bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermosolutal Natural Convection in Partially Porous Domains
Authors: Gobin Dominique , Goyeau Benoiˆt
Published: March 2011

In many industrial processes or natural phenomena coupled heat and mass transfer and fluid flow take place in configurations combining a clear fluid and a porous medium. Since the pioneering work by Beavers and Joseph (1967), the modelling of such systems has been a controversial issue, essentially due to the description of the interface between the fluid and the porous domains. The validity of the so-called one-domain approach — more intuitive and numerically simpler to implement — compared to a two-domain description where the interface is explicitly accounted for, is now clearly assessed. This paper reports recent developments and the current state of the art on this topic, concerning the numerical simulation of such flows as well as the stability studies. The continuity of the conservation equations between a fluid and a porous medium are examined and the conditions for a correct handling of the discontinuity of the macroscopic properties are analyzed. A particular class of problems dealing with thermal and double diffusive natural convection mechanisms in partially porous enclosures is presented, and it is shown that this configuration exhibits specific features in terms of the heat and mass transfer characteristics, depending on the properties of the porous domain. From the viewpoint of the stability of convection in a horizontal layer where a fluid layer lies on top of a porous medium, the analysis shows that the onset of convection is strongly influenced by the presence of the porous medium. The case of thermal convection is fully detailed and many open problems arise in the field of double diffusive convection.
Steam Jet Condensation in a Pool: From Fundamental Understanding to Engineering Scale Analysis
Authors: Song Chul-Hwa
Published: March 2011

The phenomena of direct contact condensation (DCC) of steam jet submerged into a water pool occurs due to the actuation of steam discharging devices in many industrial processes and there are practically two kinds of technical concerns to consider. The one is a concern on the thermal mixing in water pool. The other concern is on thermo-hydraulically induced mechanical loads on the structures of relevant systems. Both concerns may be inter-related with each other in terms of thermally-induced hydrodynamic loads on the relevant system. There are two kinds of viewpoints in terms of DCC-induced thermal mixing in a pool: the local hot spot, which may affect the stability of condensation phenomena, and the thermal stratification, which usually exists over the whole pool region. Both aspects can be well described only if the local behaviour of condensing steam jet and the resultant turbulent jet in a pool are well understood. In this paper, the DCC-related thermo-fluid dynamic features are discussed, based mainly on our experiences of developing the relevant engineering systems over the past years. Fundamental characteristics of condensing steam jets are discussed, including the local behaviour of condensing jets and the resultant turbulent jet to importantly affect the macroscopic circulation in a pool. Then the local analysis of condensing jet behaviour and the global analysis of thermal mixing in a pool are discussed with practical application to engineering in mind.
From Megawatt to Gigawatt: New Developments in Concentrating Solar Thermal Power
Authors: Mu¨ller-Steinhagen Hans
Published: March 2011

On October 30th 2009, a major industrial consortium initiated the so-called DESERTEC project which aims at providing by 2050 15% of the European electricity from renewable energy sources in North Africa, while at the same time securing energy, water, income and employment for this region. In the heart of this concept are solar thermal power plants which can provide affordable, reliable and dispatchable electricity. While this technology has been known for about 100 years, new developments and market introduction programs have recently triggered world-wide activities leading to the present project pipeline of 8.5 GW and 42 billion Euro. To become competitive with mid-load electricity from conventional power plants within the next 10–15 years, mass production of components, increased plant size and planning/operating experience will be accompanied by technological innovations which are presently in the development or even demonstration stage. The scale of construction, the high temperatures and the naturally transient operation provide formidable challenges for academic and industrial R&D. Experimental and theoretical research involving all mechanisms of heat transfer and fluid flow is required together with large-scale demonstration to resolve the combined challenges of performance and cost.
Optimizing Thomson’s jumping ring
Authors: Tjossem Paul J. H. , Brost Elizabeth C.
Published: March 2011

The height to which rings will jump in a Thomson jumping ring apparatus is the central question posed by this popular lecture demonstration. We develop a simple time-averaged inductive-phase-lag model for the dependence of the jump height on the ring material, its mass, and temperature and apply it to measurements of the jump height for a set of rings made by slicing copper and aluminum alloy pipe into varying lengths. The data confirm a peak jump height that grows, narrows, and shifts to smaller optimal mass when the rings are cooled to 77 K. The model explains the ratio of the cooled/warm jump heights for a given ring, the reduction in optimal mass as the ring is cooled, and the shape of the mass resonance. The ring that jumps the highest is found to have a characteristic resistance equal to the inductive reactance of the set of rings.
System-Wide Temporal Characterization of the Proteome and Phosphoproteome of Human Embryonic Stem Cell Differentiation
Authors: Rigbolt Kristoffer T. G. , Prokhorova Tatyana A. , Akimov Vyacheslav , Henningsen Jeanette , Johansen Pia T. , Kratchmarova Irina , Kassem Moustapha , Mann Matthias , Olsen Jesper V. , Blagoev Blagoy
Published: March 2011

Dynamic phosphorylation during stem cell differentiation may control recruitment of DNA methyltransferases to silence genes that maintain pluripotency.
Vancomycin Dosing in Critically Ill Patients: Robust Methods for Improved Continuous-Infusion Regimens
Authors: Roberts Jason A. , Taccone Fabio Silvio , Udy Andrew A. , Vincent Jean-Louis , Jacobs Frédérique , Lipman Jeffrey
Published: March 2011

Despite the development of novel antibiotics active against Gram-positive bacteria, vancomycin generally remains the first treatment, although rapidly achieving concentrations associated with maximal efficacy provides an unresolved challenge. The objective of this study was to conduct a population pharmacokinetic analysis of vancomycin in a large population of critically ill patients. This was a retrospective data collection of 206 adult septic critically ill patients who were administered vancomycin as a loading dose followed by continuous infusion. The concentration-versus-time data for vancomycin in serum was analyzed by a nonlinear mixed-effects modeling approach using NONMEM. Monte Carlo simulations were performed using the final covariate model. We found that the best population pharmacokinetic model consisted of a one-compartment linear model with combined proportional and additive residual unknown variability. The volume of distribution of vancomycin (1.5 liters/kg) was described by total body weight and clearance (4.6 liters/h) by 24-hour urinary creatinine clearance (CrCl), normalized to body surface area. Simulation data showed that a 35-mg/kg loading dose was necessary to rapidly achieve vancomycin concentrations of 20 mg/liter. Daily vancomycin requirements were dependent on CrCl, such that a patient with a CrCl of 100 ml/min/1.73 m
2
would require at least 35 mg/kg per day by continuous infusion to maintain target concentrations. In conclusion, we have found that higher-than-recommended loading and daily doses of vancomycin seem to be necessary to rapidly achieve therapeutic serum concentrations in these patients.
Are the Soft, Liquid-Like Structures Detected around Bacteria by Ambient Dynamic Atomic Force Microscopy Capsules?
Authors: Méndez-Vilas A. , Labajos-Broncano L. , Perera-Núñez J. , González-Martín M. L.
Published: March 2011

High-resolution imaging of bacterial capsules by microscopy is of paramount importance in microbiology due to their role in pathogenesis. This is, however, quite a challenging task due to their delicate nature. In this context, recent reports have claimed successful exploitation of the capacity of atomic force microscopy (AFM) for imaging of extremely deformable (even liquid) surfaces under ambient conditions to detect bacterial capsules in the form of tiny amounts of liquid-like substances around bacteria. In order to further explore this supposed capacity of AFM, in this work, three staphylococcal strains have been scrutinized for the presence of capsules using such an AFM-based approach with a phosphate buffer and water as the suspending liquids. Similar results were obtained with the three strains. AFM showed the presence of liquid-like substances identical to those attributed to bacterial capsules in the previous literature. Extensive imaging and chemical analysis point out the central role of the suspending liquid (buffer) in the formation of these substances. The phenomenon has been reproduced even by using nonliving particles, a finding that refutes the biological origin of the liquid-like substances visualized around the cells. Deliquescence of major components of biological buffers, such as K
2
HPO
4
, CaCl
2
, or HEPES, is proposed as the fundamental mechanism of the formation of these ultrasmall liquid-like structures. Such an origin could explain the high similarity of our results obtained with three very different strains and also the high similarity of these results to others reported in the literature based on other bacteria and suspending liquids. Finally, possible biological/biomedical implications of the presence of these ultrasmall amounts of liquids wrapping microorganisms are discussed.
Moist-Heat Resistance, Spore Aging, and Superdormancy in Clostridium difficile
Authors: Rodriguez-Palacios Alexander , LeJeune Jeffrey T.
Published: March 2011

Clostridium difficile
spores can survive extended heating at 71°C (160°F), a minimum temperature commonly recommended for adequate cooking of meats. To determine the extent to which higher temperatures would be more effective at killing
C. difficile
, we quantified (
D
values) the effect of moist heat at 85°C (145°F, for 0 to 30 min) on
C. difficile
spores and compared it to the effects at 71 and 63°C. Fresh (1-week-old) and aged (≥20-week-old)
C. difficile
spores from food and food animals were tested in multiple experiments. Heating at 85°C markedly reduced spore recovery in all experiments (5 to 6 log
10
within 15 min of heating;
P
< 0.001), regardless of spore age. In ground beef, the inhibitory effect of 85°C was also reproducible (
P
< 0.001), but heating at 96°C reduced 6 log
10
within 1 to 2 min. Mechanistically, optical density and enumeration experiments indicated that 85°C inhibits cell division but not germination, but the inhibitory effect was reversible in some spores. Heating at 63°C reduced counts for fresh spores (1 log
10
, 30 min;
P
< 0.04) but increased counts of 20-week-old spores by 30% (15 min;
P
< 0.02), indicating that sublethal heat treatment reactivates superdormant spores. Superdormancy is an increasingly recognized characteristic in
Bacillus
spp., and it is likely to occur in
C. difficile
as spores age. The potential for reactivation of (super)dormant spores with sublethal temperatures may be a food safety concern, but it also has potential diagnostic value. Ensuring that food is heated to >85°C would be a simple and important intervention to reduce the risk of inadvertent ingestion of
C. difficile
spores.
Versatile Enzyme Expression and Characterization System for Aspergillus nidulans, with the Penicillium brevicompactum Polyketide Synthase Gene from the Mycophenolic Acid Gene Cluster as a Test Case
Authors: Hansen Bjarne G. , Salomonsen Bo , Nielsen Morten T. , Nielsen Jakob B. , Hansen Niels B. , Nielsen Kristian F. , Regueira Torsten B. , Nielsen Jens , Patil Kiran R. , Mortensen Uffe H.
Published: March 2011

Assigning functions to newly discovered genes constitutes one of the major challenges en route to fully exploiting the data becoming available from the genome sequencing initiatives. Heterologous expression in an appropriate host is central in functional genomics studies. In this context, filamentous fungi offer many advantages over bacterial and yeast systems. To facilitate the use of filamentous fungi in functional genomics, we present a versatile cloning system that allows a gene of interest to be expressed from a defined genomic location of
Aspergillus nidulans
. By a single USER cloning step, genes are easily inserted into a combined targeting-expression cassette ready for rapid integration and analysis. The system comprises a vector set that allows genes to be expressed either from the constitutive PgpdA promoter or from the inducible PalcA promoter. Moreover, by using the vector set, protein variants can easily be made and expressed from the same locus, which is mandatory for proper comparative analyses. Lastly, all individual elements of the vectors can easily be substituted for other similar elements, ensuring the flexibility of the system. We have demonstrated the potential of the system by transferring the 7,745-bp large
mpaC
gene from
Penicillium brevicompactum
to
A. nidulans
. In parallel, we produced defined mutant derivatives of
mpaC
, and the combined analysis of
A. nidulans
strains expressing
mpaC
or mutated
mpaC
genes unequivocally demonstrated that
mpaC
indeed encodes a polyketide synthase that produces the first intermediate in the production of the medically important immunosuppressant mycophenolic acid.
Solute Transport Proteins and the Outer Membrane Protein NmpC Contribute to Heat Resistance of Escherichia coli AW1.7
Authors: Ruan Lifang , Pleitner Aaron , Gänzle Michael G. , McMullen Lynn M.
Published: March 2011

This study aimed to elucidate determinants of heat resistance in
Escherichia coli
by comparing the composition of membrane lipids, as well as gene expression, in heat-resistant
E. coli
AW1.7 and heat-sensitive
E. coli
GGG10 with or without heat shock. The survival of
E. coli
AW1.7 at late exponential phase was 100-fold higher than that of
E. coli
GGG10 after incubation at 60°C for 15 min. The cytoplasmic membrane of
E. coli
AW1.7 contained a higher proportion of saturated and cyclopropane fatty acids than that of
E. coli
GGG10. Microarray hybridization of cDNA libraries obtained from exponentially growing or heat-shocked cultures was performed to compare gene expression in these two strains. Expression of selected genes from different functional groups was quantified by quantitative PCR. DnaK and 30S and 50S ribosomal subunits were overexpressed in
E. coli
GGG10 relative to
E. coli
AW1.7 upon heat shock at 50°C, indicating improved ribosome stability. The outer membrane porin NmpC and several transport proteins were overexpressed in exponentially growing
E. coli
AW1.7. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of membrane properties confirmed that NmpC is present in the outer membrane of
E. coli
AW1.7 but not in that of
E. coli
GGG10. Expression of NmpC in
E. coli
GGG10 increased survival at 60°C 50- to 1,000-fold. In conclusion, the outer membrane porin NmpC contributes to heat resistance in
E. coli
AW1.7, but the heat resistance of this strain is dependent on additional factors, which likely include the composition of membrane lipids, as well as solute transport proteins.
Multiple DNA Extractions Coupled with Stable-Isotope Probing of Anthracene-Degrading Bacteria in Contaminated Soil
Authors: Jones Maiysha D. , Singleton David R. , Sun Wei , Aitken Michael D.
Published: March 2011

In many of the DNA-based stable-isotope probing (SIP) studies published to date in which soil communities were investigated, a single DNA extraction was performed on the soil sample, usually using a commercial DNA extraction kit, prior to recovering the13C-labeled (heavy) DNA by density-gradient ultracentrifugation. Recent evidence suggests, however, that a single extraction of a soil sample may not lead to representative recovery of DNA from all of the organisms in the sample. To determine whether multiple DNA extractions would affect the DNA yield, the eubacterial 16S rRNA gene copy number, or the identification of anthracene-degrading bacteria, we performed seven successive DNA extractions on the same aliquot of contaminated soil either untreated or enriched with [U-13C]anthracene. Multiple extractions were necessary to maximize the DNA yield and 16S rRNA gene copy number from both untreated and anthracene-enriched soil samples. Sequences within the orderSphingomonadales, but unrelated to any previously described genus, dominated the 16S rRNA gene clone libraries derived from13C-enriched DNA and were designated “anthracene group 1.” Sequences clustering withVariovoraxspp., which were also highly represented, and sequences related to the genusPigmentiphagawere newly associated with anthracene degradation. The bacterial groups collectively identified across all seven extracts were all recovered in the first extract, although quantitative PCR analysis of SIP-identified groups revealed quantitative differences in extraction patterns. These results suggest that performing multiple DNA extractions on soil samples improves the extractable DNA yield and the number of quantifiable eubacterial 16S rRNA gene copies but have little qualitative effect on the identification of the bacterial groups associated with the degradation of a given carbon source by SIP.
Survival of Escherichia coli O157:H7 on Cattle Hides
Authors: Arthur Terrance M. , Nou Xiangwu , Kalchayanand Norasak , Bosilevac Joseph M. , Wheeler Tommy , Koohmaraie Mohammad
Published: March 2011

The objective of this study was to determine the time period that
Escherichia coli
O157:H7 survives on the hides of cattle. Extensive research has been conducted and is ongoing to identify and develop novel preharvest intervention strategies to reduce the presence of
E. coli
O157:H7 on live cattle and subsequent transfer to processed carcasses. If a reduction of
E. coli
O157:H7 levels in feces can be achieved through preharvest intervention, it is not known how long it would take for such reductions to be seen on the hide. In the study presented herein, three trials were conducted to follow
E. coli
O157:H7 hide prevalence over time. For each trial, 36 animals were housed in individual stanchions to minimize or prevent hide contamination events. Through prevalence determination and isolate genotyping with pulsed-field gel electrophoresis, survival of
E. coli
O157:H7 on the hides of live cattle was determined to be short lived, with an approximate duration of 9 days or less. The results of this study suggest that any preharvest interventions that are to be administered at the end of the finishing period will achieve maximum effect in reducing
E. coli
O157:H7 levels on cattle hides if given 9 days before the cattle are presented for processing. However, it should be noted that interventions reducing pathogen shedding would also contribute to decreasing hide contamination through lowering the contamination load of the processing plant lairage environment, regardless of the time of application.
Intra- and Intergenerational Persistence of an Insect Nucleopolyhedrovirus: Adverse Effects of Sublethal Disease on Host Development, Reproduction, and Susceptibility to Superinfection
Authors: Cabodevilla Oihana , Villar Eduardo , Virto Cristina , Murillo Rosa , Williams Trevor , Caballero Primitivo
Published: March 2011

Sublethal infections by
Spodoptera exigua
multiple nucleopolyhedrovirus (SeMNPV) are common in field populations of the beet armyworm (
S. exigua
, Hübner) in the Almerian horticultural region of Spain. Inoculation of second, third, and fourth instars with occlusion bodies (OBs) of an isolate (VT-SeAl1) associated with vertically transmitted infections resulted in 15 to 100% of sublethal infection in adult survivors, as determined by reverse transcription-PCR (RT-PCR) detection of viral DNA polymerase transcripts, and quantitative PCR (qPCR) targeted at the DNA polymerase gene. The prevalence of adult sublethal infection was positively related to the inoculum OB concentration consumed during the larval stage. Sublethal infections persisted in OB-treated insects for at least five generations. Viral transcripts were more frequently detected in adult insects than in third instars. qPCR analysis indicated a consistently higher prevalence of sublethal infection than RT-PCR. Sublethal infection was associated with significant reductions in pupal weight, adult emergence, fecundity, and fertility (egg hatch) and significant increases in larval development time and duration of the preoviposition period. Insects taken from a persistently infected experimental population were significantly more susceptible to the OB inoculum than control insects that originated from the same virus-free colony as the persistently infected insects. We conclude that OB treatment results in rapid establishment of sublethal infections that persist between generations and which incur costs in the development and reproductive capacity of the host insect.
Evaluation of Procedures for the Collection, Processing, and Analysis of Biomolecules from Low-Biomass Surfaces
Authors: Kwan K. , Cooper M. , La Duc M. T. , Vaishampayan P. , Stam C. , Benardini J. N. , Scalzi G. , Moissl-Eichinger C. , Venkateswaran K.
Published: March 2011

To comprehensively assess microbial diversity and abundance via molecular-analysis-based methods, procedures for sample collection, processing, and analysis were evaluated in depth. A model microbial community (MMC) of known composition, representative of a typical low-biomass surface sample, was used to examine the effects of variables in sampling matrices, target cell density/molecule concentration, and cryogenic storage on the overall efficacy of the sampling regimen. The MMC used in this study comprised 11 distinct species of bacterial, archaeal, and fungal lineages associated with either spacecraft or clean-room surfaces. A known cellular density of MMC was deposited onto stainless steel coupons, and after drying, a variety of sampling devices were used to recover cells and biomolecules. The biomolecules and cells/spores recovered from each collection device were assessed by cultivable and microscopic enumeration, and quantitative and species-specific PCR assays. rRNA gene-based quantitative PCR analysis showed that cotton swabs were superior to nylon-flocked swabs for sampling of small surface areas, and for larger surfaces, biological sampling kits significantly outperformed polyester wipes. Species-specific PCR revealed differential recovery of certain species dependent upon the sampling device employed. The results of this study empower current and future molecular-analysis-based microbial sampling and processing methodologies.
Molecular Basis for Mycophenolic Acid Biosynthesis in Penicillium brevicompactum
Authors: Regueira Torsten Bak , Kildegaard Kanchana Rueksomtawin , Hansen Bjarne Gram , Mortensen Uffe H. , Hertweck Christian , Nielsen Jens
Published: March 2011

Mycophenolic acid (MPA) is the active ingredient in the increasingly important immunosuppressive pharmaceuticals CellCept (Roche) and Myfortic (Novartis). Despite the long history of MPA, the molecular basis for its biosynthesis has remained enigmatic. Here we report the discovery of a polyketide synthase (PKS), MpaC, which we successfully characterized and identified as responsible for MPA production in
Penicillium brevicompactum. mpaC
resides in what most likely is a 25-kb gene cluster in the genome of
Penicillium brevicompactum
. The gene cluster was successfully localized by targeting putative resistance genes, in this case an additional copy of the gene encoding IMP dehydrogenase (IMPDH). We report the cloning, sequencing, and the functional characterization of the MPA biosynthesis gene cluster by deletion of the polyketide synthase gene
mpaC
of
P. brevicompactum
and bioinformatic analyses. As expected, the gene deletion completely abolished MPA production as well as production of several other metabolites derived from the MPA biosynthesis pathway of
P. brevicompactum
. Our work sets the stage for engineering the production of MPA and analogues through metabolic engineering.
Driving Forces Enable High-Titer Anaerobic 1-Butanol Synthesis in Escherichia coli
Authors: Shen Claire R. , Lan Ethan I. , Dekishima Yasumasa , Baez Antonino , Cho Kwang Myung , Liao James C.
Published: March 2011

1-Butanol, an important chemical feedstock and advanced biofuel, is produced by
Clostridium
species. Various efforts have been made to transfer the clostridial 1-butanol pathway into other microorganisms. However, in contrast to similar compounds, only limited titers of 1-butanol were attained. In this work, we constructed a modified clostridial 1-butanol pathway in
Escherichia coli
to provide an irreversible reaction catalyzed by
trans
-enoyl-coenzyme A (CoA) reductase (Ter) and created NADH and acetyl-CoA driving forces to direct the flux. We achieved high-titer (30 g/liter) and high-yield (70 to 88% of the theoretical) production of 1-butanol anaerobically, comparable to or exceeding the levels demonstrated by native producers. Without the NADH and acetyl-CoA driving forces, the Ter reaction alone only achieved about 1/10 the level of production. The engineered host platform also enables the selection of essential enzymes with better catalytic efficiency or expression by anaerobic growth rescue. These results demonstrate the importance of driving forces in the efficient production of nonnative products.
Novel Tandem Biotransformation Process for the Biosynthesis of a Novel Compound, 4-(2,3,5,6-Tetramethylpyrazine-1)-4′-Demethylepipodophyllotoxin
Authors: Tang Ya-Jie , Zhao Wei , Li Hong-Mei
Published: March 2011

According to the structure of podophyllotoxin and its structure-function relationship, a novel tandem biotransformation process was developed for the directional modification of the podophyllotoxin structure to directionally synthesize a novel compound, 4-(2,3,5,6-tetramethylpyrazine-1)-4′-demethylepipodophyllotoxin (4-TMP-DMEP). In this novel tandem biotransformation process, the starting substrate of podophyllotoxin was biotransformed into 4′-demethylepipodophyllotoxin (product 1) with the demethylation of the methoxyl group at the 4′ position byGibberella fujikuroiSH-f13, which was screened out from Shennongjia prime forest humus soil (Hubei, China). 4′-Demethylepipodophyllotoxin (product 1) was then biotransformed into 4′-demethylpodophyllotoxone (product 2) with the oxidation of the hydroxyl group at the 4 position byAlternaria alternataS-f6, which was screened out from the gatheredDysosma versipellisplants in the Wuhan Botanical Garden, Chinese Academy of Sciences. Finally, 4′-demethylpodophyllotoxone (product 2) and ligustrazine were linked with a transamination reaction to synthesize the target product 4-TMP-DMEP (product 3) byAlternaria alternataS-f6. Compared with podophyllotoxin (i.e., a 50% effective concentration [EC50] of 529 μM), the EC50of 4-TMP-DMEP against the tumor cell line BGC-823 (i.e., 0.11 μM) was significantly reduced by 5,199 times. Simultaneously, the EC50of 4-TMP-DMEP against the normal human proximal tubular epithelial cell line HK-2 (i.e., 0.40 μM) was 66 times higher than that of podophyllotoxin (i.e., 0.006 μM). Furthermore, compared with podophyllotoxin (i.e., logP= 0.34), the water solubility of 4-TMP-DMEP (i.e., logP= 0.66) was significantly enhanced by 94%. For the first time, the novel compound 4-TMP-DMEP with superior antitumor activity was directionally synthesized from podophyllotoxin by the novel tandem biotransformation process developed in this work.
Orthologues of the Anaphase-Promoting Complex/Cyclosome Coactivators Cdc20p and Cdh1p Are Important for Mitotic Progression and Morphogenesis in Candida albicans
Authors: Chou Hsini , Glory Amandeep , Bachewich Catherine
Published: March 2011

The conserved anaphase-promoting complex/cyclosome (APC/C) system mediates protein degradation during mitotic progression. Conserved coactivators Cdc20p and Cdh1p regulate the APC/C during early to late mitosis and G
1
phase.
Candida albicans
is an important fungal pathogen of humans, and it forms highly polarized cells when mitosis is blocked through depletion of the polo-like kinase Cdc5p or other treatments. However, the mechanisms governing mitotic progression and associated polarized growth in the pathogen are poorly understood. In order to gain insights into these processes, we characterized
C. albicans
orthologues of Cdc20p and Cdh1p. Cdc20p-depleted cells were blocked in early or late mitosis with elevated levels of Cdc5p and the mitotic cyclin Clb2p, suggesting that Cdc20p is essential and has some conserved functions during mitosis. However, the yeast cells formed highly polarized buds in contrast to the large doublets of
S. cerevisiae
cdc20
mutants, implying a distinct role in morphogenesis. In comparison,
cdh1Δ/cdh1Δ
cells were viable but showed enrichment of Clb2p and Cdc5p, suggesting that Cdh1p may influence mitotic exit. The
cdh1Δ/cdh1Δ
phenotype was pleiotropic, consisting of normal or enlarged yeast, pseudohyphae, and some elongated buds, whereas
S. cerevisiae
cdh1Δ
yeast cells were reduced in size. Thus,
C. albicans
Cdh1p may have some distinct functions. Finally, absence of Cdh1p or Cdc20p had a minor or no effect on hyphal development, respectively. Overall, the results suggest that Cdc20p and Cdh1p may be APC/C activators that are important for mitosis but also morphogenesis in
C. albicans
. Their novel features imply additional variations in function and underscore rewiring in the emerging mitotic regulatory networks of the pathogen.
Staphylococcus epidermidis Uses Distinct Mechanisms of Biofilm Formation To Interfere with Phagocytosis and Activation of Mouse Macrophage-Like Cells 774A.1
Authors: Schommer Nina N. , Christner Martin , Hentschke Moritz , Ruckdeschel Klaus , Aepfelbacher Martin , Rohde Holger
Published: March 2011

Assembly of adherent biofilms is the key mechanism involved in
Staphylococcus epidermidis
virulence during device-associated infections. Aside from polysaccharide intercellular adhesin (PIA), the accumulation-associated protein Aap and the extracellular matrix binding protein Embp act as intercellular adhesins, mediating
S. epidermidis
cell aggregation and biofilm accumulation. The aim of this study was to investigate structural features of PIA-, Aap-, and Embp-mediated
S. epidermidis
biofilms in more detail and to evaluate their specific contributions to biofilm-related
S. epidermidis
immune escape. PIA-, Embp-, and Aap-mediated biofilms exhibited substantial morphological differences. Basically, PIA synthesis induced formation of macroscopically visible, rough cell clusters, whereas Aap- and Embp-dependent biofilms preferentially displayed a smooth layer of aggregated bacteria. On the microscopic level, PIA was found to form a string-like organized extracellular matrix connecting the bacteria, while Embp produced small deposits of intercellular matrix and Aap was strictly localized to the bacterial surface. Despite marked differences,
S. epidermidis
strains using PIA, Aap, or Embp for biofilm formation were protected from uptake by J774A.1 macrophages, with similarly efficiencies. In addition, compared to biofilm-negative
S. epidermidis
strains, isogenic biofilm-forming
S. epidermidis
induced only a diminished inflammatory J774A.1 macrophage response, leading to significantly (88.2 to 88.7%) reduced NF-κB activation and 68.8 to 83% reduced interleukin-1β (IL-1β) production. Mechanical biofilm dispersal partially restored induction of NF-κB activation, although bacterial cell surfaces remained decorated with the respective intercellular adhesins. Our results demonstrate that distinct
S. epidermidis
biofilm morphotypes are similarly effective at protecting
S. epidermidis
from phagocytic uptake and at counteracting macrophage activation, providing novel insights into mechanisms that could contribute to the chronic and persistent course of biofilm-related
S. epidermidis
foreign material infections.
Genome Sequences of Two Staphylococcus aureus Ovine Strains That Induce Severe (Strain O11) and Mild (Strain O46) Mastitis
Authors: Le Maréchal Caroline , Hernandez David , Schrenzel Jacques , Even Sergine , Berkova Nadia , Thiéry Richard , Vautor Eric , Fitzgerald J. Ross , François Patrice , Le Loir Yves
Published: March 2011

Staphylococcus aureus
is a major etiological agent of mastitis in ruminants. We report here the genome sequences of two ovine strains that were isolated from gangrenous (strain O11) and subclinical (strain O46) ewe mastitis. Both strains belong to the same clonal complex. Despite this close genotypic relationship, the two isolates were shown to reproducibly induce highly divergent types of infections, either severe (O11) or mild (O46) mastitis, in an experimental ewe model.
The
spoIIE
Homolog of Epulopiscium sp. Type B Is Expressed Early in Intracellular Offspring Development
Authors: Miller David A. , Choat John Howard , Clements Kendall D. , Angert Esther R.
Published: March 2011

Epulopiscium
sp. type B is an enormous intestinal symbiont of the surgeonfish
Naso tonganus
. Intracellular offspring production in
Epulopiscium
shares features with endospore formation. Here, we characterize the
spoIIE
homolog in
Epulopiscium
. The timing of
spoIIE
gene expression and presence of interacting partners suggest that the activation of σ
F
occurs early in
Epulopiscium
offspring development.
Cadaverine Covalently Linked to the Peptidoglycan Serves as the Correct Constituent for the Anchoring Mechanism between the Outer Membrane and Peptidoglycan in Selenomonas ruminantium
Authors: Kojima Seiji , Kaneko Jun , Abe Naoki , Takatsuka Yumiko , Kamio Yoshiyuki
Published: March 2011

In
Selenomonas ruminantium
, a strictly anaerobic and Gram-negative bacterium, cadaverine covalently linked to the peptidoglycan is required for the interaction between the peptidoglycan and the S-layer homologous (SLH) domain of the major outer membrane protein Mep45. Here, using a series of diamines with a general structure of NH
3
+
(CH
2
)

n

NH
3
+
(
n
= 3 to 6), we found that cadaverine (
n
= 5) specifically serves as the most efficient constituent of the peptidoglycan in acquiring the high resistance of the cell to external damage agents and is required for effective interaction between the SLH domain of Mep45 and the peptidoglycan, facilitating the correct anchoring of the outer membrane to the peptidoglycan.
Multilocus Sequence-Based Analysis Delineates a Clonal Population of Agrobacterium (Rhizobium) radiobacter (Agrobacterium tumefaciens) of Human Origin
Authors: Aujoulat Fabien , Jumas-Bilak Estelle , Masnou Agnès , Sallé Fanny , Faure Denis , Segonds Christine , Marchandin Hélène , Teyssier Corinne
Published: March 2011

The genus
Agrobacterium
includes plant-associated bacteria and opportunistic human pathogens. Taxonomy and nomenclature within the genus remain controversial. In particular, isolates of human origin were all affiliated with the species
Agrobacterium
(
Rhizobium
)
radiobacter
, while phytopathogenic strains were designated under the synonym denomination
Agrobacterium tumefaciens
. In order to study the relative distribution of
Agrobacterium
strains according to their origins, we performed a multilocus sequence-based analysis (MLSA) on a large collection of 89 clinical and environmental strains from various origins. We proposed an MLSA scheme based on the partial sequence of 7 housekeeping genes (
atpD
,
zwf
,
trpE
,
groEL
,
dnaK
,
glnA
, and
rpoB
) present on the circular chromosome of
A. tumefaciens
C58. Multilocus phylogeny revealed that 88% of the clinical strains belong to genovar A7, which formed a homogeneous population with linkage disequilibrium, suggesting a low rate of recombination. Comparison of genomic fingerprints obtained by pulsed-field gel electrophoresis (PFGE) showed that the strains of genovar A7 were epidemiologically unrelated. We present genetic evidence that genovar A7 may constitute a human-associated population distinct from the environmental population. Also, phenotypic characteristics, such as culture at 42°C, agree with this statement. This human-associated population might represent a potential novel species in the genus
Agrobacterium
.
Germination of Individual Bacillus subtilis Spores with Alterations in the GerD and SpoVA Proteins, Which Are Important in Spore Germination
Authors: Wang Guiwen , Yi Xuan , Li Yong-qing , Setlow Peter
Published: March 2011

Release of Ca
2+
with dipicolinic acid (CaDPA) was monitored by Raman spectroscopy and differential interference contrast microscopy during germination of individual spores of
Bacillus subtilis
strains with alterations in GerD and SpoVA proteins. Notable conclusions about germination after the addition of nutrient were as follows. (i) Following
l
-alanine addition, wild-type and
gerD
spores and spores with elevated SpoVA protein levels (↑SpoVA spores) slowly released ∼10% of their CaDPA during a variable (6- to 55-min) period ending at
T
lag
, the time when faster CaDPA release began. (ii)
T
lag
times were lower for ↑SpoVA spores than for wild-type spores and were higher for
gerD
spores. (iii) The long
T
lag
times of
gerD
spores were partially due to slow commitment to germinate. (iv) The intervals between the commitment to germinate and CaDPA release were similar for wild-type and ↑SpoVA spores but longer for
gerD
spores. (v) The times for rapid CaDPA release, Δ
T
release
=
T
release
−
T
lag
(with
T
release
being the time at which CaDPA release was complete), were similar for wild-type,
gerD
, and ↑SpoVA spores. (vi) Spores with either one of two point mutations in the s
poVA
operon (
spoVA
1
and
spoVA
2
spores) exhibited a more rapid rate of CaDPA release beginning immediately after
l
-alanine addition leading to ∼65% CaDPA release prior to
T
lag
. (vii)
T
lag
times for
spoVA
1
and
spoVA
2
spores were longer than for wild-type spores. (viii) The intervals between
spoVA
1
and
spoVA
2
spores' commitment and CaDPA release were similar to those for wild-type spores, but commitment occurred later. In contrast to germination after the addition of nutrient,
T
lag
and Δ
T
release
times were relatively similar during dodecylamine germination of spores of the five strains. These findings suggest the following. (i) GerD plays no role in CaDPA release during spore germination. (ii) SpoVA proteins are involved in CaDPA release during germination with nutrients, and probably with dodecylamine. (iii) Spores release significant CaDPA before commitment. (iv) CaDPA release during
T
lag
and Δ
T
release
may signal subsequent germination events.
Complete Genome Sequence of the Canine Pathogen Staphylococcus pseudintermedius
Authors: Zakour Nouri L. Ben , Bannoehr Jeanette , van den Broek Adri H. M. , Thoday Keith L. , Fitzgerald J. Ross
Published: March 2011

We report the first whole-genome sequence for a clinical isolate of
Staphylococcus pseudintermedius
(ED99), the major pathogen responsible for canine bacterial pyoderma.
S. pseudintermedius
contains numerous mobile genetic elements and encodes an array of putative virulence factors, including superantigenic, cytolytic, and exfoliative toxins and cell wall-associated surface proteins.
Complete Genome Sequence of Lactobacillus helveticus H10
Authors: Zhao Wenjing , Chen Yongfu , Sun Zhihong , Wang Jicheng , Zhou Zhemin , Sun Tiansong , Wang Lei , Chen Wei , Zhang Heping
Published: March 2011

Lactobacillus helveticus
strain H10 was isolated from traditional fermented milk in Tibet, China. We sequenced the whole genome of strain H10 and compared it to the published genome sequence of
Lactobacillus helveticus
DPC4571.
Complete Genome Sequence of the Commensal Enterococcus faecalis 62, Isolated from a Healthy Norwegian Infant
Authors: Brede Dag Anders , Snipen Lars Gustav , Ussery David Wayne , Nederbragt Alexander J. , Nes Ingolf F.
Published: March 2011

The genome of
Enterococcus faecalis
62, a commensal isolate from a healthy Norwegian infant, revealed multiple adaptive traits to the gastrointestinal tract (GIT) environment and the milk-containing diet of breast-fed infants. Adaptation to a commensal existence was emphasized by lactose and other carbohydrate metabolism genes within genomic islands, accompanied by the absence of virulence traits.
Complete Genome Sequence of “Vulcanisaeta moutnovskia” Strain 768-28, a Novel Member of the Hyperthermophilic Crenarchaeal Genus Vulcanisaeta
Authors: Gumerov Vadim M. , Mardanov Andrey V. , Beletsky Alexey V. , Prokofeva Maria I. , Bonch-Osmolovskaya Elizaveta A. , Ravin Nikolai V. , Skryabin Konstantin G.
Published: March 2011

Strain 768-28 was isolated from a hot spring in Kamchatka, Russia, and represents a novel member of the
Vulcanisaeta
genus. The complete genome sequence of this thermoacidophilic anaerobic crenarchaeon reveals genes for protein and carbohydrate-active enzymes, the Embden-Meyerhof and Entner-Doudoroff pathways for glucose metabolism, the tricarboxylic acid cycle, beta-oxidation of fatty acids, and sulfate reduction.
Genome Sequences of Three Acinetobacter baumannii Strains Assigned to the Multilocus Sequence Typing Genotypes ST2, ST25, and ST78
Authors: Zarrilli Raffaele , Giannouli Maria , Rocco Francesco , Loman Nicholas J. , Haines Anthony S. , Constantinidou Chrystala , Pallen Mark J. , Triassi Maria , Di Nocera Pier Paolo
Published: March 2011

Acinetobacter baumannii
is an emerging opportunistic Gram-negative pathogen responsible for hospital-acquired infections.
A. baumannii
epidemics described in Europe and worldwide were caused by a limited number of genotypic clusters of multidrug-resistant strains. Here, we report the availability of draft genome sequences for three multidrug-resistant
A. baumannii
strains assigned to multilocus sequence typing genotypes ST2, ST25, and ST78 that were more frequently isolated during outbreaks occurred in Greece, Italy, Lebanon, and Turkey.
Complete Genome Sequence of Bacillus thuringiensis Serovar finitimus Strain YBT-020
Authors: Zhu Yiguang , Shang Hui , Zhu Qian , Ji Fang , Wang Pengxia , Fu Jingjing , Deng Yun , Xu Chengchen , Ye Weixing , Zheng Jinshui , Zhu Lei , Ruan Lifang , Peng Donghai , Sun Ming
Published: March 2011

Bacillus thuringiensis
is a Gram-positive, spore-forming bacterium that forms parasporal crystals at the onset of the sporulation phase of its growth. Here, we report the complete genome sequence of
B. thuringiensis
serovar finitimus strain YBT-020, whose parasporal crystals consist of Cry26Aa and Cry28Aa crystal proteins and are located between the exosporium and the spore coat and remain adhering to the spore after sporulation.
Genome Sequence of Victivallis vadensis ATCC BAA-548, an Anaerobic Bacterium from the Phylum Lentisphaerae, Isolated from the Human Gastrointestinal Tract
Authors: van Passel Mark W. J. , Kant Ravi , Palva Airi , Lucas Susan , Copeland Alex , Lapidus Alla , Glavina del Rio Tijana , Dalin Eileen , Tice Hope , Bruce David , Goodwin Lynne , Pitluck Sam , Davenport Karen Walston , Sims David , Brettin Thomas S. , Detter John C. , Han Shunsheng , Larimer Frank W. , Land Miriam L. , Hauser Loren , Kyrpides Nikolaos , Ovchinnikova Galina , Richardson P. Paul , de Vos Willem M. , Smidt Hauke , Zoetendal Erwin G.
Published: March 2011

Victivallis vadensis
ATCC BAA-548 represents the first cultured representative from the novel phylum
Lentisphaerae
, a deep-branching bacterial lineage. Few cultured bacteria from this phylum are known, and
V. vadensis
therefore represents an important organism for evolutionary studies.
V. vadensis
is a strictly anaerobic sugar-fermenting isolate from the human gastrointestinal tract.
The Dimer Interface of Agrobacterium tumefaciens VirB8 Is Important for Type IV Secretion System Function, Stability, and Association of VirB2 with the Core Complex
Authors: Sivanesan Durga , Baron Christian
Published: March 2011

Type IV secretion systems are virulence factors used by many Gram-negative bacteria to translocate macromolecules across the cell envelope. VirB8 is an essential inner membrane component of type IV secretion systems, and it is believed to form a homodimer. In the absence of VirB8, the levels of several other VirB proteins were reduced (VirB1, VirB3, VirB4, VirB5, VirB6, VirB7, and VirB11) in
Agrobacterium tumefaciens
, underlining its importance for complex stability. To assess the importance of dimerization, we changed residues at the predicted dimer interface (V97, A100, Q93, and E94) in order to strengthen or to abolish dimerization. We verified the impact of the changes on dimerization
in vitro
with purified V97 variants, followed by analysis of the
in vivo
consequences in a complemented
virB8
deletion strain. Dimer formation was observed
in vivo
after the introduction of a cysteine residue at the predicted interface (V97C), and this variant supported DNA transfer, but the formation of elongated T pili was not detected by the standard pilus isolation technique. Variants with changes at V97 and A100 that weaken dimerization did not support type IV secretion system functions. The T-pilus component VirB2 cofractionated with high-molecular-mass core protein complexes extracted from the membranes, and the presence of VirB8 as well as its dimer interface were important for this association. We conclude that the VirB8 dimer interface is required for T4SS function, for the stabilization of many VirB proteins, and for targeting of VirB2 to the T-pilus assembly site.
Triggered Mycobacterium tuberculosis Heparin-Binding Hemagglutinin Adhesin Folding and Dimerization
Authors: Lomino Joseph V. , Tripathy Ashutosh , Redinbo Matthew R.
Published: March 2011

The heparin-binding hemagglutinin adhesin (HBHA) is a surface adhesin on the human pathogen
Mycobacterium tuberculosis
. Previously, it has been shown that HBHA exists as a dimer in solution. We investigated the detailed nature of this dimer using circular dichroism spectroscopy and analytical ultracentrifugation techniques. We demonstrate that the heparan sulfate (HS) binding region does not play a role in dimerization in solution, while the linker region between the predicted N-terminal coiled-coil and the C-terminal HS binding region does affect dimer stability. The majority of contacts responsible for dimerization, folding, and stability lie within the predicted coiled-coil region of HBHA, while the N-terminal helix preceding the coiled-coil appears to trigger the folding and dimerization of HBHA. Constructs lacking this initial helix or containing site-specific mutations produce nonhelical monomers in solution. Thus, we show that HBHA dimerization and folding are linked and that the N-terminal region of this cell surface adhesin triggers the formation of an HBHA coiled-coil dimer.