Integrating crop and livestock is being considered to improve soil health by carbon sequestration. A two-year study (2019-2021) at CPBES in Newton, MS was aimed to evaluate soil microbial diversity in the warm, humid regions, specifically southeastern USA. Amplicons targeting bacterial 16S rRNA genes and fungal ITS2 regions were sequenced. Taxonomic assignment and microbial diversity characterization were performed using QIIME2®. Soil fungal diversity showed significant differences (alpha diversity, p = 0.031 in yr. 2020 and beta diversity, p = 0.037 in yr. 2021). Canonical Correspondence Analysis (CCA) and Mantel test showed significant influence on fungal diversity due to carbon (rm = 0.2581, p = 0.022), nitrogen (rm = 0.2921, p = 0.0165) in yr. 2021, and on bacterial diversity due to EE-GRSP (rm = 0.22, p = 0.02) in yr. 2020. Long term study of ICLS can help us better understand the shift in microbiome to improve crop production sustainably.

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Student employees (N=86) at a major research institution participated in a new hire orientation training and then responded to questionnaires measuring ten transfer behaviors and eight work environment constructs measuring support, frequency of contact, cohesion, and general means efficacy. Supervisor ratings of trainee performance were used to measure transfer behaviors.

Cellular function and physiology are largely established through regulated gene expression. The first step in gene expression, transcription of the genomic DNA into RNA, is a process that is highly aligned at the levels of initiation, elongation and termination. In eukaryotes, protein-coding genes are exclusively transcribed by RNA polymerase II (Pol II). Upon transcription of the first 15-20 nucleotides (nt), the emerging nascent RNA 5’ end is modified with a 7-methylguanosyl cap. This is one of several RNA modifications and processing steps that take place during transcription, i.e. co-transcriptionally. For example, protein-coding sequences (exons) are often disrupted by non-coding sequences (introns) that are removed by RNA splicing. The two transesterification reactions required for RNA splicing are catalyzed through the action of a large macromolecular machine, the spliceosome. Several non-coding small nuclear RNAs (snRNAs) and proteins form functional spliceosomal subcomplexes, termed snRNPs. Sequentially with intron synthesis different snRNPs recognize sequence elements within introns, first the 5’ splice site (5‘ SS) at the intron start, then the branchpoint and at the end the 3’ splice site (3‘ SS). Multiple conformational changes and concerted assembly steps lead to formation of the active spliceosome, cleavage of the exon-intron junction, intron lariat formation and finally exon-exon ligation with cleavage of the 3’ intron-exon junction. Estimates on pre-mRNA splicing duration range from 15 sec to several minutes or, in terms of distance relative to the 3‘ SS, the earliest detected splicing events were 500 nt downstream of the 3‘ SS. However, the use of indirect assays, model genes and transcription induction/blocking leave the question of when pre-mRNA splicing of endogenous transcripts occurs unanswered. In recent years, global studies concluded that the majority of introns are removed during the course of transcription. In principal, co-transcriptional splicing reduces the need for post-transcriptional processing of the pre-mRNA. This could allow for quicker transcriptional responses to stimuli and optimal coordination between the different steps. In order to gain insight into how pre-mRNA splicing might be functionally linked to transcription, I wanted to determine when co-transcriptional splicing occurs, how transcripts with multiple introns are spliced and if and how the transcription termination process is influenced by pre-mRNA splicing. I chose two yeast species, S. cerevisiae and S. pombe, to study co-transcriptional splicing. Small genomes, short genes and introns, but very different number of intron-containing genes and multi-intron genes in S. pombe, made the combination of both model organisms a promising system to study by next-generation sequencing and to learn about co-transcriptional splicing in a broad context with applicability to other species. I used nascent RNA-Seq to characterize co-transcriptional splicing in S. pombe and developed two strategies to obtain single-molecule information on co-transcriptional splicing of endogenous genes: (1) with paired-end short read sequencing, I obtained the 3’ nascent transcript ends, which reflect the position of Pol II molecules during transcription, and the splicing status of the nascent RNAs. This is detected by sequencing the exon-intron or exon-exon junctions of the transcripts. Thus, this strategy links Pol II position with intron splicing of nascent RNA. The increase in the fraction of spliced transcripts with further distance from the intron end provides valuable information on when co-transcriptional splicing occurs. (2) with Pacific Biosciences sequencing (PacBio) of full-length nascent RNA, it is possible to determine the splicing pattern of transcripts with multiple introns, e.g. sequentially with transcription or also non-sequentially. Part of transcription termination is cleavage of the nascent transcript at the polyA site. The splicing status of cleaved and non-cleaved transcripts can provide insights into links between splicing and transcription termination and can be obtained from PacBio data. I found that co-transcriptional splicing in S. pombe is similarly prevalent to other species and that most introns are removed co-transcriptionally. Co-transcriptional splicing levels are dependent on intron position, adjacent exon length, and GC-content, but not splice site sequence. A high level of co-transcriptional splicing is correlated with high gene expression. In addition, I identified low abundance circular RNAs in intron-containing, as well as intronless genes, which could be side-products of RNA transcription and splicing. The analysis of co-transcriptional splicing patterns of 88 endogenous S. cerevisiae genes showed that the majority of intron splicing occurs within 100 nt downstream of the 3‘ SS. Saturation levels vary, and confirm results of a previous study. The onset of splicing is very close to the transcribing polymerase (within 27 nt) and implies that spliceosome assembly and conformational rearrangements must be completed immediately upon synthesis of the 3‘ SS. For S. pombe genes with multiple introns, most detected transcripts were completely spliced or completely unspliced. A smaller fraction showed partial splicing with the first intron being most often not spliced. Close to the polyA site, most transcripts were spliced, however uncleaved transcripts were often completely unspliced. This suggests a beneficial influence of pre-mRNA splicing for efficient transcript termination. Overall, sequencing of nascent RNA with the two strategies developed in this work offers significant potential for the analysis of co-transcriptional splicing, transcription termination and also RNA polymerase pausing by profiling nascent 3’ ends. I could define the position of pre-mRNA splicing during the process of transcription and provide evidence for fast and efficient co-transcriptional splicing in S. cerevisiae and S. pombe, which is associated with highly expressed genes in both organisms. Differences in S. pombe co-transcriptional splicing could be linked to gene architecture features, like intron position, GC-content and exon length.

Il est estimé qu'une fracture se produit toutes les trois secondes autour du monde, accompagné par un risque élevé d'invalidité ou même de mortalité. La connaissance des mécanismes de fractures dans une configuration de chargement représentatif d'une chute semble être d'un intérêt majeur pour le développement de méthodes dédiées à la prédiction du risque de fracture. La ténacité est un paramètre approprié lorsqu'on s'intéresse à ces mécanismes de fracture, elle détermine l'énergie nécessaire pour propager une fissure à travers l'architecture du tissu. L'objectif de cette étude est d'évaluer la ténacité de l'os cortical humain, considérant à la fois des conditions chargement quasi-statique et représentatif d'une chute sur sites anatomiques appariés. L'acquisition d'images en micro-tomographie ainsi qu'une mesure des cross-links ont été réalisées afin d'évaluer leur influence sur les mécanismes fracture du tissu. Les résultats ont montré que dans des conditions quasi-statiques, les différents sites anatomiques présentent des propriétés mécaniques différentes : le radius résiste mieux à une propagation de fissure. Dans des conditions de chute, il n'y a plus de différences entre ces sites, mais la ténacité décroit de façon significative par rapport au chargement standard. L'os cortical résiste mieux à une propagation de fissure dans des conditions quasi-statiques. Les analyses structurales et biochimiques ont montré des différences entre les sites anatomiques qui expliquent les différences mécaniques. Les caractéristiques architecturales du tissu sont déterminantes vis-à-vis des mécanismes de fracture dans des conditions quasi-statiques. Mais leur rôle lors d'une chute est moins évident. Ces résultats impliquent que la microstructure de l'os cortical n'est pas un déterminant majeur vis-à-vis du risque de fracture. De futures études doivent être réalisées afin de déterminer les paramètres décisifs dans des conditions représentatives d'une chute / A fracture is estimated every three seconds in the world, leading to an increased risk of impairment or even mortality. The biomechanical knowledge of bone fracture mechanisms in a fall configuration of loading is of great interests for the development of clinical method for the prediction of the risk of fracture. Toughness seems to be a good candidate to investigate this fracture process as it corresponds to the energy needed to propagate a crack through cortical bone complex microstructure. The aim of this study was thus to evaluate human cortical bone toughness parameter under both quasi-static and fall-like loading conditions paired anatomical locations. Micro-computed tomography images using synchrotron radiation and collagen cross-links maturation measurements were performed to investigate the influence of the tissue architecture on crack propagation. Results found showed that under quasi-static condition, the different anatomical locations present different mechanical behavior. Radius significantly better resist crack propagation than the other studied location. Considering a fall-like loading condition, no more difference is observed between the locations but a significant decreased is measured compare to the first configuration. Human cortical bone has a better capacity to resist crack propagation under a standard quasi-static loading condition. By investigating the tissue morphometric and biochemical parameters, we observed different organization from a location to another that explains the mechanical differences. The architectural features appear to be determinant for crack propagation mechanisms under quasi-static condition, but they play a lesser role under fall-like condition. These results imply that the tissue microstructure is not a determinant when dealing with the prediction of the risk of fracture. Further work has to be done to reach out which parameters are more determinants under a specific fall-like loading condition

La concentration de Carbone organique de sol (COS) et les émissions de gaz à effet de serre (GES) ne sont pas uniformes à travers l’espace, mais se regroupent en “hotspots” dans des endroits spécifiques. Ces différences s’expliquent principalement par les activités anthropiques telles que la gestion agricole. 40-50% de la surface de la Terre est utilisé par l’agriculture, par exemple les terres cultivées, les prairies gérées et cultures permanentes, y compris l’agro-foresterie et de bio-cultures énergétiques. En outre, 62% du carbone globale est COS, et le sol conserve plus que 3 fois plus de C que l’atmosphère. Ainsi, la séquestration du carbone dans les sols agricoles joue un rôle potentiellement important dans l’augmentation de stockage de COS et l’atténuation des GES, et il y a un intérêt considérable pour comprendre les effets de la gestion agricole sur le COS et les flux de GES aux prairies et terres cultivées, afin de mieux évaluer l’incertitude et la vulnérabilité des réservoirs de COS. Afin de découvrir les pratiques de gestion agricole qui contribuent à la séquestration efficace et durable du carbone aux terres agricoles en Europe, il est essentiel de simuler les stocks futurs de carbone terrestriel et les budgets de GES par rapport aux systèmes de gestion agricole variés sur les grands écosystèmes européens. Dans ce contexte, la modélisation est une méthode utile, et la modélisation a déjà été utilisée dans beaucoup d’études. Cependant beaucoup de résultats de la modélisation n’ont pas encore été validés avec les données mesurées sur l’horizon long-terme, et d’ailleurs d’autres études ont constaté un fort impact de l’initialisation du modèle sur le résultat du modèle. Néanmoins, la variabilité des prévisions annuelles et décennales concernant le C et le GES en Europe dépendent des résultats du modèle. Par conséquence, il est important de trouver la meilleure méthode d’initialisation des modèles pour obtenir des résultats des modèles fiables, notamment pour les modèles d’écosystèmes dits “process-based”. Au cours des dernières années, Zimmermann et al. (2007) a réussit à initialiser le modèle de Rothamsted carbone (RothC) en utilisant une méthode (physique et chimique) de fractionation des sols. Pour cette raison, j’ai fait l’hypothèse que les données COS détaillées seraient utiles pour initialiser des modèles d’écosystème, et que cette hypothèse doit être testée avec les modèles différents par rapport aux gestions agricoles différentes. Les buts de cette thèse sont les suivants: i) évaluation des influences des gestions agricoles sur le stockage de COS, en utilisant des approches expérimentales et des approches de modélisation; et ii) déterminer la meilleur méthode d’initialisation des modèles. (...) / Soil organic carbon (SOC) concentrations and greenhouse gas (GHG) emissions are not uniform across the landscape, but assemble in “hotspots” in specific areas. These differences are mainly driven by human-induced activities such as agricultural management. 40-50% of the Earth’s land surface is under agricultural land-use, for instance cropland, managed grassland and permanent crops including agro-forestry and bio-energy crops. Furthermore, 62% of the global soil C stock is SOC and the soil stores more than 3 times more C than the atmosphere. Thus, C sequestration in agricultural soil has a potentially important role in increasing SOC storage and GHG mitigation, and there is considerable interest in understanding the effects of agricultural management on SOC and GHG fluxes in both grasslands and croplands, in order to better assess the uncertainty and vulnerability of terrestrial SOC reservoirs. For the sake of discovering the agricultural management practices relating to the effective and sustainable C sequestration in agricultural lands in Europe, simulating future terrestrial C stocks and GHG budgets under varied agricultural management systems in major European ecosystems is essential. Using models is a useful method with the purpose of this and abundant studies have carried out. However, many model results have not been validated with reliable observed long-term data, while other studies have reported a strong impact of model initialisation on model result. Nevertheless, predictions of annual to decadal variability in the European terrestrial C and GHG ressources largely rely on model results. Consequently, finding the most appropriate and comprehensive model initialisation method for obtaining reliable model simulations became important, especially for process-based ecosystem models. In recent years, Zimmermann et al. (2007) have succeed in initialising the Rothamsted Carbon model (RothC) using a physical and chemical soil fractionation method. For that reason, we hypothesised that measured detailed SOC data would be useful to initialise ecosystem models, and this hypothesis should be tested for different process-based models and agricultural land-use and management. (...)

Le neurone est une cellule polarisée qui se divise en deux compartiments spécialisés : le compartiment somato-dendritique et le compartiment axonal. Généralement, le premier reçoit l'information en provenance d'autres neurones et le second génère un message en sortie lorsque la somme des entrées dépasse une valeur seuil au segment initial de l'axone. Ce signal de nature discrète appelé potentiel d'action (PA) est propagé activement jusqu'à la terminaison synaptique où il déclenche la transmission chimique de l'information. Cependant, la fonction axonale ne se résume pas à la simple transmission des séquences de PA à l'image d'un câble de télégraphe. L'axone est également capable de transmettre des variations continues de signaux électriques infraliminaires dit analogues et les combiner avec l'information digitale véhiculée par le PA. J'ai consacré la majorité de mon travail de thèse à l'étude de ce nouvel aspect de la fonction axonale dans le cadre de la transmission synaptique entre les neurones pyramidaux au sein du réseau excitateur CA3 de l'hippocampe de rat. Les résultats obtenus à partir d'enregistrements de paires de neurones pendant ma thèse mettent en évidence deux sortes de signalisation analogue et digitale qui aboutissent à la facilitation de la transmission synaptique. La facilitation analogue-digitale (FAD) a été observée lors d'une dépolarisation prolongée, mais également à la suite d'une hyperpolarisation transitoire au niveau du corps cellulaire. Ce sont deux versants d'une même plasticité à court-terme qui découle de l'état biophysique des canaux ioniques sensibles au voltage étant à l'origine du PA. / The neuron is a polarised cell divided into two specialized compartments: the somato-dendritic and the axonal compartment. Generally, the first one receives information arriving from other neurones and the second generates an output message, when the sum of inputs exceeds a threshold value at the axon initial segment. This all-or-none signal, called the action potential (AP) is propagated actively to the synaptic terminal where it triggers chemical transmission of information. However, axonal function is not limited to transmission of AP sequences like a telegraph cable. The axon is also capable of transmitting continuously changing sub-threshold electric signals called analogue signals and to combine them with the digital information carried by the AP. I devoted the majority of my thesis work to the study of these novel aspects of axonal function in the framework of synaptic transmission between pyramidal neurons in the CA3 excitatory network of the rat hippocampus. The results obtained through paired recordings brought to light two kinds of analogue and digital signalling that lead to a facilitation of synaptic transmission. Analogue-digital facilitation (ADF) was observed during prolonged presynaptic depolarization and also after a transient hyperpolarization of the neuronal cell body. These are two sides of the same form of short-term synaptic plasticity depending on the biophysical state of voltage gated ion channels responsible for AP generation. The first variant of ADF induced by depolarization (ADFD) is due to AP broadening and involves Kv1 potassium channels.

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