8,438 research outputs found
Changes in soil fertility and microbial communities following cultivation of native grassland in Horqin Sandy Land, China: a 60-year chronosequence
Background: Grassland conversion to cropland is a prevailing change of land use in traditionally nomadic areas, especially in the Mongolian Plateau. We investigated the effects of grassland conversion followed by continuous cultivation on soil properties and microbial community characteristics in Horqin Sandy Land, a typical agro-pastoral transition zone of Northern China. Soil samples were collected from the topsoil (upper 20 cm) across a 60-year cultivation chronosequence (5, 15, 25, 35 and 60 years) and unconverted native grassland. Soil physico-chemical properties were determined and high-throughput sequencing was used to assess microbial community diversity and composition. Results: Grassland cultivation resulted in changes to soil properties in both the short and longer term. Initially, it significantly increased soil bulk density (BD), electrical conductivity (EC), soil total nitrogen (TN), available phosphorus (AP) and available potassium (AK) concentrations, while reducing soil water content (SWC) and soil organic carbon content (SOC). Over the next 35–55 years of continuous cultivation, the trend for most of these characteristics was of reversion towards values nearer to those of native grassland, except for SOC which remained highly depleted. Cultivation of grassland substantially altered soil microbial communities at phylum level but there was no significant difference in microbial α-diversity between native grassland and any cropland. However, soil bacterial and fungal community structures at phylum level in the croplands of all cultivation years were different from those in the native grasslands. Heatmaps further revealed that bacterial and fungal structures in cropland tended to become more similar to native grassland after 15 and 25 years of cultivation, respectively. Redundancy analysis indicated that SOC, EC and BD were primary determinants of microbial community composition and diversity. Conclusions: These findings suggest that agricultural cultivation of grassland has considerable effects on soil fertility and microbial characteristics of Horqin Sandy Land. Intensive high-yield forage grass production is proposed as an alternative to avoid further native grassland reclamation, while meeting the grazing development needs in the ethnic minority settlements of eco-fragile regions
La identidad cultural del cultivo de maíz en México: importancia y retos ante la apertura comercial de trangénicos
El trabajo de Tesis Doctoral, La identidad cultural del cultivo de maíz en
México: importancia y retos ante la apertura comercial de transgénicos, se basa en la aplicación de técnicas
bibliométricas, análisis de productividad agrícola y herramientas de sistemas de información geográfica, orientadas
a delimitar áreas con alta diversidad de razas de maíz nativas y asociar su cultivo con la riqueza etnográfica de las
regiones, con el objetivo de establecer regiones prioritarias de conservación in situ de razas de maíz nativas donde
se restrinja el cultivo de variedades transgénicas
Investigation of a Histidine-Based Probe for the Exploration of Proteomes
Leishmaniasis is a neglected tropical disease which affects 0.7-1 million people per year. Current chemotherapies for leishmaniasis are toxic with long treatment times and reports of increasing resistance, which stresses the importance of this research area. Inositol phosphorylceramide synthase is a membrane bound enzyme that has no direct human homologue, which converts ceramide to inositol phosphorylceramide through the action of a highly conserved HHD catalytic triad. An ideal method to study this enzyme further would be through activity-based protein profiling, however, there are currently no activity-based probes reported that reacts with this type of active site. Therefore, an activity-based probe was designed based on the structure of diethyl pyrocarbonate, a compound known to bind covalently to active site histidine residues. The synthesised activity-based probe was shown to inhibit Leishmania major inositol phosphorylceramide synthase in a simple assay. In addition, the probe was shown to selectively bind to the active site histidine residue in two pure enzyme models; one of which has the same catalytic triad as inositol phosphorylceramide synthase, and the other was an acid base active site histidine residue. Further, this activity-based probe was able to isolate an overexpressed enzyme in the lysate of Escherichia coli as well as bind to intrinsic proteins. Following the function validation of the activity-based probe, preliminary work was started in Leishmania to isolate proteins identify expressed enzymes
Contemporary, decadal, and millennial-scale permafrost- and vegetation dynamics and carbon release in an alpine region of Jotunheimen, Norway
Climatic warming in northern alpine regions facilitates the thawing of permafrost, the associated release of soil carbon into the atmosphere, and the altitudinal shifts in vegetation patterns. Here, a multi-disciplinary approach is adopted to investigate the response of an alpine permafrost landscape (Jotunheimen, Norway, with focus on Galdhøpiggen) to climatic changes over long- to medium timescales. First, a gas analyser is used to explore how ecosystem respiration is affected by ecosystem (soil and vegetation) and geomorphological (cryogenic disturbance) factors during the peak growing season. A palaeoecological record is then analysed to infer the past dynamics of the alpine tree lines and the lower limit of permafrost on Galdhøpiggen over the millennial- and centennial scales. Finally, remotely sensed satellite imagery is combined with observed air temperatures to create a model that provides an estimation of land surface temperatures over the past six decades. The model is then used to predict surface ‘greenness’ over the same period. Palynological evidence from Galdhøpiggen indicates that the altitudinal limits of alpine tree lines have shifted by hundreds of metres in response to climatic changes over the millennial scale. Since 1957, the model predictions indicate substantial increases in land surface temperatures and growing season surface ‘greenness’ (i.e., vegetation abundance) in Jotunheimen, but the change has not been spatially uniform. The highest increases were recorded over the low- and mid-alpine heaths above the tree line (1050-1500 m a.s.l.), which was attributed to increased shrub cover. This trend could facilitate carbon release from the ground, as peak growing season ecosystem respiration was found to be most strongly controlled by soil microclimate and plant growth forms. The likely future scenario in response to warming in Jotunheimen will be continued permafrost degradation, with higher altitudes (≥1500 m a.s.l.) experiencing decreased cryoturbation, increased shrub encroachment and higher surface CO2 emissions
The expansion of Brachypodium rupestre in western Pyrenees: fungal endophytes and loss of ecosystem services
En esta tesis se plantean dos líneas de investigación que han quedado recogidas en los tres trabajos científicos que la conforman:
• Capítulo 1) La primera línea de investigación desarrolla un modo de cuantificar económicamente la pérdida del servicio ecosistémico de aprovisionamiento ligado a la expansión de B. rupestre, con el objetivo de sensibilizar a los sectores implicados y fomentar acciones medioambientales dirigidas a promover la conservación de los pastos de montaña, ecosistemas ambiental y económicamente valiosos. Para ello, se realizó una adaptación del método de valoración económica por sustitución y se llevaron a cabo inventarios florísticos en cubiertas de alta y baja diversidad florística. El registro de estos datos nos permitió generar unos valores pastorales transformables en cantidad de forraje disponible para los animales, tras un detallado cálculo de la superficie viable de ser pastada (200,05 ha tras excluir las zonas con grandes pendientes). Con censos de animales y con información detallada y exhaustiva del consumo de energía que tiene cada tipo de animal que pasta las estivas del valle (ovejas, vacas y caballos) se determinaron las raciones de alimento necesarias en una temporada de pastoreo estival (50007 raciones) y su coste monetario (21146€; 107€/ha). De este modo, se estimó el coste que supone la pérdida del valor de aprovisionamiento debido a la expansión de B. rupestre y que va ligado en este caso a la pérdida de riqueza y diversidad florística de las comunidades vegetales que lo constituyen.
• Capítulo 2 y 3) La segunda línea de investigación engloba dos trabajos en los que se caracteriza la desconocida comunidad de hongos endófitos de individuos de B. rupestre desarrollándose en comunidades de alta y baja diversidad florística. El estudio de los microorganismos en su ambiente natural es una disciplina relativamente nueva, dado que su interés se ha centrado tradicionalmente en las enfermedades que afectan a los humanos, los animales o las plantas. Sin embargo, los grandes avances tecnológicos y científicos de las últimas décadas nos están permitiendo conocer su altísima diversidad y las complejas redes ecológicas en las que están involucrados. El conocimiento sobre los hongos endófitos, que crecen en el interior de casi todas las plantas sin desarrollar enfermedades, está demostrando numerosas ventajas adaptativas que estos pueden llegar a conferir a su huésped ante numerosas situaciones de estrés (salinidad, herbivorismo, patógenos, etc.).This thesis encompasses two research lines comprised in three scientific papers:
• Chapter 1) First chapter quantifies economically the loss of the provisioning service related to the B. rupestre expansion, with the aim of raising awareness among stakeholders and promote environmental actions for grassland restauration. For this purpose, we adapted the substitution economic approach, that we based on field floristic surveys done in high-diversity and low-diversity grasslands. The data collected allowed the estimation of the pastoral values, that were related to energy values and eventually to animal feed rations (50007 rations). We estimated the available surface for grazing (200.05 ha excluding steep slopes) and we compiled summer livestock censuses for determining the energy needs of each type of animal (sheep, cows and horses). Eventually, we estimated the economic cost of the loss of the provisioning service related to the B. rupestre expansion (21146€; 107€/ha).
• Chapter 2 and 3) The second line of research encompasses two papers that characterize the fungal endophytic community of B. rupestre from plants developing in communities of high and low- floristic diversity. The study of microorganisms in their natural environment is a new discipline, considering that the research has usually focused on human, animal or plant diseases. The technological and scientific advances in the last decades have broadened our knowledge on the high diversity and the complex ecological networks in which they are involved. In particular, the study of fungal endophytes, which grow inside plants without developing diseases, is demonstrating the numerous adaptive advantages they confer to their host in different stressing situations (salinity, herbivory, pathogens, etc.).Ayudas de nueva solicitud para la Formación de Personal Investigador en la Universidad Pública de Navarra, convocatoria 2017. Ayudas de movilidad de doctorado 2021 para la realización de una estancia internacional en la Universidad de Camerino (Italia).
Interreg Sudoe Programme, European Regional Development Fund, Open2preserve Project 108 (SOE2/P5/E0804). Libera 2017, SEO y Ecoembes - Apadrinamiento de espacios naturales. La degradación de los ecosistemas pascícolas de la Selva de Irati: Comportamiento invasivo de especies endémicas bajo condiciones de cambio global. Libera 2018, SEO y Ecoembes-Apadrinamiento de espacios naturales. La degradación de los ecosistemas pascícolas: ZEC Roncesvalles-Selva de Irati. Proyecto de investigación en centros escolares (Gobierno de Navarra, 2018). Formando futuras investigadoras: introduciendo la ciencia ecológica y ambiental al mundo escolar.Programa de Doctorado en Agrobiología Ambiental (RD 99/2011)Ingurumen Agrobiologiako Doktoretza Programa (ED 99/2011
Evolutionary Dynamic Multi-Objective Optimisation : A survey
Peer reviewedPostprin
Endogenous mechanisms of vascular regeneration following myocardial infarction
Ischaemic heart disease remains one of the leading causes of death worldwide, responsible for over 8.9 million deaths in 2017 according to the Global Burden of Disease Study. Restoring blood perfusion in the ischaemic border via a functional vascular network may enhance myocardial perfusion, limit infarct expansion and promote cardiac regeneration. However, the pathways driving endogenous vascular regeneration following myocardial infarction (MI) remain poorly understood. The aim of this thesis was twofold; First, to investigate the origin and clonal dynamics of cardiac endothelial cells (EC) post-MI. Secondly, to analyse the transcriptional profiles of pro-angiogenic EC in MI using single cell RNA sequencing in the post-ischaemic adult mouse heart, and investigate potential therapeutic targets in human patient samples. MI was induced in an EC-specific multispectral lineage-tracing mouse, “Pdgfb-iCreERT2-Brainbow2.1”, by permanent ligation of the left anterior descending coronary artery. Blood vessel formation via clonal proliferation by resident Pdgfb-lineage EC was significantly upregulated in the ischaemic border at 7 days post-MI, compared to the healthy heart. Minimal contribution from the bone marrow was observed. Bioinformatics analyses revealed 10 transcriptionally discrete heterogeneous EC states in the 7 days post-MI heart and revealed molecular pathways through which each cluster was likely to mediate neovasculogenesis following MI. Plasmalemma Vesicle–Associated Protein (Plvap) gene expression was upregulated in MI, specifically in clusters of cells from the MI group, indicating its potential relevance to neovasculogenic pathways. I validated increased Plvap expression at the protein level, which was EC-specific and was significantly higher in the infarct border of the post-ischaemic mouse heart compared to the healthy heart. PLVAP expression was also significantly increased in EC adjacent to regions of fibrosis and scarring in the ischaemic human heart, compared to healthy human hearts. Moreover, in vitro silencing using RNAi in human umbilical vein ECs showed that PLVAP may play a direct functional role in regulating EC proliferation. The single cell gene expression atlas of cardiac resident ECs presented in this thesis can be used to unravel the neovasculogenesis pathways that are activated 7 days post-MI. Cluster
specific PLVAP was identified as a possible target for augmenting endogenous myocardial perfusion following ischaemia and validated in human cardiac ischaemic tissue. Future studies will involve further interrogation of the activated neovasculogenesis pathways from cardiac ECs using the single cell gene expression atlas as well as investigation of the molecular mechanisms of the role of PLVAP in EC proliferation
Modélisation et comparaison de la structure de gènes
La bio-informatique est un domaine de recherche multi-disciplinaire, à la croisée de différents domaines : biologie, médecine, mathématiques, statistiques, chimie, physique et informatique. Elle a pour but de concevoir et d’appliquer des modèles et outils statistiques et computationnels visant l’avancement des connaissances en biologie et dans les sciences connexes.
Dans ce contexte, la compréhension du fonctionnement et de l’évolution des gènes fait l’objet de nombreuses études en bio-informatique. Ces études sont majoritairement fondées sur la comparaison des gènes et en particulier sur l’alignement de séquences génomiques. Cependant, dans leurs calculs d’alignement de séquences génomiques, les méthodes existantes se basent uniquement sur la similarité des séquences et ne tiennent pas compte de la structure des gènes. L’alignement prenant en compte la structure des séquences offre l’opportunité d’en améliorer la précision ainsi que les résultats des méthodes développées à partir de ces alignements.
C’est dans cette hypothèse que s’inscrit l’objectif de cette thèse de doctorat : proposer des modèles tenant compte de la structure des gènes lors de l’alignement des séquences de familles de gènes. Ainsi, par cette thèse, nous avons contribué à accroître les connaissances scientifiques en développant des modèles d’alignement de séquences biologiques intégrant des informations sur la structure de codage et d’épissage des séquences. Nous avons proposé un algorithme et une nouvelle fonction du score pour l’alignement de séquences codantes d’ADN (CDS) en tenant compte de la longueur des décalages du cadre de traduction. Nous avons aussi proposé un algorithme pour aligner des paires de séquences d’une famille de gènes en considérant leurs structures d’épissage. Nous avons également développé un algorithme pour assembler des alignements épissés par paire en alignements multiples de séquences. Enfin, nous avons développé un outil pour la visualisation d’alignements épissés multiples de famille de gènes. Dans cette thèse, nous avons souligné l’importance et démontré l’utilité de tenir compte de la structure des séquences en entrée lors du calcul de leur alignement
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