OsbZIP49, complement the zinc deficiency-hypersensitive Arabidopsis bzip19bzip23 double mutant. Ectopic expression of OsbZIP50 in Arabidopsis significantly increases plant zinc accumulation under control zinc supply, suggesting an altered Zn sensing in OsbZIP50. In addition, we performed a phylogenetic analysis of F-bZIP homologs from representative monocot species that supports the branching of plant F-bZIPs into Group 1 and Group 2. Our results suggest that regulation of the zinc deficiency response in rice is conserved, with OsbZIP48 being a functional homolog of AtbZIP19 and AtbZIP23. A better understanding of the mechanisms behind the Zn deficiency response in rice and other important crops will contribute to develop plant-based strategies to address the problems of Zn deficiency in soils, crops, and cereal-based human diets.</p

Joint Scheduling, Routing and Gateway Designation in Real-Time TSCH Networks

International audienceThis research proposes a co-design framework for scheduling, routing and gateway designation to improve the real-time performance of low-power wireless mesh networks. We target time-synchronized channel hopping (TSCH) networks with centralized network management and a single gateway. The end goal is to exploit existing trade-offs between the three dimensions to enhance traffic schedulability at systems’ design time. The framework we propose considers a global Earliest-Deadline-First (EDF) scheduler that operates in conjunction with the minimal-overlap (MO) shortest-path routing, after a centrality-driven gateway designation is concluded. Simulation results over varying settings suggest our approach can lead to optimal or near-optimal real-time network performance, with 3 times more schedulable flows than a naive real-time configuration

Interference with Hemozoin Formation Represents an Important Mechanism of Schistosomicidal Action of Antimalarial Quinoline Methanols

Heme is an essential molecule to most living organisms, but once in a free state it exerts toxic effects. Blood-feeding organisms evolved efficient ways to detoxify free heme derived from hemoglobin digestion. A key mechanism present in some hematophagous organisms consists of the crystallization of heme into a pigment named hemozoin. Schistosoma mansoni is one of the etiologic agents of human schistosomiasis, a parasitic disease that affects over 200 million people in tropical and subtropical areas. Hemozoin formation represents the main heme detoxification pathway in S. mansoni. Here, we report that the antimalarial quinoline methanols quinine and quinidine exert schistosomicidal effects notably due to their capacity to interfere with hemozoin formation. When quinine or quinidine were administered intraperitoneally during seven days to S. mansoni-infected mice (75 mg/kg/day), both worm and eggs burden were significantly reduced. Interestingly, hemozoin content in female worms was drastically affected after treatment with either compound. We also found that quinine caused important changes in the cellular organization of worm gastrodermis and increased expression of genes related to musculature, protein synthesis and repair mechanisms. Together, our results indicate that interference with hemozoin formation is a valid chemotherapeutic target for development of new schistosomicidal agents

Phase angle and COVID-19: a systematic review with meta-analysis

Phase angle (PhA) has been identified as a poor prognostic factor in patients with COVID-19. This study aimed to achieve a systematic review, where we discussed the potential role of PhA value as a prognostic marker of adverse clinical outcomes such as mortality and complication in hospitalized with SARS-CoV2 infection and established the strength of recommendations for use. A systematic literature review with meta-analysis was done in the main electronic databases from 2020 to January 2023. The selected articles had to investigate adverse consequences of the COVID-19 population and raw bioimpedance parameters such as PhA and published in peer-reviewed journals. GRADE tools regarded the quality of the methodology. The review protocol was registered in PROSPERO. Only eight studies, 483 studies, were eligible for the analysis. In general, differences in PhA were seen between the comparative study groups. Patients with a low PhA experienced poor outcomes. A low PhA was associated with a significantly increased mortality risk [RR: 2.44; 95% CI (1.20–4.99), p = 0.01; I2 = 79% (p = 0.0008)] and higher complications risk [OR: 3.47, 95% CI (1.16 – 10.37), p = 0.03; I2 = 82% (p = 0.004)] in COVID-19 patients. Our analysis showed four evidence-based recommendations on the prognostic value of PhA with two strong recommendations, one of moderate and another of low-moderate quality, for predicting mortality and complications, respectively. We recommend using PhA as a prognostic marker for mortality and complications in this population. Although the results are promising, future studies must identify the PhA cut-off to guide therapeutic decisions more precisely.Funding for open access publishing: Universidad Málaga/CBUA. I.C.-P. was the recipient of a postdoctoral grant (Río Hortega CM 17/00169) and is now the recipient of a postdoctoral grant (Juan Rodes JR 19/00054) from the Instituto de Salud Carlos III and co-funded by Fondo Europeo de Desarrollo Regional-FEDER. Funding for open access charge: Universidad de Málaga / CBU

The mineralocorticoid receptor forms higher order oligomers upon DNA binding.

The mineralocorticoid and glucocorticoid receptors (MR and GR) are evolutionary related nuclear receptors with highly conserved DNA- and ligand-binding domains (DBD and LBD), which determine promiscuous activation by corticosteroid hormones (aldosterone and glucocorticoids) and binding to a shared DNA consensus sequence, the hormone response element (HRE). In addition, MR and GR functionally interact, likely through direct formation of heteromeric complexes, potentially contributing to cell-specific corticosteroid signaling. It has recently been proposed that agonist and DNA binding promote GR self-association in tetramers. Here we investigated MR quaternary arrangement after receptor activation. To that end we used a fluorescence imaging technique, Number & Brightness (N&B) analysis, in a cell system where receptor-DNA interaction can be studied in live cells in real time. Our results show that agonist-bound MR is a tetramer in the nucleoplasm, forming higher order oligomers upon binding to HREs. Antagonists form intermediate quaternary arrangements, suggesting that the formation of large oligomeric complexes is essential for function. We also show that divergence between MR and GR quaternary arrangements are driven by different functionality of multimerization interfaces in the DBD and LBD and their interplay with the N-terminal domain. In spite of contrasting quaternary structures, MR and GR are able to form heteromers. Given the importance of both receptors as pharmacological targets and the differential oligomerization induced by antagonists, our findings suggest that influencing quaternary structure may be important to provide selective modulation of corticosteroid signaling