Leaf functional traits of Neotropical savanna trees in relation to seasonal water deficit

The seasonal savannas (cerrados) of Central Brazil are characterized by a large diversity of evergreen and deciduous trees, which do not show a clear differentiation in terms of active rooting depth. Irrespective of the depth of the root system, expansion of new foliage in deciduous species occurs at the end of the dry season. In this study, we examined a suite of leaf traits related to C assimilation, water and nutrients (N, P) in five deciduous and six evergreen trees that were among the dominant families of cerrado vegetation. Maximum CO₂ assimilation on a mass basis (A_mass) was significantly correlated with leaf N and P, and specific leaf area (SLA; leaf area per unit of leaf mass). The highest leaf concentrations of both nutrients were measured in the newly mature leaves of deciduous species at the end of the dry period. The differences in terms of leaf N and P between evergreen and deciduous species decreased during the wet season. Deciduous species also invested less in the production of non-photosynthetic leaf tissues and produced leaves with higher SLA and maintained higher water use efficiency. Thus, deciduous species compensated for their shorter leaf payback period by maintaining higher potential payback capacity (higher values of A_mass) and lower leaf construction costs (higher SLA). Their short leafless period and the capacity to flush by the end of the dry season may also contribute to offset the longer payback period of evergreen species, although it may involve the higher cost of maintaining a deep-root system or a tight control of plant water balance in the shallow-rooted ones.     

Restriction factors of retroviral replication: the example of Tripartite Motif (TRIM) protein 5α and 22

Viral tropism, replication, and pathogenesis are determined by multiple interactions between the pathogen and the host. In the case of retroviruses, and in particular, the human immunodeficiency virus, the specific interaction of the envelope protein with the host receptors and co-receptors is essential to gain entry in the cells. After entry, the success of retroviruses to complete their life cycle depends on a complex interplay between the virus and host proteins. Indeed, the cell environment is endowed with a number of factors that actively block distinct stage(s) in the microbial life cycle. Among these restriction factors, Tripartite Motif-5α (TRIM5α) has been extensively studied; however, other TRIM family members have been demonstrated to be anti-retroviral effector proteins. This article reviews, in particular, the current knowledge on the anti-retroviral effects of TRIM5α and TRIM22.     

Silica-alginate composites for microencapsulation

Optimisation of membrane properties of alginate microcapsules is a key factor for the application of microencapsulation techniques to bioartificial organ elaboration. Coacervation and layer-by-layer processes involving additional biopolymers have been extensively studied. Recently, the use of silica as a membrane-forming agent was investigated. This approach was rendered possible by the development of biocompatible routes to silica formation. The composites exhibit enhanced mechanical and thermal stability as well as suitable diffusion properties. Moreover, encapsulated enzymes and cells retain their biological activities. Similarly, silica can be associated to many other biopolymers, opening a promising route for new biocomposites design and biotechnology applications.     

Increasing day-length induces spring flushing of tropical dry forest trees in the absence of rain

In many conspecific trees of >50 species highly synchronous bud break with low inter-annual variation was observed during the late dry season, around the spring equinox, in semideciduous tropical forests of Argentina, Costa Rica, Java and Thailand and in tropical savannas of Central Brazil. Bud break was 6 months out of phase between the northern and southern hemispheres and started about 1 month earlier in the subtropics than at lower latitudes. These observations indicate that "spring flushing", i.e., synchronous bud break around the spring equinox and weeks before the first rains of the wet season, is induced by an increase in photoperiod of 30 min or less. Spring flushing is common in semideciduous forests characterized by a 4-6 month dry season and annual rainfall of 800-1,500 mm, but rare in neotropical forests with a shorter dry season or lower annual precipitation. Establishment of new foliage shortly before the wet growing season is likely to optimize photosynthetic gain in tropical forests with a relatively short growing season.     

BAC-mediated transgenic expression of fluorescent autophagic protein Beclin 1 reveals a role for Beclin 1 in lymphocyte development

Beclin 1/Atg6 is an essential component of the evolutionary conserved PtdIns(3)-kinase (Vps34) protein complex that regulates macroautophagy (autophagy) in eukaryotic cells and also interacts with antiapoptotic Bcl-2 family members, Bcl-2, and Bcl-x(L). To elucidate the physiological function of Beclin 1, we generated transgenic mice producing a green fluorescent Beclin 1 protein (Beclin 1-GFP) under Beclin 1 endogenous regulation. The beclin 1-GFP transgene is functional because it completely rescues early embryonic lethality in beclin 1-deficient mice. The transgenic mice appear normal, with undetected change in basal autophagy levels in different tissues, despite the additional expression of functional Beclin 1-GFP. Staining of Beclin 1-GFP shows mostly diffuse cytoplasmic distribution in various tissues. Detailed analysis of the transgene expression by flow cytometry reveals a Bcl-2-like biphasic expression pattern in developing T and B cells, as well as differential regulation of expression in mature versus immature thymocytes following in vitro stimulation. Moreover, thymocytes expressing high Beclin 1-GFP levels appear increasingly sensitive to glucocorticoid-induced apoptosis in vitro. Our results, therefore, support a role for Beclin 1 in lymphocyte development involving cross talk between autophagy and apoptosis.     

Monitoring proteolytic processing events by quantitative mass spectrometry

Introduction: Protease activity plays a key role in a wide variety of biological processes including gene expression, protein turnover and development. misregulation of these proteins has been associated with many cancer types such as prostate, breast, and skin cancer. thus, the identification of protease substrates will provide key information to understand proteolysis-related pathologies.

Areas covered: Proteomics-based methods to investigate proteolysis activity, focusing on substrate identification, protease specificity and their applications in systems biology are reviewed. Their quantification strategies, challenges and pitfalls are underlined and the biological implications of protease malfunction are highlighted.

Expert commentary: Dysregulated protease activity is a hallmark for some disease pathologies such as cancer. Current biochemical approaches are low throughput and some are limited by the amount of sample required to obtain reliable results. Mass spectrometry based proteomics provides a suitable platform to investigate protease activity, providing information about substrate specificity and mapping cleavage sites.     

Hydrogen-Deuterium Exchange Coupled to Top- and Middle-Down Mass Spectrometry Reveals Histone Tail Dynamics before and after Nucleosome Assembly

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Recycling and adaptation of Klebsormidium flaccidum microalgae for the sustained production of gold nanoparticles

Targeting the development of cell-based bioreactors for the production of metal nanoparticles, the possibility to perform the sustained synthesis of colloidal gold using Klebsormidium flaccidum green algae was studied. A first strategy relying on successive growth/reduction/reseeding recycling steps demonstrated maintained biosynthesis capability of the microalgae but limitation in metal content due to toxic effects. An alternative approach consisting of progressive gold salt addition revealed to be suitable to favor cell adaptation to larger metal concentrations and supported particle release over month periods.     

ProDy: protein dynamics inferred from theory and experiments

SUMMARY: We developed a Python package, ProDy, for structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations in heterogeneous datasets of structures experimentally resolved for a given biomolecular system, and for comparison of these variations with the theoretically predicted equilibrium dynamics. Datasets include structural ensembles for a given family or subfamily of proteins, their mutants and sequence homologues, in the presence/absence of their substrates, ligands or inhibitors. Numerous helper functions enable comparative analysis of experimental and theoretical data, and visualization of the principal changes in conformations that are accessible in different functional states. ProDy application programming interface (API) has been designed so that users can easily extend the software and implement new methods. AVAILABILITY: ProDy is open source and freely available under GNU General Public License from http://www.csb.pitt.edu/ProDy/.     

Quasispecies composition and phylogenetic analysis of feline coronaviruses (FCoVs) in naturally infected cats

Quasispecies composition and tissue distribution of feline coronaviruses (FCoVs) were studied in naturally infected cats. The genomic complexity of FCoVs was investigated using single-strand conformational polymorphism (SSCP) analysis of N and ORF7b amplicons, and the evolutionary process was investigated by sequence-based phylogenetic analysis. SSCP analysis showed high heterogeneity of the FCoV genome which was correlated with the seriousness of the clinical form. The two genomic regions analysed showed different levels of variation; the N region demonstrated significant heterogeneity as compared to ORF7b. Phylogenetic analysis of the nucleotide sequences showed the clear separation of sequences analysed on the basis of virulence and geographical origin. A maximum likelihood analysis of N and ORF7b data sets showed a situation of strong heterogeneity for the N region.