bluuebunny/crossref_metadata_2025 huggingface dataset:
Monte Carlo calculations of , the beam quality conversion factor
Authors: Muir B. R. , Rogers D. W. O.
Published: November 2010

Purpose:

To use EGSnrc Monte Carlo simulations to directly calculate beam quality conversion factors,, for 32 cylindrical ionization chambers over a range of beam qualities and to quantify the effect of systematic uncertainties on Monte Carlo calculations of . These factors are required to use the TG‐51 or TRS‐398 clinical dosimetry protocols for calibrating external radiotherapy beams.

Methods:

Ionization chambers are modeled either from blueprints or manufacturers' user's manuals. The dose‐to‐air in the chamber is calculated using the EGSnrc user‐code egs_chamber using 11 different tabulated clinical photon spectra for the incident beams. The dose to a small volume of water is also calculated in the absence of the chamber at the midpoint of the chamber on its central axis. Using a simple equation, is calculated from these quantities under the assumption that is constant with energy and compared to TG‐51 protocol and measured values.

Results:

Polynomial fits to the Monte Carlo calculated factors as a function of beam quality expressed as and are given for each ionization chamber. Differences are explained between Monte Carlo calculated values and values from the TG‐51 protocol or calculated using the computer program used for TG‐51 calculations. Systematic uncertainties in calculated values are analyzed and amount to a maximum of one standard deviation uncertainty of 0.99% if one assumes that photon cross‐section uncertainties are uncorrelated and 0.63% if they are assumed correlated. The largest components of the uncertainty are the constancy of and the uncertainty in the cross‐section for photons in water.

Conclusions:

It is now possible to calculate directly using Monte Carlo simulations. Monte Carlo calculations for most ionization chambers give results which are comparable to TG‐51 values. Discrepancies can be explained using individual Monte Carlo calculations of various correction factors which are more accurate than previously used values. For small ionization chambers with central electrodes composed of high‐Z materials, the effect of the central electrode is much larger than that for the aluminum electrodes in Farmer chambers.
Patient radiation dose in prospectively gated axial CT coronary angiography and retrospectively gated helical technique with a 320‐detector row CT scanner
Authors: Seguchi Shigenobu , Aoyama Takahiko , Koyama Shuji , Fujii Keisuke , Yamauchi‐Kawaura Chiyo
Published: November 2010

Purpose:

The aim of this study was to evaluate radiation dose to patients undergoing computed tomography coronary angiography (CTCA) for prospectively gated axial (PGA) technique and retrospectively gated helical (RGH) technique.

Methods:

Radiation doses were measured for a 320‐detector row CT scanner (Toshiba Aquilion ONE) using small sized silicon‐photodiode dosimeters, which were implanted at various tissue and organ positions within an anthropomorphic phantom for a standard Japanese adult male. Output signals from photodiode dosimeters were read out on a personal computer, from which organ and effective doses were computed according to guidelines published in the International Commission on Radiological Protection Publication 103.

Results:

Organs that received high doses were breast, followed by lung, esophagus, and liver. Breast doses obtained with PGA technique and a phase window width of 16% at a simulated heart rate of 60 beats per minute were 13 mGy compared to 53 mGy with RGH technique using electrocardiographically dependent dose modulation at the same phase window width as that in PGA technique. Effective doses obtained in this case were 4.7 and 20 mSv for the PGA and RGH techniques, respectively. Conversion factors of dose length product to the effective dose in PGA and RGH were 0.022 and with a scan length of 140 mm.

Conclusions:

CTCA performed with PGA technique provided a substantial effective dose reduction, i.e., 70%–76%, compared to RGH technique using the dose modulation at the same phase windows as those in PGA technique. Though radiation doses in CTCA with RGH technique were the same level as, or some higher than, those in conventional coronary angiography (CCA), the use of PGA technique reduced organ and effective doses to levels less than CCA except for breast dose.
Inverse planning for four‐dimensional (4D) volumetric modulated arc therapya)
Authors: Ma Yunzhi , Chang Daniel , Keall Paul , Xie Yiaoqin , Park Jae‐yoon , Suh Tae‐Suk , Xing Lei
Published: November 2010

Purpose:

To develop a 4D volumetric modulated arc therapy (VMAT) inverse planning framework.

Methods:

4D VMAT inverse planning aims to derive an aperture and weight modulated arc therapy treatment plan that optimizes the accumulated dose distribution from all gantry angles and breathing phases. Under an assumption that the gantry rotation and patient breathing are synchronized (i.e., there is a functional relationship between the phase of the patient breathing cycle and the beam angle), the authors compute the contribution from different respiration phases through the registration of the phased CT images. The accumulative dose distribution is optimized by iteratively adjusting the aperture shape and weight of each beam through the minimization of the planning objective function. For comparison, traditional 3D VMAT plans are also performed for the two cases and the performance of the proposed technique is demonstrated.

Results:

A framework for 4D VMAT inverse planning has been proposed. With the consideration of the extra dimension of time in VMAT, a tighter target margin can be achieved with a full duty cycle, which is otherwise not achievable simultaneously by either 3D VMAT optimization or gated VMAT.

Conclusions:

The 4D VMAT planning formulism proposed here provides useful insight on how the “time” dimension can be exploited in rotational arc therapy to maximally compensate for the intrafraction organ motion.
Maximum intensity projection (MIP) imaging using slice‐stacking MRIa)
Authors: Adamson Justus , Chang Zheng , Wang Zhiheng , Yin Fang‐Fang , Cai Jing
Published: November 2010

Purpose:

To evaluate the feasibility of acquiring maximum intensity projection (MIP) images using a novel slice‐stacking MRI (SS‐MRI) technique.

Methods:

The proposed technique employed a steady state acquisition sequence to image multiple axial slices. At each axial slice, the scan is repeated throughout one respiratory cycle. Four objects (small, medium, and large triangles, and a cylinder) moving with a patient breathing trajectory were imaged repeatedly for six times using the slice‐stacking MRI and 4D‐CT. and were reconstructed. The internal target volume (ITV) was segmented for each object on the six scans and compared between and . The medium triangle was also imaged with various motion patterns using slice‐stacking MRI, 4D‐CT, and sagittal cine‐MRI. The corresponding MIP images were reconstructed and volume/area measurements were performed and compared between different imaging methods. Three healthy volunteers underwent the slice‐stacking MRI and sagittal cine‐MRI scans. A region of interest (ROI) was selected and contoured for each subject in both and . The area of the selected ROI was computed and compared.

Results:

Volume comparison between and showed statistically insignificant ( in all cases) difference in the mean ITVs for all four objects. For the study of the medium triangle with multiple motion patterns, there was a good agreement in the measured ITVs between and (, correlation ), with a mean difference of . The area measurements between and also showed good agreement (, correlation ), with a mean difference of . For the healthy volunteer study, the average difference in the area of selected ROI was between and .

Conclusions:

These preliminary results showed good agreement in volume/area measurements between the slice‐stacking MRI technique and 4D‐CT/cine‐MRI, indicating that it is feasible to use this technique for MIP imaging.
Total variation superiorization schemes in proton computed tomography image reconstruction
Authors: Penfold S. N. , Schulte R. W. , Censor Y. , Rosenfeld A. B.
Published: November 2010

Purpose: Iterative projection reconstruction algorithms are currently the preferred reconstruction method in proton computed tomography (pCT). However, due to inconsistencies in the measured data arising from proton energy straggling and multiple Coulomb scattering, the noise in the reconstructed image increases with successive iterations. In the current work, the authors investigated the use of total variation superiorization (TVS) schemes that can be applied as an algorithmic add‐on to perturbation‐resilient iterative projection algorithms for pCT image reconstruction.

Methods: The block‐iterative diagonally relaxed orthogonal projections (DROP) algorithm was used for reconstructing GEANT4 Monte Carlo simulated pCT data sets. Two TVS schemes added on to DROP were investigated; the first carried out the superiorization steps once per cycle and the second once per block. Simplifications of these schemes, involving the elimination of the computationally expensive feasibility proximity checking step of the TVS framework, were also investigated. The modulation transfer function and contrast discrimination function were used to quantify spatial and density resolution, respectively.

Results: With both TVS schemes, superior spatial and density resolution was achieved compared to the standard DROP algorithm. Eliminating the feasibility proximity check improved the image quality, in particular image noise, in the once‐per‐block superiorization, while also halving image reconstruction time. Overall, the greatest image quality was observed when carrying out the superiorization once per block and eliminating the feasibility proximity check.

Conclusions: The low‐contrast imaging made possible with TVS holds a promise for its incorporation into future pCT studies.
Characterization of a multi‐axis ion chamber array
Authors: Simon Thomas A. , Kozelka Jakub , Simon William E. , Kahler Darren , Li Jonathan , Liu Chihray
Published: November 2010

Purpose:

The aim of this work was to characterize a multi‐axis ion chamber array (IC PROFILER™; Sun Nuclear Corporation, Melbourne, FL USA) that has the potential to simplify the acquisition of LINAC beam data.

Methods:

The IC PROFILER™ (orpanel) measurement response was characterized with respect to radiation beam properties, including dose, dose per pulse, pulse rate frequency (PRF), and energy. Panel properties were also studied, including detector‐calibration stability, power‐on time, backscatter dependence, and the panel's agreement with water tank measurements [profiles, fractional depth dose (FDD), and output factors].

Results:

The panel's relative deviation was typically within (±) 1% of an independent (or nominal) response for all properties that were tested. Notable results were (a) a detectable relative field shape change of with linear accelerator PRF changes; (b) a large range in backscatter thickness had a minimal effect on the measured dose distribution (typically less than 1%); (c) the error spread in profile comparison between the panel and scanning water tank (Blue Phantom™, CC13™; IBA Schwarzenbruck, DE) was approximately (±) 0.75%.

Conclusions:

The ability of the panel to accurately reproduce water tank profiles, FDDs, and output factors is an indication of its abilities as a dosimetry system. The benefits of using the panel versus a scanning water tank are less setup time and less error susceptibility. The same measurements (including device setup and breakdown) for both systems took 180 min with the water tank versus 30 min with the panel. The time‐savings increase as the measurement load is increased.
New Species Genetic Approach To Identify Strains of Mitis Group Streptococci That Are Donors of Rifampin Resistance to
Streptococcus pneumoniae
Authors: Ferrándiz María-José , Ardanuy Carmen , Liñares Josefina , Balsalobre Luz , García María Teresa , de la Campa Adela G.
Published: November 2010

Eight rifampin-resistant streptococci of the mitis group were identified at the species level by using a concatenated 16S rRNA gene-
sodA-rpoB-hlpA
sequence. Characterization of their
rpoB
alleles showed single amino acid changes involved in rifampin resistance. Comparison of RpoB sequences from pneumococcal recombinant isolates, viridans isolates, and type strains revealed a species-specific amino acid signature, which allowed it to be ascertained that recombinant RpoBs were originated in genetic interchanges with
Streptococcus mitis
and
Streptococcus oralis
.
Evaluation of Ceftazidime and NXL104 in Two Murine Models of Infection Due to KPC-Producing
Klebsiella pneumoniae
Authors: Endimiani Andrea , Hujer Kristine M. , Hujer Andrea M. , Pulse Mark E. , Weiss William J. , Bonomo Robert A.
Published: November 2010

We evaluated the efficacy of NXL104, a novel β-lactamase inhibitor, in combination with ceftazidime (CAZ) in two murine infection models (septicemia and thigh infection). We chose two KPC-producing
Klebsiella pneumoniae
strains (VA-361 and VA-406) showing MICs of CAZ of ≥256 μg/ml. Septicemia was induced by the intraperitoneal injection of KPC-producing
K. pneumoniae
followed 30 min later by a single subcutaneous treatment with CAZ alone or CAZ-NXL104 in ratios of 2:1, 4:1, 8:1, and 16:1. In this model, the median effective doses for 50% (ED
50
) of the animals for CAZ alone versus VA-361 and VA-406 were 1,578 and 709 mg/kg of body weight, respectively. When combined with NXL104 at 2:1, 4:1, 8:1, and 16:1 ratios, the CAZ ED
50
s for VA-361 and VA-406 were reduced to 8.1 and 3.5 mg/kg, 15.1 and 3.8 mg/kg, 16.9 and 7.2 mg/kg, and 29.5 and 12.1 mg/kg, respectively. For thigh infection, neutropenia was induced by the intraperitoneal injection of cyclophosphamide at days −4 and −1 preinfection. Infection was established by the intramuscular injection of KPC-producing
K. pneumoniae
into the right thigh. Mice were treated 1.5 h postinfection with either CAZ alone or CAZ-NXL104 at constant ratios of 4:1. When thighs were removed at 24 h postinfection, a >2-log CFU reduction was observed for mice treated with CAZ-NXL104 at doses of ≥128:32 mg/kg. In contrast, CAZ doses of ≥1,024 mg/kg were unable to reduce the numbers of CFU. Despite resistance to CAZ and possessing a complex β-lactamase background, NXL104 combined with CAZ proved to be very effective in murine models of infection due to contemporary highly resistant KPC-producing
K. pneumoniae
isolates.
Sawyeria marylandensis (Heterolobosea) Has a Hydrogenosome with Novel Metabolic Properties
Authors: Barberà Maria José , Ruiz-Trillo Iñaki , Tufts Julia Y. A. , Bery Amandine , Silberman Jeffrey D. , Roger Andrew J.
Published: October 2010

Protists that live under low-oxygen conditions often lack conventional mitochondria and instead possess mitochondrion-related organelles (MROs) with distinct biochemical functions. Studies of mostly parasitic organisms have suggested that these organelles could be classified into two general types: hydrogenosomes and mitosomes. Hydrogenosomes, found in parabasalids, anaerobic chytrid fungi, and ciliates, metabolize pyruvate anaerobically to generate ATP, acetate, CO
2
, and hydrogen gas, employing enzymes not typically associated with mitochondria. Mitosomes that have been studied have no apparent role in energy metabolism. Recent investigations of free-living anaerobic protists have revealed a diversity of MROs with a wider array of metabolic properties that defy a simple functional classification. Here we describe an expressed sequence tag (EST) survey and ultrastructural investigation of the anaerobic heteroloboseid amoeba
Sawyeria marylandensis
aimed at understanding the properties of its MROs. This organism expresses typical anaerobic energy metabolic enzymes, such as pyruvate:ferredoxin oxidoreductase, [FeFe]-hydrogenase, and associated hydrogenase maturases with apparent organelle-targeting peptides, indicating that its MRO likely functions as a hydrogenosome. We also identified 38 genes encoding canonical mitochondrial proteins in
S. marylandensis
, many of which possess putative targeting peptides and are phylogenetically related to putative mitochondrial proteins of its heteroloboseid relative
Naegleria gruberi
. Several of these proteins, such as a branched-chain alpha keto acid dehydrogenase, likely function in pathways that have not been previously associated with the well-studied hydrogenosomes of parabasalids. Finally, morphological reconstructions based on transmission electron microscopy indicate that the
S. marylandensis
MROs form novel cup-like structures within the cells. Overall, these data suggest that
Sawyeria marylandensis
possesses a hydrogenosome of mitochondrial origin with a novel combination of biochemical and structural properties.
Histidine Kinase Two-Component Response Regulator Proteins Regulate Reproductive Development, Virulence, and Stress Responses of the Fungal Cereal Pathogens Cochliobolus heterostrophus and Gibberella zeae
Authors: Oide Shinichi , Liu Jinyuan , Yun Sung-Hwan , Wu Dongliang , Michev Alex , Choi May Yee , Horwitz Benjamin A. , Turgeon B. Gillian
Published: October 2010

Histidine kinase (HK) phosphorelay signaling is a major mechanism by which fungi sense their environment. The maize pathogen
Cochliobolus heterostrophus
has 21 HK genes, 4 candidate response regulator (RR) genes (
SSK1
,
SKN7
,
RIM15
,
REC1
), and 1 gene (
HPT1
) encoding a histidine phosphotransfer domain protein. Because most HKs are expected to signal through RRs, these were chosen for deletion. Except for pigment and slight growth alterations for
rim15
mutants, no measurable altered phenotypes were detected in
rim15
or
rec1
mutants. Ssk1p is required for virulence and affects fertility and proper timing of sexual development of heterothallic
C. heterostrophus
. Pseudothecia from crosses involving
ssk1
mutants ooze masses of single ascospores, and tetrads cannot be found. Wild-type pseudothecia do not ooze. Ssk1p represses asexual spore proliferation during the sexual phase, and lack of it dampens asexual spore proliferation during vegetative growth, compared to that of the wild type.
ssk1
mutants are heavily pigmented. Mutants lacking Skn7p do not display any of the above phenotypes; however, both
ssk1
and
skn7
mutants are hypersensitive to oxidative and osmotic stresses and
ssk1 skn7
mutants are more exaggerated in their spore-type balance phenotype and more sensitive to stress than single mutants.
ssk1
mutant phenotypes largely overlap
hog1
mutant phenotypes, and in both types of mutant, the Hog1 target gene,
MST1
, is not induced.
ssk1
and
hog1
mutants were examined in the homothallic cereal pathogen
Gibberella zeae
, and pathogenic and reproductive phases of development regulated by Ssk1 and Hog1 were found to mirror, but also vary from, those of
C. heterostrophus
.
The Yeast-Phase Virulence Requirement for α-Glucan Synthase Differs among Histoplasma capsulatum Chemotypes
Authors: Edwards Jessica A. , Alore Elizabeth A. , Rappleye Chad A.
Published: October 2010

Histoplasma capsulatumstrains can be classified into two chemotypes based on cell wall composition. The cell wall of chemotype II yeast contains a layer of α-(1,3)-glucan that masks immunostimulatory β-(1,3)-glucans from detection by the Dectin-1 receptor on host phagocytes. This α-(1,3)-glucan cell wall component is essential for chemotype IIHistoplasmavirulence. In contrast, chemotype I yeast cells lack α-(1,3)-glucanin vitro, yet they remain fully virulentin vivo. Analysis of the chemotype I α-glucan synthase (AGS1) locus revealed a 2.7-kb insertion in the promoter region that diminishesAGS1expression. Nonetheless,AGS1mRNA can be detected during respiratory infection with chemotype I yeast, suggesting that α-(1,3)-glucan could be produced duringin vivogrowth despite its absencein vitro. To directly test whetherAGS1contributes to chemotype I strain virulence, we preventedAGS1function by RNA interference and by insertional mutation. Loss ofAGS1function in chemotype I does not impair the cytotoxicity ofags1(−) mutant yeast to cultured macrophages, nor does it affect the intracellular growth of yeast. In a murine model of histoplasmosis, theags1(−) chemotype I mutant strains show no defect in lung infection or in extrapulmonary dissemination. Together, these studies demonstrate thatAGS1expression is dispensable for chemotype I yeast virulence, in contrast to the case for chemotype II yeast. Despite the absence of cell wall α-(1,3)-glucan, chemotype I yeast can avoid detection by Dectin-1 in a growth stage-dependent manner. This suggests the production of a uniqueHistoplasmachemotype I factor that, at least partially, circumvents the α-(1,3)-glucan requirement for yeast virulence.
Effect of Factor H-Binding Protein Sequence Variation on Factor H Binding and Survival ofNeisseria meningitidisin Human Blood
Authors: Dunphy Kathleen Y. , Beernink Peter T. , Brogioni Barbara , Granoff Dan M.
Published: November 2010

Binding of the complement inhibitor factor H (fH) to the surface ofNeisseria meningitidisis critical for evasion of innate host defenses. The meningococcal vaccine candidate factor H-binding protein (fHbp) serves as an fH ligand. We prepared 16 recombinant fHbp natural sequence variants. By enzyme-linked immunosorbent assay (ELISA), the variants from a New Zealand epidemic strain (fHbp ID 14) and from an endemic United Kingdom strain (ID 15) showed 10-fold lower fH binding than a reference fHbp from an epidemic Norwegian strain (ID 1). By surface plasmon resonance, association rate constants (ka) for fHbp ID 14 and 15 were similar to those for ID 1, but dissociation rate constants (kd) were 4- to 10-fold higher than those for ID 1. To determine the effect of fH affinity on fHbp fitness, we prepared isogenic mutants of strain H44/76 that expressed fHbp ID 1, 14, or 15. By flow cytometry, mutants expressing fHbp ID 14 or 15 had lower fH binding than ID 1. When incubated in plasma or blood of nonimmune donors, all three mutants showed similar increases in CFU/ml. In contrast, an isogenic fHbp knockout mutant, which grew well in broth, was rapidly killed in plasma or blood. Thus, although fHbp expression was required for survival of strain H44/76 in blood or plasma, expression of two natural fHbp sequence variants with lower fH affinity had minimal or no effect on nonimmune clearance. One reason may be the high fH concentrations in normal serum, which favor saturation of fH binding to fHbp, even when dissociation rates varied over 10-fold.
Cadherin Domains in the Polysaccharide-Degrading Marine Bacterium
Saccharophagus degradans
2-40 Are Carbohydrate-Binding Modules
Authors: Fraiberg Milana , Borovok Ilya , Bayer Edward A. , Weiner Ronald M. , Lamed Raphael
Published: October 2010

The complex polysaccharide-degrading marine bacterium S
accharophagus degradans
strain 2-40 produces putative proteins that contain numerous cadherin and cadherin-like domains involved in intercellular contact interactions. The current study reveals that both domain types exhibit reversible calcium-dependent binding to different complex polysaccharides which serve as growth substrates for the bacterium.
Draft Genome Sequence of the Anoxygenic Filamentous Phototrophic Bacterium
Oscillochloris trichoides
subsp. DG-6
Authors: Kuznetsov Boris B. , Ivanovsky Ruslan N. , Keppen Olga I. , Sukhacheva Marina V. , Bumazhkin Boris K. , Patutina Ekaterina O. , Beletsky Alexey V. , Mardanov Andrey V. , Baslerov Roman V. , Panteleeva Angela N. , Kolganova Tatjana V. , Ravin Nikolai V. , Skryabin Konstantin G.
Published: October 2010

Oscillochloris trichoides
is a mesophilic, filamentous, photoautotrophic, nonsulfur, diazotrophic bacterium which is capable of carbon dioxide fixation via the reductive pentose phosphate cycle and possesses no assimilative sulfate reduction. Here, we present the draft genome sequence of
Oscillochloris trichoides
subsp. DG-6, the type strain of the species, which has permitted the prediction of genes for carbon and nitrogen metabolism and for the light-harvesting apparatus.
Adhesive Activity of the
Haemophilus
Cryptic Genospecies Cha Autotransporter Is Modulated by Variation in Tandem Peptide Repeats
Authors: Sheets Amanda J. , St. Geme Joseph W.
Published: October 2010

The
Haemophilus
cryptic genospecies is an important cause of maternal genital tract and neonatal systemic infections and initiates infection by colonizing the genital or respiratory epithelium. In recent work, we identified a unique
Haemophilus
cryptic genospecies protein called Cha, which mediates efficient adherence to genital and respiratory epithelia. The Cha adhesin belongs to the trimeric autotransporter family and contains an N-terminal signal peptide, an internal passenger domain that harbors adhesive activity, and a C-terminal membrane anchor domain. The passenger domain in Cha contains clusters of YadA-like head domains and neck motifs as well as a series of tandem 28-amino-acid peptide repeats. In the current study, we report that variation in peptide repeat number gradually modulates Cha adhesive activity, associated with a direct effect on the length of Cha fibers on the bacterial cell surface. The N-terminal 404 residues of the Cha passenger domain mediate binding to host cells and also facilitate bacterial aggregation through intermolecular Cha-Cha binding. As the tandem peptide repeats expand, the Cha fiber becomes longer and Cha adherence activity decreases. The expansion and contraction of peptide repeats represent a novel mechanism for modulating adhesive capacity, potentially balancing the need of the organism to colonize the genital and respiratory tracts with the ability to attach to alternative substrates, disperse within the host, or evade the host immune system.
A Small Protein Required for the Switch from σ
F
to σ
G
during Sporulation in
Bacillus subtilis
Authors: Camp Amy H. , Wang Anna F. , Losick Richard
Published: October 2010

A cascade of alternative sigma factors governs the program of developmental gene expression during sporulation in
Bacillus subtilis
. Little is known, however, about how the early-acting sigma factors are inactivated and replaced by the later-acting factors. Here we identify a small protein, Fin (formerly known as YabK), that is required for efficient switching from σ
F
- to σ
G
-directed gene expression in the forespore compartment of the developing sporangium. The
fin
gene, which is conserved among
Bacillus
species and species of related genera, is transcribed in the forespore under the control of both σ
F
and σ
G
. Cells mutant for
fin
are unable to fully deactivate σ
F
and, conversely, are unable to fully activate σ
G
. Consistent with their deficiency in σ
G
-directed gene expression,
fin
cells are arrested in large numbers following the engulfment stage of sporulation, ultimately forming 50-fold fewer heat-resistant spores than the wild type. Based in part on the similarity of Fin to the anti-σ
G
factor CsfB (also called Gin), we speculate that Fin is an anti-σ
F
factor which, by disabling σ
F
, promotes the switch to late developmental gene expression in the forespore.
Activation of the SoxR Regulon in
Streptomyces coelicolor
by the Extracellular Form of the Pigmented Antibiotic Actinorhodin
Authors: Shin Jung-Ho , Singh Atul K. , Cheon Dong-Joo , Roe Jung-Hye
Published: October 2010

The redox-sensitive transcription factor SoxR in enteric bacteria senses and regulates the cellular response to superoxide and nitric oxide. In other bacterial groups, however, it may respond to redox-active small molecules, as demonstrated for pyocyanin sensing in pseudomonads. The antibiotic-producing soil bacterium
Streptomyces coelicolor
contains a gene for an SoxR homologue (SCO1697) whose DNA recognition helix is identical to that of
Escherichia coli
SoxR. Using the
E. coli
SoxR binding sequence, we predicted five candidate genes of the SoxR regulon and demonstrated that SoxR binds to their promoter regions and activates their expression concurrently with the production of the blue antibiotic actinorhodin (a benzoisochromanequinone). These genes encode a probable NADPH-dependent flavin reductase (SCO2478), an NADPH-dependent quinone reductase (SCO4266), an ABC transporter (SCO7008), a monooxygenase (SCO1909), and a hypothetical protein (SCO1178). Addition of actinorhodin to exponentially growing cells activated the expression of SoxR target genes in an SoxR-dependent manner. The secreted γ-actinorhodin was over 10-fold more effective in activation than the intracellular form of actinorhodin, suggesting that SoxR is specified to respond more to exogenous signals than to intracellular metabolites. The
ΔsoxR
mutant was not compromised in resistance against oxidants but was slow in forming aerial mycelium on R2YE medium with reduced sporulation, and its production of actinorhodin and undecylprodigiosin was lowered by about 50% and 30%, respectively, compared to that of the wild type. These results support the proposal that SoxR senses redox-active molecules, such as actinorhodin in
S. coelicolor
, and induces a protective function against them. It also functions to ensure that cells undergo optimal differentiation and secondary metabolite production.
Inactivation of the RluD Pseudouridine Synthase Has Minimal Effects on Growth and Ribosome Function in Wild-TypeEscherichia coliandSalmonella enterica
Authors: O'Connor Michael , Gregory Steven T.
Published: October 2010

TheEscherichia coli rluDgene encodes a pseudouridine synthase responsible for the pseudouridine (Ψ) modifications at positions 1911, 1915, and 1917 in helix 69 of 23S rRNA. It has been reported that deletion ofrluDin K-12 strains ofE. coliis associated with extremely slow growth, increased readthrough of stop codons, and defects in 50S ribosomal subunit assembly and 30S-50S subunit association. Suppressor mutations in theprfBandprfCgenes encoding release factor 2 (RF2) and RF3 that restore the wild type-growth rate and also correct the ribosomal defects have now been isolated. These suppressors link helix 69 Ψ residues with the termination phase of protein synthesis. However, further genetic analysis reported here also reveals that the slow growth and other defects associated with inactivation ofrluDinE. coliK-12 strains are due to a defective RF2 protein, with a threonine at position 246, which is present in all K-12 strains. This is in contrast to the more typical alanine found at this position in most bacterial RF2s, including those of otherE. colistrains. Inactivation ofrluDinE. colistrains containing theprfBallele fromE. coliB or inSalmonella enterica, both carrying an RF2 with Ala246, has negligible effects on growth, termination, or ribosome function. The results indicate that, in contrast to those in wild bacteria, termination functions inE. coliK-12 strains carrying a partially defective RF2 protein are especially susceptible to perturbation of ribosome-RF interactions, such as that caused by loss of h69 Ψ modifications.
Orientation of SecA and SecB in Complex, Derived from Disulfide Cross-Linking
Authors: Suo Yuying , Hardy Simon J. S. , Randall Linda L.
Published: October 2010

SecA is the ATPase that acts as the motor for protein export in the general secretory, or Sec, system of
Escherichia coli
. The tetrameric cytoplasmic chaperone SecB binds to precursors of exported proteins before they can become stably folded and delivers them to SecA. During this delivery step, SecB binds to SecA. The complex between SecA and SecB that is maximally active in translocation contains two protomers of SecA bound to a tetramer of SecB. The aminoacyl residues on each protein that are involved in binding the other have previously been identified by site-directed spin labeling and electron paramagnetic resonance (EPR) spectroscopy; however, that study provided no information concerning the relative orientation of the proteins within the complex. Here we used our extensive collection of single-cysteine variants of the two proteins and subjected pairwise combinations of SecA and SecB to brief oxidation to identify residues in close proximity. These data were used to generate a model for the orientation of the two proteins within the complex.
Distinct Roles of Multiple NDH-1 Complexes in the Cyanobacterial Electron Transport Network as Revealed by Kinetic Analysis of P700
+
Reduction in Various
ndh
-Deficient Mutants of
Synechocystis
sp. Strain PCC6803
Authors: Bernát Gábor , Appel Jens , Ogawa Teruo , Rögner Matthias
Published: October 2010

While methyl viologen had only a small effect on P700
+
rereduction kinetics after far-red pulses in KCN-treated wild-type
Synechocystis
sp. strain PCC6803 and an NdhF3/NdhF4 (NdhF3/F4)-defective mutant, it involved a rather slow P700
+
rereduction in an NdhF1-defective mutant. This strongly indicates that (i) active electron flow from metabolites to plastoquinone is suppressed upon deletion of
ndhF1
and (ii) photosystem 1-mediated cyclic electron transport is dependent on NdhF3/F4-type NDH-1 complexes.
Characterization of the
Bacteroides
CTnDOT Regulatory Protein RteC
Authors: Park Jiyeon , Salyers Abigail A.
Published: October 2010

Excision of the
Bacteroides
conjugative transposon CTnDOT is stimulated by tetracycline. It was shown previously that a gene,
rteC
, is necessary for tetracycline-stimulated transcriptional regulation of the
orf2c
operon, which contains the excision genes. The protein encoded by this gene, RteC, did not have primary amino acid sequence homology to any known proteins in the databases. Accordingly, we sought structural homologs of RteC. A three-dimensional structure prediction by Robetta suggested that RteC might have two domains and that the C-terminal domain might have a winged helix motif. Based on the Robetta prediction, the human transcriptional factors E2F-4 and DP2 were identified as the most likely structural homologs of RteC. We made alanine substitutions within the putative DNA binding helix 3 region of RteC. Assays of
orf2c
::
uidA
activation by alanine mutants indicated that residues 174, 175, 178, 180, and 184 in helix 3 might contact the upstream region of P
E
. The upstream region of
orf2c
contained two inverted-repeat half sites. Mutational analysis of these half sites showed that both half sites are important for activity. Thus, we have identified the DNA binding portion of RteC and the DNA site to which it binds.
X-Ray Structure and Site-Directed Mutagenesis Analysis of theEscherichia coliColicin M Immunity Protein
Authors: Gérard Fabien , Brooks Mark A. , Barreteau Hélène , Touzé Thierry , Graille Marc , Bouhss Ahmed , Blanot Didier , van Tilbeurgh Herman , Mengin-Lecreulx Dominique
Published: October 2010

Colicin M (ColM), which is produced by someEscherichia colistrains to kill competitor strains from the same or related species, was recently shown to inhibit cell wall peptidoglycan biosynthesis through enzymatic degradation of its lipid II precursor. ColM-producing strains are protected from the toxin that they produce by coexpression of a specific immunity protein, named Cmi, whose mode of action still remains to be identified. We report here the resolution of the crystal structure of Cmi, which is composed of four β strands and four α helices. This rather compact structure revealed a disulfide bond between residues Cys31 and Cys107. Interestingly, these two cysteines and several other residues appeared to be conserved in the sequences of several proteins of unknown function belonging to the YebF family which exhibit 25 to 35% overall sequence similarity with Cmi. Site-directed mutagenesis was performed to assess the role of these residues in the ColM immunity-conferring activity of Cmi, which showed that the disulfide bond and residues from the C-terminal extremity of the protein were functionally essential. The involvement of DsbA oxidase in the formation of the Cmi disulfide bond is also demonstrated.
Catabolite Control Protein A Controls Hydrogen Peroxide Production and Cell Death inStreptococcus sanguinis
Authors: Zheng Lanyan , Chen Zhijun , Itzek Andreas , Ashby Michael , Kreth Jens
Published: October 2010

Streptococcus sanguinisis a commensal oral bacterium producing hydrogen peroxide (H2O2) that is dependent on pyruvate oxidase (Spx) activity. In addition to its well-known role in bacterial antagonism during interspecies competition, H2O2causes cell death in about 10% of theS. sanguinispopulation. As a consequence of H2O2-induced cell death, largely intact chromosomal DNA is released into the environment. This extracellular DNA (eDNA) contributes to the self-aggregation phenotype under aerobic conditions. To further investigate the regulation ofspxgene expression, we assessed the role of catabolite control protein A (CcpA) inspxexpression control. We report here that CcpA repressesspxexpression. An isogenic ΔccpAmutant showed elevatedspxexpression, increased Spx abundance, and H2O2production, whereas the wild type did not respond with alteredspxexpression in the presence of glucose and other carbohydrates. Since H2O2is directly involved in the release of eDNA and bacterial cell death, the presented data suggest that CcpA is a central control element in this important developmental process inS. sanguinis.
Pseudomonas aeruginosaMucD Regulates the Alginate Pathway through Activation of MucA Degradation via MucP Proteolytic Activity
Authors: Damron F. Heath , Yu Hongwei D.
Published: October 2010

Alginate overproduction inPseudomonas aeruginosacan be caused by the proteolysis of the anti-sigma factor MucA regulated by the AlgW protease. Here, we show that inactivation of MucD, an HtrA/DegP homolog and alginate regulator, can bypass AlgW, leading to an atypical proteolysis of MucA that is dependent on the MucP protease.
Regulation of Horizontal Gene Transfer in
Bacillus subtilis
by Activation of a Conserved Site-Specific Protease
Authors: Bose Baundauna , Grossman Alan D.
Published: October 2010

The mobile genetic element ICE
Bs1
is an integrative and conjugative element (a conjugative transposon) found in
Bacillus subtilis
. The RecA-dependent SOS response and the RapI-PhrI cell sensory system activate ICE
Bs1
gene expression by stimulating cleavage of ImmR, the ICE
Bs1
immunity repressor, by the protease ImmA. We found that increasing the amount of wild-type ImmA
in vivo
caused partial derepression of ICE
Bs1
gene expression. However, during RapI-mediated derepression of ICE
Bs1
gene expression, ImmA levels did not detectably increase, indicating that RapI likely activates the protease ImmA by increasing its specific activity. We also isolated and characterized mutations in
immA
(
immA

h

) that cause partial derepression of ICE
Bs1
gene expression in the absence of inducing signals. We obtained two types of
immA

h

mutations: one type caused increased amounts of the mutant proteins
in vivo
but no detectable effect on specific activity
in vitro
; the other type had no detectable effect on the amount of the mutant protein
in vivo
but caused increased specific activity of the protein (as measured
in vitro
). Together, these findings indicate that derepression of ICE
Bs1
gene expression is likely caused by an increase in the specific activity of ImmA. Homologs of ImmA and ImmR are found in many mobile genetic elements, so the mechanisms that regulate ImmA-mediated cleavage of ImmR may be widely conserved.
Complete Genome Sequence of the Probiotic
Lactobacillus plantarum
ST-III
Authors: Wang Yinyu , Chen Chen , Ai Lianzhong , Zhou Fangfang , Zhou Zhemin , Wang Lei , Zhang Hao , Chen Wei , Guo Benheng
Published: October 2010

Lactobacillus plantarum
strain ST-III, a probiotic strain with several functions, was isolated from kimchi. Here we report the complete genome sequence of ST-III and compared it with two published
L. plantarum
genomes.
Complete Genome Sequence of
Cronobacter turicensis
LMG 23827, a Food-Borne Pathogen Causing Deaths in Neonates
Authors: Stephan Roger , Lehner Angelika , Tischler Patrick , Rattei Thomas
Published: October 2010

Here, we report the complete and annotated genome sequence of
Cronobacter turicensis
, an opportunistic food-borne pathogen, which is known as a rare but important cause of life-threatening neonatal infections. Among all proteins of
C. turicensis
, 223 have been annotated as virulence- and disease-related proteins.
Complete Genome Sequence of
Bifidobacterium bifidum
S17
Authors: Zhurina Daria , Zomer Aldert , Gleinser Marita , Brancaccio Vincenco Francesco , Auchter Marc , Waidmann Mark S. , Westermann Christina , van Sinderen Douwe , Riedel Christian U.
Published: October 2010

Here, we report on the first completely annotated genome sequence of a
Bifidobacterium bifidum
strain.
B. bifidum
S17, isolated from feces of a breast-fed infant, was shown to strongly adhere to intestinal epithelial cells and has potent anti-inflammatory activity
in vitro
and
in vivo
. The genome sequence will provide new insights into the biology of this potential probiotic organism and allow for the characterization of the molecular mechanisms underlying its beneficial properties.
Complete Genome Sequence of the BacteriumKetogulonicigenium vulgareY25
Authors: Xiong Xiang-hua , Han Shuang , Wang Jian-hua , Jiang Ze-hui , Chen Wei , Jia Ning , Wei Hong-li , Cheng Hong , Yang Yan-xin , Zhu Bin , You Song , He Jian-yong , Hou Wei , Chen Meng-xia , Yu Chun-jie , Jiao Ying-hui , Zhang Wei-cai
Published: October 2010

Ketogulonicigenium vulgareis characterized by the efficient production of 2KGA froml-sorbose.Ketogulonicigenium vulgareY25 is known as a 2-keto-l-gulonic acid-producing strain in the vitamin C industry. Here we report the finished, annotated genome sequence ofKetogulonicigenium vulgareY25.
dnaX36
Mutator of
Escherichia coli
: Effects of the τ Subunit of the DNA Polymerase III Holoenzyme on Chromosomal DNA Replication Fidelity
Authors: Gawel Damian , Jonczyk Piotr , Fijalkowska Iwona J. , Schaaper Roel M.
Published: October 2010

The
Escherichia coli dnaX36
mutant displays a mutator effect, reflecting a fidelity function of the
dnaX
-encoded τ subunit of the DNA polymerase III (Pol III) holoenzyme. We have shown that this fidelity function (i) applies to both leading- and lagging-strand synthesis, (ii) is independent of Pol IV, and (iii) is limited by Pol II.
Complete Genome Sequence of Strain HTCC2503
T
of
Parvularcula bermudensis
, the Type Species of the Order “
Parvularculales
” in the Class
Alphaproteobacteria
Authors: Oh Hyun-Myung , Kang Ilnam , Vergin Kevin L. , Kang Dongmin , Rhee Kwang-Hyun , Giovannoni Stephen J. , Cho Jang-Cheon
Published: October 2010

The order “
Parvularculales
” represents the seventh order in the class
Alphaproteobacteria. Parvularcula bermudensis
, the type species of the order, was isolated from the Sargasso Sea using dilution-to-extinction culturing. We present here the complete genome sequence of
Parvularcula bermudensis
HTCC2503
T
, which contains genes for carotenoid biosynthesis, dimethylsulfoniopropionate demethylase, and transduction-like gene transfer agents.
Complete Genome Sequence of Strain HTCC2170, a Novel Member of the Genus
Maribacter
in the Family
Flavobacteriaceae
Authors: Oh Hyun-Myung , Kang Ilnam , Yang Seung-Jo , Jang Yoonra , Vergin Kevin L. , Giovannoni Stephen J. , Cho Jang-Cheon
Published: October 2010

Strain HTCC2170 was isolated from surface waters off the Oregon coast using dilution-to-extinction culturing. Here, we present the finished genome sequence of a marine bacterium,
Maribacter
sp. strain HTCC2170. Strain sp. HTCC2170 is predicted to be a facultatively aerobic chemoorganotroph that, based on genomic sequence analysis, is capable of macromolecule degradation and anaerobic respiration.
Complete Genome Sequence of
Corynebacterium pseudotuberculosis
I19, a Strain Isolated from a Cow in Israel with Bovine Mastitis
Authors: Silva Artur , Schneider Maria Paula C. , Cerdeira Louise , Barbosa Maria Silvanira , Ramos Rommel Thiago J. , Carneiro Adriana R. , Santos Rodrigo , Lima Marília , D'Afonseca Vivian , Almeida Sintia S. , Santos Anderson R. , Soares Siomar C. , Pinto Anne C. , Ali Amjad , Dorella Fernanda A. , Rocha Flavia , de Abreu Vinicius Augusto Carvalho , Trost Eva , Tauch Andreas , Shpigel Nahum , Miyoshi Anderson , Azevedo Vasco
Published: October 2010

This work reports the completion and annotation of the genome sequence of
Corynebacterium pseudotuberculosis
I19, isolated from an Israeli dairy cow with severe clinical mastitis. To present the whole-genome sequence, a
de novo
assembly approach using 33 million short (25-bp) mate-paired SOLiD reads only was applied. Furthermore, the automatic, functional, and manual annotations were attained with the use of several algorithms in a multistep process.
Complete Genome Sequence of a Carbon Monoxide-Utilizing Acetogen,
Eubacterium limosum
KIST612
Authors: Roh Hanseong , Ko Hyeok-Jin , Kim Daehee , Choi Dong Geon , Park Shinyoung , Kim Sujin , Chang In Seop , Choi In-Geol
Published: October 2010

Eubacterium limosum
KIST612 is an anaerobic acetogenic bacterium that uses CO as the sole carbon/energy source and produces acetate, butyrate, and ethanol. To evaluate its potential as a syngas microbial catalyst, we have sequenced the complete 4.3-Mb genome of
E. limosum
KIST612.
Complete Genome Sequence of
Paenibacillus polymyxa
SC2, a Strain of Plant Growth-Promoting Rhizobacterium with Broad-Spectrum Antimicrobial Activity
Authors: Ma Mingchao , Wang Cuicui , Ding Yanqin , Li Li , Shen Delong , Jiang Xin , Guan Dawei , Cao Fengming , Chen Huijun , Feng Ruihua , Wang Xuan , Ge Yifan , Yao Liangtong , Bing Xiaohui , Yang Xiaohong , Li Jun , Du Binghai
Published: October 2010

Paenibacillus polymyxa
SC2 is an important plant growth-promoting rhizobacterium (PGPR). Here, we report the complete genome sequence of
P. polymyxa
SC2. Multiple sets of functional genes have been found in the genome. As far as we know, this is the first complete genome sequence of
Paenibacillus polymyxa
.
Genome Sequence of
Oceanicaulis
sp. Strain HTCC2633, Isolated from the Western Sargasso Sea
Authors: Oh Hyun-Myung , Kang Ilnam , Vergin Kevin L. , Lee Kiyoung , Giovannoni Stephen J. , Cho Jang-Cheon
Published: October 2010

The genus
Oceanicaulis
represents dimorphic rods that were originally isolated from a marine dinoflagellate. Here, we announce the genome sequence of
Oceanicaulis
sp. strain HTCC2633, isolated by dilution-to-extinction culturing from the Sargasso Sea. The genome information of strain HTCC2633 indicates a chemoorganotrophic way of life of this strain.
Genome Sequence of Strain HTCC2083, a Novel Member of the Marine Clade
Roseobacter
Authors: Kang Ilnam , Vergin Kevin L. , Oh Hyun-Myung , Choi Ahyoung , Giovannoni Stephen J. , Cho Jang-Cheon
Published: October 2010

Strain HTCC2083 was isolated from Oregon seawater using dilution-to-extinction culturing and represents a novel member of the
Roseobacter
clade. The draft genome sequence of HTCC2083 is presented here. The genome is predicted to contain genes for aerobic anoxygenic phototrophy, sulfite-oxidizing chemolithotrophy, anapleurotic CO
2
fixation, carbon monoxide oxidation, and dimethylsulfoniopropionate (DMSP) utilization.