D-ASSIRC: distributed program for finding sequence similarities in genomes

MOTIVATION: Locating the regions of similarity in a genome requires the availability of appropriate tools such as 'Accelerated Search for SImilar Regions in Chromosomes' (ASSIRC; Vincens et al., Bioinformatics, 14, 715-725, 1998). The aim of this paper is to present different strategies for improving this program by distributing the operations and data to multiple processing units and to assess the efficiency of the different implementations in terms of running time as a function of the number of processing units. RESULTS: The new version D-ASSIRCis based on three alternative strategies of task sharing: (1) a distributed search using the splitting of studied sequences into large overlapping subsequences (strategy ASS); (2) two distributed searches for repeated exact motifs of fixed size either managed by a central processor (strategy AGD) or locally managed by numerous processors (strategy ALD). The result is that the strategy ASSis suitable for a large number of processing units (the time was divided by a factor of 12 when the number of processing units was increased from 1 to 16) wheras the strategy ALDis better for a small set of processors (typically for four or six).The different proposed strategies are efficient for various applications in genomic research, particularly for locating similarities of nucleic sequences in large genomes. AVAILABILITY: D-ASSIRCis freely available by anonymous FTP at ftp://ftp.ens.fr/pub/molbio/dassirc.tar.gz. Sources and binaries for Solaris and Linux are included in the distribution.     

Physics-based gene identification: proof of concept for Plasmodium falciparum

The ab initio prediction of new genes in eukaryotic genomes represents a difficult task, notably for the identification of complex split genes. A Physics-Based Gene Identification (PBGI) method was formulated recently (Yeramian, Gene, 255, 139-150, 151-168, 2000a,b) to address this problem, taking as a model the Plasmodium falciparum genome. Here, the predictive power of this method is put under experimental test for this genome. The presented results demonstrate the usefulness of the PBGI as a gene-identification tool for P. falciparum, notably for the discovery of new genes with no homology to known genes. Perspectives opened by this new method for other eukaryotic genomes are also mentioned.     

Characterization of free radical defense system in high glucose cultured HeLa-tat cells: consequences for glucose-induced cytotoxicity

HeLa cell line stably transfected with the tat gene from human immunodeficiency virus type 1 has a decreased antioxidant potential. In this work, we used this model to investigate the effect of a high glucose level (20 mM) on the glucose induced cytotoxicity and on the antioxidant system. In comparison to cell culture under control medium, HeLa-wild cell cultured under 20 mM glucose did not exhibit necrosis or apoptosis, contrary to HeLa-tat cell presenting a significant increase in necrotic or apoptotic state. Moreover after 48 h culture under high glucose level the HeLa-tat proliferation rate was not higher than the one of HeLa-wild cells. In HeLa-wild cell high glucose level resulted in an induction of glutathione reductase activity in opposition to HeLa-tat cells where no change was observed. High glucose level resulted in 20% increase in GSSG/GSH ratio in HeLa-wild cells and 38% increase in HeLa-tat cells. Moreover, high glucose level resulted in a dramatic cytosolic thiol decrease and an important lipid peroxidation in HeLa-tat cells. No significant change of these two parameters was observed in HeLa-wild cells. In both cell lines, high glucose resulted in an increase of total SOD activity, as a consequence of the increase in Cu,Zn-SOD activity. High glucose did not result in an increase of Mn-SOD activity in both cell lines. As a consequence of tat tranfection Mn-SOD activity was 50% lower in HeLa-tat cells in comparison to HeLa-wild cells. This work emphasizes the importance of the antioxidant system in the glucose induced cytotoxicity.     

A revised diagnosis of the feather mite genus Magimelia Gaud, 1961 (Pterolichoidea: Pterolichidae: Magimeliinae) and the description of three new species

Three new mite species of the genus Magimelia (Astigmata: Pterolichidae) are described from the plumage of various lapwings (Charadriidae: Vanellinae): M. breviloba n. sp. from Vanellus miles miles; M. thailandica n. sp. from V. indicus (type-host), V. duvaucelii and V. tricolor; and M. chilensis n. sp. from V. chilensis. An extended host range for M. dolichosikya Gaud, 1961 is given. A revised diagnosis of the genus and a key to known species are presented.     

Flow cytometry and factor analysis evaluation of confocal image sequences of morphologic and functional changes occurring at the mitochondrial level during 7-ketocholesterol-induced cell death

OBJECTIVE: To analyze functional and morphologic alterations that occur at the mitochondrial level by flow cytometry and laser scanning confocal microscopy (CLSM) combined with factor analysis of biomedical image sequences (FAMIS). STUDY DESIGN: Under treatment of U937 cells with 7-ketocholesterol, functional alterations that occur at the mitochondrial level (especially loss of transmembrane mitochondrial potential [delta psi m]) were assessed with 3,3'-dihexyloxacarbocyanine iodide (DiOC6(3)) and mitotracker red (CMXRos), whereas morphologic changes were analyzed with nonyl acridine orange (NAO). By flow cytometry, these different dyes were excited at 488 nm, whereas on CLSM, excitation of NAO and CMXRos was performed by lines of an argon laser. By CLSM, spectral sequences were performed to characterize NAO and CMXRos. FAMIS was used to transform the image sequences in factor images. RESULTS: By flow cytometry, rapid loss of delta psi m induced by 7-ketocholesterol was detected with both DiOC6(3) and CMXRos, which gave similar results. Morphologic alterations of mitochondria were revealed with NAO. The factor images obtained from confocal image sequences confirmed these results. CONCLUSION: The simultaneous use of NAO, CMXRos and FAMIS constitutes a new method to detect morphologic and functional alterations occurring at the mitochondrial level during cell death.     

The HIV nef and the Kaposi-sarcoma-associated virus K3/K5 proteins: "parasites"of the endocytosis pathway

The modulation of plasma membrane proteins involved in the communication with the immune system is a general mechanism developed by viruses to escape the immune response. Most of the studied examples have focused on viral proteins that missort cellular proteins during their biosynthesis. However, an increasing number of examples show that the down-modulation can also be achieved after membrane delivery by targeting into the endocytic pathway. For both human immunodeficiency virus (HIV) and Kaposi sarcoma-associated herpesvirus (KSHV), the proteins required for this process are identified, Nef and K3/K5 respectively. The extensive studies in this field have shown that the mechanisms by which these proteins "parasite" the endocytic pathway are completely different. Nef directly interacts with components of the cellular machinery involved in the vesicular transport between the endocytic compartments, mainly the clathrin adaptor complexes (AP), inducing the misrouting of numerous cellular proteins, including CD4, MHC-I, LIGHT, DC-SIGN, CD28 and MHC-II to the endosomal degradation compartment or the trans Golgi-network. The K3 and K5 proteins from KSHV act by inducing the ubiquitylation of the target proteins, such as CMH-I and B7.2, triggering their internalization and subsequent degradation by the highly conserved Tsg101/vps23 ubiquitin-dependent endosomal pathway. While these findings show that the strategies used by viruses to target cellular proteins to the endocytic pathway are extremely diverse, additional investigations are needed for the complete understanding of the specific roles of Nef and K3/K5 in the physiopathology of HIV and KSHV infections, respectively. In addition, these viral factors represent valuable tools to study the pathway they are perturbing.     

Molecular cloning and biological activity of alpha-, beta-, and gamma-megaspermin,three elicitins secreted by Phytophthora megasperma H20

We report on the molecular cloning of the Phytophthora megasperma H20 (PmH20) glycoprotein shown previously as an inducer of the hypersensitive response, of localized acquired resistance and of systemic acquired resistance in tobacco (Nicotiana tabacum), and of the PmH20 alpha- and beta-megaspermin, two elicitins of class I-A and I-B, respectively. The structure of the glycoprotein shows a signal peptide of 20 amino acids followed by the typical elicitin 98-amino acid-long domain and a 77-amino acid-long C-terminal domain carrying an O-glycosylated moiety. The molecular mass deduced from the translated cDNA sequence is 14,920 and 18,676 D as determined by mass spectrometry. This structure together with multiple sequence alignments and phylogenetic analyses indicate that the glycoprotein belongs to class III elicitins. It is the first class III elicitin protein characterized, which we named gamma-megaspermin. We compared the biological activity of the three PmH20 elicitins when applied to tobacco cv Samsun NN plants. Although alpha- and gamma-megaspermin were similarly active, beta-megaspermin was the most active in inducing the hypersensitive response and localized acquired resistance, which was assessed by measuring the levels of acidic and basic pathogenesis-related proteins and of the antioxidant phytoalexin scopoletin. The three elicitins induced similar levels of systemic acquired resistance measured as the expression of acidic PR proteins and is increased resistance to challenge tobacco mosaic virus infection.