bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Sequence and Global Gene Expression of Q54, a New Phage Species Linking the 936 and c2 Phage Species ofLactococcus lactis
Authors: Fortier Louis-Charles , Bransi Ali , Moineau Sylvain 
Published: August 2006

ABSTRACTThe lytic lactococcal phage Q54 was previously isolated from a failed sour cream production. Its complete genomic sequence (26,537 bp) is reported here, and the analysis indicated that it represents a newLactococcus lactisphage species. A striking feature of phage Q54 is the low level of similarity of its proteome (47 open reading frames) with proteins in databases. A global gene expression study confirmed the presence of two early gene modules in Q54. The unusual configuration of these modules, combined with results of comparative analysis with other lactococcal phage genomes, suggests that one of these modules was acquired through recombination events between c2- and 936-like phages. Proteolytic cleavage and cross-linking of the major capsid protein were demonstrated through structural protein analyses. A programmed translational frameshift between the major tail protein (MTP) and the receptor-binding protein (RBP) was also discovered. A “shifty stop” signal followed by putative secondary structures is likely involved in frameshifting. To our knowledge, this is only the second report of translational frameshifting (+1) in double-stranded DNA bacteriophages and the first case of translational coupling between an MTP and an RBP. Thus, phage Q54 represents a fascinating member of a new species with unusual characteristics that brings new insights into lactococcal phage evolution.
Compensatory Functions of Two Alkyl Hydroperoxide Reductases in the Oxidative Defense System ofLegionella pneumophila
Authors: LeBlanc Jason J. , Davidson Ross J. , Hoffman Paul S. 
Published: August 2006

ABSTRACTLegionella pneumophilaexpresses two catalase-peroxidase enzymes that exhibit strong peroxidatic but weak catalatic activities, suggesting that other enzymes participate in decomposition of hydrogen peroxide (H2O2). Comparative genomics revealed thatL. pneumophilaand its close relativeCoxiella burnetiieach contain two peroxide-scavenging alkyl hydroperoxide reductase (AhpC) systems: AhpC1, which is similar to theHelicobacter pyloriAhpC system, and AhpC2 AhpD (AhpC2D), which is similar to the AhpC AhpD system ofMycobacterium tuberculosis. To establish a catalatic function for these two systems, we expressedL. pneumophila ahpC1orahpC2in a catalase/peroxidase mutant ofEscherichia coliand demonstrated restoration of H2O2resistance by a disk diffusion assay.ahpC1::Km andahpC2D::Km chromosomal deletion mutants were two- to eightfold more sensitive to H2O2,tert-butyl hydroperoxide, cumene hydroperoxide, and paraquat than the wild-typeL. pneumophila, a phenotype that could be restored bytrans-complementation. Reciprocal strategies to construct double mutants were unsuccessful. Mutant strains were not enfeebled for growth in vitro or in a U937 cell infection model. Green fluorescence protein reporter assays revealed expression to be dependent on the stage of growth, withahpC1appearing after the exponential phase andahpC2appearing during early exponential phase. Quantitative real-time PCR showed thatahpC1mRNA levels were ∼7- to 10-fold higher thanahpC2DmRNA levels. However, expression ofahpC2Dwas significantly increased in theahpC1mutant, whereasahpC1expression was unchanged in theahpC2Dmutant. These results indicate that AhpC1 or AhpC2D (or both) provide an essential hydrogen peroxide-scavenging function toL. pneumophilaand that the compensatory activity of theahpC2Dsystem is most likely induced in response to oxidative stress.
Sensor Domains Encoded in
Bacillus anthracis
Virulence Plasmids Prevent Sporulation by Hijacking a Sporulation Sensor Histidine Kinase
Authors: White Andrea K. , Hoch James A. , Grynberg Marcin , Godzik Adam , Perego Marta 
Published: August 2006

ABSTRACT

Anthrax toxin and capsule, determinants for successful infection by
Bacillus anthracis
, are encoded on the virulence plasmids pXO1 and pXO2, respectively. Each of these plasmids also encodes proteins that are highly homologous to the signal sensor domain of a chromosomally encoded major sporulation sensor histidine kinase (BA2291) in this organism.
B. anthracis
Sterne overexpressing the plasmid pXO2-61-encoded signal sensor domain exhibited a significant decrease in sporulation that was suppressed by the deletion of the BA2291 gene. Expression of the sensor domains from the pXO1-118 and pXO2-61 genes in
Bacillus subtilis
strains carrying the
B. anthracis
sporulation sensor kinase BA2291 gene resulted in BA2291-dependent inhibition of sporulation. These results indicate that sporulation sensor kinase BA2291 is converted from an activator to an inhibitor of sporulation in its native host by the virulence plasmid-encoded signal sensor domains. We speculate that activation of these signal sensor domains contributes to the initiation of
B. anthracis
sporulation in the bloodstream of its infected host, a salient characteristic in the virulence of this organism, and provides an additional role for the virulence plasmids in anthrax pathogenesis.
Control of the
Streptomyces
Subtilisin Inhibitor Gene by AdpA in the A-Factor Regulatory Cascade in
Streptomyces griseus
Authors: Hirano Setsu , Kato Jun-ya , Ohnishi Yasuo , Horinouchi Sueharu 
Published: August 2006

ABSTRACT

AdpA in the A-factor regulatory cascade in
Streptomyces griseus
activates a number of genes required for secondary metabolism and morphological differentiation, forming an AdpA regulon. The
Streptomyces
subtilisin inhibitor (SSI) gene,
sgiA
, in
S. griseus
was transcribed in response to AdpA, showing that
sgiA
is a member of the AdpA regulon. AdpA bound a single site upstream of the
sgiA
promoter at approximately position −70 with respect to its transcriptional start point. Mutational analysis of the AdpA-binding site showed that the AdpA-binding site was essential for transcriptional activation. Mutants in which
sgiA
was disrupted had higher trypsin, chymotrypsin, metalloendopeptidase, and total protease activities than the wild-type strain, which showed that SgiA modulated the activities of these extracellularly produced proteases. Because a number of genes encoding chymotrypsins, trypsins, and metalloendopeptidases, most of which are SSI-sensitive proteases, are also under the control of AdpA, the A-factor regulatory cascade was thought to play a crucial role in modulating the extracellular protease activities by triggering simultaneous production of the proteases and their inhibitor at a specific timing during growth. Mutants in which
sgiA
was disrupted grew normally and formed aerial hyphae and spores with the same time course as the wild-type strain. However, exogenous addition of purified SgiA to substrate mycelium grown on agar medium resulted in a delay in aerial mycelium formation, indicating that SgiA is involved in aerial hypha formation in conjunction with proteases.
Transposon Mutagenesis Identifies Genes Associated with
Mycoplasma pneumoniae
Gliding Motility
Authors: Hasselbring Benjamin M. , Page Clinton A. , Sheppard Edward S. , Krause Duncan C. 
Published: August 2006

ABSTRACT

The wall-less prokaryote
Mycoplasma pneumoniae
, a common cause of chronic respiratory tract infections in humans, is considered to be among the smallest and simplest known cells capable of self-replication, yet it has a complex architecture with a novel cytoskeleton and a differentiated terminal organelle that function in adherence, cell division, and gliding motility. Recent findings have begun to elucidate the hierarchy of protein interactions required for terminal organelle assembly, but the engineering of its gliding machinery is largely unknown. In the current study, we assessed gliding in cytadherence mutants lacking terminal organelle proteins B, C, P1, and HMW1. Furthermore, we screened over 3,500
M. pneumoniae
transposon mutants individually to identify genes associated with gliding but dispensable for cytadherence. Forty-seven transformants having motility defects were characterized further, with transposon insertions mapping to 32 different open reading frames widely distributed throughout the
M. pneumoniae
genome; 30 of these were dispensable for cytadherence. We confirmed the clonality of selected transformants by Southern blot hybridization and PCR analysis and characterized satellite growth and gliding by microcinematography. For some mutants, satellite growth was absent or developed more slowly than that of the wild type. Others produced lawn-like growth largely devoid of typical microcolonies, while still others had a dull, asymmetrical leading edge or a filamentous appearance of colony spreading. All mutants exhibited substantially reduced gliding velocities and/or frequencies. These findings significantly expand our understanding of the complexity of
M. pneumoniae
gliding and the identity of possible elements of the gliding machinery, providing a foundation for a detailed analysis of the engineering and regulation of motility in this unusual prokaryote.
Crowding and Confinement Effects on Protein Diffusion In Vivo
Authors: Konopka Michael C. , Shkel Irina A. , Cayley Scott , Record M. Thomas , Weisshaar James C. 
Published: August 2006

ABSTRACT

The first in vivo measurements of a protein diffusion coefficient versus cytoplasmic biopolymer volume fraction are presented. Fluorescence recovery after photobleaching yields the effective diffusion coefficient on a 1-μm-length scale of green fluorescent protein within the cytoplasm of
Escherichia coli
grown in rich medium. Resuspension into hyperosmotic buffer lacking K
+
and nutrients extracts cytoplasmic water, systematically increasing mean biopolymer volume fraction, <φ>, and thus the severity of possible crowding, binding, and confinement effects. For resuspension in isosmotic buffer (osmotic upshift, or Δ, of 0), the mean diffusion coefficient, <
D
>, in cytoplasm (6.1 ± 2.4 μm
2
s
−1
) is only 0.07 of the in vitro value (87 μm
2
s
−1
); the relative dispersion among cells, σ

D

/<
D
> (standard deviation, σ

D

, relative to the mean), is 0.39. Both <
D
> and σ

D

/<
D
> remain remarkably constant over the range of Δ values of 0 to 0.28 osmolal. For a Δ value of ≥0.28 osmolal, formation of visible plasmolysis spaces (VPSs) coincides with the onset of a rapid decrease in <
D
> by a factor of 380 over the range of Δ values of 0.28 to 0.70 osmolal and a substantial increase in σ

D

/<
D
>. Individual values of
D
vary by a factor of 9 × 10
4
but correlate well with
f
VPS
, the fractional change in cytoplasmic volume on VPS formation. The analysis reveals two levels of dispersion in
D
among cells: moderate dispersion at low Δ values for cells lacking a VPS, perhaps related to variation in φ or biopolymer organization during the cell cycle, and stronger dispersion at high Δ values related to variation in
f
VPS
. Crowding effects alone cannot explain the data, nor do these data alone distinguish crowding from possible binding or confinement effects within a cytoplasmic meshwork.
A NONLINEAR DYNAMICS PERSPECTIVE OF WOLFRAM'S NEW KIND OF SCIENCE PART VI: FROM TIME-REVERSIBLE ATTRACTORS TO THE ARROW OF TIME
Authors: CHUA LEON O. , SBITNEV VALERY I. , YOON SOOK 
Published: August 2006

This paper proves, via an analytical approach, that 170 (out of 256) Boolean CA rules in a one-dimensional cellular automata (CA) are time-reversible in a generalized sense. The dynamics on each attractor of a time-reversible rule N is exactly mirrored, in both space and time, by its bilateral twin ruleN†. In particular, all 69 period-1 rules, 17 (out of 25) period-2 rules, and 84 (out of 112) Bernoulli rules are time-reversible. The remaining 86 CA rules are time-irreversible in the sense that N and N† mirror their dynamics only in space, but not in time. In this case, each attractor of N defines a unique arrow of time. A simple "time-reversal test" is given for testing whether an attractor of a CA rule is time-reversible or time-irreversible. For a time-reversible attractor of a CA rule N the past can be uniquely recovered from the future of N†, and vice versa. This remarkable property provides 170 concrete examples of CA time machines where time travel can be routinely achieved by merely hopping from one attractor to its bilateral twin attractor, and vice versa. Moreover, the time-reversal property of some local rules can be programmed to mimic the matter–antimatter "annihilation" or "pair-production" phenomenon from high-energy physics, as well as to mimic the "contraction" or "expansion" scenarios associated with the Big Bang from cosmology. Unlike the conventional laws of physics, which are based on a unique universe, most CA rules have multiple universes (i.e. attractors), each blessed with its own laws. Moreover, some CA rules are endowed with both time-reversible attractors and time-irreversible attractors. Using an analytical approach, the time-τ return map of each Bernoulli στ-shift attractor of all 112 Bernoulli rules are shown to obey an ultra-compact formula in closed form, namely,. [Formula: see text] or its inverse map. These maps completely characterize the time-asymptotic (steady state) behavior of the nonlinear dynamics on the attractors. In-depth analysis of all but 18 global equivalence classes of CA rules have been derived, along with their basins of attraction, which characterize their transient regimes. Above all, this paper provides a rigorous nonlinear dynamics foundation for a paradigm shift from an empirical-based approach à la Wolfram to an attractor-based analytical theory of cellular automata.
Bortezomib inhibits docetaxel-induced apoptosis via a p21-dependent mechanism in human prostate cancer cells
Authors: Canfield Steven E. , Zhu Keyi , Williams Simon A. , McConkey David J. 
Published: August 2006

AbstractBortezomib (PS-341, Velcade) is a peptide boronate inhibitor of the 20S proteasome that is currently being combined with taxanes in several clinical trials in patients with prostate cancer. Here, we report that bortezomib inhibited docetaxel-induced M-phase arrest and apoptosis in androgen-dependent LNCaP-Pro5 cells. Direct analysis of kinase activity in immune complex kinase assays revealed that docetaxel activated cyclin-dependent kinase (CDK) 1 (CDC2) and that bortezomib blocked this activation. The effects of bortezomib were associated with accumulation of p21 and mimicked by chemical CDK inhibitors or by transfecting cells with a small interfering RNA construct specific for CDK1. Transient transfection with p21 also inhibited docetaxel-induced apoptosis; conversely, p21 silencing reversed the antagonistic effects of bortezomib on docetaxel-induced apoptosis. Together, our data show that bortezomib interferes with docetaxel-induced apoptosis via a p21-dependent mechanism that is associated with CDK1 inhibition. These observations may have important implications for the ongoing bortezomib-docetaxel combination trials as well as trials using bortezomib and other cell cycle–sensitive agents. [Mol Cancer Ther 2006;5(8):2043–50]
Mechanism of action of isothiocyanates: the induction of ARE-regulated genes is associated with activation of ERK and JNK and the phosphorylation and nuclear translocation of Nrf2
Authors: Xu Changjiang , Yuan Xiaoling , Pan Zui , Shen Guoxiang , Kim Jung-Hwan , Yu Siwang , Khor Tin Oo , Li Wenge , Ma Jianjie , Kong Ah-Ng Tony 
Published: August 2006

Abstract
The up-regulation of phase II detoxifying and stress-responsive genes is believed to play an important role in cancer prevention, and many natural compounds have been shown to be potent inducers of these genes. Previous studies showed that the antioxidant responsive element (ARE), found in these genes, can be bound by the transcription factor Nrf2, and is responsive to the activation by chemopreventive compounds and by oxidative stress. In the present study, we investigated the roles of extracellular signal-regulated kinase (ERK) and c-Jun-NH2-kinase (JNK) in the regulation of phenethyl isothiocyanate (PEITC)–induced and Nrf2-dependent ARE activity and ARE-driven heme oxygenase-1 (HO-1) gene expression in PC-3 cells. ARE activity and HO-1 expression were strongly increased after treatment with PEITC. PEITC also increased the phosphorylation of ERK1/2 and JNK1/2 and caused release of Nrf2 from sequestration by Keap1, and its subsequent translocation into the nucleus. Importantly, Nrf2 was also translocated into the nucleus after transfection with ERK or JNK and that these activated ERK and JNK colocalized with Nrf2 in the nucleus. Activation of ERK and JNK signaling also resulted in the elevation of ARE activity and HO-1 expression. Importantly, PEITC-induced ARE activity was attenuated by inhibition of ERK and JNK signaling. In vitro kinase assays showed that both ERK2 and JNK1 could directly phosphorylate glutathione S-transferase–Nrf2 protein. Taken together, these results strongly suggest a model in which PEITC treatment of PC-3 cells activates ERK and JNK, which, in turn, phosphorylate Nrf2 and induce its translocation to the nucleus. Nuclear Nrf2 activates ARE elements and induces expression of stress-responsive genes, including HO-1. [Mol Cancer Ther 2006;5(8):1918–26]
Therapeutic advantage of combining calcium channel blockers and TRAIL in prostate cancer
Authors: Kaddour-Djebbar Ismail , Lakshmikanthan Vijayabaskar , Shirley Robert B. , Ma Yulin , Lewis Ronald W. , Kumar M. Vijay 
Published: August 2006

Abstract
Disruption of intracellular calcium initiates multiple cell-damaging processes, such as apoptosis. In normal cells, the levels of Ca2+ are low in the mitochondria, whereas in apoptotic cells, Ca2+ increases. Mitochondria uptake Ca2+ via an inner membrane channel called the uniporter and extrude it into the cytoplasm through a Na+/Ca2+ exchanger. Overload of Ca2+ in the mitochondria in CGP-treated cells leads to its damage, thus affecting cellular function and survival. The goal of these experiments was to determine the importance of mitochondrial calcium ([Ca2+]m) in apoptosis of prostate cancer cells. Furthermore, we have examined the advantages of increasing the [Ca2+]m and treating the cells with tumor necrosis factor–related apoptosis-inducing ligand (TRAIL), a potent apoptotic agent. Our results show that, under these treatment conditions, inhibiting the Na+/Ca2+ exchanger using benzothiazepin CGP-37157 (CGP) did not induce apoptosis. However, combination of CGP and TRAIL increased the apoptotic response ∼25-fold compared with control. Increase in apoptosis followed enhanced levels of [Ca2+]m and was accompanied by pronounced mitochondrial changes characteristic of mitochondria-mediated apoptosis. Experiments with calcium ionophores showed that mere increase in cytosolic and/or mitochondrial Ca2+ was not sufficient to induce apoptosis. These results have therapeutic implications as inhibitors of Na+/Ca2+ exchanger are being used for treating some neurologic and cardiologic ailments, and TRAIL induces apoptosis preferentially in cancer cells. Furthermore, this system provides an excellent model to investigate the role of [Ca2+]m in apoptosis. [Mol Cancer Ther 2006;5(8):1958–66]
Vorinostat, a histone deacetylase inhibitor, enhances the response of human tumor cells to ionizing radiation through prolongation of γ-H2AX foci
Authors: Munshi Anupama , Tanaka Toshimitsu , Hobbs Marvette L. , Tucker Susan L. , Richon Victoria M. , Meyn Raymond E. 
Published: August 2006

AbstractVorinostat (suberoylanilide hydroxamic acid) is the prototype of a family of hybrid polar compounds that can induce growth arrest in transformed cells and shows promise for the treatment of cancer. Vorinostat specifically binds to and inhibits the activity of histone deacetylases resulting in acetylation of nucleosomal histones and an activation of gene transcription. Because histone deacetylases modulate chromatin structure and gene expression, both of which can influence radioresponse, this study was designed to examine the capacity of Vorinostat to influence radiation response in human tumor cells and investigate the mechanism underlying these interactions. Vorinostat induced hyperacetylation of histone H4 in a dose-dependent manner. We tested its ability to radiosensitize three human tumor cell lines (A375, MeWo, and A549) using clonogenic cell survival assays. Clonogenic cell survival assay showed that Vorinostat significantly radiosensitized all three tumor cell lines, substantially reducing the surviving fraction at 2 Gy. We examined potential mechanisms that may contribute to the enhanced radiation response induced by Vorinostat. Vorinostat and radiation alone did not induce apoptosis in the melanoma cell line. However, enhanced apoptosis was observed when cells were exposed to both Vorinostat and radiation, suggesting that Vorinostat renders tumor cells more susceptible to radiation-induced apoptosis. Results from DNA damage repair analysis in cultured A375 cells showed that Vorinostat had a strong inhibitory effect on the nonhomologous end joining pathway after radiation. A detailed examination of the involvement of the DNA repair pathway following Vorinostat treatment showed that Vorinostat reduced the expression of the repair-related genes Ku70, Ku80, and Rad50 in A375 cells as detected by Western blot analysis. We also examined γ-H2AX phosphorylation as a predictive marker of radiotherapy response to Vorinostat and observed that the combination of Vorinostat and radiation caused a prolongation of expression of DNA repair proteins such as γ-H2AX. Overall, we conclude that Vorinostat enhances tumor radioresponse by multiple mechanisms that may involve antiproliferative growth inhibition and effects on DNA repair after exposure to radiation. [Mol Cancer Ther 2006;5(8):1967–74]
Sequential oral 9-nitrocamptothecin and etoposide: a pharmacodynamic- and pharmacokinetic-based phase I trial
Authors: Simon George R. , Lush Richard M. , Gump Jana , Tetteh Leticia , Williams Charles , Cantor Alan , Antonia Scott , Garrett Christopher , Rocha-Lima Caio , Fishman Mayer , Sullivan Daniel M. , Munster Pamela N. 
Published: August 2006

Abstract
Purpose: Resistance to topoisomerase (topo) I inhibitors has been related to down-regulation of nuclear target enzyme, whereas sensitization to topo II inhibitors may result from induction of topo II by topo I inhibitors. Here, we evaluated a sequence-specific administration of a topo I inhibitor followed by a topo II inhibitor. Experimental Design: Twenty-five patients with advanced or metastatic malignancies were treated with increasing doses (0.75, 1.0, 1.25, 1.5, 1.75, or 2.0 mg/m2) of 9-nitrocamptothecin (9-NC) on days 1 to 3, followed by etoposide (100 or 150 mg/d) on days 4 and 5. At the maximally tolerated dose, 20 additional patients were enrolled. The median age was 60 years (range, 40–84 years). Endpoints included pharmacokinetic analyses of 9-NC and etoposide, and treatment-induced modulations of topo I and II expression in peripheral blood mononuclear cells. Results: Neutropenia, thrombocytopenia, nausea, vomiting, diarrhea, and fatigue were dose-limiting toxicities and occurred in six patients. Despite a median number of four prior regimens (range 1–12), 2 (4%) patients had an objective response and 13 (29%) patients had stable disease. In contrast to the expected modulation in topo I and IIα levels, we observed a decrease in topo IIα levels, whereas topo I levels were not significantly altered by 9-NC treatment. Conclusions: Sequence-specific administration of 9-NC and etoposide is tolerable and active. However, peripheral blood mononuclear cells may not be a predictive biological surrogate for drug-induced modulation of topo levels in tumor tissues and should be further explored in larger studies. [Mol Cancer Ther 2006;5(8):2130–7]