Predicting spatial patterns of plant biodiversity : from species to communities

Understanding the distribution and composition of species assemblages and being able to predict them in space and time are highly important tasks io investigate the fate of biodiversity in the current global changes context. Species distribution models are tools that have proven useful to predict the potential distribution of species by relating their occurrences to environmental variables. Species assemblages can then be predicted by combining the prediction of individual species models. In the first part of my thesis, I tested the importance of new environmental predictors to improve species distribution prediction. I showed that edaphic variables, above all soil pH and nitrogen content could be important in species distribution models. In a second chapter, I tested the influence of different resolution of predictors on the predictive ability of species distribution models. I showed that fine resolution predictors could ameliorate the models for some species by giving a better estimation of the micro-topographic condition that species tolerate, but that fine resolution predictors for climatic factors still need to be ameliorated. The second goal of my thesis was to test the ability of empirical models to predict species assemblages' characteristics such as species richness or functional attributes. I showed that species richness could be modelled efficiently and that the resulting prediction gave a more realistic estimate of the number of species than when obtaining it by stacking outputs of single species distribution models. Regarding the prediction of functional characteristics (plant height, leaf surface, seed mass) of plant assemblages, mean and extreme values of functional traits were better predictable than indices reflecting the diversity of traits in the community. This approach proved interesting to understand which environmental conditions influence particular aspects of the vegetation functioning. It could also be useful to predict climate change impacts on the vegetation. In the last part of my thesis, I studied the capacity of stacked species distribution models to predict the plant assemblages. I showed that this method tended to over-predict the number of species and that the composition of the community was not predicted exactly either. Finally, I combined the results of macro- ecological models obtained in the preceding chapters with stacked species distribution models and showed that this approach reduced significantly the number of species predicted and that the prediction of the composition is also ameliorated in some cases. These results showed that this method is promising. It needs now to be tested on further data sets. - Comprendre la manière dont les plantes se répartissent dans l'environnement et s'organisent en communauté est une question primordiale dans le contexte actuel de changements globaux. Cette connaissance peut nous aider à sauvegarder la diversité des espèces et les écosystèmes. Des méthodes statistiques nous permettent de prédire la distribution des espèces de plantes dans l'espace géographique et dans le temps. Ces modèles de distribution d'espèces, relient les occurrences d'une espèce avec des variables environnementales pour décrire sa distribution potentielle. Cette méthode a fait ses preuves pour ce qui est de la prédiction d'espèces individuelles. Plus récemment plusieurs tentatives de cumul de modèles d'espèces individuelles ont été réalisées afin de prédire la composition des communautés végétales. Le premier objectif de mon travail est d'améliorer les modèles de distribution en testant l'importance de nouvelles variables prédictives. Parmi différentes variables édaphiques, le pH et la teneur en azote du sol se sont avérés des facteurs non négligeables pour prédire la distribution des plantes. Je démontre aussi dans un second chapitre que les prédicteurs environnementaux à fine résolution permettent de refléter les conditions micro-topographiques subies par les plantes mais qu'ils doivent encore être améliorés avant de pouvoir être employés de manière efficace dans les modèles. Le deuxième objectif de ce travail consistait à étudier le développement de modèles prédictifs pour des attributs des communautés végétales tels que, par exemple, la richesse en espèces rencontrée à chaque point. Je démontre qu'il est possible de prédire par ce biais des valeurs de richesse spécifiques plus réalistes qu'en sommant les prédictions obtenues précédemment pour des espèces individuelles. J'ai également prédit dans l'espace et dans le temps des caractéristiques de la végétation telles que sa hauteur moyenne, minimale et maximale. Cette approche peut être utile pour comprendre quels facteurs environnementaux promeuvent différents types de végétation ainsi que pour évaluer les changements à attendre au niveau de la végétation dans le futur sous différents régimes de changements climatiques. Dans une troisième partie de ma thèse, j'ai exploré la possibilité de prédire les assemblages de plantes premièrement en cumulant les prédictions obtenues à partir de modèles individuels pour chaque espèce. Cette méthode a le défaut de prédire trop d'espèces par rapport à ce qui est observé en réalité. J'ai finalement employé le modèle de richesse en espèce développé précédemment pour contraindre les résultats du modèle d'assemblage de plantes. Cela a permis l'amélioration des modèles en réduisant la sur-prédiction et en améliorant la prédiction de la composition en espèces. Cette méthode semble prometteuse mais de nouveaux tests sont nécessaires pour bien évaluer ses capacités.

Aversive Stimuli and Functional Networks of Fear Learning in PTSD : 734

Background: One characteristic of post traumatic stress disorder is an inability to adapt to a safe environment i.e. to change behavior when predictions of adverse outcomes are not met. Recent studies have also indicated that PTSD patients have altered pain processing, with hyperactivation of the putamen and insula to aversive stimuli (Geuze et al, 2007). The present study examined neuronal responses to aversive and predicted aversive events. Methods: Twenty-four trauma exposed non-PTSD controls and nineteen subjects with PTSD underwent fMRI imaging during a partial reinforcement fear conditioning paradigm, with a mild electric shock as the unconditioned stimuli (UCS). Three conditions were analyzed: actual presentations of the UCS, events when a UCS was expected, but omitted (CS+), and events when the UCS was neither expected nor delivered (CS-). Results: The UCS evoked significant alterations in the pain matrix consisting of the brainstem, the midbrain, the thalamus, the insula, the anterior and middle cingulate and the contralateral somatosensory cortex. PTSD subjects displayed bilaterally elevated putamen activity to the electric shock, as compared to controls. In trials when USC was expected, but omitted, significant activations were observed in the brainstem, the midbrain, the anterior insula and the anterior cingulate. PTSD subjects displayed similar activations, but also elevated activations in the amygdala and the posterior insula. Conclusions: These results indicate altered fear and safety learning in PTSD, and neuronal activations are further explored in terms of functional connectivity using psychophysiological interaction analyses.

Molecular evidence for a functional ecdysone signaling system in Brugia malayi.

BACKGROUND: Filarial nematodes, including Brugia malayi, the causative agent of lymphatic filariasis, undergo molting in both arthropod and mammalian hosts to complete their life cycles. An understanding of how these parasites cross developmental checkpoints may reveal potential targets for intervention. Pharmacological evidence suggests that ecdysteroids play a role in parasitic nematode molting and fertility although their specific function remains unknown. In insects, ecdysone triggers molting through the activation of the ecdysone receptor: a heterodimer of EcR (ecdysone receptor) and USP (Ultraspiracle). METHODS AND FINDINGS: We report the cloning and characterization of a B. malayi EcR homologue (Bma-EcR). Bma-EcR dimerizes with insect and nematode USP/RXRs and binds to DNA encoding a canonical ecdysone response element (EcRE). In support of the existence of an active ecdysone receptor in Brugia we also cloned a Brugia rxr (retinoid X receptor) homolog (Bma-RXR) and demonstrate that Bma-EcR and Bma-RXR interact to form an active heterodimer using a mammalian two-hybrid activation assay. The Bma-EcR ligand-binding domain (LBD) exhibits ligand-dependent transactivation via a GAL4 fusion protein combined with a chimeric RXR in mammalian cells treated with Ponasterone-A or a synthetic ecdysone agonist. Furthermore, we demonstrate specific up-regulation of reporter gene activity in transgenic B. malayi embryos transfected with a luciferase construct controlled by an EcRE engineered in a B. malayi promoter, in the presence of 20-hydroxy-ecdysone. CONCLUSIONS: Our study identifies and characterizes the two components (Bma-EcR and Bma-RXR) necessary for constituting a functional ecdysteroid receptor in B. malayi. Importantly, the ligand binding domain of BmaEcR is shown to be capable of responding to ecdysteroid ligands, and conversely, ecdysteroids can activate transcription of genes downstream of an EcRE in live B. malayi embryos. These results together confirm that an ecdysone signaling system operates in B. malayi and strongly suggest that Bma-EcR plays a central role in it. Furthermore, our study proposes that existing compounds targeting the insect ecdysone signaling pathway should be considered as potential pharmacological agents against filarial parasites.

Anatomic and functional outcome after 23-gauge vitrectomy, peeling, and intravitreal triamcinolone for idiopathic macular epiretinal membrane.

PURPOSE: To report both the functional and anatomic outcome and safety profile of 23-gauge pars plana vitrectomy combined with membrane peeling and intravitreal injection of triamcinolone acetonide in eyes with idiopathic macular epiretinal membranes. METHODS: Retrospective study of 39 consecutive patients who underwent 23-gauge transconjunctival sutureless vitrectomy, membrane peeling, and intravitreal triamcinolone acetonide injection for an idiopathic macular epiretinal membrane between February 2007 and February 2008. Minimum follow-up was 6 months. RESULTS: Thirty-nine eyes of 39 patients were included in the study. The mean follow-up was 7 +/- 2.2 months (range, 6-15 months). Twenty-two eyes (56%) were pseudophakic and 17 (44%) were phakic at the time of surgery. Five of the phakic eyes (29.4%) had worsening of cataracts during the follow-up period. Mean preoperative intraocular pressure was 14 +/- 3.5 mmHg. At the final follow-up, mean intraocular pressure was 14.5 +/- 2.7 mmHg, which did not differ significantly from the intraocular pressure at baseline (P = 0.14, two-tailed t-test). Five (13%) patients needed topical antiglaucoma treatment. Mean preoperative best-corrected visual acuity (BCVA) was 0.28 decimal equivalent (20/71 Snellen equivalent; logarithm of the minimum angle of resolution 0.54 +/- 0.2, range: 1.0-0.2) and improved significantly (P < 0.0001, two-tailed t-test) to a mean of 0.6 decimal equivalent (20/33 Snellen equivalent; logarithm of the minimum angle of resolution 0.22 +/- 0.16, range: 0.6-0) at the final follow-up. The BCVA improved by a mean of 3.2 +/- 2.1 lines (range: 0-8). Twenty-nine patients (74%) demonstrated a gain of > or =3 lines. Mean central macular thickness was 456 +/- 77 microm (mean +/- SD) at baseline, which was significantly reduced at the final follow-up to 327 +/- 79 microm (mean +/- SD; P < 0.0001, two-tailed t-test). Average central macular thickness reduction was 131 +/- 77 microm (mean +/- SD; range: 36-380 microm). A subgroup analysis of 15 selected cases, which had central macular thickness and BCVA measurements after the first postoperative week, demonstrated that 84% of the total final reduction in central macular thickness and 84% of the total final improvement in BCVA occurred already during the first postoperative week. CONCLUSION: Twenty-three-gauge sutureless transconjunctival vitrectomy is a safe and effective technique for the treatment of idiopathic macular epiretinal membranes. The concomitant administration of intravitreal triamcinolone acetonide after pars plana vitrectomy may speed up and improve the anatomic and functional outcome.

Structural components in functional data

Analyzing functional data often leads to finding common factors, for which functional principal component analysis proves to be a useful tool to summarize and characterize the random variation in a function space. The representation in terms of eigenfunctions is optimal in the sense of L-2 approximation. However, the eigenfunctions are not always directed towards an interesting and interpretable direction in the context of functional data and thus could obscure the underlying structure. To overcome such difficulty, an alternative to functional principal component analysis is proposed that produces directed components which may be more informative and easier to interpret. These structural components are similar to principal components, but are adapted to situations in which the domain of the function may be decomposed into disjoint intervals such that there is effectively independence between intervals and positive correlation within intervals. The approach is demonstrated with synthetic examples as well as real data. Properties for special cases are also studied.

Prospective, multicenter validation of prediction scores for major bleeding in elderly patients with venous thromboembolism.

BACKGROUND: The Outpatient Bleeding Risk Index (OBRI) and the Kuijer, RIETE and Kearon scores are clinical prognostic scores for bleeding in patients receiving oral anticoagulants for venous thromboembolism (VTE). We prospectively compared the performance of these scores in elderly patients with VTE. METHODS: In a prospective multicenter Swiss cohort study, we studied 663 patients aged ≥ 65 years with acute VTE. The outcome was a first major bleeding at 90 days. We classified patients into three categories of bleeding risk (low, intermediate and high) according to each score and dichotomized patients as high vs. low or intermediate risk. We calculated the area under the receiver-operating characteristic (ROC) curve, positive predictive values and likelihood ratios for each score. RESULTS: Overall, 28 out of 663 patients (4.2%, 95% confidence interval [CI] 2.8-6.0%) had a first major bleeding within 90 days. According to different scores, the rate of major bleeding varied from 1.9% to 2.1% in low-risk, from 4.2% to 5.0% in intermediate-risk and from 3.1% to 6.6% in high-risk patients. The discriminative power of the scores was poor to moderate, with areas under the ROC curve ranging from 0.49 to 0.60 (P = 0.21). The positive predictive values and positive likelihood ratios were low and varied from 3.1% to 6.6% and from 0.72 to 1.59, respectively. CONCLUSION: In elderly patients with VTE, existing bleeding risk scores do not have sufficient accuracy and power to discriminate between patients with VTE who are at a high risk of short-term major bleeding and those who are not.

An integrated genetic and functional analysis of the role of type II transmembrane serine proteases (TMPRSSs) in hearing loss.

Building on our discovery that mutations in the transmembrane serine protease, TMPRSS3, cause nonsyndromic deafness, we have investigated the contribution of other TMPRSS family members to the auditory function. To identify which of the 16 known TMPRSS genes had a strong likelihood of involvement in hearing function, three types of biological evidence were examined: 1) expression in inner ear tissues; 2) location in a genomic interval that contains a yet unidentified gene for deafness; and 3) evaluation of hearing status of any available Tmprss knockout mouse strains. This analysis demonstrated that, besides TMPRSS3, another TMPRSS gene was essential for hearing and, indeed, mice deficient for Hepsin (Hpn) also known as Tmprss1 exhibited profound hearing loss. In addition, TMPRSS2, TMPRSS5, and CORIN, also named TMPRSS10, showed strong likelihood of involvement based on their inner ear expression and mapping position within deafness loci PKSR7, DFNB24, and DFNB25, respectively. These four TMPRSS genes were then screened for mutations in affected members of the DFNB24 and DFNB25 deafness families, and in a cohort of 362 sporadic deaf cases. This large mutation screen revealed numerous novel sequence variations including three potential pathogenic mutations in the TMPRSS5 gene. The mutant forms of TMPRSS5 showed reduced or absent proteolytic activity. Subsequently, TMPRSS genes with evidence of involvement in deafness were further characterized, and their sites of expression were determined. Tmprss1, 3, and 5 proteins were detected in spiral ganglion neurons. Tmprss3 was also present in the organ of Corti. TMPRSS1 and 3 proteins appeared stably anchored to the endoplasmic reticulum membranes, whereas TMPRSS5 was also detected at the plasma membrane. Collectively, these results provide evidence that TMPRSS1 and TMPRSS3 play and TMPRSS5 may play important and specific roles in hearing.

The use of clinical risk factors enhances the performance of BMD in the prediction of hip and osteoporotic fractures in men and women.

SUMMARY: BMD and clinical risk factors predict hip and other osteoporotic fractures. The combination of clinical risk factors and BMD provide higher specificity and sensitivity than either alone. INTRODUCTION AND HYPOTHESES: To develop a risk assessment tool based on clinical risk factors (CRFs) with and without BMD. METHODS: Nine population-based studies were studied in which BMD and CRFs were documented at baseline. Poisson regression models were developed for hip fracture and other osteoporotic fractures, with and without hip BMD. Fracture risk was expressed as gradient of risk (GR, risk ratio/SD change in risk score). RESULTS: CRFs alone predicted hip fracture with a GR of 2.1/SD at the age of 50 years and decreased with age. The use of BMD alone provided a higher GR (3.7/SD), and was improved further with the combined use of CRFs and BMD (4.2/SD). For other osteoporotic fractures, the GRs were lower than for hip fracture. The GR with CRFs alone was 1.4/SD at the age of 50 years, similar to that provided by BMD (GR = 1.4/SD) and was not markedly increased by the combination (GR = 1.4/SD). The performance characteristics of clinical risk factors with and without BMD were validated in eleven independent population-based cohorts. CONCLUSIONS: The models developed provide the basis for the integrated use of validated clinical risk factors in men and women to aid in fracture risk prediction.

La cohorte OstéoLaus: évaluation des outils de routine clinique pour la prédiction de la fracture ostéoporotique [OsteoLaus: prediction of osteoporotic fractures by clinical risk factors and DXA, IVA and TBS].

OsteoLaus is a cohort of 1400 women 50 to 80 years living in Lausanne, Switzerland. Clinical risk factors for osteoporosis, bone ultrasound of the heel, lumbar spine and hip bone mineral density (BMD), assessment of vertebral fracture by DXA, and microarchitecture evaluation by TBS (Trabecular Bone Score) will be recorded. TBS is a new parameter obtained after a re-analysis of a DXA exam. TBS is correlated with parameters of microarchitecture. His reproducibility is good. TBS give an added diagnostic value to BMD, and predict osteoporotic fracture (partially) independently to BMD. The position of TBS in clinical routine in complement to BMD and clinical risk factors will be evaluated in the OsteoLaus cohort.

Identification of new MHC class I-restricted human tumor antigens for immunotherapy

Summary Cancer is a leading cause of morbidity and mortality in Western countries (as an example, colorectal cancer accounts for about 300'000 new cases and 200'000 deaths each year in Europe and in the USA). Despite that many patients with cancer have complete macroscopic clearance of their disease after resection, radiotherapy and/or chemotherapy, many of these patients develop fatal recurrence. Vaccination with immunogenic peptide tumor antigens has shown encouraging progresses in the last decade; immunotherapy might therefore constitute a fourth therapeutic option in the future. We dissect here and critically evaluate the numerous steps of reverse immunology, a forecast procedure to identify antigenic peptides from the sequence of a gene of interest. Bioinformatic algorithms were applied to mine sequence databases for tumor-specific transcripts. A quality assessment of publicly available sequence databanks allowed defining strengths and weaknesses of bioinformatics-based prediction of colon cancer-specific alternative splicing: new splice variants could be identified, however cancer-restricted expression could not be significantly predicted. Other sources of target transcripts were quantitatively investigated by polymerase chain reactions, as cancer-testis genes or reported overexpressed transcripts. Based on the relative expression of a defined set of housekeeping genes in colon cancer tissues, we characterized a precise procedure for accurate normalization and determined a threshold for the definition of significant overexpression of genes in cancers versus normal tissues. Further steps of reverse immunology were applied on a splice variant of the Melan¬A gene. Since it is known that the C-termini of antigenic peptides are directly produced by the proteasome, longer precursor and overlapping peptides encoded by the target sequence were synthesized chemically and digested in vitro with purified proteasome. The resulting fragments were identified by mass spectroscopy to detect cleavage sites. Using this information and based on the available anchor motifs for defined HLA class I molecules, putative antigenic peptides could be predicted. Their relative affinity for HLA molecules was confirmed experimentally with functional competitive binding assays and they were used to search patients' peripheral blood lymphocytes for the presence of specific cytolytic T lymphocytes (CTL). CTL clones specific for a splice variant of Melan-A could be isolated; although they recognized peptide-pulsed cells, they failed to lyse melanoma cells in functional assays of antigen recognition. In the conclusion, we discuss advantages and bottlenecks of reverse immunology and compare the technical aspects of this approach with the more classical procedure of direct immunology, a technique introduced by Boon and colleagues more than 10 years ago to successfully clone tumor antigens.

Functional heterogeneity of memory CD4 T cell responses in different conditions of antigen exposure and persistence.

Memory CD4 T cell responses are functionally and phenotypically heterogeneous. In the present study, memory CD4 T cell responses were analyzed in different models of Ag-specific immune responses differing on Ag exposure and/or persistence. Ag-specific CD4 T cell responses for tetanus toxoid, HSV, EBV, CMV, and HIV-1 were compared. Three distinct patterns of T cell response were observed. A dominant single IL-2 CD4 T cell response was associated with the model in which the Ag can be cleared. Polyfunctional (single IL-2 plus IL-2/IFN-gamma plus single IFN-gamma) CD4 T cell responses were associated with Ag persistence and low Ag levels. A dominant single IFN-gamma CD4 T cell response was associated with the model of Ag persistence and high Ag levels. The results obtained supported the hypothesis that the different patterns observed were substantially influenced by different conditions of Ag exposure and persistence.

Evolutionary simulations to detect functional lineage-specific genes.

MOTIVATION: Supporting the functionality of recent duplicate gene copies is usually difficult, owing to high sequence similarity between duplicate counterparts and shallow phylogenies, which hamper both the statistical and experimental inference. RESULTS: We developed an integrated evolutionary approach to identify functional duplicate gene copies and other lineage-specific genes. By repeatedly simulating neutral evolution, our method estimates the probability that an ORF was selectively conserved and is therefore likely to represent a bona fide coding region. In parallel, our method tests whether the accumulation of non-synonymous substitutions reveals signatures of selective constraint. We show that our approach has high power to identify functional lineage-specific genes using simulated and real data. For example, a coding region of average length (approximately 1400 bp), restricted to hominoids, can be predicted to be functional in approximately 94-100% of cases. Notably, the method may support functionality for instances where classical selection tests based on the ratio of non-synonymous to synonymous substitutions fail to reveal signatures of selection. Our method is available as an automated tool, ReEVOLVER, which will also be useful to systematically detect functional lineage-specific genes of closely related species on a large scale. AVAILABILITY: ReEVOLVER is available at http://www.unil.ch/cig/page7858.html.

Structural and functional studies of nonstructural protein 2 of the hepatitis C virus reveal its key role as organizer of virion assembly.

Non-structural protein 2 (NS2) plays an important role in hepatitis C virus (HCV) assembly, but neither the exact contribution of this protein to the assembly process nor its complete structure are known. In this study we used a combination of genetic, biochemical and structural methods to decipher the role of NS2 in infectious virus particle formation. A large panel of NS2 mutations targeting the N-terminal membrane binding region was generated. They were selected based on a membrane topology model that we established by determining the NMR structures of N-terminal NS2 transmembrane segments. Mutants affected in virion assembly, but not RNA replication, were selected for pseudoreversion in cell culture. Rescue mutations restoring virus assembly to various degrees emerged in E2, p7, NS3 and NS2 itself arguing for an interaction between these proteins. To confirm this assumption we developed a fully functional JFH1 genome expressing an N-terminally tagged NS2 demonstrating efficient pull-down of NS2 with p7, E2 and NS3 and, to a lower extent, NS5A. Several of the mutations blocking virus assembly disrupted some of these interactions that were restored to various degrees by those pseudoreversions that also restored assembly. Immunofluorescence analyses revealed a time-dependent NS2 colocalization with E2 at sites close to lipid droplets (LDs) together with NS3 and NS5A. Importantly, NS2 of a mutant defective in assembly abrogates NS2 colocalization around LDs with E2 and NS3, which is restored by a pseudoreversion in p7, whereas NS5A is recruited to LDs in an NS2-independent manner. In conclusion, our results suggest that NS2 orchestrates HCV particle formation by participation in multiple protein-protein interactions required for their recruitment to assembly sites in close proximity of LDs.