A comparison of methods for counting viruses in aquatic systems.
(33/1313)
In this study, we compared different methods-including transmission electron microscopy-and various nucleic acid labeling methods in which we used the fluorochromes 4',6'-diamidino-2-phenylindole (DAPI), 4-[3-methyl-2,3-dihydro-(benzo-1, 3-oxazole)-2-methylmethyledene]-1-(3'-trimethyl ammoniumpropyl)-quinilinium diioide (YOPRO-1), and SYBR Green I, which can be detected by epifluorescence microscopy (EM), for counting viruses in samples obtained from freshwater ecosystems whose trophic status varied and from a culture of T7 phages. From a quantitative and qualitative viewpoint, our results showed that the greatest efficiency for all ecosystems was obtained when we used the EM counting protocol in which YOPRO-1 was the label, as this fluorochrome exhibited strong and very stable fluorescence. A modification of the original protocol in which YOPRO-1 was used is recommended, because this modification makes the protocol faster and allows it to be used for routine analysis of fixed samples. Because SYBR Green I fades very quickly, the use of this fluorochrome is not recommended for systems in which the viral content is very high (>10(8) particles/ml), such as treated domestic sewage effluents. Experiments in which we used DNase and RNase revealed that the number of viruses determined by EM was slightly overestimated (by approximately 15%) because of interference caused by the presence of free nucleic acids. (+info)
Arenaviruses: purification and physicochemical nature.
(34/1313)
The arenaviruses are a group of enveloped viruses having as a unique morphological finding the presence in the virion of granules instead of a defined core. The viruses contain a single-stranded RNA genome, but appreciable amounts of ribosomal-like RNA and 4-6S RNA of host cell origin have been detected. Little information is available on the mode of replication of the viral nucleic acids. A virion-associated RNA-dependent RNA polymerase has been described and there is indirect evidence to suggest that host cell RNA or DNA participates in virus replication. However, the steps in viral RNA synthesis and expression have not yet been elucidated.Pichinde virus contains 2 glycoproteins and 2 polypeptides. Cells infected with Pichinde virus or LCM virus have been shown to produce 2 antigens detectable by immunodiffusion. Both antigens appear to be components of the virion, but the relation between the antigens detected by immunodiffusion and the polypeptides detected by polyacrylamide gel electrophoresis has not yet been clarified. (+info)
Identification of functionally important domains in the N-terminal region of telomerase reverse transcriptase.
(35/1313)
Telomerase is a ribonucleoprotein reverse transcriptase responsible for the maintenance of one strand of telomere terminal repeats. The key protein subunit of the telomerase complex, known as TERT, possesses reverse transcriptase-like motifs that presumably mediate catalysis. These motifs are located in the C-terminal region of the polypeptide. Hidden Markov model-based sequence analysis revealed in the N-terminal region of all TERTs the presence of four conserved motifs, named GQ, CP, QFP, and T. Point mutation analysis of conserved residues confirmed the functional importance of the GQ motif. In addition, the distinct phenotypes of the GQ mutants suggest that this motif may play at least two distinct functions in telomere maintenance. Deletion analysis indicates that even the most N-terminal nonconserved region of yeast TERT (N region) is required for telomerase function. This N region exhibits a nonspecific nucleic acid binding activity that probably reflects an important physiologic function. Expression studies of various portions of the yeast TERT in Escherichia coli suggest that the N region and the GQ motif together may constitute a stable domain. We propose that all TERTs may have a bipartite organization, with an N-GQ domain connected to the other motifs through a flexible linker. (+info)
TrExML: a maximum-likelihood approach for extensive tree-space exploration.
(36/1313)
MOTIVATION: Maximum-likelihood analysis of nucleotide and amino acid sequences is a powerful approach for inferring phylogenetic relationships and for comparing evolutionary hypotheses. Because it is a computationally demanding and time-consuming process, most algorithms explore only a minute portion of tree-space, with the emphasis on finding the most likely tree while ignoring the less likely, but not significantly worse, trees. However, when such trees exist, it is equally important to identify them to give due consideration to the phylogenetic uncertainty. Consequently, it is necessary to change the focus of these algorithms such that near optimal trees are also identified. RESULTS: This paper presents the Advanced Stepwise Addition Algorithm for exploring tree-space and two algorithms for generating all binary trees on a set of sequences. The Advanced Stepwise Addition Algorithm has been implemented in TrExML, a phylogenetic program for maximum-likelihood analysis of nucleotide sequences. TrExML is shown to be more effective at finding near optimal trees than a similar program, fastDNAml, implying that TrExML offers a better approach to account for phylogenetic uncertainty than has previously been possible. A program, TreeGen, is also described; it generates binary trees on a set of sequences allowing for extensive exploration of tree-space using other programs. AVAILABILITY: TreeGen, TrExML, and the sequence data used to test the programs are available from the following two WWW sites: http://whitetail.bemidji.msus. edu/trexml/and http://jcsmr.anu.edu.au/dmm/humgen.+ ++html. (+info)
Glycotargeting: influence of the sugar moiety on both the uptake and the intracellular trafficking of nucleic acid carried by glycosylated polymers.
(37/1313)
Nucleic acids (plasmids as well as oligonucleotides) used to specifically express or modulate the expression of a gene, must reach the cytosol and/or the nucleus. Several systems have been developed to increase their uptake and their efficiency. Glycosylated polylysines have been shown to specifically help nucleic acids to be taken up in cells expressing a given cell surface membrane lectin. However, it appeared that the efficiency of the imported nucleic acid was not directly related to the extent of the uptake. Indeed, some glycosylated polylysines bearing sugar moities which are poor ligands of the cell surface lectins of a given cell were found to be more efficient than those bearing better sugar ligands. The interpretation of this paradoxal result is discussed with regards to the nature of the compartment allowing the nucleic acid to cross the membrane and to be delivered in the cytosol on the one hand, and to the presence of intracellular lectins on the other hand. (+info)
Uptake of adenosine 5'-monophosphate by Escherichia coli.
(38/1313)
Adenosine 5'-monophosphate is dephosphorylated before its uptake by cells of Escherichia coli. This is demonstrated by using a radioactive double-labeled culture, and with a 5'-nucleotidase-deficient, mutant strain. The adenosine formed is further phosphorolyzed to adenine as a prerequisite for its uptake and incorporation. The cellular localization of the enzymes involved in the catabolism of adenosine 5'-monophosphate is discussed. (+info)
Isolation and chemical characterization of plasma membranes from the yeast and mycelial forms of Candida albicans.
(39/1313)
It has been possible to induce the yeast-mycelium transformation in Candida albicans by growth of the organism under completely defined conditions in batch culture. Protoplasts have been obtained from the two forms by using a lytic enzyme preparation from Streptomyces violaceus. A plasma membrane fraction was prepared by osmotic lysis of these protoplasts and fractionated by using a combination of differential and discontinuous sucrose density-gradient flotation centrifugation. The purity of this fraction was determined by radioactive dansylation and iodination of plasma membranes of intact protoplasts followed by localization of the radioactivity upon fractionation. This procedure demonstrated less than 4% contamination of the plasma membrane fraction with other cell membranes. Chemical analysis of this fraction revealed that the major components were protein and lipid. Membranes from the yeast form contained (w/w): 50% protein, 45% lipid, 9% carbohydrate and 0.3% nucleic acid. Plasma membranes from the mycelial form contained significantly more carbohydrate and were found to be composed of (w/w): 43% protein, 31% lipid, 25% carbohydrate and 0.5% nucleic acid. Marked differences were also observed between the phospholipid, free and esterified sterols, and total fatty acids of membranes from the two forms of the organism. (+info)
Utilization of nucleoside monophosphates per Se for intraperiplasmic growth of Bdellovibrio bacteriovorus.
(40/1313)
During growth of Bdellovibrio bacteriovorus on Escherichia coli, there was a marked preferential use of E. coli phosphorus over exogenous orthophosphate even though the latter permeated into the intraperiplasmic space where the bdellovibrio was growing. This preferential use occurred to an equal extent for lipid phosphorus and nucleic acid phosphorus. Exogenous thymidine-5'-monophosphate competed effectively with [3H]thymine residues of E. coli as a precursor for bdellovibrio deoxyribonucleic acid; exogenous thymidine competed less effectively and thymine and uridine not at all. A mixture of exogenous nucleoside-5'-monophosphates equilibrated effectively with E. coli phosphorus as a phosphorus source for B. bacteriovorus; the nucleotide phosphorus entered preferentially into bdellovibrio nucleic acids. A comparable mixture of exogenous nucleosides plus orthophosphate had only a small effect on utilization of E. coli phosphorus by B. bacteriovorus, as did orthophosphate alone. A mixture of exogenous deoxyriboside monophosphates equilibrium effectively with E. coli phosphorus as a phosphorus source for bdellovibrio growth; the phosphorus from this source entered preferentially into deoxyribonucleic acid. These data show that nucleoside monophosphates derived from the substrate organism are utilized directly for n-cleic acid biosynthesis by B. bacteriovorus growing intraperiplasmically. As a consequence, the phosphate ester bonds preexisting in the nucleic acids of the substrate organism are conserved by the bdellovibrio, presumably lessening its energy requirement for intraperiplasmic growth. The data also suggest, but do not prove, that the phosphate ester bonds of phospholipids are also conserved. (+info)