Analysis of interval‐grouped data in weed science: The binnednp Rcpp package

[Abstract] Weed scientists are usually interested in the study of the distribution and density functions of the random variable that relates weed emergence with environmental indices like the hydrothermal time (HTT). However, in many situations, experimental data are presented in a grouped way and, therefore, the standard nonparametric kernel estimators cannot be computed. Kernel estimators for the density and distribution functions for interval‐grouped data, as well as bootstrap confidence bands for these functions, have been proposed and implemented in the binnednp package. Analysis with different treatments can also be performed using a bootstrap approach and a Cramér‐von Mises type distance. Several bandwidth selection procedures were also implemented. This package also allows to estimate different emergence indices that measure the shape of the data distribution. The values of these indices are useful for the selection of the soil depth at which HTT should be measured which, in turn, would maximize the predictive power of the proposed methods. This paper presents the functions of the package and provides an example using an emergence data set of Avena sterilis (wild oat). The binnednp package provides investigators with a unique set of tools allowing the weed science research community to analyze interval‐grouped data.Ministerio de Economía y Competitividad; AGL2015-64130-RMinisterio de Economía y Competitividad; MTM2014-52876-RMinisterio de Economía y Competitividad; MTM2017-82724-RMinisterio de Economía y Competitividad; AGL2012-33736Xunta de Galicia; ED431C-2016-015Xunta de Galicia; ED431G/0

Androgen receptor gene and sociosexuality. Does fighting ability moderate the effect of genetics in reproductive strategies?

Springer Nature remains neutral with regard to juris dictional claims in published maps and institutional affiliations.Sociosexuality is a reliable proxy to evaluate the trade-off between short-term and long-term human mating strategies. The androgen receptor (AR) gene CAG-repeats polymorphism regulates the effect of testosterone and the expression of testosterone-related traits commonly associated with short-term mating strategies. According to the strategic pluralism hypothesis, a more effective receptor would prompt a short-term mating strategy to maximize the number of sexual partners, but studies are inconclusive and contradictory. The effect of a particular gene in behavior is frequently small and affected by the social environment and other variables, particularly psychological and personality traits. In the current study we propose the effect of the AR gene polymorphism in sociosexuality to be moderated by self-perceived fighting ability, a psychological attribute relevant in intrasexual competition. Our objective is to reveal if the CAG polymorphism is associated with a short-term strategy as expected from the strategic pluralism hypothesis, or conversely with long-term investments to maximize parental care. We fail to find any effect of the CAG polymorphism over mating strategies. However, self-perceived fighting ability is related to short-term mating orientation but not to the number of past sexual partners. In conclusion, we find no clear evidence about the potential role of CAG polymorphism of the AR gene over sociosexual attitudes and behavior. However, results from other studies suggest that there is evidence that genetic factors influence sociosexuality, but it is necessary to consider simultaneously more than a single genetic polymorphism and other psychological and physiological variablesThis study was supported by a postdoctoral proj ect from Universidad del Desarrollo for author Nohelia T. Valenzuela and funded by the project BIOUAM03-2019 of the Departmento de Biología of the Universidad Autónoma de Madri

Porcine Protein Hydrolysates (PEPTEIVA®) Promote Growth and Enhance Systemic Immunity in Gilthead Sea Bream (Sparus aurata)

The effects of porcine plasma protein hydrolysate (PPH) on growth, feed efficiency, and immune responses was evaluated in Sparus aurata. Fish were fed two isoproteic (48% protein), isolipidic (17% fat), and isoenergetic diets (21.7 MJ/kg) diets, one of them containing 5% PPH at the expense of fishmeal. Both diets were tested for 92 days. A significant increase in growth was observed in fish fed the PPH diet in comparison to the control group (182.2 ± 4.4 vs. 173.8 ± 4.1 g), as well as an increase in feed intake without worsening FCR values. An ex vivo assay, with splenocytes incubated with lipopolysaccharide, was conducted to evaluate the cellular immune competence of fish. Genes involved in humoral immunity (lys, IgM), pro- (tnf-α, il-1β), and anti-inflammatory (tgf-β1, il10) cytokines were upregulated in the PPH group in comparison to the control group. The inclusion of PPH in diets enhanced the antibacterial capacity of skin mucus, as the co-culture of selected bacteria (E. coli, V. anguillarum, and P. anguilliseptica) with skin mucus indicated. The present results showed that the PPH in low fishmeal diets (2%) promoted growth and feed efficiency, as well as enhancing the immune response, which indicates that this is a safe and functional ingredient for aquafeeds.info:eu-repo/semantics/publishedVersio

Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides

Phosphorothioates (PS) have proven their effectiveness in the area of therapeutic oligonucleotides with applications spanning from cancer treatment to neurodegenerative disorders. Initially, PS substitution was introduced for the antisense oligonucleotides (PS ASOs) because it confers an increased nuclease resistance meanwhile ameliorates cellular uptake and in-vivo bioavailability. Thus, PS oligonucleotides have been elevated to a fundamental asset in the realm of gene silencing therapeutic methodologies. But, despite their wide use, little is known on the possibly different structural changes PS-substitutions may provoke in DNA·RNA hybrids. Additionally, scarce information and significant controversy exists on the role of phosphorothioate chirality in modulating PS properties. Here, through comprehensive computational investigations and experimental measurements, we shed light on the impact of PS chirality in DNA-based antisense oligonucleotides; how the different phosphorothioate diastereomers impact DNA topology, stability and flexibility to ultimately disclose pro-Sp S and pro-Rp S roles at the catalytic core of DNA Exonuclease and Human Ribonuclease H; two major obstacles in ASOs-based therapies. Altogether, our results provide full-atom and mechanistic insights on the structural aberrations PS-substitutions provoke and explain the origin of nuclease resistance PS-linkages confer to DNA·RNA hybrids; crucial information to improve current ASOs-based therapies.© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research

Porcine Protein Hydrolysates (PEPTEIVA ) Promote Growth and Enhance Systemic Immunity in Gilthead Sea Bream (Sparus aurata)

The effects of porcine plasma protein hydrolysate (PPH) on growth, feed efficiency, and immune responses was evaluated in Sparus aurata. Fish were fed two isoproteic (48% protein), isolipidic (17% fat), and isoenergetic diets (21.7 MJ/kg) diets, one of them containing 5% PPH at the expense of fishmeal. Both diets were tested for 92 days. A significant increase in growth was observed in fish fed the PPH diet in comparison to the control group (182.2 ± 4.4 vs. 173.8 ± 4.1 g), as well as an increase in feed intake without worsening FCR values. An ex vivo assay, with splenocytes incubated with lipopolysaccharide, was conducted to evaluate the cellular immune competence of fish. Genes involved in humoral immunity (lys, IgM), pro- (tnf-α, il-1β), and anti-inflammatory (tgf-β1, il10) cytokines were upregulated in the PPH group in comparison to the control group. The inclusion of PPH in diets enhanced the antibacterial capacity of skin mucus, as the co-culture of selected bacteria (E. coli, V. anguillarum, and P. anguilliseptica) with skin mucus indicated. The present results showed that the PPH in low fishmeal diets (2%) promoted growth and feed efficiency, as well as enhancing the immune response, which indicates that this is a safe and functional ingredient for aquafeeds

Evaluating the functional properties of spray-dried porcine plasma in gilthead seabream (Sparus aurata) fed low fish meal diets.

Blood by-products are an untapped source of high-quality ingredients for aquafeeds, containing a broad variety of cytokines, hormones, growth factors, proteins, bioactive peptides, and amino acids. The effects of the spray-dried porcine plasma (SDPP), a type of processed animal protein on several immune parameters, were evaluated in sea bream using ex vivo and in vitro assays. In this study, fish were fed with two isoproteic, isolipidic, and isoenergetic diets: control diet (7% fish meal, FM) and SDPP diet (2% FM and 5% SDPP). At the end of the 92-days trial, those fed the SDPP diet were larger in body weight (p 0.05). The ex vivo immune stimulation of splenocytes indicated that SDPP had a beneficial effect in promoting systemic immunity, since the surface cell marker (cd4), pro- (il-1β), and anti-inflammatory (tgf-β1) cytokines, and genes involved in humoral immunity (IgM) were up-regulated. The co-culture assays of skin mucus corroborated that SDPP enhanced the antibacterial capacity of mucus against V. anguillarum. In addition, main mucus biomarkers did not show significant differences, except for cortisol levels which were lower in the SDPP diet. The present study indicated that SDPP may be considered a functional ingredient in aquafeeds formulated with low FM levels

Skin multi-omics-based interactome analysis: integrating the tissue and mucus exuded layer for a comprehensive understanding of the teleost mucosa functionality as model of study

From a general structural perspective, a mucosal tissue is constituted by two main matrices: the tissue and the secreted mucus. Jointly, they fulfill a wide range of functions including the protection of the epithelial layer. In this study, we simultaneously analyzed the epithelial tissue and the secreted mucus response using a holistic interactome-based multi-omics approach. The effect of the gilthead sea bream (Sparus aurata) skin mucosa to a dietary inclusion of spray-dried porcine plasma (SDPP) was evaluated. The epithelial skin microarrays-based transcriptome data showed 194 differentially expressed genes, meanwhile the exuded mucus proteome analysis 35 differentially synthesized proteins. Separately, the skin transcripteractome revealed an expression profile that favored biological mechanisms associated to gene expression, biogenesis, vesicle function, protein transport and localization to the membrane. Mucus proteome showed an enhanced protective role with putatively higher antioxidant and antimicrobial properties. The integrated skin mucosa multi-interactome analysis evidenced the interrelationship and synergy between the metabolism and the exuded mucus functions improving specifically the tissue development, innate defenses, and environment recognition. Histologically, the skin increased in thickness and in number of mucous cells. A positive impact on animal performance, growth and feed efficiency was also registered. Collectively, the results suggest an intimate crosstalk between skin tissue and its exuded mucus in response to the nutritional stimulus (SDPP supplementation) that favors the stimulation of cell protein turnover and the activation of the exudation machinery in the skin mucosa. Thus, the multi-omics-based interactome analysis provides a comprehensive understanding of the biological context of response that takes place in a mucosal tissue. In perspective, this strategy is applicable for evaluating the effect of any experimental variable on any mucosal tissue functionality, including the benefits this assessment may provide on the study of the mammalian mucosa

Operationalizing local ecological knowledge in climate change research : challenges and opportunities of citizen science

Current research on the local impacts of climate change is based on contrasting results from the simulation of historical trends in climatic variables produced with global models against climate data from independent observations. To date, these observations have mostly consisted of weather data from standardized meteorological stations. Given that the spatial distribution of weather stations is patchy, climate scientists have called for the exploration of new data sources. Knowledge developed by Indigenous Peoples and local communities with a long history of interaction with their environment has been proposed as a data source with untapped potential to contribute to our understanding of the local impacts of climate change. In this chapter, we discuss an approach that aims to bring insights from local knowledge systems to climate change research. First, we present a number of theoretical arguments that give support to the idea that local knowledge systems can contribute in original ways to the endeavors of climate change research. Then, we explore the potential of using information and communication technologies to gather and share local knowledge of climate change impacts. We do so through the examination of a citizen science initiative aiming to collect local indicators of climate change impacts: the LICCI project (www.licci.eu). Our findings illustrate that citizen science can inspire new approaches to articulate the inclusion of local knowledge systems in climate change research. However, this requires outlining careful approaches, with high ethical standards, toward knowledge validation and recognizing that there are aspects of local ecological knowledge that are incommensurable with scientific knowledge