bluuebunny/crossref_metadata_2025_split huggingface dataset:
VISIONAIR: A European Infrastructure to Support Research Based on Visualization and Interaction Techniques
Authors: Noël Frédéric 
Published: December 2013

VISIONAIR is an acronym for “VISION Advanced Infrastructure for Research”. VISIONAIR is a European infrastructure for high level visualization facilities that is open to research communities across Europe and around the world. By integrating existing facilities, VISIONAIR creates a world-class research infrastructure for conducting state-of-the-art research, thus significantly enhancing the attractiveness and visibility of the European Research Area (ERA).
VISIONAIR allows researches into Scientific Visualization, Ultra High Definition Networks, Virtual Reality, and Augmented Collaborative Environments. VISIONAIR expects high level research inside these fields and enables new research perspectives. This paper presents the aims of VISIONAIR and analyzes some challenges and opportunities open by such an infrastructure.
Modal Modeling of Micro-Machining Center
Authors: Chodźko Marcin , Marchelek Krzysztof 
Published: December 2013

Modeling of dynamic properties of machine tools has a significant influence on improvement of its construction. This process is extremely important when a new construction of machine tool is under development. Experimental modal analysis provides information about frequency bandwidths with significant amplitudes of resonances, damping values and mode shapes. This information can be used in FEM model updating, stability prediction or finding weak elements of the machine tool structure as well.
In the paper the modal model of prototype of the micro machining center is presented. Polymax algorithm was used to estimate the poles (frequency, damping) of modal model and modal shapes. Modal model was built on the basis of the impact test results. Methodology of conducted experimental test is presented. Tested machine tool was made of different materials (steel, aluminum, stone and others) which causes difficulties during experimental investigations. In the construction different types of guideways were implemented — rolling, slide and pneumatic ones. Maximum rotational speed of the tool is about 100 000 rev/min, so the frequency range where poles of modal model are estimated is wide (high frequencies of excitation during machining). Weight of sensors used during testing is an important issue due to a low mass of the structure. Also the excitation of the structure is troublesome because of vulnerability of precise guideways and forces sensors used in machine tool construction.
Validation of the modal model is also presented in the paper and practical problems of modal testing are discussed.
Exposure of Escherichia coli ATCC 12806 to Sublethal Concentrations of Food-Grade Biocides Influences Its Ability To Form Biofilm, Resistance to Antimicrobials, and Ultrastructure
Authors: Capita Rosa , Riesco-Peláez Félix , Alonso-Hernando Alicia , Alonso-Calleja Carlos 
Published: December 2013

ABSTRACT

Escherichia coli
ATCC 12806 was exposed to increasing subinhibitory concentrations of three biocides widely used in food industry facilities: trisodium phosphate (TSP), sodium nitrite (SNI), and sodium hypochlorite (SHY). The cultures exhibited an acquired tolerance to biocides (especially to SNI and SHY) after exposure to such compounds.
E. coli
produced biofilms (as observed by confocal laser scanning microscopy) on polystyrene microtiter plates. Previous adaptation to SNI or SHY enhanced the formation of biofilms (with an increase in biovolume and surface coverage) both in the absence and in the presence (MIC/2) of such compounds. TSP reduced the ability of
E. coli
to produce biofilms. The concentration of suspended cells in the culture broth in contact with the polystyrene surfaces did not influence the biofilm structure. The increase in cell surface hydrophobicity (assessed by a test of microbial adhesion to solvents) after contact with SNI or SHY appeared to be associated with a strong capacity to form biofilms. Cultures exposed to biocides displayed a stable reduced susceptibility to a range of antibiotics (mainly aminoglycosides, cephalosporins, and quinolones) compared with cultures that were not exposed. SNI caused the greatest increase in resistances (14 antibiotics [48.3% of the total tested]) compared with TSP (1 antibiotic [3.4%]) and SHY (3 antibiotics [10.3%]). Adaptation to SHY involved changes in cell morphology (as observed by scanning electron microscopy) and ultrastructure (as observed by transmission electron microscopy) which allowed this bacterium to persist in the presence of severe SHY challenges. The findings of the present study suggest that the use of biocides at subinhibitory concentrations could represent a public health risk.
High Salinity Alters the Germination Behavior of Bacillus subtilis Spores with Nutrient and Nonnutrient Germinants
Authors: Nagler Katja , Setlow Peter , Li Yong-Qing , Moeller Ralf 
Published: December 2013

ABSTRACT

The effect of high NaCl concentrations on nutrient and nonnutrient germination of
Bacillus subtilis
spores was systematically investigated. Under all conditions, increasing NaCl concentrations caused increasing, albeit reversible, inhibition of germination. High salinity delayed and increased the heterogeneity of germination initiation, slowed the germination kinetics of individual spores and the whole spore population, and decreased the overall germination efficiency, as observed by a variety of different analytical techniques. Germination triggered by nutrients which interact with different germinant receptors (GRs) was affected differently by NaCl, suggesting that GRs are targets of NaCl inhibition. However, NaCl also inhibited GR-independent germination, suggesting that there is at least one additional target for NaCl inhibition. Strikingly, a portion of the spore population could initiate germination with
l
-alanine even at NaCl concentrations near saturation (∼5.4 M), suggesting that spores lack a salt-sensing system preventing them from germinating in a hostile high-salinity environment. Spores that initiated germination at very high NaCl concentrations excreted their large depot of Ca
2+
-pyridine-2,6-dicarboxylic acid and lost their heat resistance, but they remained in a phase-gray state in the phase-contrast microscope, suggesting that there was incomplete germination. However, some metabolic activity could be detected at up to 4.8 M NaCl. Overall, high salinity seems to exert complex effects on spore germination and outgrowth whose detailed elucidation in future investigations could give valuable insights on these processes in general.
Mechanism for Stabilizing mRNAs Involved in Methanol-Dependent Methanogenesis of Cold-Adaptive Methanosarcina mazei zm-15
Authors: Cao Yi , Li Jie , Jiang Na , Dong Xiuzhu 
Published: December 2013

ABSTRACT

Methylotrophic methanogenesis predominates at low temperatures in the cold Zoige wetland in Tibet. To elucidate the basis of cold-adapted methanogenesis in these habitats,
Methanosarcina mazei
zm-15 was isolated, and the molecular basis of its cold activity was studied. For this strain, aceticlastic methanogenesis was reduced 7.7-fold during growth at 15°C versus 30°C. Methanol-derived methanogenesis decreased only 3-fold under the same conditions, suggesting that it is more cold adaptive. Reverse transcription-quantitative PCR (RT-qPCR) detected <2-fold difference in the transcript abundances of
mtaA1
,
mtaB1
, and
mtaC1
, the methanol methyltransferase (Mta) genes, in 30°C versus 15°C culture, while
ackA
and
pta
mRNAs, encoding acetate kinase (Ack) and phosphotransacetylase (Pta) in aceticlastic methanogenesis, were 4.5- and 6.8-fold higher in 30°C culture than in 15°C culture. The
in vivo
half-lives of
mtaA1
and
mtaC1B1
mRNAs were similar in 30°C and 15°C cultures. However, the
pta-ackA
mRNA half-life was significantly reduced in 15°C culture compared to 30°C culture. Using circularized RNA RT-PCR, large 5′ untranslated regions (UTRs) (270 nucleotides [nt] and 238 nt) were identified for
mtaA1
and
mtaC1B1
mRNAs, while only a 27-nt 5′ UTR was present in the
pta-ackA
transcript. Removal of the 5′ UTRs significantly reduced the
in vitro
half-lives of
mtaA1
and
mtaC1B1
mRNAs. Remarkably, fusion of the
mtaA1
or
mtaC1B1
5′ UTRs to
pta-ackA
mRNA increased its
in vitro
half-life at both 30°C and 15°C. These results demonstrate that the large 5′ UTRs significantly enhance the stability of the mRNAs involved in methanol-derived methanogenesis in the cold-adaptive
M. mazei
zm-15.
Strain Design of Ashbya gossypii for Single-Cell Oil Production
Authors: Ledesma-Amaro Rodrigo , Santos María A. , Jiménez Alberto , Revuelta José Luis 
Published: December 2013

ABSTRACT

Single-cell oil (SCO) represents a sustainable alternative for the oil industry. Accordingly, the identification of microorganisms with either higher lipidogenic ability or novel capacities for the transformation of raw materials constitutes a major challenge for the field of oil biotechnology. With this in mind, here, we were prompted to address the lipidogenic profile of the filamentous hemiascomycete
Ashbya gossypii
, which is currently used for the microbial production of vitamins. We found that
A. gossypii
mostly accumulates unsaturated fatty acids (FAs), with more than 50% of the total FA content corresponding to oleic acid. In addition, we engineered
A. gossypii
strains both lacking the beta-oxidation pathway and also providing ATP-citrate lyase (ACL) activity to block the degradation of FA and to increase the cytosolic acetyl-coenzyme A (CoA) content, respectively. The lipidogenic profile of the newly developed strains demonstrates that the mere elimination of the beta-oxidation pathway in
A. gossypii
triggers a significant increase in lipid accumulation that can reach 70% of cell dry weight. The use of
A. gossypii
as a novel and robust tool for the production of added-value oils is further discussed.
Ecology and Genetic Structure of Zoonotic Anisakis spp. from Adriatic Commercial Fish Species
Authors: Mladineo Ivona , Poljak Vedran 
Published: December 2013

ABSTRACTConsumption of raw or thermally inadequately treated fishery products represents a public health risk, with the possibility of propagation of liveAnisakislarvae, the causative agent of the zoonotic disease anisakidosis, or anisakiasis. We investigated the population dynamics ofAnisakisspp. in commercially important fish—anchovies (Anisakis), sardines (Sardina pilchardus), European hake (Merluccius merluccius), whiting (Merlangius merlangus), chub mackerel (Scomber japonicus), and Atlantic bluefin tuna (Thunnus thynnus)—captured in the main Adriatic Sea fishing ground. We observed a significant difference in the numbers of parasite larvae (1 to 32) in individual hosts and between species, with most fish showing high or very highAnisakispopulation indices. Phylogenetic analysis confirmed that commercial fish in the Adriatic Sea are parasitized byAnisakis pegreffii(95.95%) andAnisakis simplexsensu stricto(4.05%). The genetic structure ofA. pegreffiiin demersal, pelagic, and top predator hosts was unstructured, and the highest frequency of haplotype sharing (n= 10) was between demersal and pelagic fish.
Kinetics and Yields of Pesticide Biodegradation at Low Substrate Concentrations and under Conditions Restricting Assimilable Organic Carbon
Authors: Helbling Damian E. , Hammes Frederik , Egli Thomas , Kohler Hans-Peter E. 
Published: December 2013

ABSTRACT

The fundamentals of growth-linked biodegradation occurring at low substrate concentrations are poorly understood. Substrate utilization kinetics and microbial growth yields are two critically important process parameters that can be influenced by low substrate concentrations. Standard biodegradation tests aimed at measuring these parameters generally ignore the ubiquitous occurrence of assimilable organic carbon (AOC) in experimental systems which can be present at concentrations exceeding the concentration of the target substrate. The occurrence of AOC effectively makes biodegradation assays conducted at low substrate concentrations mixed-substrate assays, which can have profound effects on observed substrate utilization kinetics and microbial growth yields. In this work, we introduce a novel methodology for investigating biodegradation at low concentrations by restricting AOC in our experiments. We modified an existing method designed to measure trace concentrations of AOC in water samples and applied it to systems in which pure bacterial strains were growing on pesticide substrates between 0.01 and 50 mg liter
−1
. We simultaneously measured substrate concentrations by means of high-performance liquid chromatography with UV detection (HPLC-UV) or mass spectrometry (MS) and cell densities by means of flow cytometry. Our data demonstrate that substrate utilization kinetic parameters estimated from high-concentration experiments can be used to predict substrate utilization at low concentrations under AOC-restricted conditions. Further, restricting AOC in our experiments enabled accurate and direct measurement of microbial growth yields at environmentally relevant concentrations for the first time. These are critical measurements for evaluating the degradation potential of natural or engineered remediation systems. Our work provides novel insights into the kinetics of biodegradation processes and growth yields at low substrate concentrations.
Nonredundant Roles for Cytochrome
c
2
and Two High-Potential Iron-Sulfur Proteins in the Photoferrotroph Rhodopseudomonas palustris TIE-1
Authors: Bird Lina J. , Saraiva Ivo H. , Park Shannon , Calçada Eduardo O. , Salgueiro Carlos A. , Nitschke Wolfgang , Louro Ricardo O. , Newman Dianne K. 
Published: December 2013

ABSTRACT

The purple bacterium
Rhodopseudomonas palustris
TIE-1 expresses multiple small high-potential redox proteins during photoautotrophic growth, including two high-potential iron-sulfur proteins (HiPIPs) (PioC and Rpal_4085) and a cytochrome
c
2
. We evaluated the role of these proteins in TIE-1 through genetic, physiological, and biochemical analyses. Deleting the gene encoding cytochrome
c
2
resulted in a loss of photosynthetic ability by TIE-1, indicating that this protein cannot be replaced by either HiPIP in cyclic electron flow. PioC was previously implicated in photoferrotrophy, an unusual form of photosynthesis in which reducing power is provided through ferrous iron oxidation. Using cyclic voltammetry (CV), electron paramagnetic resonance (EPR) spectroscopy, and flash-induced spectrometry, we show that PioC has a midpoint potential of 450 mV, contains all the typical features of a HiPIP, and can reduce the reaction centers of membrane suspensions in a light-dependent manner at a much lower rate than cytochrome
c
2
. These data support the hypothesis that PioC linearly transfers electrons from iron, while cytochrome
c
2
is required for cyclic electron flow. Rpal_4085, despite having spectroscopic characteristics and a reduction potential similar to those of PioC, is unable to reduce the reaction center. Rpal_4085 is upregulated by the divalent metals Fe(II), Ni(II), and Co(II), suggesting that it might play a role in sensing or oxidizing metals in the periplasm. Taken together, our results suggest that these three small electron transfer proteins perform different functions in the cell.
Cell Growth Inhibition upon Deletion of Four Toxin-Antitoxin Loci from the Megaplasmids of Sinorhizobium meliloti
Authors: Milunovic Branislava , diCenzo George C. , Morton Richard A. , Finan Turlough M. 
Published: December 2013

ABSTRACT

Toxin and antitoxin (TA) gene pairs are addiction systems that are present in many microbial genomes.
Sinorhizobium meliloti
is an N
2
-fixing bacterial symbiont of alfalfa and other leguminous plants, and its genome consists of three large replicons, a circular chromosome (3.7 Mb) and the megaplasmids pSymA (1.4 Mb) and pSymB (1.7 Mb).
S. meliloti
carries 211 predicted type II TA genes, each encoding a toxin or an antitoxin. We constructed defined deletion strains that collectively removed the entire pSymA and pSymB megaplasmids except for their
oriV
regions. Of approximately 100 TA genes on pSymA and pSymB, we identified four whose loss was associated with cell death or stasis unless copies of the genes were supplied in
trans
. Orthologs of three of these loci have been characterized in other organisms (
relB/E
[
sma0471/sma0473
],
Fic
[
DOC
] [
sma2105
], and
VapC
[
PIN
] [
orf2230/sma2231
]), and this report contains the first experimental proof that
RES/Xre
(
smb21127/smb21128
) loci can function as a TA system. Transcriptome sequencing (RNA-seq) analysis did not reveal transcriptional differences between the TA systems to account for why deletion of the four “active” systems resulted in cell toxicity. These data suggest that severe cell growth phenotypes result from the loss of a few TA systems and that loss of most TA systems may result in more subtle phenotypes. These four TA systems do not appear to play a direct role in the
S. meliloti
-alfalfa symbiosis, as strains lacking these TA systems had a symbiotic N
2
fixation phenotype that was indistinguishable from the wild type.
Structural Modeling and Physicochemical Characterization Provide Evidence that P66 Forms a β-Barrel in the Borrelia burgdorferi Outer Membrane
Authors: Kenedy Melisha R. , Luthra Amit , Anand Arvind , Dunn Joshua P. , Radolf Justin D. , Akins Darrin R. 
Published: December 2013

ABSTRACT

The
Borrelia burgdorferi
outer membrane (OM) contains numerous surface-exposed lipoproteins but a relatively low density of integral OM proteins (OMPs). Few membrane-spanning OMPs of
B. burgdorferi
have been definitively identified, and none are well characterized structurally. Here, we provide evidence that the borrelial OMP P66, a known adhesin with pore-forming activity, forms a β-barrel in the
B. burgdorferi
OM. Multiple computer-based algorithms predict that P66 forms a β-barrel with either 22 or 24 transmembrane domains. According to our predicted P66 topology, a lysine residue (K487) known to be sensitive to trypsin cleavage is located within a surface-exposed loop. When we aligned the mature P66 amino acid sequences from
B. burgdorferi
and
B. garinii
, we found that K487 was present only in the
B. burgdorferi
P66 protein sequence. When intact cells from each strain were treated with trypsin, only
B. burgdorferi
P66 was trypsin sensitive, indicating that K487 is surface exposed, as predicted. Consistent with this observation, when we inserted a c-Myc tag adjacent to K487 and utilized surface localization immunofluorescence, we detected the loop containing K487 on the surface of
B. burgdorferi
. P66 was examined by both Triton X-114 phase partitioning and circular dichroism, confirming that the protein is amphiphilic and contains extensive (48%) β-sheets, respectively. Moreover, P66 also was able to incorporate into liposomes and form channels in large unilamellar vesicles. Finally, blue native PAGE (BN-PAGE) revealed that under nondenaturing conditions, P66 is found in large complexes of ∼400 kDa and ∼600 kDa. Outer surface lipoprotein A (OspA) and OspB both coimmunoprecipitate with P66, demonstrating that P66 associates with OspA and OspB in
B. burgdorferi
. The combined computer-based structural analyses and supporting physicochemical properties of P66 provide a working model to further examine the porin and integrin-binding activities of this OMP as they relate to
B. burgdorferi
physiology and Lyme disease pathogenesis.
Identification of 3-Sulfinopropionyl Coenzyme A (CoA) Desulfinases within the Acyl-CoA Dehydrogenase Superfamily
Authors: Schürmann Marc , Demming Rebecca Michaela , Krewing Marco , Rose Judith , Wübbeler Jan Hendrik , Steinbüchel Alexander 
Published: December 2013

ABSTRACT

In a previous study, the essential role of 3-sulfinopropionyl coenzyme A (3SP-CoA) desulfinase acyl-CoA dehydrogenase (Acd) in
Advenella mimigardefordensis
strain DPN7
T
(Acd
DPN7
) during degradation of 3,3′-dithiodipropionic acid (DTDP) was elucidated. DTDP is a sulfur-containing precursor substrate for biosynthesis of polythioesters (PTEs). Acd
DPN7
showed high amino acid sequence similarity to acyl-CoA dehydrogenases but was unable to catalyze a dehydrogenation reaction. Hence, it was investigated in the present study whether 3SP-CoA desulfinase activity is an uncommon or a widespread property within the acyl-CoA dehydrogenase superfamily. Therefore, proteins of the acyl-CoA dehydrogenase superfamily from
Advenella kashmirensis
WT001,
Bacillus cereus
DSM31,
Cupriavidus necator
N-1,
Escherichia coli
BL21,
Pseudomonas putida
KT2440,
Burkholderia xenovorans
LB400,
Ralstonia eutropha
H16,
Variovorax paradoxus
B4,
Variovorax paradoxus
S110, and
Variovorax paradoxus
TBEA6 were expressed in
E. coli
strains. All purified acyl-CoA dehydrogenases appeared as homotetramers, as revealed by size exclusion chromatography. Acd
S110
, Acd
B4
, Acd
H16
, and Acd
KT2440
were able to dehydrogenate isobutyryl-CoA. Acd
KT2440
additionally dehydrogenated butyryl-CoA and valeryl-CoA, whereas Acd
DSM31
dehydrogenated only butyryl-CoA and valeryl-CoA. No dehydrogenation reactions were observed with propionyl-CoA, isovaleryl-CoA, succinyl-CoA, and glutaryl-CoA for any of the investigated acyl-CoA dehydrogenases. Only Acd
TBEA6
, Acd
N-1
, and Acd
LB400
desulfinated 3SP-CoA and were thus identified as 3SP-CoA desulfinases within the acyl-CoA dehydrogenase family, although none of these three Acds dehydrogenated any of the tested acyl-CoA thioesters. No appropriate substrates were identified for Acd
BL21
and Acd
WT001
. Spectrophotometric assays provided apparent

K
m

and
V
max
values for active substrates and indicated the applicability of phylogenetic analyses to predict the substrate range of uncharacterized acyl-CoA dehydrogenases. Furthermore,
C. necator
N-1 was found to utilize 3SP as the sole source of carbon and energy.
Regulation of the Response Regulator Gene
degU
through the Binding of SinR/SlrR and Exclusion of SinR/SlrR by DegU in Bacillus subtilis
Authors: Ogura Mitsuo , Yoshikawa Hirofumi , Chibazakura Taku 
Published: December 2013

ABSTRACT

Bacillus subtilis
DegU is a response regulator of the DegS-DegU two-component regulatory system. Phosphorylated DegU (DegU-P) controls many genes and biological processes, such as exoprotease and γ-polyglutamic acid production, in addition to the
degU
gene, by binding to target gene promoters. Nonphosphorylated DegU and low levels of DegU-P are required for swarming motility and genetic competence. The DNA-binding repressors SinR and SlrR are part of a double-negative feedback loop and comprise the epigenetic switch governing biofilm formation. In this study, we found that SinR repressed
degU
. Furthermore, SlrR, which interacts with SinR through protein-protein interaction, seems to have an active role in
degU
expression in
in vivo lacZ
analysis. An
in vitro
transcription assay supported this observation. An electrophoretic mobility shift assay (EMSA) showed that SinR bound to the
degU
promoter and that SlrR formed a complex with SinR on the
degU
promoter. In EMSA, DegU-P excluded the SinR/SlrR complex but not SinR from the
degU
promoter in the presence of RNA polymerase. These findings suggest that DegU-P interacts with SlrR. In support of this hypothesis, disruption of the
slrR
gene resulted in decreased
degU
expression. This newly identified regulatory mechanism for
degU
is considered to be sequential transcription factor replacement.