bluuebunny/crossref_metadata_2025 huggingface dataset:
Topical Photodynamic Therapy Using Different Porphyrin Precursors Leads to Differences in Vascular Photosensitization and Vascular Damage in Normal Mouse Skin
Authors: Middelburg Tom A. , de Vijlder Hannah C. , de Bruijn Henriette S. , van der Ploeg‐van den Heuvel Angélique , Neumann H. A. Martino , de Haas Ellen R. M. , Robinson Dominic J.
Published: March 2014

Different distributions of hexyl aminolevulinate (HAL), aminolevulinic acid (ALA) and methyl aminolevulinate (MAL) in the superficial vasculature are not well studied but they are hypothesized to play an important role in topical photodynamic therapy (PDT). The colocalization of fluorescent CD31 and protoporphyrin IX (PpIX) was calculated using confocal microscopy of mouse skin sections to investigate the vascular distribution after topical application. Vascular damage leads to disruption of the normal endothelial adherens junction complex, of which CD144 is an integral component. Therefore, normal CD31 combined with loss of normal fluorescent CD144 staining was visually scored to assess vascular damage. Both the vascular PpIX concentration and the vascular damage were highest for HAL, then ALA and then MAL. Vascular damage in MAL was not different from normal contralateral control skin. This pattern is consistent with literature data on vasoconstriction after PDT, and with the hypothesis that the vasculature plays a role in light fractionation that increases efficacy for HAL and ALA‐PDT but not for MAL. These findings indicate that endothelial cells of superficial blood vessels synthesize biologically relevant PpIX concentrations, leading to vascular damage. Such vascular effects are expected to influence the oxygenation of tissue after PDT which can be important for treatment efficacy.
Localized Analytical Solutions and Parameters Analysis in the Nonlinear Dispersive Gross–Pitaevskii Mean‐Field GP (m,n) Model with Space‐Modulated Nonlinearity and Potential
Authors: Yan Zhenya
Published: March 2014

The novel nonlinear dispersive Gross–Pitaevskii (GP) mean‐field model with the space‐modulated nonlinearity and potential (called GP equation) is investigated in this paper. By using self‐similar transformations and some powerful methods, we obtain some families of novel envelope compacton‐like solutions spikon‐like solutions to the GP equation. These solutions possess abundant localized structures because of infinite choices of the self‐similar function . In particular, we choose as the Jacobi amplitude function and the combination of linear and trigonometric functions of space x so that the novel localized structures of the GP(2, 2) equation are illustrated, which are much different from the usual compacton and spikon solutions reported. Moreover, it is shown that GP(m, 1) equation with linear dispersion also admits the compacton‐like solutions for the case and spikon‐like solutions for the case .
Measuring health literacy – the Swedish Functional Health Literacy scale
Authors: Wångdahl Josefin M. , Mårtensson Lena I.
Published: March 2014

Background

The benefits of health promotion efforts vary due to a complexity of reasons. One possible reason for an absence of effects is the level of functional health literacy among the individuals that participate in the interventions. Thus, valid and reliable instruments that capture these kinds of skills are needed. The aim of this study was to develop a Swedish Functional Health Literacy scale to use in health promotion and health prevention by translating the Japanese Functional Health Literacy scale into Swedish and testing some aspects of its validity and test–retest reliability.

Methods

The research project comprised six phases including translation and back translation, validity tests of the two first versions of the instrument based on interviews with professionals and representatives for the target group of the instrument, and a test–retest of the first version among target groups.

Results

The items in the first two versions were experienced as unclear, which led to improvements of the next version. The final version of the translated instrument (the Swedish Functional Literacy scale) showed evidence of content validity, and the test–retest confirmed that the instrument had stability over time with a percentage agreement for the items ranging from 63% to 92% (M = 77.2%).

Conclusion

The items in the Swedish version of the scale are equivalent to the original Japanese scale in terms of language and contents and cover the major aspects of functional health literacy as it is defined in the literature. The translated instrument shows stability over time, that is, reliability, at least for a part of the Swedish population. More validity tests of the Swedish Functional Health Literacy scale based on a broader population are needed.
From Yuppies to Yupps: Family Gentrifiers Consuming Spaces and Re‐inventing Cities
Authors: Karsten Lia
Published: March 2014

This is a study of family consumption in an upgraded Amsterdam neighbourhood. It aims to unravel the relationship between the increase of middle‐class families and the establishing of new family‐related consumption spaces, both commercial and public. Based on observations and interviews in Amsterdam, we identify an increase in family and child directed consumption spaces. They reflect parental wishes to continue their former childless lifestyle, the need to combine work and care, and the wish to educate children in a wide range of skills. The more intensive consumption of parks and sidewalks reveals new practices of public parenting in urban contexts. It is argued that the transformation from childless yuppie to young urban professional parent (yupp) not only goes along with new consumption cultures but also with the production of a new city. This re‐invented city has potentials for age and gender equality, however unequal class relations appear to continue.
Acute enteritis associated with Coxsackievirus A19 in a kidney transplant patient
Authors: Melica G. , Langlois A.‐L. , Le Goff J. , Viglietti D. , Glotz D. , Molina J.‐M. , Peraldi M.‐N.
Published: March 2014

Diarrhea is a frequent complication after kidney transplantation, with an incidence rate between 22% and 51%. In many cases, the cause remains unknown. We describe here the first case, to our knowledge, of persistent diarrhea associated with Coxsackievirus A19 (CVA19) in a kidney transplant recipient. The patient was a 46‐year‐old man who received a deceased‐donor kidney. He experienced delayed graft function because of donor kidney donation after circulatory determination of death. Maintenance immunosuppression consisted of low‐dose cyclosporine, high‐dose mycophenolate mofetil (MMF) (3 g/day), and prednisone (10 mg/day). He had severe diarrhea for 2 weeks associated with acute renal failure. No pathogens were found in the stool cultures. Enterovirus detection was positive by real‐time polymerase chain reaction, and sequence analysis found CVA19 (from Enterovirus C group). Area under the curve of MMF was 48 mg.h/L. Because of the persistence of diarrhea, MMF was stopped and replaced by azathioprine. The diarrhea disappeared, but serum creatinine did not return to baseline. CVA19 rarely causes gastroenteritis. This case illustrates that MMF is not always the direct cause of diarrhea, and that new clinical infectious diseases will be detected with the expansion of molecular‐based DNA diagnostics.
MHF1 plays Fanconi anaemia complementation group M protein (FANCM)‐dependent and FANCM‐independent roles in DNA repair and homologous recombination in plants
Authors: Dangel Natalie J. , Knoll Alexander , Puchta Holger
Published: March 2014

Fanconi anaemia complementation group M protein (FANCM), a component of the human Fanconi anemia pathway, acts as DNA translocase that is essential during the repair of DNA interstrand cross‐links. The DNA‐damage‐binding function of FANCM is strongly enhanced by the histone fold‐containing FANCM‐associated protein MHF1. We identified a single homologue of MHF1 in the genome of Arabidopsis thaliana. Similar to the loss of AtFANCM, the loss of AtMHF1 leads to several meiotic defects, such as chromosome bridges between bivalents and an unequal distribution of chromosomes. Moreover, MHF1, together with FANCM, is involved in interstrand cross‐link repair in plants. This phenotype is detectable only in double mutants of the RecQ helicase and BLM homologue RECQ4A, which appears to function in a parallel pathway to the FANCM/MHF1 complex. However, in somatic cells, FANCM has an MHF1‐independent function in replicative repair in a parallel pathway to the endonuclease MUS81. Furthermore, MHF1 is required for efficient somatic homologous recombination (HR) – a role antagonistic to FANCM. FANCM and RECQ4A define two parallel pathways of HR suppression in Arabidopsis. Hyperrecombination in the fancm but not the recq4A mutant can be abolished by MHF1 mutations. This finding indicates that MHF1 and FANCM act at different steps of a single, common, HR pathway.
Effects of acute hypoxia on cerebrovascular responses to carbon dioxide
Authors: Ogoh Shigehiko , Nakahara Hidehiro , Ueda Shinya , Okazaki Kazunobu , Shibasaki Manabu , Subudhi Andrew W. , Miyamoto Tadayoshi
Published: March 2014

New Findings

What is the central question of this study?

In acute hypoxia, the reduction in arterial CO2 tension due to the hypoxic ventilatory response (respiratory chemoreflex) stimulates cerebral vasoconstriction, which opposes the degree of hypoxic cerebral vasodilatation. The aim was to examine this interaction further. Specifically, we questioned whether arterial CO2 tension‐mediated effects on cerebrovascular regulation are attenuated during acute hypoxia.

What is the main finding and its importance?

Cerebrovascular CO2 reactivity and CO2‐mediated effects on dynamic cerebral autoregulation were attenuated during acute hypoxia. These findings suggest that blunted cerebrovascular responses to CO2 may limit the degree of CO2‐mediated vasoconstriction to help maintain adequate cerebral blood flow for cerebral O2 homeostasis during acute hypoxia.

In normoxic conditions, a reduction in arterial carbon dioxide tension causes cerebral vasoconstriction, thereby reducing cerebral blood flow and modifying dynamic cerebral autoregulation (dCA). It is unclear to what extent these effects are altered by acute hypoxia and the associated hypoxic ventilatory response (respiratory chemoreflex). This study tested the hypothesis that acute hypoxia attenuates arterial CO2 tension‐mediated regulation of cerebral blood flow to help maintain cerebral O2 homeostasis. Eight subjects performed three randomly assigned respiratory interventions following a resting baseline period, as follows: (1) normoxia (21% O2); (2) hypoxia (12% O2); and (3) hypoxia with wilful restraint of the respiratory chemoreflex. During each intervention, 0, 2.0, 3.5 or 5.0% CO2 was sequentially added (8 min stages) to inspired gas mixtures to assess changes in steady‐state cerebrovascular CO2 reactivity and dCA. During normoxia, the addition of CO2 increased internal carotid artery blood flow and middle cerebral artery mean blood velocity (MCA Vmean), while reducing dCA (change in phase = −0.73 ± 0.22 rad, P = 0.005). During acute hypoxia, internal carotid artery blood flow and MCA Vmean remained unchanged, but cerebrovascular CO2 reactivity (internal carotid artery, P = 0.003; MCA Vmean, P = 0.031) and CO2‐mediated effects on dCA (P = 0.008) were attenuated. The effects of hypoxia were not further altered when the respiratory chemoreflex was restrained. These findings support the hypothesis that arterial CO2 tension‐mediated effects on the cerebral vasculature are reduced during acute hypoxia. These effects could limit the degree of hypocapnic vasoconstriction and may help to regulate cerebral blood flow and cerebral O2 homeostasis during acute periods of hypoxia.
Laser surface structuring of AZ31 Mg alloy for controlled wettability
Authors: Gökhan Demir Ali , Furlan Valentina , Lecis Nora , Previtali Barbara
Published: March 2014

Structured surfaces exhibit functional properties that can enhance the performance of a bioimplant in terms of biocompatibility, adhesion, or corrosion behavior. In order to tailor the surface property, chemical and physical methods can be used in a sequence of many steps. On the other hand, laser surface processing can provide a single step solution to achieve the designated surface function with the use of simpler equipment and high repeatability. This work provides the details on the surface structuring of AZ31, a biocompatible and biodegradable Mg alloy, by a single-step laser surface structuring based on remelting. The surfaces are characterized in terms of topography, chemistry, and physical integrity, as well as the effective change in the surface wetting behavior is demonstrated. The results imply a great potential in local or complete surface structuring of medical implants for functionalization by the flexible positioning of the laser beam.
Advanced methodology for electrical characterization of metal/high-k interfaces
Authors: Rao Rosario , Lorenzi Paolo , Irrera Fernanda
Published: March 2014

A methodology for the quantitative electrical characterization of defects at metal/high-k interfaces is proposed. It includes modelling of trapping in the oxide, fit of experiments, and calculation of the system band diagram after trapping. As a result, the defect concentrations and energy levels are extracted. The methodology is demonstrated on metal-oxide–semiconductor systems, but its results can be extended on whatever structure containing an interface between a metal and a high-k dielectric film.
Monte Carlo simulation of a quantum noise limited Čerenkov detector based on air‐spaced light guiding taper for megavoltage x‐ray imaging
Authors: Teymurazyan A. , Rowlands J. A. , Pang G.
Published: March 2014

Purpose:

Electronic Portal Imaging Devices (EPIDs) have been widely used in radiation therapy and are still needed on linear accelerators (Linacs) equipped with kilovoltage cone beam CT (kV‐CBCT) or MRI systems. Our aim is to develop a new high quantum efficiency (QE) Čerenkov Portal Imaging Device (CPID) that is quantum noise limited at dose levels corresponding to a single Linac pulse.

Methods:

Recently a new concept of CPID for MV x‐ray imaging in radiation therapy was introduced. It relies on Čerenkov effect for x‐ray detection. The proposed design consisted of a matrix of optical fibers aligned with the incident x‐rays and coupled to an active matrix flat panel imager (AMFPI) for image readout. A weakness of such design is that too few Čerenkov light photons reach the AMFPI for each incident x‐ray and an AMFPI with an avalanche gain is required in order to overcome the readout noise for portal imaging application. In this work the authors propose to replace the optical fibers in the CPID with light guides without a cladding layer that are suspended in air. The air between the light guides takes on the role of the cladding layer found in a regular optical fiber. Since air has a significantly lower refractive index (∼1 versus 1.38 in a typical cladding layer), a much superior light collection efficiency is achieved.

Results:

A Monte Carlo simulation of the new design has been conducted to investigate its feasibility. Detector quantities such as quantum efficiency (QE), spatial resolution (MTF), and frequency dependent detective quantum efficiency (DQE) have been evaluated. The detector signal and the quantum noise have been compared to the readout noise.

Conclusions:

Our studies show that the modified new CPID has a QE and DQE more than an order of magnitude greater than that of current clinical systems and yet a spatial resolution similar to that of current low‐QE flat‐panel based EPIDs. Furthermore it was demonstrated that the new CPID does not require an avalanche gain in the AMFPI and is quantum noise limited at dose levels corresponding to a single Linac pulse.
Genetic Divergence of Bradyrhizobium Strains Nodulating Soybeans as Revealed by Multilocus Sequence Analysis of Genes Inside and Outside the Symbiosis Island
Authors: Zhang Xing Xing , Guo Hui Juan , Wang Rui , Sui Xin Hua , Zhang Yan Ming , Wang En Tao , Tian Chang Fu , Chen Wen Xin
Published: March 2014

The genus
Bradyrhizobium
has been considered to be a taxonomically difficult group. In this study, phylogenetics and evolutionary genetics analyses were used to investigate divergence levels among
Bradyrhizobium
strains nodulating soybeans in China. Eleven genospecies were identified by sequence analysis of three phylogenetic and taxonomic markers (
SMc00019
,
thrA
, and
truA
). This was also supported by analyses of eight genes outside the symbiosis island (“off-island” genes;
SMc00019
,
thrA
,
truA
,
fabB
,
glyA
,
phyR
,
exoN
, and
hsfA
). However, seven genes inside the symbiosis island (“island” genes;
nifA
,
nifH
,
nodC
,
nodV
,
fixA
,
trpD
, and
rhcC2
) showed contrasting lower levels of nucleotide diversity and recombination rates than did off-island genes. Island genes had significantly incongruent gene phylogenies compared to the species tree. Four phylogenetic clusters were observed in island genes, and the epidemic cluster IV (harbored by
Bradyrhizobium japonicum
,
Bradyrhizobium diazoefficiens
,
Bradyrhizobium huanghuaihaiense
,
Bradyrhizobium liaoningense
,
Bradyrhizobium daqingense
,
Bradyrhizobium
sp. I,
Bradyrhizobium
sp. III, and
Bradyrhizobium
sp. IV) was not found in
Bradyrhizobium yuanmingense
,
Bradyrhizobium
sp. II, or
Bradyrhizobium elkanii
. The gene flow level of island genes among genospecies is discussed in the context of the divergence level of off-island genes.
Unveiling of the Diversity of Prasinoviruses (Phycodnaviridae) in Marine Samples by Using High-Throughput Sequencing Analyses of PCR-Amplified DNA Polymerase and Major Capsid Protein Genes
Authors: Clerissi Camille , Grimsley Nigel , Ogata Hiroyuki , Hingamp Pascal , Poulain Julie , Desdevises Yves
Published: March 2014

Viruses strongly influence the ecology and evolution of their eukaryotic hosts in the marine environment, but little is known about their diversity and distribution. Prasinoviruses infect an abundant and widespread class of phytoplankton, the Mamiellophyceae, and thereby exert a specific and important role in microbial ecosystems. However, molecular tools to specifically identify this viral genus in environmental samples are still lacking. We developed two primer sets, designed for use with polymerase chain reactions and 454 pyrosequencing technologies, to target two conserved genes, encoding the DNA polymerase (PolB gene) and the major capsid protein (MCP gene). While only one copy of the PolB gene is present in
Prasinovirus
genomes, there are at least seven paralogs for MCP, the copy we named number 6 being shared with other eukaryotic alga-infecting viruses. Primer sets for PolB and MCP6 were thus designed and tested on 6 samples from the Tara Oceans project. The results suggest that the MCP6 amplicons show greater richness but that PolB gave a wider coverage of
Prasinovirus
diversity. As a consequence, we recommend use of the PolB primer set, which will certainly reveal exciting new insights about the diversity and distribution of prasinoviruses at the community scale.
Safely Coupling Livestock and Crop Production Systems: How Rapidly Do Antibiotic Resistance Genes Dissipate in Soil following a Commercial Application of Swine or Dairy Manure?
Authors: Marti Romain , Tien Yuan-Ching , Murray Roger , Scott Andrew , Sabourin Lyne , Topp Edward
Published: March 2014

Animal manures recycled onto crop production land carry antibiotic-resistant bacteria. The present study evaluated the fate in soil of selected genes associated with antibiotic resistance or genetic mobility in field plots cropped to vegetables and managed according to normal farming practice. Referenced to unmanured soil, fertilization with swine or dairy manure increased the relative abundance of the gene targets
sul1
,
erm
(B),
str
(B),
int1
, and IncW
repA
. Following manure application in the spring of 2012, gene copy number decayed exponentially, reaching background levels by the fall of 2012. In contrast, gene copy number following manure application in the fall of 2012 or spring of 2013 increased significantly in the weeks following application and then declined. In both cases, the relative abundance of gene copy numbers had not returned to background levels by the fall of 2013. Overall, these results suggest that under conditions characteristic of agriculture in a humid continental climate, a 1-year period following a commercial application of raw manure is sufficient to ensure that an additional soil burden of antibiotic resistance genes approaches background. The relative abundance of several gene targets exceeded background during the growing season following a spring application or an application done the previous fall. Results from the present study reinforce the advisability of treating manure prior to use in crop production systems.
Arsenic(V) Reduction in Relation to Iron(III) Transformation and Molecular Characterization of the Structural and Functional Microbial Community in Sediments of a Basin-Fill Aquifer in Northern Utah
Authors: Mirza Babur S. , Muruganandam Subathra , Meng Xianyu , Sorensen Darwin L. , Dupont R. Ryan , McLean Joan E.
Published: March 2014

Basin-fill aquifers of the Southwestern United States are associated with elevated concentrations of arsenic (As) in groundwater. Many private domestic wells in the Cache Valley Basin, UT, have As concentrations in excess of the U.S. EPA drinking water limit. Thirteen sediment cores were collected from the center of the valley at the depth of the shallow groundwater and were sectioned into layers based on redoxmorphic features. Three of the layers, two from redox transition zones and one from a depletion zone, were used to establish microcosms. Microcosms were treated with groundwater (GW) or groundwater plus glucose (GW+G) to investigate the extent of As reduction in relation to iron (Fe) transformation and characterize the microbial community structure and function by sequencing 16S rRNA and arsenate dissimilatory reductase (
arrA
) genes. Under the carbon-limited conditions of the GW treatment, As reduction was independent of Fe reduction, despite the abundance of sequences related to
Geobacter
and
Shewanella
, genera that include a variety of dissimilatory iron-reducing bacteria. The addition of glucose, an electron donor and carbon source, caused substantial shifts toward domination of the bacterial community by
Clostridium
-related organisms, and As reduction was correlated with Fe reduction for the sediments from the redox transition zone. The
arrA
gene sequencing from microcosms at day 54 of incubation showed the presence of 14 unique phylotypes, none of which were related to any previously described
arrA
gene sequence, suggesting a unique community of dissimilatory arsenate-respiring bacteria in the Cache Valley Basin.
Clostridium botulinum Strains Producing BoNT/F4 or BoNT/F5
Authors: Raphael Brian H. , Bradshaw Marite , Kalb Suzanne R. , Joseph Lavin A. , Lúquez Carolina , Barr John R. , Johnson Eric A. , Maslanka Susan E.
Published: March 2014

Botulinum neurotoxin type F (BoNT/F) may be produced by
Clostridium botulinum
alone or in combination with another toxin type such as BoNT/A or BoNT/B. Type F neurotoxin gene sequences have been further classified into seven toxin subtypes. Recently, the genome sequence of one strain of
C. botulinum
(Af84) was shown to contain three neurotoxin genes (
bont
/
F4
,
bont
/
F5
, and
bont
/
A2
). In this study, eight strains containing
bont
/
F4
and seven strains containing
bont
/
F5
were examined. Culture supernatants produced by these strains were incubated with BoNT/F-specific peptide substrates. Cleavage products of these peptides were subjected to mass spectral analysis, allowing detection of the BoNT/F subtypes present in the culture supernatants. PCR analysis demonstrated that a plasmid-specific marker (PL-6) was observed only among strains containing
bont
/
F5
. Among these strains, Southern hybridization revealed the presence of an approximately 242-kb plasmid harboring
bont
/
F5
. Genome sequencing of four of these strains revealed that the genomic backgrounds of strains harboring either
bont
/
F4
or
bont
/
F5
are diverse. None of the strains analyzed in this study were shown to produce BoNT/F4 and BoNT/F5 simultaneously, suggesting that strain Af84 is unusual. Finally, these data support a role for the mobility of a
bont
/
F5
-carrying plasmid among strains of diverse genomic backgrounds.
Diversity of the Lactic Acid Bacterium and Yeast Microbiota in the Switch from Firm- to Liquid-Sourdough Fermentation
Authors: Di Cagno Raffaella , Pontonio Erica , Buchin Solange , De Angelis Maria , Lattanzi Anna , Valerio Francesca , Gobbetti Marco , Calasso Maria
Published: March 2014

Four traditional type I sourdoughs were comparatively propagated (28 days) under firm (dough yield, 160) and liquid (dough yield, 280) conditions to mimic the alternative technology options frequently used for making baked goods. After 28 days of propagation, liquid sourdoughs had the lowest pH and total titratable acidity (TTA), the lowest concentrations of lactic and acetic acids and free amino acids, and the most stable density of presumptive lactic acid bacteria. The cell density of yeasts was the highest in liquid sourdoughs. Liquid sourdoughs showed simplified microbial diversity and harbored a low number of strains, which were persistent.
Lactobacillus plantarum
dominated firm sourdoughs over time.
Leuconostoc lactis
and
Lactobacillus brevis
dominated only some firm sourdoughs, and
Lactobacillus sanfranciscensis
persisted for some time only in some firm sourdoughs.
Leuconostoc citreum
persisted in all firm and liquid sourdoughs, and it was the only species detected in liquid sourdoughs at all times; it was flanked by
Leuconostoc mesenteroides
in some sourdoughs.
Saccharomyces cerevisiae
,
Candida humilis
,
Saccharomyces servazzii
,
Saccharomyces bayanus-Kazachstania
sp., and
Torulaspora delbrueckii
were variously identified in firm and liquid sourdoughs. A total of 197 volatile components were identified through purge and trap–/solid-phase microextraction–gas chromatography-mass spectrometry (PT–/SPME–GC-MS). Aldehydes, several alcohols, and some esters were at the highest levels in liquid sourdoughs. Firm sourdoughs mainly contained ethyl acetate, acetic acid, some sulfur compounds, and terpenes. The use of liquid fermentation would change the main microbial and biochemical features of traditional baked goods, which have been manufactured under firm conditions for a long time.
Rapid TaqMan-Based Quantification of Chlorophyll
d
-Containing Cyanobacteria in the Genus Acaryochloris
Authors: Behrendt Lars , Nielsen Jeppe L. , Sørensen Søren J. , Larkum Anthony W. D. , Winther Jakob R. , Kühl Michael
Published: March 2014

Reports of the chlorophyll (Chl)
d
-containing cyanobacterium
Acaryochloris
have accumulated since its initial discovery in 1996. The majority of this evidence is based on amplification of the gene coding for the 16S rRNA, and due to the wide geographical distribution of these sequences, a global distribution of
Acaryochloris
species was suggested. Here, we present a rapid, reliable, and cost-effective TaqMan-based quantitative PCR (qPCR) assay that was developed for the specific detection of
Acaryochloris
species in complex environmental samples. The TaqMan probe showed detection limits of ∼10 16S rRNA gene copy numbers based on standard curves consisting of plasmid inserts. DNA from five
Acaryochloris
strains, i.e., MBIC11017, CCMEE5410, HICR111A, CRS, and Awaji-1, exhibited amplification efficiencies of >94% when tested in the TaqMan assay. When used on complex natural communities, the TaqMan assay detected the presence of
Acaryochloris
species in four out of eight samples of crustose coralline algae (CCA), collected from temperate and tropical regions. In three out of these TaqMan-positive samples, the presence of Chl
d
was confirmed via high-performance liquid chromatography (HPLC), and corresponding cell estimates of
Acaryochloris
species amounted to 7.6 × 10
1
to 3.0 × 10
3
per mg of CCA. These numbers indicate a substantial contribution of Chl
d
-containing cyanobacteria to primary productivity in endolithic niches. The new TaqMan assay allows quick and easy screening of environmental samples for the presence of
Acaryochloris
species and is an important tool to further resolve the global distribution and significance of this unique oxyphototroph.
The Canonical Twin-Arginine Translocase Components Are Not Required for Secretion of Folded Green Fluorescent Protein from the Ancestral Strain of Bacillus subtilis
Authors: Snyder Anthony J. , Mukherjee Sampriti , Glass J. Kyle , Kearns Daniel B. , Mukhopadhyay Suchetana
Published: March 2014

Cellular processes, such as the digestion of macromolecules, phosphate acquisition, and cell motility, require bacterial secretion systems. In
Bacillus subtilis
, the predominant protein export pathways are Sec (generalized secretory pathway) and Tat (twin-arginine translocase). Unlike Sec, which secretes unfolded proteins, the Tat machinery secretes fully folded proteins across the plasma membrane and into the medium. Proteins are directed for Tat-dependent export by N-terminal signal peptides that contain a conserved twin-arginine motif. Thus, utilizing the Tat secretion system by fusing a Tat signal peptide is an attractive strategy for the production and export of heterologous proteins. As a proof of concept, we expressed green fluorescent protein (GFP) fused to the PhoD Tat signal peptide in the laboratory and ancestral strains of
B. subtilis
. Secretion of the Tat-GFP construct, as well as secretion of proteins in general, was substantially increased in the ancestral strain. Furthermore, our results show that secreted, fluorescent GFP could be purified directly from the extracellular medium. Nonetheless, export was not dependent on the known Tat secretion components or the signal peptide twin-arginine motif. We propose that the ancestral strain contains additional Tat components and/or secretion regulators that were abrogated following domestication.
Xanthomonas perforans Colonization Influences Salmonella enterica in the Tomato Phyllosphere
Authors: Potnis Neha , Soto-Arias José Pablo , Cowles Kimberly N. , van Bruggen Ariena H. C. , Jones Jeffrey B. , Barak Jeri D.
Published: March 2014

Salmonella enterica
rarely grows on healthy, undamaged plants, but its persistence is influenced by bacterial plant pathogens. The interactions between
S. enterica
,
Xanthomonas perforans
(a tomato bacterial spot pathogen), and tomato were characterized. We observed that virulent
X. perforans
, which establishes disease by suppressing pathogen-associated molecular pattern (PAMP)-triggered immunity that leads to effector-triggered susceptibility, created a conducive environment for persistence of
S. enterica
in the tomato phyllosphere, while activation of effector-triggered immunity by avirulent
X. perforans
resulted in a dramatic reduction in
S. enterica
populations.
S. enterica
populations persisted at ∼10 times higher levels in leaves coinoculated with virulent
X. perforans
than in those where
S. enterica
was applied alone. In contrast,
S. enterica
populations were ∼5 times smaller in leaves coinoculated with avirulent
X. perforans
than in leaves inoculated with
S. enterica
alone. Coinoculation with virulent
X. perforans
increased
S. enterica
aggregate formation; however,
S. enterica
was not found in mixed aggregates with
X. perforans
. Increased aggregate formation by
S. enterica
may serve as the mechanism of persistence on leaves cocolonized by virulent
X. perforans
.
S. enterica
association with stomata was altered by
X. perforans
; however, it did not result in appreciable populations of
S. enterica
in the apoplast even in the presence of large virulent
X. perforans
populations. Gene-for-gene resistance against
X. perforans
successively restricted
S. enterica
populations. Given the effect of this interaction, breeding for disease-resistant cultivars may be an effective strategy to limit both plant disease and
S. enterica
populations and, consequently, human illness.
Determination of Thermal Inactivation Kinetics of Hepatitis A Virus in Blue Mussel (Mytilus edulis) Homogenate
Authors: Bozkurt Hayriye , D'Souza Doris H. , Davidson P. Michael
Published: March 2014

Hepatitis A virus (HAV) is a food-borne enteric virus responsible for outbreaks of hepatitis associated with shellfish consumption. The objectives of this study were to determine the thermal inactivation behavior of HAV in blue mussels, to compare the first-order and Weibull models to describe the data, to calculate Arrhenius activation energy for each model, and to evaluate model efficiency by using selected statistical criteria. The times required to reduce the population by 1 log cycle (D-values) calculated from the first-order model (50 to 72°C) ranged from 1.07 to 54.17 min for HAV. Using the Weibull model, the times required to destroy 1 log unit (

t
D

= 1
) of HAV at the same temperatures were 1.57 to 37.91 min. At 72°C, the treatment times required to achieve a 6-log reduction were 7.49 min for the first-order model and 8.47 min for the Weibull model. The z-values (changes in temperature required for a 90% change in the log D-values) calculated for HAV were 15.88 ± 3.97°C (
R
2
, 0.94) with the Weibull model and 12.97 ± 0.59°C (
R
2
, 0.93) with the first-order model. The calculated activation energies for the first-order model and the Weibull model were 165 and 153 kJ/mol, respectively. The results revealed that the Weibull model was more appropriate for representing the thermal inactivation behavior of HAV in blue mussels. Correct understanding of the thermal inactivation behavior of HAV could allow precise determination of the thermal process conditions to prevent food-borne viral outbreaks associated with the consumption of contaminated mussels.
Bacillus thuringiensis DB27 Produces Two Novel Protoxins, Cry21Fa1 and Cry21Ha1, Which Act Synergistically against Nematodes
Authors: Iatsenko Igor , Boichenko Iuliia , Sommer Ralf J.
Published: March 2014

Bacillus thuringiensis
has been widely used as a biopesticide, primarily for the control of insect pests, but some
B. thuringiensis
strains specifically target nematodes. However, nematicidal virulence factors of
B. thuringiensis
are poorly investigated. Here, we describe virulence factors of nematicidal
B. thuringiensis
DB27 using
Caenorhabditis elegans
as a model. We show that
B. thuringiensis
DB27 kills a number of free-living and animal-parasitic nematodes via intestinal damage. Its virulence factors are plasmid-encoded Cry protoxins, since plasmid-cured derivatives do not produce Cry proteins and are not toxic to nematodes. Whole-genome sequencing of
B. thuringiensis
DB27 revealed multiple potential nematicidal factors, including several Cry-like proteins encoded by different plasmids. Two of these proteins appear to be novel and show high similarity to Cry21Ba1. Named Cry21Fa1 and Cry21Ha1, they were expressed in
Escherichia coli
and fed to
C. elegans
, resulting in intoxication, intestinal damage, and death of nematodes. Interestingly, the effects of the two protoxins on
C. elegans
are synergistic (synergism factor, 1.8 to 2.5). Using purified proteins, we determined the 50% lethal concentrations (LC
50
s) for Cry21Fa1 and Cry21Ha1 to be 13.6 μg/ml and 23.9 μg/ml, respectively, which are comparable to the LC
50
of nematicidal Cry5B. Finally, we found that signaling pathways which protect
C. elegans
against Cry5B toxin are also required for protection against Cry21Fa1. Thus,
B. thuringiensis
DB27 produces novel nematicidal protoxins Cry21Fa1 and Cry21Ha1 with synergistic action, which highlights the importance of naturally isolated strains as a source of novel toxins.
An Uncultivated Nitrate-Reducing Member of the Genus Herminiimonas Degrades Toluene
Authors: Kim So-Jeong , Park Soo-Je , Jung Man-Young , Kim Jong-Geol , Madsen Eugene L. , Rhee Sung-Keun
Published: March 2014

Stable isotope probing (SIP) is a cultivation-free methodology that provides information about the identity of microorganisms participating in assimilatory processes in complex communities. In this study, a
Herminiimonas
-related bacterium was identified as the dominant member of a denitrifying microcosm fed [
13
C]toluene. The genome of the uncultivated toluene-degrading bacterium was obtained by applying pyrosequencing to the heavy DNA fraction. The draft genome comprised ∼3.8 Mb, in 131 assembled contigs. Metabolic reconstruction of aromatic hydrocarbon (toluene, benzoate,
p
-cresol, 4-hydroxybenzoate, phenylacetate, and cyclohexane carboxylate) degradation indicated that the bacterium might specialize in anaerobic hydrocarbon degradation. This characteristic is novel for the order
Burkholderiales
within the class
Betaproteobacteria
. Under aerobic conditions, the benzoate oxidation gene cluster (BOX) system is likely involved in the degradation of benzoate via benzoyl coenzyme A. Many putative genes for aromatic hydrocarbon degradation were closely related to those in the
Rhodocyclaceae
(particularly
Aromatoleum aromaticum
EbN1) with respect to organization and sequence similarity. Putative mobile genetic elements associated with these catabolic genes were highly abundant, suggesting gene acquisition by
Herminiimonas
via horizontal gene transfer.
Identification of Biomarker Genes To Predict Biodegradation of 1,4-Dioxane
Authors: Gedalanga Phillip B. , Pornwongthong Peerapong , Mora Rebecca , Chiang Sheau-Yun Dora , Baldwin Brett , Ogles Dora , Mahendra Shaily
Published: March 2014

Bacterial multicomponent monooxygenase gene targets in
Pseudonocardia dioxanivorans
CB1190 were evaluated for their use as biomarkers to identify the potential for 1,4-dioxane biodegradation in pure cultures and environmental samples. Our studies using laboratory pure cultures and industrial activated sludge samples suggest that the presence of genes associated with dioxane monooxygenase, propane monooxygenase, alcohol dehydrogenase, and aldehyde dehydrogenase are promising indicators of 1,4-dioxane biotransformation; however, gene abundance was insufficient to predict actual biodegradation. A time course gene expression analysis of dioxane and propane monooxygenases in
Pseudonocardia dioxanivorans
CB1190 and mixed communities in wastewater samples revealed important associations with the rates of 1,4-dioxane removal. In addition, transcripts of alcohol dehydrogenase and aldehyde dehydrogenase genes were upregulated during biodegradation, although only the aldehyde dehydrogenase was significantly correlated with 1,4-dioxane concentrations. Expression of the propane monooxygenase demonstrated a time-dependent relationship with 1,4-dioxane biodegradation in
P. dioxanivorans
CB1190, with increased expression occurring after over 50% of the 1,4-dioxane had been removed. While the fraction of
P. dioxanivorans
CB1190-like bacteria among the total bacterial population significantly increased with decrease in 1,4-dioxane concentrations in wastewater treatment samples undergoing active biodegradation, the abundance and expression of monooxygenase-based biomarkers were better predictors of 1,4-dioxane degradation than taxonomic 16S rRNA genes. This study illustrates that specific bacterial monooxygenase and dehydrogenase gene targets together can serve as effective biomarkers for 1,4-dioxane biodegradation in the environment.
Detection of Streptococcus suis in Bioaerosols of Swine Confinement Buildings
Authors: Bonifait Laetitia , Veillette Marc , Létourneau Valérie , Grenier Daniel , Duchaine Caroline
Published: March 2014

Streptococcus suisis an important swine pathogen that can cause septicemia, meningitis, and pneumonia. Also recognized as an emerging zoonotic agent, it is responsible for outbreaks of human infections in Asian countries. Serotype 2 is the predominant isolate from diseased animals and humans. The aerosolization ofS. suisin the air of swine confinement buildings (SCB) was studied. The presence ofS. suisin bioaerosols was monitored in SCB where cases of infection had been reported and in healthy SCB without reported infections. Using a quantitative-PCR (qPCR) method, we determined the total number of bacteria (1 × 108to 2 × 108airborne/m3), total number ofS. suisbacteria (4 × 105to 10 × 105airborne/m3), and number ofS. suisserotype 2 and 1/2 bacteria (1 × 103to 30 × 103airborne/m3) present in the air.S. suisserotypes 2 and 1/2 were detected in the air of all growing/finishing SCB that had documented cases ofS. suisinfection and in 50% of healthy SCB. The total number of bacteria and total numbers ofS. suisandS. suisserotype 2 and 1/2 bacteria were monitored in one positive SCB during a 5-week period, and it was shown that the aerosolizedS. suisserotypes 2 and 1/2 remain airborne for a prolonged period. When the effect of aerosolization onS. suiswas observed, the percentage of intactS. suisbacteria (showing cell membrane integrity) in the air might have been up to 13%. FinallyS. suiswas found in nasal swabs from 14 out of 21 healthy finishing-SCB workers, suggesting significant exposure to the pathogen. This report provides a better understanding of the aerosolization, prevalence, and persistence ofS. suisin SCB.
Sulfur Species as Redox Partners and Electron Shuttles for Ferrihydrite Reduction by Sulfurospirillum deleyianum
Authors: Lohmayer Regina , Kappler Andreas , Lösekann-Behrens Tina , Planer-Friedrich Britta
Published: March 2014

Iron(III) (oxyhydr)oxides can represent the dominant microbial electron acceptors under anoxic conditions in many aquatic environments, which makes understanding the mechanisms and processes regulating their dissolution and transformation particularly important. In a previous laboratory-based study, it has been shown that 0.05 mM thiosulfate can reduce 6 mM ferrihydrite indirectly via enzymatic reduction of thiosulfate to sulfide by the sulfur-reducing bacterium
Sulfurospirillum deleyianum
, followed by abiotic reduction of ferrihydrite coupled to reoxidation of sulfide. Thiosulfate, elemental sulfur, and polysulfides were proposed as reoxidized sulfur species functioning as electron shuttles. However, the exact electron transfer pathway remained unknown. Here, we present a detailed analysis of the sulfur species involved. Apart from thiosulfate, substoichiometric amounts of sulfite, tetrathionate, sulfide, or polysulfides also initiated ferrihydrite reduction. The portion of thiosulfate produced during abiotic ferrihydrite-dependent reoxidation of sulfide was about 10% of the total sulfur at maximum. The main abiotic oxidation product was elemental sulfur attached to the iron mineral surface, which indicates that direct contact between microorganisms and ferrihydrite is necessary to maintain the iron reduction process. Polysulfides were not detected in the liquid phase. Minor amounts were found associated either with microorganisms or the mineral phase. The abiotic oxidation of sulfide in the reaction with ferrihydrite was identified as rate determining. Cysteine, added as a sulfur source and a reducing agent, also led to abiotic ferrihydrite reduction and therefore should be eliminated when sulfur redox reactions are investigated. Overall, we could demonstrate the large impact of intermediate sulfur species on biogeochemical iron transformations.
Requirements for Hirano Body Formation
Authors: Griffin Paul , Furukawa Ruth , Piggott Cleveland , Maselli Andrew , Fechheimer Marcus
Published: March 2014

Hirano bodies are paracrystalline F-actin-rich structures associated with diverse conditions, including neurodegeneration and aging. Generation of model Hirano bodies using altered forms of
Dictyostelium
34-kDa actin-bundling protein allows studies of their physiological function and mechanism of formation. We describe a novel 34-kDa protein mutant, E60K, with a point mutation within the inhibitory domain of the 34-kDa protein. Expression of E60K in
Dictyostelium
induces the formation of model Hirano bodies. The E60K protein has activated actin binding and is calcium regulated, unlike other forms of the 34-kDa protein that induce Hirano bodies and that have activated actin binding but lack calcium regulation. Actin filaments in the presence of E60K
in vitro
show enhanced resistance to disassembly induced by latrunculin B. Actin filaments in model Hirano bodies are also protected from latrunculin-induced depolymerization. We used nocodazole and blebbistatin to probe the role of the microtubules and myosin II, respectively, in the formation of model Hirano bodies. In the presence of these inhibitors, model Hirano bodies can form but are smaller than controls at early times of formation. The ultrastructure of model Hirano bodies did not reveal any major difference in structure and organization in the presence of inhibitors. In summary, these results support the conclusion that formation of model Hirano bodies is promoted by gain-of-function actin filament bundling, which enhances actin filament stabilization. Microtubules and myosin II contribute to but are not required for formation of model Hirano bodies.
Sex-Specific Posttranslational Regulation of the Gamete Fusogen GCS1 in the Isogamous Volvocine Alga Gonium pectorale
Authors: Kawai-Toyooka Hiroko , Mori Toshiyuki , Hamaji Takashi , Suzuki Masahiro , Olson Bradley J. S. C. , Uemura Tomohiro , Ueda Takashi , Nakano Akihiko , Toyoda Atsushi , Fujiyama Asao , Nozaki Hisayoshi
Published: March 2014

Male and female, generally defined based on differences in gamete size and motility, likely have multiple independent origins, appearing to have evolved from isogamous organisms in various eukaryotic lineages. Recent studies of the gamete fusogen GCS1/HAP2 indicate that this protein is deeply conserved across eukaryotes, and its exclusive and/or functional expression generally resides in males or in male homologues. However, little is known regarding the conserved or primitive molecular traits of males and females within eukaryotes. Here, using morphologically indistinguishable isogametes of the colonial volvocine
Gonium pectorale
, we demonstrated that GCS1 is differently regulated between the sexes.
G. pectorale
GCS1 molecules in one sex (homologous to male) are transported from the gamete cytoplasm to the protruded fusion site, whereas those of the other sex (females) are quickly degraded within the cytoplasm upon gamete activation. This molecular trait difference might be conserved across various eukaryotic lineages and may represent male and female prototypes originating from a common eukaryotic ancestor.
The Precarious Prokaryotic Chromosome
Authors: Kuzminov Andrei
Published: March 2014

Evolutionary selection for optimal genome preservation, replication, and expression should yield similar chromosome organizations in any type of cells. And yet, the chromosome organization is surprisingly different between eukaryotes and prokaryotes. The nuclear versus cytoplasmic accommodation of genetic material accounts for the distinct eukaryotic and prokaryotic modes of genome evolution, but it falls short of explaining the differences in the chromosome organization. I propose that the two distinct ways to organize chromosomes are driven by the differences between the global-consecutive chromosome cycle of eukaryotes and the local-concurrent chromosome cycle of prokaryotes. Specifically, progressive chromosome segregation in prokaryotes demands a single duplicon per chromosome, while other “precarious” features of the prokaryotic chromosomes can be viewed as compensations for this severe restriction.