Sliding MinPD: building evolutionary networks of serial samples via an automated recombination detection approach

MOTIVATION: Traditional phylogenetic methods assume tree-like evolutionary models and are likely to perform poorly when provided with sequence data from fast-evolving, recombining viruses. Furthermore, these methods assume that all the sequence data are from contemporaneous taxa, which is not valid for serially-sampled data. A more general approach is proposed here, referred to as the Sliding MinPD method, that reconstructs evolutionary networks for serially-sampled sequences in the presence of recombination. RESULTS: Sliding MinPD combines distance-based phylogenetic methods with automated recombination detection based on the best-known sliding window approaches to reconstruct serial evolutionary networks. Its performance was evaluated through comprehensive simulation studies and was also applied to a set of serially-sampled HIV sequences from a single patient. The resulting network organizations reveal unique patterns of viral evolution and may help explain the emergence of disease-associated mutants and drug-resistant strains with implications for patient prognosis and treatment strategies.     

Three novel ABCC5 splice variants in human retina and their role as regulators of ABCC5 gene expression

Background  

The ABCC5 gene encodes an organic anion pump of the ATP-binding cassette (ABC) transporter family, subclass C. The exact physiological function of ABCC5 however is not known. Here, we have isolated three novel ABCC5 splice variants and characterized their role in the regulation of ABCC5 gene expression.     

Cytoskeletal control of centrioles movement during the establishment of polarity in Madin-Darby canine kidney cells

The two centrioles that are localized close to each other and to the nucleus in single Madin-Darby Canine kidney cells (MDCK) move apart by distances as large as 13 microns after the establishment of extensive cellular junctions. Microfilaments, and possibly microtubules appear to be responsible for this separation. In fully polarized cells, the centrioles are localized just beneath the apical membrane. After disruption of intercellular junctions in low calcium medium, the centrioles move back towards the cell center. This process requires intact microtubules but happens even in the absence of microfilaments. These results indicate that the position of centrioles is determined by opposing forces produced by microtubules and microfilaments and suggest that the balance between these forces is modulated by the assembly of cellular junctions. Centriole separation appears to be an early event in the process that precedes their final positioning in the apical-most region of the polarized cell.     

Postembedding α-tubulin immunolabelling of isolated centrosomes

Summary Accurate ultrastructural localization of the components of centrosomes is an important step toward the determination of their function. We have used an electron microscopy procedure to preserve centrosome-associated antigens which enables their high-resolution localization. The unique part of our procedure is the application of a post-sectioning fixation step which overcomes the poor section contrast and morphological appearance that limits the use of low-temperature processing and Lowicryl embedding. The efficacy of our approach is demonstrated by the efficient labelling of α-tubulin in the well-preserved and contrasted microtubule barrels of the centrides of isolated mammalian centrosomes.     

Effects of water stress and rootstocks on fruit phenolic composition and physical/chemical quality in Suncrest peach

The aim of the present work was to evaluate the effects of water stress and different rootstocks on the quality indices and nutritional characteristics of peach fruit, cv. Suncrest. The results show how pre‐harvest factors, such as the type of rootstock and water stress, can influence the quality indices and nutritional properties of peach fruits. Rootstocks type influenced both quality indices such as flesh firmness (FF) and soluble solid content (SSC), but it is unclear how rootstock exerted its influence. Also water stress induced changes in quality indices of peach fruit grafted on GF 677 and Montclar whereas minor effects were recorded when water stress was applied on Penta. The content of hydroxycinnamic acids was similar in control fruits of GF677, Montclar and Penta and it increased significantly only in fruit of trees grafted on GF 677 following water stress. Anthocyanins content in fruit of control plants was higher in Montclar in comparison with the fruit grafted on the other two rootstocks while procyanidin content was higher in fruit of control plants grafted on Penta. Following the water stress an increase in total anthocyanins was observed in GF 677 and Penta whereas no significant differences were found for Montclar. Water stress induced a significant decrease in procyanidin content in Penta. In conclusion in fruits of trees grafted on Penta following water stress quality indices did not show changes but significant variations in some phytochemicals, i.e. anthocyanins and procyanindins were observed. The results suggest that the regulation of water management is an important factor to maintain a good quality of the fruits. In fact, if irrigation stress can induce a higher biosynthesis of phytochemical compounds and an increase of SSC, at the same time, it can change fruit quality traits, such as a lower FW in Montclar, a higher titratable acidity (TA) in GF 677 and Penta and a lower FF in Gf 677 and Montclar.     

In vitro and in vivo synthesis of the hepatitis B virus surface antigen and of the receptor for polymerized human serum albumin from recombinant human adenoviruses.

We have developed an adenovirus vector to express foreign proteins under the control of the adenovirus E1a promoter. Two recombinant plasmids, harbouring either the S gene or the pre-S2 region and the S gene of hepatitis B virus under the control of the E1a promoter, were used to construct two recombinant adenoviruses. These two viruses direct the synthesis of hepatitis B virus surface antigen (HBsAg) particles during the time course of an infectious cycle. When the pre-S2 region is present in the constructed virus, the synthesis of particles carrying the receptor for polymerized human serum albumin (pHSA) is observed. Moreover, the inoculation of rabbits with this latter purified recombinant adenovirus elicits the production of antibodies that react with both HBsAg and pHSA receptor.