Soil seed bank characteristics in Cameroonian rainforests and implications for post-logging forest recovery

The soil seed bank is considered as an important component for resilience of climacic vegetation. Whereas several related studies have been conducted in Asian, American and some African tropical forests, no investigation has ever been conducted in Central African rainforests, especially in logged forests where the soil seed bank could contribute to regeneration of timber of trees species. We studied the soil seed bank characteristics in relation to the standing vegetation in three Cameroonian forest zones with different disturbance regimes. There was no significant difference between sites in terms of density of the seed bank; the average mean density was 87.6 seeds m⁻². But dissimilarities of the floristic compositions between sites were quite high. Overall, seeds came from 43 species including three commercial tree species. Whereas the seedlings emerging from soil samples mostly came from weedy and short-lived pioneer species, climax species predominated in the extant vegetation, leading to a very weak similarity between soil seed flora and the surrounding vegetation: Sorensen's index ranged from 3.5 to 7.6%. Canopy openness could significantly affect the species richness of soil seed stocks but not the seed density. These results show that the soil seed bank contribution to the resilience of mature tropical forests is low. In particular, very few timber tree species could benefit from soil seed stocks for their regeneration. Therefore, the development of enrichment techniques including use of the soil seed bank as a source of tree regeneration in such a context would be irrelevant.     

Using logic programming for modeling the one-carbon metabolism network to study the impact of folate deficiency on methylation processes

Dynamical modeling is an accurate tool for describing the dynamic regulation of one-carbon metabolism (1CM) with emphasis on the alteration of DNA methylation and/or dUMP methylation into dTMP. Using logic programming we present a comprehensive and adaptative mathematical model to study the impact of folate deficiency, including folate transport and enzymes activities. 5-Methyltetrahydrofolate (5mTHF) uptake and DNA and dUMP methylation were studied by simulating nutritional 5mTHF deficiency and methylenetetrahydrofolate reductase (MTHFR) gene defects. Both conditions had distinct effects on 1CM metabolite synthesis. Simulating severe 5mTHF deficiency (25% of normal levels) modulated 11 metabolites. However, simulating a severe decrease in MTHFR activity (25% of normal activity) modulated another set of metabolites. Two oscillations of varying amplitude were observed at the steady state for DNA methylation with severe 5mTHF deficiency, and the dUMP/dTMP ratio reached a steady state after 2 h, compared to 2.5 h for 100% 5mTHF. MTHFR activity with 25% of V(max) resulted in an increased methylated DNA pool after half an hour. We observed a deviation earlier in the profile compared to 50% and 100% V(max). For dUMP methylation, the highest level was observed with 25%, suggesting a low rate of dUMP methylation into dTMP with 25% of MTHFR activity. In conclusion, using logic programming we were able to construct the 1CM for analyzing the dynamic system behavior. This model may be used to refine biological interpretations of data or as a tool that can provide new hypotheses for pathogenesis.     

Scalable rules for coherent group motion in a gregarious vertebrate

Individuals of gregarious species that initiate collective movement require mechanisms of cohesion in order to maintain advantages of group living. One fundamental question in the study of collective movement is what individual rules are employed when making movement decisions. Previous studies have revealed that group movements often depend on social interactions among individual members and specifically that collective decisions to move often follow a quorum-like response. However, these studies either did not quantify the response function at the individual scale (but rather tested hypotheses based on group-level behaviours), or they used a single group size and did not demonstrate which social stimuli influence the individual decision-making process. One challenge in the study of collective movement has been to discriminate between a common response to an external stimulus and the synchronization of behaviours resulting from social interactions. Here we discriminate between these two mechanisms by triggering the departure of one trained Merino sheep (Ovis aries) from groups containing one, three, five and seven naïve individuals. Each individual was thus exposed to various combinations of already-departed and non-departed individuals, depending on its rank of departure. To investigate which individual mechanisms are involved in maintaining group cohesion under conditions of leadership, we quantified the temporal dynamic of response at the individual scale. We found that individuals'' decisions to move do not follow a quorum response but rather follow a rule based on a double mimetic effect: attraction to already-departed individuals and attraction to non-departed individuals. This rule is shown to be in agreement with an adaptive strategy that is inherently scalable as a function of group size.     

Chemical Synthesis of 4-Thiouridine-Containing Substrate Analogues of tRNA:Pseudouridine-55 Synthase: Photocross-Linking Studies

Abstract

For site specific incorporation of 4-thiouridine into oligoribonucleotides a new phosphoramidite is proposed. It makes use of the S-pivaloyloxymethyl group for the protection of the thiol function. This group is easily introduced and removed without modification of the standard protocol for solid phase synthesis of RNA. Three 4-thiouridine-containing oligoribonucleotides (21-mers), corresponding to tRNA minisubstrates of yeast tRNA:pseudouridine-55 synthase (Pus4) were prepared. These 4-thiouridine containing substrates were characterized and used as photoaffinity probe of the enzyme:substrate complex. Irradiation resulted in the specific photocross-linking of these oligoribonucleotides with purified recombinant tRNA:pseudouridine-55 synthase.     

Human Endogenous Retrovirus Protein Activates Innate Immunity and Promotes Experimental Allergic Encephalomyelitis in Mice

Multiple sclerosis (MS) is a complex multifactorial disease of the central nervous system (CNS) for which animal models have mainly addressed downstream immunopathology but not potential inducers of autoimmunity. In the absence of a pathogen known to cause neuroinflammation in MS, Mycobacterial lysate is commonly used in the form of complete Freund''s adjuvant to induce autoimmunity to myelin proteins in Experimental Allergic Encephalomyelitis (EAE), an animal model for MS. The present study demonstrates that a protein from the human endogenous retrovirus HERV-W family (MSRV-Env) can be used instead of mycobacterial lysate to induce autoimmunity and EAE in mice injected with MOG, with typical anti-myelin response and CNS lesions normally seen in this model. MSRV-Env was shown to induce proinflammatory response in human macrophage cells through TLR4 activation pathway. The present results demonstrate a similar activation of murine dendritic cells and show the ability of MSRV-Env to trigger EAE in mice. In previous studies, MSRV-Env protein was reproducibly detected in MS brain lesions within microglia and perivascular macrophages. The present results are therefore likely to provide a model for MS, in which the upstream adjuvant triggering neuroinflammation is the one detected in MS active lesions. This model now allows pre-clinical studies with therapeutic agents targeting this endogenous retroviral protein in MS.     

Experimental and statistical analysis of nutritional requirements for the growth of the extremophile Deinococcus geothermalis DSM 11300

Few studies concerning the nutritional requirements of Deinococcus geothermalis DSM 11300 have been conducted to date. Three defined media compositions have been published for the growth of this strain but they were found to be inadequate to achieve growth without limitation. Furthermore, growth curves, biomass concentration and growth rates were generally not available. Analysis in Principal Components was used in this work to compare and consequently to highlight the main compounds which differ between published chemically defined media. When available, biomass concentration, and/or growth rate were superimposed to the PCA analysis. The formulations of the media were collected from existing literature; media compositions designed for the growth of several strains of Deinococcaceae or Micrococcaceae were included. The results showed that a defined medium adapted from Holland et al. (Appl Microbiol Biotechnol 72:1074–1082, 2006) was the best basal medium and was chosen for further studies. A growth rate of 0.03 h^?1 and a final OD_600nm of 0.55 were obtained, but the growth was linear. Then, the effects of several medium components on oxygen uptake and biomass production by Deinococcus geothermalis DSM 11300 were studied using a respirometry-based method, to search for the nutritional limitation. The results revealed that the whole yeast extract in the medium with glucose is necessary to obtain a non-limiting growth of Deinococcus geothermalis DSM 11300 at a maximum growth rate of 0.64 h^?1 at 45 °C.     

A novel anti‐apoptotic role for apolipoprotein L2 in IFN‐γ‐induced cytotoxicity in human bronchial epithelial cells

Airway epithelium functions not only as a physical barrier, but also a regulator of lung inflammation. IFN‐γ plays a critical role in airway inflammation associated with respiratory viral infection. We investigated differential protein profiling in IFN‐γ‐stimulated normal human bronchial epithelial cells (HBEC) using a 2‐dimensional gel electrophoresis followed by MALDI‐TOF‐MS/MS. IFN‐γ markedly stimulated apolipoprotein L2 (ApoL2) protein expression in normal HBEC. ApoL2 mRNA expression was also elevated in normal human lung fibroblasts and smooth muscle cells stimulated with IFN‐γ, in lung tissues from an IFN‐γ‐predominant influenza A virus‐infected mouse lung injury model, and in cancer lung tissues from human patients. Normal HBEC showed strong resistance to IFN‐γ‐induced cytotoxicity. ApoL2 knockdown by siRNA promoted IFN‐γ‐induced cytotoxicity as revealed by a significant drop in cell viability using MTT and CyQUANT NF cell proliferation assays, and a marked increase in hypodiploid sub‐G1 cell population in cell cycle analysis. Furthermore, depletion of ApoL2 facilitated IFN‐γ‐induced membrane damage and chromatin condensation as observed in Hoechst and propidium iodide‐double staining and in transmission electron microscopy, and DNA fragmentation using a DNA laddering assay, in a caspase‐dependent manner. Our results reveal a novel function for ApoL2 in conferring anti‐apoptotic ability of human bronchial epithelium to the cytotoxic effects of IFN‐γ, in maintaining airway epithelial layer integrity. J. Cell. Physiol. 226: 397–406, 2011. © 2010 Wiley‐Liss, Inc.     

Characterization of boar sperm cytoskeletal cylicin II as an actin-binding protein

The presence of actin-binding proteins in the perinuclear theca of boar spermatozoa has been investigated, using stepwise extractions of proteins from sperm heads. Proteins extracted with the alkaline buffer 1M Na(2)CO(3), pH 11, were found to contain a 66kDa protein that binds F-actin in actin pelleting assays. Sequence studies and immunological characterization with antibodies specific for human cylicin II identified the 66kDa protein as the homologue of bovine and human cylicin II. Immunocytochemical studies showed the presence of porcine cylicin II in the acrosomal region of round spermatids and in the postacrosomal region of late spermatids and spermatozoa, in agreement with the previously described localization of cylicins. Taken together, the results suggest that cylicin II, a protein of the sperm perinuclear cytoskeleton, is a novel actin-binding protein, which probably plays a role in the actin-related events that occur during spermiogenesis and the early events of fertilization.     

REML estimation of variance parameters in nonlinear mixed effects models using the SAEM algorithm

Nonlinear mixed effects models are now widely used in biometrical studies, especially in pharmacokinetic research or for the analysis of growth traits for agricultural and laboratory species. Most of these studies, however, are often based on ML estimation procedures, which are known to be biased downwards. A few REML extensions have been proposed, but only for approximated methods. The aim of this paper is to present a REML implementation for nonlinear mixed effects models within an exact estimation scheme, based on an integration of the fixed effects and a stochastic estimation procedure. This method was implemented via a stochastic EM, namely the SAEM algorithm. The simulation study showed that the proposed REML estimation procedure considerably reduced the bias observed with the ML estimation, as well as the residual mean squared error of the variance parameter estimations, especially in the unbalanced cases. ML and REML based estimators of fixed effects were also compared via simulation. Although the two kinds of estimates were very close in terms of bias and mean square error, predictions of individual profiles were clearly improved when using REML vs. ML. An application of this estimation procedure is presented for the modelling of growth in lines of chicken.