Phylogeny of gammaproteobacteria.

The phylogeny of the large bacterial class Gammaproteobacteria has been difficult to resolve. Here we apply a telescoping multiprotein approach to the problem for 104 diverse gammaproteobacterial genomes, based on a set of 356 protein families for the whole class and even larger sets for each of four cohesive subregions of the tree. Although the deepest divergences were resistant to full resolution, some surprising patterns were strongly supported.

Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle.

The facultative intracellular bacterial pathogen Brucella infects a wide range of warm-blooded land and marine vertebrates and causes brucellosis. Currently, there are nine recognized Brucella species based on host preferences and phenotypic differences. The availability of 10 different genomes consisting of two chromosomes and representing six of the species allowed for a detailed comparison among themselves and relatives in the order Rhizobiales.

Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life.

Background: Completed genome sequences are rapidly increasing for Rickettsia, obligate intracellular alpha-proteobacteria responsible for various human diseases, including epidemic typhus and Rocky Mountain spotted fever. In light of phylogeny, the establishment of orthologous groups (OGs) of open reading frames (ORFs) will distinguish the core rickettsial genes and other group specific genes (class 1 OGs or C1OGs) from those distributed indiscriminately throughout the rickettsial tree (class 2 OG or C2OGs).

Methodology/principal Findings: We present 1823 representative (no gene duplications) and 259 non-representative (at least one gene duplication) rickettsial OGs.

Plasmids and rickettsial evolution: insight from Rickettsia felis.

Background: The genome sequence of Rickettsia felis revealed a number of rickettsial genetic anomalies that likely contribute not only to a large genome size relative to other rickettsiae, but also to phenotypic oddities that have confounded the categorization of R. felis as either typhus group (TG) or spotted fever group (SFG) rickettsiae. Most intriguing was the first report from rickettsiae of a conjugative plasmid (pRF) that contains 68 putative open reading frames, several of which are predicted to encode proteins with high similarity to conjugative machinery in other plasmid-containing bacteria.

PATRIC: the VBI PathoSystems Resource Integration Center.

The PathoSystems Resource Integration Center (PATRIC) is one of eight Bioinformatics Resource Centers (BRCs) funded by the National Institute of Allergy and Infection Diseases (NIAID) to create a data and analysis resource for selected NIAID priority pathogens, specifically proteobacteria of the genera Brucella, Rickettsia and Coxiella, and corona-, calici- and lyssaviruses and viruses associated with hepatitis A and E. The goal of the project is to provide a comprehensive bioinformatics resource for these pathogens, including consistently annotated genome, proteome and metabolic pathway data to facilitate research into counter-measures, including drugs, vaccines and diagnostics. The project's curation strategy has three prongs: 'breadth first' beginning with whole-genome and proteome curation using standardized protocols, a 'targeted' approach addressing the specific needs of researchers and an integrative strategy to leverage high-throughput experimental data (e.

The genome of the African trypanosome Trypanosoma brucei.

African trypanosomes cause human sleeping sickness and livestock trypanosomiasis in sub-Saharan Africa. We present the sequence and analysis of the 11 megabase-sized chromosomes of Trypanosoma brucei. The 26-megabase genome contains 9068 predicted genes, including approximately 900 pseudogenes and approximately 1700 T.

Comparative genomics of trypanosomatid parasitic protozoa.

A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that-along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions-have shaped the genomes of each parasite.

Microwave exposure induces Hsp70 and confers protection against hypoxia in chick embryos.

To determine if microwave exposure could elicit a biological effect in the absence of thermal stress, studies were designed in which chick embryos were exposed to athermal microwave radiation (915 MHz) to look for induction of Hsp70, a protein produced during times of cellular stress that aids in the protection of cellular components. Levels of Hsp70 were found to increase within 2 h, with maximum expression ( approximately 30% higher than controls) typically occurring by 3 h from the start of exposure. Other embryos were exposed to microwave radiation prior to being subjected to hypoxic stress, and were found to have significantly higher survival (P < 0.

PDR2 Gain-of-function mutations eliminate the need for Pdr1 and require the UBP6 product for resistance to translational inhibitors.

The yeast YRR1 gene was identified as a sequence encoding a protein that is related in structure to the Pdr1 and Pdr3 zinc cluster transcription factors. Dominant gain-of-function mutations were recovered that cause a multidrug resistance to inhibitors transported by the SNQ2 and YOR1 proteins. It was previously reported by others that null mutations in YRR1 cause hypersensitivity to these agents.

A PDR5-independent pathway of multi-drug resistance regulated by the SIN4 gene product.

The SIN4 locus encodes a global transcriptional regulator of various yeast genes. In this report, we demonstrate that loss of function mutations in SIN4 create a multi-drug hypersensitive phenotype that is independent of PDR5 mediated resistance. Thus, double sin4, pdr5 mutants are more sensitive than single mutants.

The unusual inheritance of multidrug-resistance factors in Saccharomyces.

The yeast PDR5 locus encodes a 160-kDa member of the ABC family of transport proteins. Strains bearing a deletion of this locus are drug hypersensitive. Resistant revertants arise when cells are plated on cycloheximide medium.

Selenium (Se) cytotoxicity in drug sensitive and drug resistant murine tumour.

Selenium is known to inhibit growth rate of neoplastic cells. We have investigated the role of selenium (Se) in resensitization of the adriamycin (ADR) resistant murine P388/ADR cells to the action of ADR. The experiments were performed in the ADR sensitive parental P388 murine leukemia (P388/S) and its subline P388/ADR, resistant to ADR, developed in our laboratory.

Novel, quinone-thiosemicarbazone hybrid (QTSCHY) non-platinum antitumor agents: inhibition of DNA biosynthesis in P388 lymphocytic cells by coordinatively unsaturated copper(II) and iron(III) complexes of naphthoquinone thiosemicarbazones.

Coordinately unsaturated Cu(II) and Fe(III) complexes of the stoichiometry [Cu(L)Cl] and [Fe(L)Cl2], where L = tridentate anion of 2-hydroxy-1,4-naphthoquinone 1-thiosemicarbazone (2HNQTSC) and its 3-methyl derivative (3M2HNQTSC), were screened in vitro against P388 lymphocytic leukemia cells. Copper complexes were found to be more effective inhibitors of DNA synthesis than analogous Fe(III) compounds. The inhibitory activities are suggested to be related to Cu(II)-Cu(I) redox couple or nitrogen adduct formation.

Response of human chronic myeloid leukemia cells to mitoxantrone cytotoxicity: potentiation by bepridil, a calcium channel antagonist.

The ability of bepridil, a calcium channel blocker, to potentiate the antitumor activity of mitoxantrone (MITO) in human chronic myeloid leukemia (CML) cells was evaluated. MITO and bepridil, when incubated alone with the CML cells for 4 h, indicated a dose-dependent increase in the inhibition of 3H-thymidine incorporation. Incorporation rate of the radiolabeled thymidine into DNA was used as a measure of cell growth.

Syntheses and spectroscopic studies of potential antitumor copper(II) complexes with 5-phenylazo-3-methoxy salicylidene thiosemicarbazone and N4 substituted thiosemicarbazones.

Five new copper(II) complexes of 5-phenylazo-3-methoxy salicylidene thiosemicarbazone and N4 substituted thiosemicarbazones have been synthesized. They have been characterized by chemical analyses, magnetic, conductance data, and by ultraviolet (UV)--visible, infrared, and electron spin resonance spectra. The complexes have the general formula CuL2, where HL is the ligand.

Altered cerebral protein turnover in rats following prolonged in vivo treatment with nicotine.

Turnover rates of cerebral proteins were examined in control adult rats and in those subjected to prolonged in vivo treatment with "low" (0.02 mg/ml) or "high" (0.04 mg/ml) doses of nicotine (added to drinking water), using [14C]bicarbonate as the label.

Altered synaptosomal ATPase activity in rat brain following prolonged in vivo treatment with nicotine.

Effects of prolonged in vivo treatment with nicotine on synaptosomal ATPase activity in rat brain were examined by employing doses of nicotine (0.02 and 0.04 mg/ml in the drinking water) which simulated intake by moderate and heavy smokers.