375 research outputs found
Environmental stress is the major cause of transcriptomic and proteomic changes in GM and non-GM plants
The approval of genetically modified (GM) crops is preceded by years of intensive research to
demonstrate safety to humans and environment. We recently showed that in vitro culture stress is
the major factor influencing proteomic differences of GM vs. non-GM plants. This made us question
the number of generations needed to erase such âmemoryâ. We also wondered about the relevance of
alterations promoted by transgenesis as compared to environment-induced ones. Here we followed
three rice lines (1-control, 1-transgenic and 1-negative segregant) throughout eight generations
after transgenesis combining proteomics and transcriptomics, and further analyzed their response to
salinity stress on the F6 generation. Our results show that: (a) differences promoted during genetic
modification are mainly short-term physiological changes, attenuating throughout generations, and
(b) environmental stress may cause far more proteomic/transcriptomic alterations than transgenesis.
Based on our data, we question what is really relevant in risk assessment design for GM food crops.This work was supported by Fundação para a CiĂȘncia e a Tecnologia (FCT) Project PTDC/EBB-BIO/098983/2008 and research unit GREEN-it âBioresources for Sustainabilityâ (UID/Multi/04551/2013). S.N. acknowledges funding from King Abdullah University of Science and Technology (KAUST).info:eu-repo/semantics/publishedVersio
CALIDAD DEL ENSILADO DE CAĂA DE AZĂCAR (Socchorum offĂcinorum L.) INFLUENCIADO POR LA UTILlZACIĂN DE ADITIVOS PARA EL CONTROL DE ETANOL
La caña de azĂșcar es una de las plantas forrajeras de mayor potencial de producciĂłn de masa y energĂa por unidad de ĂĄrea, mantiene su valor nutritivo durante varios meses de sequĂa y es una alternativa vĂĄlida para el ensilaje. Teniendo en cuenta la calidad de la caña de azĂșcar se ha realizado un experimento con el objetivo de determinar la calidad bromatolĂłgica del mismo en la Granja - Escuela de la Facultad de Ciencias Agrarias- Filial San Pedro. Los tratamientos consistieron en caña de azĂșcar (CA) aditivadas con urea (U); sulfato de amonio (SA); Lactobacillus Cap (LC) en distintas proporciones con cinco tratamientos y cuatro repeticiones en un diseño completamente al azar, los cuales fueron T1 (testigo); T2 (CA + U + SA); T3 (CA + LC); T4(CA + U + SA +LC); T5 (CA + U + SA +LC). La caña de azĂșcar picada y aditivada fue cargada y compactada en microsilos preparados para el efecto, los parĂĄmetros determinados mediante anĂĄlisis fueron ProteĂna bruta(PB), EnergĂa (E), Fibra bruta (FB), Grasa (G), Carbohidratos (Ch), Ceniza (Cz), Humedad (H). El anĂĄlisis laboratorial se realizĂł 60 dĂas depĂșes de haber cerrado los microsilos cuyos resultados una vez analizados arrojaron diferencias estadĂsticas significativas (P< 0,01). En tanto el T4 (CA + 500gr.U + 0,55gr. SA +0,2gr. LC) con 3,7175 % de PB y 60,5225 Kcal/100 de E, resultĂł ser la proporciĂłn mĂĄs conveniente para ensilar. Al aditivar el ensilado de caña de azĂșcar mejora la calidad bromatolĂłgica del mismo
Mandated data archiving greatly improves access to research data
The data underlying scientific papers should be accessible to researchers
both now and in the future, but how best can we ensure that these data are
available? Here we examine the effectiveness of four approaches to data
archiving: no stated archiving policy, recommending (but not requiring)
archiving, and two versions of mandating data deposition at acceptance. We
control for differences between data types by trying to obtain data from papers
that use a single, widespread population genetic analysis, STRUCTURE. At one
extreme, we found that mandated data archiving policies that require the
inclusion of a data availability statement in the manuscript improve the odds
of finding the data online almost a thousand-fold compared to having no policy.
However, archiving rates at journals with less stringent policies were only
very slightly higher than those with no policy at all. At one extreme, we found
that mandated data archiving policies that require the inclusion of a data
availability statement in the manuscript improve the odds of finding the data
online almost a thousand fold compared to having no policy. However, archiving
rates at journals with less stringent policies were only very slightly higher
than those with no policy at all. We also assessed the effectiveness of asking
for data directly from authors and obtained over half of the requested
datasets, albeit with about 8 days delay and some disagreement with authors.
Given the long term benefits of data accessibility to the academic community,
we believe that journal based mandatory data archiving policies and mandatory
data availability statements should be more widely adopted
Deciphering the Link between Doubly Uniparental Inheritance of mtDNA and Sex Determination in Bivalves: Clues from Comparative Transcriptomics
Bivalves exhibit an astonishing diversity of sexual systems and sex-determining mechanisms. They can be gonochoric, hermaphroditic or androgenetic, with both genetic and environmental factors known to determine or influence sex. One unique sex-determining system involving the mitochondrial genome has also been hypothesized to exist in bivalves with doubly uniparental inheritance (DUI) of mtDNA. However, the link between DUI and sex determination remains obscure. In this study, we performed a comparative gonad transcriptomics analysis for two DUI-possessing freshwater mussel species to better understand the mechanisms underlying sex determination and DUI in these bivalves. We used a BLAST reciprocal analysis to identify orthologs between Venustaconcha ellipsiformis and Utterbackia peninsularis and compared our results with previously published sex-specific bivalve transcriptomes to identify conserved sex-determining genes. We also compared our data with other DUI species to identify candidate genes possibly involved in the regulation of DUI. A total of 3c12,000 orthologous relationships were found, with 2,583 genes differentially expressed in both species. Among these genes, key sex-determining factors previously reported in vertebrates and in bivalves (e.g., Sry, Dmrt1, Foxl2) were identified, suggesting that some steps of the sex-determination pathway may be deeply conserved in metazoans. Our results also support the hypothesis that a modified ubiquitination mechanism could be responsible for the retention of the paternal mtDNA in male bivalves, and revealed that DNA methylation could also be involved in the regulation of DUI. Globally, our results suggest that sets of genes associated with sex determination and DUI are similar in distantly-related DUI species
An inâplanta comparative study of Plasmopara viticola proteome reveals diferent infection strategies towards susceptible and Rpv3âmediated resistance hosts
Plasmopara viticola, an obligate biotrophic oomycete, is the causal agent of one of the most harmful grapevine diseases, downy mildew. Within this pathosystem, much information is gathered on the host, as characterization of pathogenicity and infection strategy of a biotrophic pathogen is quite challenging. Molecular insights into P. viticola development and pathogenicity are just beginning to be uncovered, mainly by transcriptomic studies. Plasmopara viticola proteome and secretome were only predicted based on transcriptome data. In this study, we have identified the in-planta proteome of P. viticola during infection of a susceptible ('Trincadeira') and a Rpv3-mediated resistance ('Regent') grapevine cultivar. Four hundred and twenty P. viticola proteins were identified on a label-free mass spectrometry-based approach of the apoplastic fluid of grapevine leaves. Overall, our study suggests that, in the compatible interaction, P. viticola manipulates salicylic-acid pathway and isoprenoid biosynthesis to enhance plant colonization. Furthermore, during the incompatible interaction, development-associated proteins increased while oxidoreductases protect P. viticola from ROS-associated plant defence mechanism. Up to our knowledge this is the first in-planta proteome characterization of this biotrophic pathogen, thus this study will open new insights into our understanding of this pathogen colonization strategy of both susceptible and Rpv3-mediated resistance grapevine genotypes.info:eu-repo/semantics/publishedVersio
Proteomic analysis of three Coffee Leaf Rust races with different pathogenic behavior
info:eu-repo/semantics/publishedVersio
Dynamics of precipitation pattern formation at geothermal hot springs
We formulate and model the dynamics of spatial patterns arising during the
precipitation of calcium carbonate from a supersaturated shallow water flow.
The model describes the formation of travertine deposits at geothermal hot
springs and rimstone dams of calcite in caves. We find explicit solutions for
travertine domes at low flow rates, identify the linear instabilities which
generate dam and pond formation on sloped substrates, and present simulations
of statistical landscape evolution
Flowering under stress: phenomics and proteomics approaches to chickpea grain yield and quality.
Chickpea (Cicer arietinum) is a major player in the FAO Zero Hunger program âtoolkitâ. It is the second most cultivated food legume, a source of sustainable protein (and other nutrients) and contributes to improved soil health and lower fertilization input. Grain yield, seed protein content and nutritional quality were found to be largely affected by Genotype x Environment. In the Mediterranean regions, higher frequency, intensity and duration of droughts, as well as hotter droughts are being registered, thus interfering with agroecosystemsâ structure, composition, and functions. A controlled conditions assay (non-invasive phenotyping@PhenoLab) was undertaken in two genotypes from the Portuguese chickpea breeding program (Elvas, INIAV). Results revealed that high temperature (32Âș C during the reproductive phase) and water regime (40% vs 10% soil water content) play a significant role in chickpea development, seed production and composition, and protein content. As seed biochemical signatures allow to discriminate between genotypes, the power protein-based methodologies in genotype assessment are highlighted. Because some proteins can resist gastrointestinal digestion and influence human health, the processed seed proteome (i.e. following soaking, boiling and in-vitro digestion) in three consecutive years was further analysed in field-grown chickpeas (Elvas, INIAV). The seed proteome was found to be highly conserved, with minor changes being attributed to the seed development conditions. Furthermore, in vitro digestion efficiently removed many anti-nutritional proteins. Combined phenotyping and omicÂŽs approaches contribute to the mechanistic knowledge of how severe terminal drought and high temperature modulate sink capacity and productivity (yield and quality). The integrated use of phenomics and omics methodologies has significant potential to increase our understanding of plant growth and development and, thus, an efficient, knowledge-based management of crops and resources.Work supported by EMPHASIS-GO (HORIZON-INFRA-2021-DEV-02 contract n. 101079772), by the European Plant Phenotyping Network 2020 (EXCELLENT SCIENCE - Research Infrastructures contract n. 731013) and by national funds from FCT - Fundação para a CiĂȘncia e a Tecnologia, I.P. namelly: UCIBIO â Research Unit on Applied Molecular Biosciences (FCT UIDP/04378/2020; FCT UIDB/04378/ 2020); 4HB - Associate Laboratory Institute for Health and Bioeconomy (FCT LA/P/0140/2020); LEAF â Linking Landscape, Environment, Agriculture and Food (FCT UID/AGR/04129/2020); PhD fellowship SFRH/BD/70345/2010.info:eu-repo/semantics/publishedVersio
Specialisation events of fungal metacommunities exposed to a persistent organic pollutant are suggestive of augmented pathogenic potential
Background: The impacts of man-made chemicals, in particular of persistent organic pollutants, are multifactorial as they may affect the integrity of ecosystems, alter biodiversity and have undesirable effects on many organisms. We have previously demonstrated that the belowground mycobiota of forest soils acts as a buffer against the biocide pollutant pentachlorophenol. However, the trade-offs made by mycobiota to mitigate this pollutant remain cryptic. Results: Herein, we demonstrate using a culture-dependent approach that exposure to pentachlorophenol led to alterations in the composition and functioning of the metacommunity, many of which were not fully alleviated when most of the biocide was degraded. Proteomic and physiological analyses showed that the carbon and nitrogen metabolisms were particularly affected. This dysregulation is possibly linked to the higher pathogenic potential of the metacommunity following exposure to the biocide, supported by the secretion of proteins related to pathogenicity and reduced susceptibility to a fungicide. Our findings provide additional evidence for the silent risks of environmental pollution, particularly as it may favour the development of pathogenic trade-offs in fungi, which may impose serious threats to animals and plant hosts
Academic freedom in Europe: reviewing UNESCOâs recommendation
This paper examines the compliance of universities in the European Union with the UNESCO Recommendation concerning the Status of HigherâEducation Teaching Personnel, which deals primarily with protection for academic freedom. The paper briefly surveys the European genesis of the modern research university and academic freedom, before evaluating compliance with the UNESCO recommendation on institutional autonomy, academic freedom, university governance and tenure. Following from this, the paper examines the reasons for the generally low level of compliance with the UNESCO Recommendation within the EU states, and considers how such compliance could be improved
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