bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved proton computed tomography by dual modality image reconstruction
Authors: Hansen David C. , Petersen Jørgen Breede Baltzer , Bassler Niels , Sørensen Thomas Sangild 
Published: February 2014

Purpose:Proton computed tomography (CT) is a promising image modality for improving the stopping power estimates and dose calculations for particle therapy. However, the finite range of about 33 cm of water of most commercial proton therapy systems limits the sites that can be scanned from a full 360° rotation. In this paper the authors propose a method to overcome the problem using a dual modality reconstruction (DMR) combining the proton data with a cone‐beam x‐ray prior.Methods:A Catphan 600 phantom was scanned using a cone beam x‐ray CT scanner. A digital replica of the phantom was created in the Monte Carlo code Geant4 and a 360° proton CT scan was simulated, storing the entrance and exit position and momentum vector of every proton. Proton CT images were reconstructed using a varying number of angles from the scan. The proton CT images were reconstructed using a constrained nonlinear conjugate gradient algorithm, minimizing total variation and the x‐ray CT prior while remaining consistent with the proton projection data. The proton histories were reconstructed along curved cubic‐spline paths.Results:The spatial resolution of the cone beam CT prior was retained for the fully sampled case and the 90° interval case, with the MTF = 0.5 (modulation transfer function) ranging from 5.22 to 5.65 linepairs/cm. In the 45° interval case, the MTF = 0.5 dropped to 3.91 linepairs/cm For the fully sampled DMR, the maximal root mean square (RMS) error was 0.006 in units of relative stopping power. For the limited angle cases the maximal RMS error was 0.18, an almost five‐fold improvement over the cone beam CT estimate.Conclusions:Dual modality reconstruction yields the high spatial resolution of cone beam x‐ray CT while maintaining the improved stopping power estimation of proton CT. In the case of limited angles, the use of prior image proton CT greatly improves the resolution and stopping power estimate, but does not fully achieve the quality of a 360° proton CT scan.
Altered Fecal Microbiota Composition Associated with Food Allergy in Infants
Authors: Ling Zongxin , Li Zailing , Liu Xia , Cheng Yiwen , Luo Yueqiu , Tong Xiaojuan , Yuan Li , Wang Yuezhu , Sun Jinbo , Li Lanjuan , Xiang Charlie 
Published: February 2014

ABSTRACT

Increasing evidence suggests that perturbations in the intestinal microbiota composition of infants are implicated in the pathogenesis of food allergy (FA), while the actual structure and composition of the intestinal microbiota in human beings with FA remain unclear. Microbial diversity and composition were analyzed with parallel barcoded 454 pyrosequencing targeting the 16S rRNA gene hypervariable V1-V3 regions in the feces of 34 infants with FA (17 IgE mediated and 17 non-IgE mediated) and 45 healthy controls. Here, we showed that several key FA-associated bacterial phylotypes, but not the overall microbiota diversity, significantly changed in infancy fecal microbiota with FA and were associated with the development of FA. The proportion of abundant
Bacteroidetes
,
Proteobacteria
, and
Actinobacteria
phyla were significantly reduced, while the
Firmicutes
phylum was highly enriched in the FA group (
P
< 0.05). Abundant
Clostridiaceae
1 organisms were prevalent in infants with FA at the family level (
P
= 0.016). FA-enriched phylotypes negatively correlated with interleukin-10, for example, the genera
Enterococcus
and
Staphylococcus
. Despite profound interindividual variability, levels of 20 predominant genera were significantly different between the FA and healthy control groups (
P
< 0.05). Infants with IgE-mediated FA had increased levels of
Clostridium sensu stricto
and
Anaerobacter
and decreased levels of
Bacteroides
and
Clostridium
XVIII (
P
< 0.05). A positive correlation was observed between
Clostridium sensu stricto
and serum-specific IgE (
R
= 0.655,
P
< 0.001). The specific microbiota signature could distinguish infants with IgE-mediated FA from non-IgE-mediated ones. Detailed microbiota analysis of a well-characterized cohort of infants with FA showed that dysbiosis of fecal microbiota with several FA-associated key phylotypes may play a pathogenic role in FA.
New Vectors for Chromosomal Integration Enable High-Level Constitutive or Inducible Magnetosome Expression of Fusion Proteins in Magnetospirillum gryphiswaldense
Authors: Borg Sarah , Hofmann Julia , Pollithy Anna , Lang Claus , Schüler Dirk 
Published: February 2014

ABSTRACT

The alphaproteobacterium
Magnetospirillum gryphiswaldense
biomineralizes magnetosomes, which consist of monocrystalline magnetite cores enveloped by a phospholipid bilayer containing specific proteins. Magnetosomes represent magnetic nanoparticles with unprecedented magnetic and physicochemical characteristics. These make them potentially useful in a number of biotechnological and biomedical applications. Further functionalization can be achieved by expression of foreign proteins via genetic fusion to magnetosome anchor peptides. However, the available genetic tool set for strong and controlled protein expression in magnetotactic bacteria is very limited. Here, we describe versatile vectors for either inducible or high-level constitutive expression of proteins in
M. gryphiswaldense
. The combination of an engineered native P

mamDC

promoter with a codon-optimized
egfp
gene (Mag-
egfp
) resulted in an 8-fold increase in constitutive expression and in brighter fluorescence. We further demonstrate that the widely used P

tet

promoter is functional and tunable in
M. gryphiswaldense
. Stable and uniform expression of the EGFP and β-glucuronidase (GusA) reporters was achieved by single-copy chromosomal insertion via Tn
5
-mediated transposition. In addition, gene duplication by Mag-EGFP–EGFP fusions to MamC resulted in further increased magnetosome expression and fluorescence. Between 80 and 210 (for single MamC–Mag-EGFP) and 200 and 520 (for MamC–Mag-EGFP–EGFP) GFP copies were estimated to be expressed per individual magnetosome particle.
Characterization of Temperate Phages Infecting Clostridium difficile Isolates of Human and Animal Origins
Authors: Sekulovic Ognjen , Garneau Julian R. , Néron Audrey , Fortier Louis-Charles 
Published: February 2014

ABSTRACT

Clostridium difficile
is a Gram-positive pathogen infecting humans and animals. Recent studies suggest that animals could represent potential reservoirs of
C. difficile
that could then transfer to humans. Temperate phages contribute to the evolution of most bacteria, for example, by promoting the transduction of virulence, fitness, and antibiotic resistance genes. In
C. difficile
, little is known about their role, mainly because suitable propagating hosts and conditions are lacking. Here we report the isolation, propagation, and preliminary characterization of nine temperate phages from animal and human
C. difficile
isolates. Prophages were induced by UV light from 58
C. difficile
isolates of animal and human origins. Using soft agar overlays with 27 different
C. difficile
test strains, we isolated and further propagated nine temperate phages: two from horse isolates (ϕCD481-1 and ϕCD481-2), three from dog isolates (ϕCD505, ϕCD506, and ϕCD508), and four from human isolates (ϕCD24-2, ϕCD111, ϕCD146, and ϕCD526). Two phages are members of the
Siphoviridae
family (ϕCD111 and ϕCD146), while the others are
Myoviridae
phages. Pulsed-field gel electrophoresis and restriction enzyme analyses showed that all of the phages had unique double-stranded DNA genomes of 30 to 60 kb. Phages induced from human
C. difficile
isolates, especially the members of the
Siphoviridae
family, had a broader host range than phages from animal
C. difficile
isolates. Nevertheless, most of the phages could infect both human and animal strains. Phage transduction of antibiotic resistance was recently reported in
C. difficile
. Our findings therefore call for further investigation of the potential risk of transduction between animal and human
C. difficile
isolates.
Role of the Alternaria alternata Blue-Light Receptor LreA (White-Collar 1) in Spore Formation and Secondary Metabolism
Authors: Pruß Sonja , Fetzner Ramona , Seither Kristin , Herr Andreas , Pfeiffer Erika , Metzler Manfred , Lawrence Christopher B. , Fischer Reinhard 
Published: February 2014

ABSTRACT

Alternaria alternata
is a filamentous fungus that causes considerable loss of crops of economically important feed and food worldwide. It produces more than 60 different secondary metabolites, among which alternariol (AOH) and altertoxin (ATX) are the most important mycotoxins. We found that mycotoxin production and spore formation are regulated by light in opposite ways. Whereas spore formation was largely decreased under light conditions, the production of AOH was stimulated 2- to 3-fold. ATX production was even strictly dependent on light. All light effects observed could be triggered by blue light, whereas red light had only a minor effect. Inhibition of spore formation by light was reversible after 1 day of incubation in the dark. We identified orthologues of genes encoding the
Neurospora crassa
blue-light-perceiving white-collar proteins, a cryptochrome, a phytochrome, and an opsin-related protein in the genome of
A. alternata
. Deletion of the white-collar 1 (WC-1) gene (
lreA
) resulted in derepression of spore formation in dark and in light. ATX formation was strongly induced in the dark in the
lreA
mutant, suggesting a repressing function of LreA, which appears to be released in the wild type after blue-light exposure. In addition, light induction of AOH formation was partially dependent on LreA, suggesting also an activating function.
A. alternata
Δ
lreA
was still able to partially respond to blue light, indicating the action of another blue-light receptor system.
Reduction of Ethanol Yield and Improvement of Glycerol Formation by Adaptive Evolution of the Wine Yeast Saccharomyces cerevisiae under Hyperosmotic Conditions
Authors: Tilloy Valentin , Ortiz-Julien Anne , Dequin Sylvie 
Published: February 2014

ABSTRACTThere is a strong demand from the wine industry for methodologies to reduce the alcohol content of wine without compromising wine's sensory characteristics. We assessed the potential of adaptive laboratory evolution strategies under hyperosmotic stress for generation ofSaccharomyces cerevisiaewine yeast strains with enhanced glycerol and reduced ethanol yields. Experimental evolution on KCl resulted, after 200 generations, in strains that had higher glycerol and lower ethanol production than the ancestral strain. This major metabolic shift was accompanied by reduced fermentative capacities, suggesting a trade-off between high glycerol production and fermentation rate. Several evolved strains retaining good fermentation performance were selected. These strains produced more succinate and 2,3-butanediol than the ancestral strain and did not accumulate undesirable organoleptic compounds, such as acetate, acetaldehyde, or acetoin. They survived better under osmotic stress and glucose starvation conditions than the ancestral strain, suggesting that the forces that drove the redirection of carbon fluxes involved a combination of osmotic and salt stresses and carbon limitation. To further decrease the ethanol yield, a breeding strategy was used, generating intrastrain hybrids that produced more glycerol than the evolved strain. Pilot-scale fermentation on Syrah using evolved and hybrid strains produced wine with 0.6% (vol/vol) and 1.3% (vol/vol) less ethanol, more glycerol and 2,3-butanediol, and less acetate than the ancestral strain. This work demonstrates that the combination of adaptive evolution and breeding is a valuable alternative to rational design for remodeling the yeast metabolic network.
Microbial Species Diversity, Community Dynamics, and Metabolite Kinetics of Water Kefir Fermentation
Authors: Laureys David , De Vuyst Luc 
Published: February 2014

ABSTRACTWater kefir is a sour, alcoholic, and fruity fermented beverage of which the fermentation is started with water kefir grains. These water kefir grains consist of polysaccharide and contain the microorganisms responsible for the water kefir fermentation. In this work, a water kefir fermentation process was followed as a function of time during 192 h to unravel the community dynamics, the species diversity, and the kinetics of substrate consumption and metabolite production. The majority of the water kefir ecosystem was found to be present on the water kefir grains. The most important microbial species present wereLactobacillus casei/paracasei,Lactobacillus harbinensis,Lactobacillus hilgardii,Bifidobacterium psychraerophilum/crudilactis,Saccharomyces cerevisiae, andDekkera bruxellensis. The microbial species diversities in the water kefir liquor and on the water kefir grains were similar and remained stable during the whole fermentation process. The major substrate, sucrose, was completely converted after 24 h of fermentation, which coincided with the production of the major part of the water kefir grain polysaccharide. The main metabolites of the fermentation were ethanol and lactic acid. Glycerol, acetic acid, and mannitol were produced in low concentrations. The major part of these metabolites was produced during the first 72 h of fermentation, during which the pH decreased from 4.26 to 3.45. The most prevalent volatile aroma compounds were ethyl acetate, isoamyl acetate, ethyl hexanoate, ethyl octanoate, and ethyl decanoate, which might be of significance with respect to the aroma of the end product.
TiO
2
Photocatalysis Damages Lipids and Proteins in Escherichia coli
Authors: Carré Gaëlle , Hamon Erwann , Ennahar Saïd , Estner Maxime , Lett Marie-Claire , Horvatovich Peter , Gies Jean-Pierre , Keller Valérie , Keller Nicolas , Andre Philippe 
Published: February 2014

ABSTRACT

This study investigates the mechanisms of UV-A (315 to 400 nm) photocatalysis with titanium dioxide (TiO
2
) applied to the degradation of
Escherichia coli
and their effects on two key cellular components: lipids and proteins. The impact of TiO
2
photocatalysis on
E. coli
survival was monitored by counting on agar plate and by assessing lipid peroxidation and performing proteomic analysis. We observed through malondialdehyde quantification that lipid peroxidation occurred during the photocatalytic process, and the addition of superoxide dismutase, which acts as a scavenger of the superoxide anion radical (O
2
·
−
), inhibited this effect by half, showing us that O
2
·
−
radicals participate in the photocatalytic antimicrobial effect. Qualitative analysis using two-dimensional electrophoresis allowed selection of proteins for which spot modifications were observed during the applied treatments. Two-dimensional electrophoresis highlighted that among the selected protein spots, 7 and 19 spots had already disappeared in the dark in the presence of 0.1 g/liter and 0.4 g/liter TiO
2
, respectively, which is accounted for by the cytotoxic effect of TiO
2
. Exposure to 30 min of UV-A radiation in the presence of 0.1 g/liter and 0.4 g/liter TiO
2
increased the numbers of missing spots to 14 and 22, respectively. The proteins affected by photocatalytic oxidation were strongly heterogeneous in terms of location and functional category. We identified several porins, proteins implicated in stress response, in transport, and in bacterial metabolism. This study reveals the simultaneous effects of O
2
·
−
on lipid peroxidation and on the proteome during photocatalytic treatment and therefore contributes to a better understanding of molecular mechanisms in antibacterial photocatalytic treatment.
Conversion of 4-Hydroxybutyrate to Acetyl Coenzyme A and Its Anapleurosis in the Metallosphaera sedula 3-Hydroxypropionate/4-Hydroxybutyrate Carbon Fixation Pathway
Authors: Hawkins Aaron B. , Adams Michael W. W. , Kelly Robert M. 
Published: February 2014

ABSTRACT

The extremely thermoacidophilic archaeon
Metallosphaera sedula
(optimum growth temperature, 73°C, pH 2.0) grows chemolithoautotrophically on metal sulfides or molecular hydrogen by employing the 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) carbon fixation cycle. This cycle adds two CO
2
molecules to acetyl coenzyme A (acetyl-CoA) to generate 4HB, which is then rearranged and cleaved to form two acetyl-CoA molecules. Previous metabolic flux analysis showed that two-thirds of central carbon precursor molecules are derived from succinyl-CoA, which is oxidized to malate and oxaloacetate. The remaining one-third is apparently derived from acetyl-CoA. As such, the steps beyond succinyl-CoA are essential for completing the carbon fixation cycle and for anapleurosis of acetyl-CoA. Here, the final four enzymes of the 3HP/4HB cycle, 4-hydroxybutyrate-CoA ligase (AMP forming) (Msed_0406), 4-hydroxybutyryl-CoA dehydratase (Msed_1321), crotonyl-CoA hydratase/(
S
)-3-hydroxybutyryl-CoA dehydrogenase (Msed_0399), and acetoacetyl-CoA β-ketothiolase (Msed_0656), were produced recombinantly in
Escherichia coli
, combined
in vitro
, and shown to convert 4HB to acetyl-CoA. Metabolic pathways connecting CO
2
fixation and central metabolism were examined using a gas-intensive bioreactor system in which
M. sedula
was grown under autotrophic (CO
2
-limited) and heterotrophic conditions. Transcriptomic analysis revealed the importance of the 3HP/4HB pathway in supplying acetyl-CoA to anabolic pathways generating intermediates in
M. sedula
metabolism. The results indicated that flux between the succinate and acetyl-CoA branches in the 3HP/4HB pathway is governed by 4-hydroxybutyrate-CoA ligase, possibly regulated posttranslationally by the protein acetyltransferase (Pat)/Sir2-dependent system. Taken together, this work confirms the final four steps of the 3HP/4HB pathway, thereby providing the framework for examining connections between CO
2
fixation and central metabolism in
M. sedula.
Infection by Toxoplasma gondii Specifically Induces Host c-Myc and the Genes This Pivotal Transcription Factor Regulates
Authors: Franco Magdalena , Shastri Anjali J. , Boothroyd John C. 
Published: February 2014

ABSTRACT

Toxoplasma gondii
infection has previously been described to cause dramatic changes in the host transcriptome by manipulating key regulators, including STATs, NF-κB, and microRNAs. Here, we report that
Toxoplasma
tachyzoites also mediate rapid and sustained induction of another pivotal regulator of host cell transcription, c-Myc. This induction is seen in cells infected with all three canonical types of
Toxoplasma
but not the closely related apicomplexan parasite
Neospora caninum
. Coinfection of cells with both
Toxoplasma
and
Neospora
still results in an increase in the level of host c-Myc, showing that c-Myc is actively upregulated by
Toxoplasma
infection (rather than repressed by
Neospora
). We further demonstrate that this upregulation may be mediated through c-Jun N-terminal protein kinase (JNK) and is unlikely to be a nonspecific host response, as heat-killed
Toxoplasma
parasites do not induce this increase and neither do nonviable parasites inside the host cell. Finally, we show that the induced c-Myc is active and that transcripts dependent on its function are upregulated, as predicted. Hence, c-Myc represents an additional way in which
Toxoplasma
tachyzoites have evolved to specifically alter host cell functions during intracellular growth.
Differential Transcriptional Regulation of Aggregatibacter actinomycetemcomitans
lsrACDBFG
and
lsrRK
Operons by Integration Host Factor Protein
Authors: Torres-Escobar Ascención , Juárez-Rodríguez María Dolores , Demuth Donald R. 
Published: February 2014

ABSTRACT

We previously showed that the
Aggregatibacter actinomycetemcomitans
lsrACDBFG
and
lsrRK
operons are regulated by LsrR and cyclic AMP receptor protein (CRP) and that proper regulation of the
lsr
locus is required for optimal biofilm growth by
A. actinomycetemcomitans
. Here, we identified sequences that reside immediately upstream from both the
lsrA
and
lsrR
start codons that closely resemble the consensus recognition sequence of
Escherichia coli
integration host factor (IHF) protein.
A. actinomycetemcomitans
IHFα and IHFβ were expressed and purified as hexahistidine fusion proteins, and using electrophoretic mobility shift assays (EMSAs), the IHFα-IHFβ protein complex was shown to bind to probes containing the putative IHF recognition sequences. In addition, single-copy chromosomal insertions of
lsrR
promoter-
lacZ
and
lsrA
promoter-
lacZ
transcriptional fusions in wild-type
A. actinomycetemcomitans
and Δ
ihfA
and Δ
ihfB
mutant strains showed that IHF differentially regulates the
lsr
locus and functions as a negative regulator of
lsrRK
and a positive regulator of
lsrACDBFG
. Deletion of
ihfA
or
ihfB
also reduced biofilm formation and altered biofilm architecture relative to the wild-type strain, and these phenotypes were partially complemented by a plasmid-borne copy of
ihfA
or
ihfB
. Finally, using 5′ rapid amplification of cDNA ends (RACE), two transcriptional start sites (TSSs) and two putative promoters were identified for
lsrRK
and three TSSs and putative promoters were identified for
lsrACDBFG
. The function of the two
lsrRK
promoters and the positive regulatory role of IHF in regulating
lsrACDBFG
expression were confirmed with a series of
lacZ
transcriptional fusion constructs. Together, our results highlight the complex transcriptional regulation of the
lsrACDBFG
and
lsrRK
operons and suggest that multiple promoters and the architecture of the
lsrACDBFG-lsrRK
intergenic region may control the expression of these operons.
The Bifunctional Cell Wall Hydrolase CwlT Is Needed for Conjugation of the Integrative and Conjugative Element ICEBs1in Bacillus subtilis and B. anthracis
Authors: DeWitt Tyler , Grossman Alan D. 
Published: February 2014

ABSTRACTThe mobile genetic element ICEBs1is an integrative and conjugative element (ICE) found inBacillus subtilis. One of the ICEBs1genes,cwlT, encodes a cell wall hydrolase with two catalytic domains, a muramidase and a peptidase. We found thatcwlTis required for ICEBs1conjugation. We examined the role of each of the two catalytic domains and found that the muramidase is essential, whereas the peptidase is partially dispensable for transfer of ICEBs1. We also found that the putative signal peptide in CwlT is required for CwlT to function in conjugation, consistent with the notion that CwlT is normally secreted from the cytoplasm. We found that alteration of the putative lipid attachment site on CwlT had no effect on its role in conjugation, indicating that if CwlT is a lipoprotein, the lipid attachment is not required for conjugation. Finally, we found conditions supporting efficient transfer of ICEBs1into and out ofBacillus anthracisand thatcwlTwas needed for ICEBs1to function inB. anthracis. The mature cell wall ofB. anthracisis resistant to digestion by CwlT, indicating that CwlT might act during cell wall synthesis, before modifications of the peptidoglycan are complete.