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R Lavigne

Publications and source records attributed to R Lavigne.

11 recordsLinked to original sources
PubMed2006

Stability analysis of the bacteriophage phiKMV lysin gp36C and its putative role during infection.

The kinetic, thermodynamic and structural stability of gp36C, the virion-associated peptidoglycan hydrolase domain of bacteriophage phiKMV, is analyzed. Recombinant gp36C is highly thermoresistant (k = 0.595 h(-1) at 95 degrees C), but not thermostable (T(m) = 50.2 degrees C, DeltaH(cal) = 6.86 x 10(4) cal mol(-1)). However, aggregation influences kinetic stability in an unusual manner since aggregation is more pronounced at 55 degrees C than at higher temperatures. Furthermore, gp36C reversibly unfolds in a two-state endothermic transition, and circular dichroism analysis shows that gp36C almost completely refolds after a 3-h heat treatment at 85 degrees C. These properties are in agreement with gp36C being part of the extensible tail which is ejected in an unfolded state during phage infection.

Amino Acid Sequence↗
PubMed2006

[Comparison of new giant bacteriophages OBP and Lu11 of soil pseudomonads with bacteriophages of phiKZ-supergroup of Pseudomonas aeruginosa].

Study of two recently isolated giant bacteriophages Lu11 and OBP that are active on Pseudomonas putida var. Manila and Pseudomonas fluorescens, respectively, demonstrated their similarity in morphology, genome size, and size of phage particles, with giant bacteriophages of Pseudomonas aeruginosa assigned to the supergroup of phiKZ-like phages of the family Myoviridae designated in this manner according to the best studied phage phiKZ that belongs to the species of this group widely distributed in nature. Comparison of major polypeptide sizes of mature particles suggests the similarity of certain proteins in the phages examined. In OBP particles visualized with an electron microscope, an "inner body" was detected, which points to the specific DNA package intrinsic to phages of phiKZ group. In the meantime, phages Lul11 and OBP do not exhibit resemblance among themselves or with any of earlier described phiKZ-like phages in respect to other traits; particularly, they have no detectable DNA homology. Note that phage Lu11 of P. putida var. Manila exhibits very slight homology with phage Lin68 of the family of P. aeruginosa phiKZ-like phages detected only in blot hybridization. This suggests the possible involvement of these phages in interspecies recombination ("gene shuffling") between phages of various bacterial species. Results of partial sequencing of phage genomes confirmed the phylogenetic relatedness of phage OBP to phages of the phiKZ-supergroup, whereas phage Lu11 most probably belongs to a novel species that is not a member of supergroup phiKZ composition. The results of the study are discussed in terms of the evolution of these phages.

Genome, Viral↗
PubMed2005

Characterization of the bacteriophage PhiKMV DNA ligase.

Gene 17 product (gp17) of the Pseudomonas aeruginosa-infecting bacteriophage phiKMV shows in silico similarity to T7 DNA ligase. In a semi-quantitative activity assay, it is shown that gp17 is a functional, ATP-dependent DNA ligase, in spite of some structural differences related to DNA-binding properties). Enzymatic activity of His6-based purified expression product was optimised (4 degrees C at 24h for sticky end double-stranded DNA fragments) and estimated at 0.5 Weiss U/microg.

Amino Acid Sequence↗
PubMed2005

[Comparison of the genome for phylogenetically related bacteriophages phiKZ and EL of Pseudomonas aeruginosa: evolutionary aspects and minimal genome size].

Bacteriophages of the family Myoviridae represent one of the most widespread domains of the biosphere substantially affecting the ecological balance of microorganisms. Interestingly, sequence analysis of genomic DNAs of large bacteriophages revealed many genes coding for proteins with unknown functions. A new approach is proposed to improve the functional identification of genes. This approach is based on comparing the genome sequence for phylogenetically and morphologically related phages showing no considerable homology at the level of genomic DNA. It is assumed that gene functions essential for the development of phages of a given family are conserved and that the corresponding genes code for similar orthologous proteins even when lacking sequence homology. The genome was sequenced and compared for two Pseudomonas aeruginosa giant bacteriophages, phiKZ and EL, which belong to a group of (phiKZ-related phages. A substantial difference in genome organization was observed, suggesting specific features of phage evolution. In addition, the problem of the minimal genome of the superfamily is discussed on the basis of the difference in size and structure between the phiKZ and EL genomes.

Base Sequence↗
PubMed2004

PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes.

MOTIVATION: In silico genome analysis of bacteriophage genomes focuses mainly on gene discovery and functional assignment. The search for regulatory elements contained within these genome sequences is often based on prior knowledge of other genomic elements or on learning algorithms of experimentally determined data, potentially leading to a biased prediction output. The PHage In silico Regulatory Elements (PHIRE) program is a standalone program in Visual Basic. It performs an algorithmic string-based search on bacteriophage genome sequences to uncover and extract subsequence alignments hinting at regulatory elements contained within these genomes, in a deterministic manner without any prior experimental or predictive knowledge. RESULTS: The PHIRE program was tested on known phage genomes with experimentally verified regulatory elements. PHIRE was able to extract phage regulatory sequences correctly for bacteriophages T7, T3, YeO3-12 and lambda, based solely on the genome sequence. For 11 bacteriophages, new predictions of conserved phage-specific putative regulatory elements were made, further corroborating this approach. AVAILABILITY: http://www.agr.kuleuven.ac.be/logt/PHIRE.htm. Freely available for academic use. Commercial users should contact the corresponding author.

Bacteriophages↗
PubMed2004

Identification and characterization of a highly thermostable bacteriophage lysozyme.

Pseudomonas aeruginosa bacteriophage phiKMV is a T7-like lytic phage. Liquid chromatography-mass spectrometry of the structural proteins revealed gene product 36 (gp36) as part of the phiKMV phage particle. The presence of a lysozyme domain in the C terminal of this protein (gp36C) was verified by turbidimetric assays on chloroform-treated P. aeruginosa PAO1 and Escherichia coli WK6 cells. The molecular mass (20,884 Da) and pI (6.4) of recombinant gp36C were determined, as were the optimal enzymatic conditions (pH 6.0 in 16.7 mM phosphate buffer) and activity (4800 U/mg). Recombinant gp36C is a highly thermostable lysozyme, retaining 26% of its activity after 2 h at 100 degrees C and 21% after autoclaving. This thermostability could prove an interesting characteristic for food conservation technology.

Amino Acid Sequence↗
PubMed1989

Organo-tins in sediments and mussels from the Sado estuarine system (Portugal).

Analyses of methyl- and butyl-tin levels in freshwater, estuarine and marine sediments from the Sado estuarine system, and in mussels (Mytilus galloprovincialis) from its adjacent coast, have been performed in order to detect the contaminated areas. The main inputs of tributyl-tin (TBT), along with degradation products di- and monobutyl-tin (DBT and MBT), were detected in the estuarine zone, due to high discharge from shipyards located in this area. These levels are sometimes very high, ranging from 235 to 12,200 ng g(-1) total butyl-tins in sediments. Such inputs lead to higher bioconcentration values in mussels in the estuarine zone, as well as in a harbour located along the adjacent coast. The bioconcentration of organo-tins in mussel tissues could be enhanced in estuarine turbid waters, due to an ingestion of butyl-tins adsorbed onto fine particles, in comparison with non-turbid coastal waters. Debutylation processes occur in both sediments and mussel tissues; in organisms, these processes may lead to the formation of inorganic tin, which may be methylated differently according to the period of the year.

Journal Article↗
PubMed1989

Impact of industrial and mine drainage wastes on the heavy metal distribution in the drainage basin and estuary of the Sado River (Portugal).

This paper presents results from a survey of the heavy metal distribution in sediments in the drainage basin and estuary of the Sado River (Portugal). In the drainage basin, heavy metals originate mostly from pyrite outcrop erosion and mining activities (Cd, Zn, Cu and locally Hg, Pg), and also from crust erosion (Sn, Ni, Ti, Zr). These sources are not correlated with the particulate organic carbon (POC) and so the metals are thought to be in inorganic forms in this area. Anthropogenic heavy metal sources (urban and industrial) are found in the lower estuary (Sn, Cd, Hg, Zn, Pb and Cu) along with high POC concentrations. In this zone, these metals are thought to be strongly adsorbed onto organic particles. Furthermore, organo-metallic species are likely to be present, as demonstrated in the case of Sn, since methyl- and butyl-tin species were detected in sediments from this area. This suggests the need for the detection of organo-metallic species to understand the heavy metal geochemical cycles. No long-term changes in metal concentrations are found in sediment cores, except in the middle estuary (Zn, Cu) due to the development of mining activities on an industrial scale in the 1860s.

Journal Article↗
PubMed1979

Epidermoid carcinoma of the breast.

Two patients with squamous cell carcinoma of the breast are described. In one patient the lesion represented a primary breast tumor; in the second, a metastases from primary bonchogenic carcinoma. Neither lesion possessed estrogen receptor protein. This report emphasizes the rarity of epidermoid lesions of the breast and the importance of identifying an extramammary primary source of metastases to the breast.

Aged↗