Microtubule dynamics and the role of molecular motors in Neurospora crassa.

Live-cell imaging methods were used to study microtubule dynamics in the apical regions of leading hyphae and germ tubes of Neurospora crassa expressing beta-tubulin-GFP. Microtubule polymerization rates in hyphae of N. crassa were much faster than those previously reported in any other eukaryotic organism. In order to address the roles of motor proteins in microtubule dynamic instability in N. crassa, the microtubule-motor mutant strains, Deltankin and ro-1, were examined. Polymerization and depolymerization rates in leading hyphae of these strains were reduced by one half relative to the wild type. Furthermore, microtubules in germ tubes of wild type and microtubule-motor mutants exhibited similar dynamic characteristics as those in hyphae of mutant strains. Small microtubule fragments exhibiting anterograde and retrograde motility were present in leading hyphae of all strains and germ tubes of wild-type strains. Our data suggest that microtubule motors play important roles in regulating microtubule dynamic instability in leading hyphae but not in germ tubes.     

Chlamydia trachomatis detection in a population of asymptomatic and symptomatic women: correlation with the presence of serological markers for this infection

A study of 371 women (261 asymptomatic and 110 symptomatic subjects with clinical PID) was performed to detect the presence of Chlamydia trachomatis (C.t.) and to correlate the serological markers against this microrganism, such as antibody to chlamydial hsp60 (Ab-Chsp60) and different levels of IgG, IgM and IgA, with epidemiology, pathology, sexual habits, age, diagnostic methods in the groups of women with and without pelvic inflammatory disease (PID). We found a statistically significant difference between the asymptomatic and symptomatic women regarding the presence of C.t. (3.4% versus 20%; p<0.0001). This presence was affected by the age of women (more in the group < or =25 years old), by having sex with new partners mainly if they did not undergo an antibiotic treatment. The association of antibody Chsp60 with the presence of clinical PID was quite striking. We also found a strict correlation between the detection of Ab-Chsp60 and previous chlamydial infection as well as between Ab-Chsp60 and elevated serum chlamydial IgG or IgA levels. Due to these findings, we can say that the use of serological markers for C.t. in clinical practice may be an important tool for an early screening and diagnosis of women at high risk of chlamydial infection.     

ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays

MOTIVATION: Affymetrix SNP arrays can be used to determine the DNA copy number measurement of 11 000-500 000 SNPs along the genome. Their high density facilitates the precise localization of genomic alterations and makes them a powerful tool for studies of cancers and copy number polymorphism. Like other microarray technologies it is influenced by non-relevant sources of variation, requiring correction. Moreover, the amplitude of variation induced by non-relevant effects is similar or greater than the biologically relevant effect (i.e. true copy number), making it difficult to estimate non-relevant effects accurately without including the biologically relevant effect. RESULTS: We addressed this problem by developing ITALICS, a normalization method that estimates both biological and non-relevant effects in an alternate, iterative manner, accurately eliminating irrelevant effects. We compared our normalization method with other existing and available methods, and found that ITALICS outperformed these methods for several in-house datasets and one public dataset. These results were validated biologically by quantitative PCR. AVAILABILITY: The R package ITALICS (ITerative and Alternative normaLIzation and Copy number calling for affymetrix Snp arrays) has been submitted to Bioconductor.     

Gypsy endogenous retrovirus maintains potential infectivity in several species of Drosophilids

Background  

Sequences homologous to the gypsy retroelement from Drosophila melanogaster are widely distributed among drosophilids. The structure of gypsy includes an open reading frame resembling the retroviral gene env, which is responsible for the infectious properties of retroviruses.     

Allosteric properties of hemoglobin and the plasma membrane of the erythrocyte: new insights in gas transport and metabolic modulation

Within the red blood cell the hemoglobin molecule is subjected to modulation mechanisms, namely homo- and heterotropic interactions, which optimize its functional behavior to the specific physiological requirements. At the cellular level, these modulation mechanisms are utilized to perform a number of other functions that are not minor with respect to the basic function of oxygen transport. Here we report some key examples concerning: (i) the interaction of hemoglobin with band 3 and its influence on glucose metabolism; (ii) the role of the ligand-linked quaternary transition of hemoglobin in the control of "NO bioactivity" and of gas diffusion; (iii) the interaction of plasma membrane with the various oxidative derivatives of the hemoglobin molecule.     

Gene expression analysis of a human enterocyte cell line reveals downregulation of cholesterol biosynthesis in response to short-chain fatty acids

It has been suggested that the short-chain fatty acids (SCFAs) produced by anaerobic bacterial intestinal fermentation of soluble fiber may regulate lipid metabolism in intestine, thus reducing plasma cholesterol levels. However, the exact mechanism of action of SCFAs in lowering cholesterol levels is not fully understood. The aims of this study were to test the effects of SCFAs on gene expression in a human enterocyte cell line Caco-2/TC-7 and to validate microarray data by real-time PCR. Human Caco-2/TC-7 enterocytes were cultured on transwell filter inserts and incubated with the SCFAs acetate (Ac), propionate (Pr), and butyrate (Bu). Total RNA was then isolated for microarrays and quantitative real-time PCR analysis. Treatment of human enterocytes with Pr and Bu affects a wide variety of genes. These genes were classified according to the PANTHER classification system, and the results showed that different biological processes and metabolic pathways were modified by Pr and Bu treatment, including the intestinal cholesterol biosynthesis pathway. Differential array expression analysis showed that nine genes were downregulated in this pathway, and these results were validated by real-time PCR. This in vitro study allowed us to identify a wide variety of biological processes and metabolic pathways affected by the SCFAs tested. Importantly, our results show that the global effect of Pr and Bu is to downregulate the expression of nine key genes involved in intestinal cholesterol biosynthesis, thus possibly inhibiting this pathway.     

Live analysis of endodermal layer formation identifies random walk as a novel gastrulation movement

During gastrulation, dramatic movements rearrange cells into three germ layers expanded over the entire embryo [1-3]. In fish, both endoderm and mesoderm are specified as a belt at the embryo margin. Mesodermal layer expansion is achieved through the combination of two directed migrations. The outer ring of precursors moves toward the vegetal pole and continuously seeds mesodermal cells inside the embryo, which then reverse their movement in the direction of the animal pole [3-6]. Unlike mesoderm, endodermal cells internalize at once and must therefore adopt a different strategy to expand over the embryo [7, 8]. With live imaging of YFP-expressing zebrafish endodermal cells, we demonstrate that in contrast to mesoderm, internalized endodermal cells display a nonoriented/noncoordinated movement fit by a random walk that rapidly disperses them over the yolk surface. Transplantation experiments reveal that this behaviour is largely cell autonomous, induced by TGF-beta/Nodal, and dependent on the downstream effector Casanova. At midgastrulation, endodermal cells switch to a convergence movement. We demonstrate that this switch is triggered by environmental cues. These results uncover random walk as a novel Nodal-induced gastrulation movement and as an efficient strategy to transform a localized cell group into a layer expanded over the embryo.     

Multiple origins of vagrant Subantarctic fur seals: a long journey to the Brazilian coast detected by molecular markers

In this study, we present the first data about putative source populations of the vagrant Subantarctic fur seal, Arctocephalus tropicalis, found on the Brazilian coast, through the comparison of their mitochondrial DNA control sequences to exclusive haplotypes from the main breeding colonies of the species. The results indicated that, despite the majority of the vagrant individuals are from Gough Island (the closest breeding site to the Brazilian coast), they also come from other reproductive colonies, such as Crozet Island, a distance around 16,500 km from the Brazilian coast. Furthermore, the molecular data identified three possible management units: (1) Gough, (2) Amsterdam, and (3) Marion, Macquarie and Crozet. This significant genetic subdivision must be taken into account in any future management plan for the species conservation, including rehabilitation and even reintroduction of vagrant fur seals. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The most widespread desmosomal cadherin, desmoglein 2, is a novel target of caspase 3-mediated apoptotic machinery

Apoptotic cells are known to regulate the ordered dismantling of intercellular contacts through caspase activity. Despite the important role of desmoglein (Dsg) 2 in epithelial cell-cell adhesion, the fate of this widespread desmosomal cadherin during apoptosis is yet poorly understood. Here, by means of pharmacological approaches, we investigated whether Dsg2 was targeted by caspases in HaCaT and HT-29 cell lines undergoing staurosporine (STS)-induced apoptosis. Results showed that STS induced a caspase-dependent form of cell-death in both keratinocytes (HaCaT) and enterocytes (HT-29), that associated with progressive depletion of Dsg2 from cell lysates. The proteolytic processing of full-length Dsg2 resulted in the appearance of a 70-kDa fragment which was released into the cytosol. Consistently, immunofluorescence studies revealed that Dsg2 staining was abolished from cell surface whereas the cytoplasmic region of Dsg2 did localize intracellularly. Plakoglobin (Pg) also underwent cleavage and detached from Dsg2. Apoptotic changes paralleled with progressive loss of intercellular adhesion strength. All these biochemical, morphological, and functional changes were regulated by caspase 3. Indeed, in the presence of the caspase 3-inhibitor z-DEVD-fmk, full-length Dsg2 protein levels were preserved, whereas the amount of the 70-kDa fragment was maintained on control levels. Furthermore, cells pretreated with z-DEVD-fmk retained the membrane labeling of Dsg2. Taken together, our data demonstrate that the apoptotic processing of Dsg2 is mediated by caspase 3 in epithelial cells.