Succession stage variation in population size in an early-successional herb in a peri-urban forest

Urban and peri-urban forests incur high anthropogenic pressures (e.g. recreational activities, artificialization, and eutrophication). Plant species from early-successional, transient, forest habitats, often characterized by a short life span and a persistent seed bank in the soil may differ from late-successional species in key-factors for population persistence. This study investigated variation in population size and seedling recruitment for different forest succession stages and three consecutive years in Centaurium erythraea, an early-successional biennial herb, occurring in a peri-urban forest of Brussels urban zone (Belgium). Forest succession stage had a significant impact on C. erythraea population size and on its temporal fluctuation. Populations in closing vegetation (evolving to late-succession stages) showed small population sizes and a low number of recruits compared to populations from stable early-succession vegetation and clearcuts. The number of recruits was the highest after clearcutting, which can be related to the expression of the soil seed bank. Populations showed year-to-year variation in size (flowering individuals and recruits), even in stable (over three years) early-succession forest vegetation. In the absence of disturbance changing succession stage, population size is expected to depend on seed set of the previous years and subsequent seedling recruitment, which can be affected by environmental stochasticity. Opening gaps in the herbaceous vegetation may stimulate seedling recruitment, also in unoccupied patches where “cryptic” seed populations are present in the soil. Forest path and road verges, despite their potential negative impact on forests, can constitute refuge habitats for early-successional forest plant species. Their management should involve the preservation of these species.     

Efficient protection and isolation of ubiquitylated proteins using tandem ubiquitin‐binding entities

Post‐translational modification with ubiquitin is one of the most important mechanisms in the regulation of protein stability and function. However, the high reversibility of this modification is the main obstacle for the isolation and characterization of ubiquitylated proteins. To overcome this problem, we have developed tandem‐repeated ubiquitin‐binding entities (TUBEs) based on ubiquitin‐associated (UBA) domains. TUBEs recognize tetra‐ubiquitin with a markedly higher affinity than single UBA domains, allowing poly‐ubiquitylated proteins to be efficiently purified from cell extracts in native conditions. More significant is the fact that TUBEs protect poly‐ubiquitin‐conjugated proteins, such as p53 and IκBα, both from proteasomal degradation and de‐ubiquitylating activity present in cell extracts, as well as from existing proteasome and cysteine protease inhibitors. Therefore, these new ‘molecular traps’ should become valuable tools for purifying endogenous poly‐ubiquitylated proteins, thus contributing to a better characterization of many essential functions regulated by these post‐translational modifications.     

Carbon and arsenic metabolism in Thiomonas strains: differences revealed diverse adaptation processes

Background  

Thiomonas strains are ubiquitous in arsenic-contaminated environments. Differences between Thiomonas strains in the way they have adapted and respond to arsenic have never been studied in detail. For this purpose, five Thiomonas strains, that are interesting in terms of arsenic metabolism were selected: T. arsenivorans, Thiomonas spp. WJ68 and 3As are able to oxidise As(III), while Thiomonas sp. Ynys1 and T. perometabolis are not. Moreover, T. arsenivorans and 3As present interesting physiological traits, in particular that these strains are able to use As(III) as an electron donor.     

Desulfosporosinus acidiphilus sp. nov.: a moderately acidophilic sulfate-reducing bacterium isolated from acid mining drainage sediments

An obligately anaerobic, spore-forming, acidophilic sulfate-reducing bacterium, strain SJ4^T, was isolated from an acid mining effluent decantation pond sediment sample (pH around 3.0). Cells were Gram negative, non-motile, curved rods occurring singly. Strain SJ4^T grew at pH 3.6–5.5 with an optimum at pH 5.2. Strain SJ4^T utilized H₂, lactate, pyruvate, glycerol, glucose, and fructose as electron donors. Lactate and glucose were weakly used. Sulfate was used as electron acceptors, but not sulfite, elemental sulfur, arsenate (V), and fumarate. The G + C content of genomic DNA was 42.3 mol% (HPLC). 16S rRNA gene sequence analysis indicated that strain SJ4^T belonged to the genus Desulfosporosinus within the family Peptococcaceae in the phylum Firmicutes. The level of 16S rRNA gene sequence similarity with other Desulfosporosinus species was 94.7–96.2%, D. orientis DSM 765^T (similarity of 96.2%) and D. auripigmenti DSM 13351^T (similarity of 95%) being its closest relatives. DNA–DNA relatedness values with D. orientis and D. auripigmenti were 16.5 and 31.8%, respectively. On the basis of phenotypic, phylogenetic, and genetic characteristics, strain SJ4^T represents a novel species within the genus Desulfosporosinus, for which the name Desulfosporosinus acidiphilus sp. nov. is proposed. The type strain is SJ4^T (=DSM 22704^T = JCM 16185^T).     

Assembly of infectious HIV-1 in human epithelial and T-lymphoblastic cell lines

The canonical view of the ultimate steps of HIV-1 replication is that virus assembly and budding are taking place at the plasma membrane of infected cells. Surprisingly, recent studies revealed that these steps also occur on endosomal membranes in the interior of infected cells, such as macrophages. This prompted us to revisit the site of HIV-1 assembly in human epithelial-like cells and in infected human T-lymphoblastic cells. To address this question, we investigated the intracellular location of the major viral structural components of HIV-1, namely Gag, Env and the genomic RNA. Using a sub-cellular fractionation method, as well as immuno-confocal and electron microscopy, we show that Gag, the Env glycoproteins and the genomic RNA accumulate in late endosomes that contain infectious HIV-1 particles. In epithelial-like 293T cells, HIV-1 assembles and buds both at the plasma membrane and in endosomes, while in chronically infected human T lymphocytes, viral assembly mostly occurs within the cell where large amounts of infectious virions accumulate in endosomal compartments. In addition, HIV-1 release could be enhanced by ionomycin, a drug stimulating calcium-dependent exocytosis. These results favour the view that newly made Gag molecules associate with the genomic RNA in the cytosol, then viral core complexes can be targeted to late endosomes together with Env, where infectious HIV-1 are made and subsequently released by exocytosis.     

The Grey Mouse Lemur Uses Season-Dependent Fat or Protein Sparing Strategies to Face Chronic Food Restriction

During moderate calorie restriction (CR) the heterotherm Microcebus murinus is able to maintain a stable energy balance whatever the season, even if only wintering animals enter into torpor. To understand its energy saving strategies to respond to food shortages, we assessed protein and energy metabolisms associated with wintering torpor expression or summering torpor avoidance. We investigated body composition, whole body protein turnover, and daily energy expenditure (DEE), during a graded (40 and 80%) 35-day CR in short-days (winter; SD40 and SD80, respectively) and long-days (summer; LD40 and LD80, respectively) acclimated animals. LD40 animals showed no change in fat mass (FM) but a 12% fat free mass (FFM) reduction. Protein balance being positive after CR, the FFM loss was early and rapid. The 25% DEE reduction, in LD40 group was mainly explained by FFM changes. LD80 animals showed a steady body mass loss and were excluded from the CR trial at day 22, reaching a survival-threatened body mass. No data were available for this group. SD40 animals significantly decreased their FM level by 21%, but maintained FFM. Protein sparing was achieved through a 35 and 39% decrease in protein synthesis and catabolism (protein turnover), respectively, overall maintaining nitrogen balance. The 21% reduction in energy requirement was explained by the 30% nitrogen flux drop but also by torpor as DEE FFM-adjusted remained 13% lower compared to ad-libitum. SD80 animals were unable to maintain energy and nitrogen balances, losing both FM and FFM. Thus summering mouse lemurs equilibrate energy balance by a rapid loss of active metabolic mass without using torpor, whereas wintering animals spare protein and energy through increased torpor expression. Both strategies have direct fitness implication: 1) to maintain activities at a lower body size during the mating season and 2) to preserve an optimal wintering muscle mass and function.     

A rotating bed system bioreactor enables cultivation of primary osteoblasts on well‐characterized sponceram® regarding structural and flow properties

The development of bone tissue engineering depends on the availability of suitable biomaterials, a well‐defined and controlled bioreactor system, and on the use of adequate cells. The biomaterial must fulfill chemical, biological, and mechanical requirements. Besides biocompatibility, the structural and flow characteristics of the biomaterial are of utmost importance for a successful dynamic cultivation of osteoblasts, since fluid percolation within the microstructure must be assured to supply to cells nutrients and waste removal. Therefore, the biomaterial must consist of a three‐dimensional structure, exhibit high porosity and present an interconnected porous network. Sponceram®, a ZrO₂ based porous ceramic, is characterized in the presented work with regard to its microstructural design. Intrinsic permeability is obtained through a standard Darcy's experiment, while Young's modulus is derived from a two plates stress–strain test in the linear range. Furthermore, the material is applied for the dynamic cultivation of primary osteoblasts in a newly developed rotating bed bioreactor. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Cyan fluorescent protein carries a constitutive mutation that prevents its dimerization

The tendency of GFP-like fluorescent proteins to dimerize in vitro is a permanent concern as it may lead to artifacts in FRET imaging applications. However, we have found recently that CFP and YFP (the couple of GFP variants mostly used in FRET studies) show no trace of association in the cytosol of living cells up to millimolar concentrations. In this study, we investigated the oligomerization properties of purified CFP, by fluorescence anisotropy and sedimentation velocity. Surprisingly, we found that CFP has a much weaker homoaffinity than other fluorescent proteins (K(d) ≥ 3 × 10(-3) M), and that this is due to the constitutive N146I mutation, originally introduced into CFP to improve its brightness.