Vertical variation in photosynthetic parameters in two different tropical forest ecosystems

Màster project submitted to obtain the degree of Master in Biology, specialisation Biodiversity: conservation and restoration. Universiteit Antwerpen. Faculty of Science. Department of Biology. Academic year 2015-2016Forests contribute to the carbon balance as the largest vegetative sink for atmospheric carbon (CO2). Anthropogenic emissions are counteracted by carbon sequestration in trees, but nutrients could be limiting photosynthesis and the effect could possibly be not as large as believed. In tropical forests, phosphorus (P) is only available from weathered bedrock and is thereby in an imbalance with the rising levels of carbon and nitrogen in the atmosphere. If P is limiting carbon uptake in tropical forests, global carbon cycle models are likely overestimating uptake by forests. Another overestimation might be to only conduct photosynthesis measurements on sunlit leaves of the canopy and take this as an overall canopy average, whilst a vertical profile in photosynthesis is very likely. Our study was conducted on two sites of the Amazonian rain forest in French Guiana. Photosynthesis and dark respiration (Rd) was measured of 120 trees in 12 plots per site. The plots were situated along a geographical gradient (at top, slope and bottom) to cover a large variety in soil P concentration. We derived the photosynthetic parameters Vcmax and Jmax from the photosynthesis measurements using the Farquhar model (Farquhar et al., 1980). The measurements were performed at two different height levels in the canopy to investigate the vertical profile. In this study we aimed to relate the spatial and vertical variability to parameters such as leaf P concentration, leaf height, light availability, the specific leaf area and the chlorophyll content (SPAD). Soil P concentrations were correlated with the leaf P concentrations, which indicates P uptake from the soil is limited. There were significant vertical differences in the leaves in Vcmax, Jmax, Rd and leaf P concentrations. We conclude that P limits the photosynthetic capacity in our study areas and vertical profiles of photosynthesis should be taken into account when estimating carbon uptake by a tropical forest ecosystem

Increased IL-10-producing regulatory T cells are characteristic of severe cases of COVID-19.

OBJECTIVES: The pandemic spread of the coronavirus SARS-CoV-2 is due, in part, to the immunological properties of the host-virus interaction. The clinical presentation varies from individual to individual, with asymptomatic carriers, mild-to-moderate-presenting patients and severely affected patients. Variation in immune response to SARS-CoV-2 may underlie this clinical variation. METHODS: Using a high-dimensional systems immunology platform, we have analysed the peripheral blood compartment of 6 healthy individuals, 23 mild-to-moderate and 20 severe COVID-19 patients. RESULTS: We identify distinct immunological signatures in the peripheral blood of the mild-to-moderate and severe COVID-19 patients, including T-cell lymphopenia, more consistent with peripheral hypo- than hyper-immune activation. Unique to the severe COVID-19 cases was a large increase in the proportion of IL-10-secreting regulatory T cells, a lineage known to possess anti-inflammatory properties in the lung. CONCLUSION: As IL-10-secreting regulatory T cells are known to possess anti-inflammatory properties in the lung, their proportional increase could contribute to a more severe COVID-19 phenotype. We openly provide annotated data (https://flowrepository.org/experiments/2713) with clinical correlates as a systems immunology resource for the COVID-19 research community

Different "metabolomic niches" of the highly diverse tree species of the French Guiana rainforests

Tropical rainforests harbor a particularly high plant diversity. We hypothesize that potential causes underlying this high diversity should be linked to distinct overall functionality (defense and growth allocation, anti-stress mechanisms, reproduction) among the different sympatric taxa. In this study we tested the hypothesis of the existence of a metabolomic niche related to a species-specific differential use and allocation of metabolites. We tested this hypothesis by comparing leaf metabolomic profiles of 54 species in two rainforests of French Guiana. Species identity explained most of the variation in the metabolome, with a species-specific metabolomic profile across dry and wet seasons. In addition to this "homeostatic" species-specific metabolomic profile significantly linked to phylogenetic distances, also part of the variance (flexibility) of the metabolomic profile was explained by season within a single species. Our results support the hypothesis of the high diversity in tropical forest being related to a species-specific metabolomic niche and highlight ecometabolomics as a tool to identify this species functional diversity related and consistent with the ecological niche theory

Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections

Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples

31P-NMR metabolomics revealed species-specific use of phosphorous in trees of a French Guiana rainforest

Productivity of tropical lowland moist forests is often limited by availability and functional allocation of phosphorus (P) that drives competition among tree species and becomes a key factor in determining forestall community diversity. We used non-target³¹P-NMR metabolic profiling to study the foliar P-metabolism of trees of a French Guiana rainforest. The objective was to test the hypotheses that P-use is species-specific, and that species diversity relates to species P-use and concentrations of P-containing compounds, including inorganic phosphates, orthophosphate monoesters and diesters, phosphonates and organic polyphosphates. We found that tree species explained the 59% of variance in ³¹P-NMR metabolite profiling of leaves. A principal component analysis showed that tree species were separated along PC 1 and PC 2 of detected P-containing compounds, which represented a continuum going from high concentrations of metabolites related to non-active P and P-storage, low total P concentrations and high N:P ratios, to high concentrations of P-containing metabolites related to energy and anabolic metabolism, high total P concentrations and low N:P ratios. These results highlight the species-specific use of P and the existence of species-specific P-use niches that are driven by the distinct species-specific position in a continuum in the P-allocation from P-storage compounds to P-containing molecules related to energy and anabolic metabolism

Decay of similarity across tropical forest communities : integrating spatial distance with soil nutrients

Altres ajuts: Acord transformatiu CRUE-CSICUnderstanding the mechanisms that drive the change of biotic assemblages over space and time is the main quest of community ecology. Assessing the relative importance of dispersal and environmental species selection in a range of organismic sizes and motilities has been a fruitful strategy. A consensus for whether spatial and environmental distances operate similarly across spatial scales and taxa, however, has yet to emerge. We used censuses of four major groups of organisms (soil bacteria, fungi, ground insects, and trees) at two observation scales (1-m sampling point vs. 2,500-m plots) in a topographically standardized sampling design replicated in two tropical rainforests with contrasting relationships between spatial distance and nutrient availability. We modeled the decay of assemblage similarity for each taxon set and site to assess the relative contributions of spatial distance and nutrient availability distance. Then, we evaluated the potentially structuring effect of tree composition over all other taxa. The similarity of nutrient content in the litter and topsoil had a stronger and more consistent selective effect than did dispersal limitation, particularly for bacteria, fungi, and trees at the plot level. Ground insects, the only group assessed with the capacity of active dispersal, had the highest species turnover and the flattest nonsignificant distance−decay relationship, suggesting that neither dispersal limitation nor nutrient availability were fundamental drivers of their community assembly at this scale of analysis. Only the fungal communities at one of our study sites were clearly coordinated with tree composition. The spatial distance at the smallest scale was more important than nutrient selection for the bacteria, fungi, and insects. The lower initial similarity and the moderate variation in composition identified by these distance-decay models, however, suggested that the effects of stochastic sampling were important at this smaller spatial scale. Our results highlight the importance of nutrients as one of the main environmental drivers of rainforest communities irrespective of organismic or propagule size and how the overriding effect of the analytical scale influences the interpretation, leading to the perception of greater importance of dispersal limitation and ecological drift over selection associated with environmental niches at decreasing observation scales

Performance and Diagnostic Value of Genome-Wide Noninvasive Prenatal Testing in Multiple Gestations.

OBJECTIVE: To evaluate the accuracy and diagnostic value of genome-wide noninvasive prenatal testing (NIPT) for the detection of fetal aneuploidies in multiple gestations, with a focus on dichorionic-diamniotic twin pregnancies. METHODS: We performed a retrospective cohort study including data from pregnant women with a twin or higher-order gestation who underwent genome-wide NIPT at one of the eight Belgian genetic centers between November 1, 2013, and March 1, 2020. Chorionicity and amnionicity were determined by ultrasonography. Follow-up invasive testing was carried out in the event of positive NIPT results. Sensitivity and specificity were calculated for the detection of trisomy 21, 18, and 13 in the dichorionic-diamniotic twin cohort. RESULTS: Unique NIPT analyses were performed for 4,150 pregnant women with a multiple gestation and an additional 767 with vanishing gestations. The failure rate in multiple gestations excluding vanishing gestations ranged from 0% to 11.7% among the different genetic centers. Overall, the failure rate was 4.8%, which could be reduced to 1.2% after single resampling. There were no common fetal trisomies detected among the 86 monochorionic-monoamniotic and 25 triplet cases. Two monochorionic-diamniotic twins had an NIPT result indicative of a trisomy 21, which was confirmed in both fetuses. Among 2,716 dichorionic-diamniotic twin gestations, a sensitivity of 100% (95% CI 74.12-100%) and a specificity of 100% (95% CI 99.86-100%) was reached for trisomy 21 (n=12). For trisomy 18 (n=3), the respective values were 75% (95% CI 30.06-95.44%) sensitivity and 100% (95% CI 99.86-100%) specificity, and for trisomy 13 (n=2), 100% (95% CI 20.65-100%) sensitivity and 99.96% (95% CI 99.79-99.99%) specificity. In the vanishing gestation group, 28 NIPT results were positive for trisomy 21, 18, or 13, with only five confirmed trisomies. CONCLUSION: Genome-wide NIPT performed accurately for detection of aneuploidy in dichorionic-diamniotic twin gestations

Synthèse - Analyse des impacts de Miriam 2.0 au regard se son contexte organisationnel et territorial. Retour réflexif et mise en lumière d’indicateurs clés pour améliorer l’implémentation du projet au sein des CPAS. Rapport d’évaluation du projet Miriam 2.0

MIRIAM 2.0 est le deuxième volet du projet que le SPP Intégration Sociale a mis en place avec le Conseil des femmes néerlandophone pour soutenir les femmes monoparentales bénéficiant d’un RIS (ou équivalent). Dans six CPAS (Anvers, Bruxelles, Genk, Mons, Liège et Ostende) une case manager a été nommée et a passé une année entière avec un groupe de femmes volontaires à travailler leur‘empowerment’ tant individuel que collectif. L’approche de l’accompagnement Miriam se veut holistique ce qui implique d’intervenir sur différents domaines de la vie en interrelation plutôt que de tendre vers un objectif unique. L’équipe de recherche du CIRTES (Prof. M. Wagener, C. Bonnetier) s’est engagée dans l’évaluation scientifique du projet Miriam 2.0 en 2018. Il s’est agi de mettre en perspective l’analyse des impacts du projet avec le contexte d’implémentation de celui-ci, à savoir l’organisation interne des CPAS et le rayonnement de leurs actions au niveau local

Analyse van de effecten van Miriam 2.0 ten opzichte van de organisatorische en territoriale context. Reflexieve feedback en toelichting van de kernindicatoren ter verbetering van de implementatie van het project binnen de OCMW's. Evaluatie rapport van het project Miriam 2.0

Miriam 2.0 vormt het tweede luik van het project dat de POD Maatschappelijke Integratie op touw heeft gezet met de Nederlandstalige Vrouwenraad om alleenstaande moeders met een (equivalent) leefloon te ondersteunen. In zes OCMW’s (Antwerpen, Brussel, Genk, Bergen, Luik en Oostende) is er een casemanager aangeduid die een volledig jaar heeft doorgebracht met een groep vrouwen om te werken aan hun individueel en collectief ‘empowerment’. De aanpak van de Miriam-begeleiding is holistisch bedoeld en richt zich dus op verschillende aspecten van het leven die met elkaar verbonden zijn in plaats van een enkel doel na te streven. Het onderzoeksteam van CIRTES (Prof. M. Wagener, C. Bonnetier) heeft in 2018 zijn schouders gezet onder de wetenschappelijke evaluatie van het project Miriam 2.0. Het was de bedoeling om de analyse van de effecten van het project in het juiste perspectief te plaatsen, samen met de context waarin het wordt geïmplementeerd, met name de interne organisatie van de OCMW’s en de uitstraling van hun acties op lokaal niveau

Analyse des impacts de Miriam 2.0 au regard se son contexte organisationnel et territorial. Retour réflexif et mise en lumière d’indicateurs clés pour améliorer l’implémentation du projet au sein des CPAS. Rapport d’évaluation du projet Miriam 2.0

MIRIAM 2.0 est le deuxième volet du projet que le SPP Intégration Sociale a mis en place avec le Conseil des femmes néerlandophone pour soutenir les femmes monoparentales bénéficiant d’un RIS (ou équivalent). Dans six CPAS (Anvers, Bruxelles, Genk, Mons, Liège et Ostende) une case manager a été nommée et a passé une année entière avec un groupe de femmes volontaires à travailler leur‘empowerment’ tant individuel que collectif. L’approche de l’accompagnement Miriam se veut holistique ce qui implique d’intervenir sur différents domaines de la vie en interrelation plutôt que de tendre vers un objectif unique. L’équipe de recherche du CIRTES (Prof. M. Wagener, C. Bonnetier) s’est engagée dans l’évaluation scientifique du projet Miriam 2.0 en 2018. Il s’est agi de mettre en perspective l’analyse des impacts du projet avec le contexte d’implémentation de celui-ci, à savoir l’organisation interne des CPAS et le rayonnement de leurs actions au niveau local