Rab and Arf proteins at the crossroad between membrane transport and cytoskeleton dynamics

The intracellular movement and positioning of organelles and vesicles is mediated by the cytoskeleton and molecular motors. Small GTPases like Rab and Arf proteins are main regulators of intracellular transport by connecting membranes to cytoskeleton motors or adaptors. However, it is becoming clear that interactions between these small GTPases and the cytoskeleton are important not only for the regulation of membrane transport. In this review, we will cover our current understanding of the mechanisms underlying the connection between Rab and Arf GTPases and the cytoskeleton, with special emphasis on the double role of these interactions, not only in membrane trafficking but also in membrane and cytoskeleton remodeling. Furthermore, we will highlight the most recent findings about the fine control mechanisms of crosstalk between different members of Rab, Arf, and Rho families of small GTPases in the regulation of cytoskeleton organization.     

Production of fumonisins by endophytic strains of <Emphasis Type="Italic">Tolypocladium cylindrosporum</Emphasis> and its relation to fungal virus infection

Fumonisins were first discovered in Fusarium verticillioides, a fungus associated to disease and asymptomatic infections in maize. Afterwards, other fungal taxa have been found to produce fumonisins. The entomopathogenic ascomycete Tolypocladium cylindrosporum has been isolated from soil and also as an endophyte from leaves of grasses. The objectives of this work were to determine the in vitro production of fumonisin B (FB) mycotoxins and the immunosuppressive compound cyclosporine A (CyA) in several strains of T. cylindrosporum, and to examine the effect of fungal virus infection and temperature in FB production. FB₁ was detected in 30% of the strains, ranging from 0.16 to 5.52 μg cm^?2 in solid media, and FB₂ was detected in 78% of the strains, ranging from 0.764 to 40.92 μg cm^?2. CyA was not detected in any strain. The mean FB₂ concentration of the endophytic strain Tc37W was three times greater (p?<?0.05) than that of any other strain. Up to 34% more of FB₂ was detected in strains infected by the virus TcV3 than in the corresponding virus-free versions. The effect of temperature on FB₂ content was interactively significantly dependent on fungal strain and growth medium; in the YES medium, the FB₂ of virus-infected strains Tc37-1V and Tc37W increased by 67 and 16%, respectively, at 26 °C as compared to 20 °C. The FB concentration in some fungal strains was similar to that in fungi associated to food and feed intoxications.     

Two-Photon Bidirectional Control and Imaging of Neuronal Excitability with High Spatial Resolution In Vivo

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Description and Phylogeny of Urostyla grandis wiackowskii subsp. nov. (Ciliophora,Hypotricha) from an Estuarine Mangrove in Brazil

Interphase specimens, aspects of physiological reorganization and divisional morphogenesis were investigated in a strain of a hypotrichous ciliate highly similar to Urostyla grandis Ehrenberg, 1830 (type species of Urostyla), collected from a mangrove area in the estuary of the Paraíba do Sul river (Rio de Janeiro, Brazil). The results revealed that albeit interphase specimens match with the known morphologic variability in U. grandis, morphogenetic processes have conspicuous differences. Parental adoral zone is entirely renewed during morphogenesis, and marginal cirri exhibit a unique combination of developmental modes, in which left marginal rows originate from multiple anlagen arising from innermost left marginal cirral row, whereas right marginal ciliature originates from individual within‐row anlagen. Based on such characteristics, a new subspecies, namely U. grandis wiackowskii subsp. nov. is proposed, and consequently, U. grandis grandis Ehrenberg, 1830 stat. nov. is established. Bayesian and maximum‐likelihood analyses of the 18S rDNA unambiguously placed U. grandis wiackowskii as adelphotaxon of a cluster formed by other U. grandis sequences. The implications of such findings to the systematics of Urostyla are discussed.     

Studies on the reactivity of malondialdehyde. I. Effects of acid concentration and solvent composition on deuterium exchange reactions

The rates of deuterium exchange reactions of malondialdehyde (MDA) and deuterated malondialdehyde (MDAd) have been studied as a function of acidity and the content of dimethyl sulfoxide (DMSO) in binary mixtures with D₂O . MDA incorporates deuterium from D₂O solutions in a first-order reaction with a rate constant (k_obs) that depends on the acid concentration. From this dependence, a catalytic constant, k_cat, can be derived (k_cat^MDA = 2.25 × 10⁵M^?s^?1). Similar kinetic behavior was found for MDAd in H₂O solutions, and in this case, k_cat^MDA = 1.56 × 10⁵M^?1s^?1. Results from reactions of MDA and MDAd in identical H₂OD₂O mixtures show that primary and secondary isotope effects are small (k_H/k_D = 1.13) and that solvent isotope effects cause most of the differences found between reactions in D₂O and H₂O. Reactions in binary DMSOd₆D₂O mixtures show a six-fold rate increase as the proportion of DMSOd₆ increases from 50% to 90%. These results also illustrate the relatively high reactivity of MDA at pH values well above its pK_a and the importance of medium composition on its reaction rate.     

Increased amidophosphoribosyltransferase and decreased xanthine oxidase activity in human and rat renal cell carcinoma

The behavior of the activity of the rate-limiting enzyme of the biosynthesis of purines, amidophosphoribosyltransferase (EC 2.4.2.14), and of the catabolism, xanthine oxidase (EC 1.2.3.2), was elucidated in primary renal cell carcinomas in human and in chemically-induced, transplantable renal cell carcinomas in rat. Enzyme activities were measured in the supernatant fluid prepared by centrifugation of 5% homogenates at 100,000 X $\text{g}$ for 30 min. The activities in human and rat kidney for amidotransferase were 2.0 ± 0.2 and 8.9 ± 0.4 and for xanthine oxidase 0.4 ± 0.09 and 5.5 ± 0.3 μmol per hr/per mg protein x 10^?2, respectively. In the human and rat tumors the activities of amidotransferase increased 1.5? to 2.7-fold and of xanthine oxidase decreased to 25 to 69% of those of the respective controls. The ratios of the activities of amidotransferase/xanthine oxidase were increased 2.1? and 5.3-fold in the tumors.Since amidotransferase activity increased and xanthine oxidase decreased in all examined kidney tumors, the alterations in the activities of these enzymes appeared to be linked with neoplastic transformation. With the reciprocal alterations in activity of the synthetic enzyme, amidotransferase, and the concurrent decrease in that of the catabolic enzyme, xanthine oxidase, the reprogramming of gene expression resulted in an imbalance that favors the synthetic over the degradative capacity. These results indicate the applicability of the pattern of enzymic imbalance discovered in rat hepatomas to human and rat kidney neoplasia.     

Contribution of Genome-Wide Association Studies to Scientific Research: A Pragmatic Approach to Evaluate Their Impact

The factual value of genome-wide association studies (GWAS) for the understanding of multifactorial diseases is a matter of intense debate. Practical consequences for the development of more effective therapies do not seem to be around the corner. Here we propose a pragmatic and objective evaluation of how much new biology is arising from these studies, with particular attention to the information that can help prioritize therapeutic targets. We chose multiple sclerosis (MS) as a paradigm disease and assumed that, in pre-GWAS candidate-gene studies, the knowledge behind the choice of each gene reflected the understanding of the disease prior to the advent of GWAS. Importantly, this knowledge was based mainly on non-genetic, phenotypic grounds. We performed single-gene and pathway-oriented comparisons of old and new knowledge in MS by confronting an unbiased list of candidate genes in pre-GWAS association studies with those genes exceeding the genome-wide significance threshold in GWAS published from 2007 on. At the single gene level, the majority (94 out of 125) of GWAS-discovered variants had never been contemplated as plausible candidates in pre-GWAS association studies. The 31 genes that were present in both pre- and post-GWAS lists may be of particular interest in that they represent disease-associated variants whose pathogenetic relevance is supported at the phenotypic level (i.e. the phenotypic information that steered their selection as candidate genes in pre-GWAS association studies). As such they represent attractive therapeutic targets. Interestingly, our analysis shows that some of these variants are targets of pharmacologically active compounds, including drugs that are already registered for human use. Compared with the above single-gene analysis, at the pathway level GWAS results appear more coherent with previous knowledge, reinforcing some of the current views on MS pathogenesis and related therapeutic research. This study presents a pragmatic approach that helps interpret and exploit GWAS knowledge.     

Constraints Shape Cell Function and Morphology by Canalizing the Developmental Path along the Waddington's Landscape

Studies performed in absence of gravitational constraint show that a living system is unable to choose between two different phenotypes, thus leading cells to segregate into different, alternative stable states. This finding demonstrates that the genotype does not determine by itself the phenotype but requires additional, physical constraints to finalize cell differentiation. Constraints belong to two classes: holonomic (independent of the system's dynamical states, as being established by the space-time geometry of the field) and non-holonomic (modified during those biological processes to which they contribute in shaping). This latter kind of “constraints”, in which dynamics works on the constraint to recreate them, have emerged as critical determinants of self-organizing systems, by manifesting a “closure of constraints.” Overall, the constraints act by harnessing the “randomness” represented by the simultaneous presence of equiprobable events restraining the system within one attractor. These results cast doubt on the mainstream scientific concept and call for a better understanding of causation in cell biology.     

Population genomics reveals evolution and variation of Saccharomyces cerevisiae in the human and insects gut

The quest to discover the variety of ecological niches inhabited by Saccharomyces cerevisiae has led to research in areas as diverse as wineries, oak trees and insect guts. The discovery of fungal communities in the human gastrointestinal tract suggested the host's gut as a potential reservoir for yeast adaptation. Here, we report the existence of yeast populations associated with the human gut (HG) that differ from those isolated from other human body sites. Phylogenetic analysis on 12 microsatellite loci and 1715 combined CDSs from whole-genome sequencing revealed three subclusters of HG strains with further evidence of clonal colonization within the host's gut. The presence of such subclusters was supported by other genomic features, such as copy number variation, absence/introgressions of CDSs and relative polymorphism frequency. Functional analysis of CDSs specific of the different subclusters suggested possible alterations in cell wall composition and sporulation features. The phenotypic analysis combined with immunological profiling of these strains further showed that sporulation was related with strain-specific genomic characteristics in the immune recognition pattern. We conclude that both genetic and environmental factors involved in cell wall remodelling and sporulation are the main drivers of adaptation in S. cerevisiae populations in the human gut.     

Proteomic analysis of activity-dependent synaptic plasticity in hippocampal neurons

Following long-term treatment with bicuculline and tetrodotoxin (TTX) aimed at modifying synaptic activity in cultured neurons, we used a proteomic approach to identify the associated changes in protein expression. The neurons were left untreated, or treated with bicuculline or TTX, and fractionated by means of differential detergent extraction, after which the proteins in each fraction were separated by means of two-dimensional (2D) gel electrophoresis, and 57 proteins of interest were identified by mass spectrometry. The proteins that showed altered expression and/or post-translational modifications include proteins or enzymes involved in regulating cell and protein metabolism, the cytoskeleton, or mitochondrial activity. These results suggest that extensive alterations in neuronal protein expression take place as a result of increased or decreased synaptic activity.