bluuebunny/crossref_metadata_2025 huggingface dataset:
The Thermal Design of a Next Generation Data Center: A Conceptual Exposition
Authors: Samadiani Emad , Joshi Yogendra , Mistree Farrokh
Published: November 2008

In the near future, electronic cabinets of data centers will house high performance chips with heat fluxes approaching 100 W/cm2 and associated high volumetric heat generation rates. With the power trends in the electronic cabinets indicating 60 kW cabinets in the near future, the current cooling systems of data centers will be insufficient and new solutions will need to be explored. Accordingly, the key issue that merits investigation is identifying and satisfying the needed specifications of the new thermal solutions, considering the design environment of the next generation data centers. Anchoring our work in the open engineering system paradigm, we identify the requirements of the future thermal solutions and explore various design specifications of an ideally open thermal solution for a next generation data center. To approach an open cooling system for the future data centers, the concept of a thermal solution centered on the multiscale (multilevel) nature of the data centers is discussed. The potential of this solution to be open, along with its theoretical advantages compared with the typical air-cooling solutions, is demonstrated through some scenarios. The realization problems and the future research needs are highlighted to achieve a practical open multiscale thermal solution in data centers. Such solution is believed to be both effective and efficient for the next generation data centers.
Oxygen-Mediated Regulation of Biofilm Development Is Controlled by the Alternative Sigma Factor σ
B
in
Staphylococcus epidermidis
Authors: Cotter John J. , O'Gara James P. , Mack Dietrich , Casey Eoin
Published: November 2008

Using a modified rotating-disk reactor to sparge oxygen to
Staphylococcus epidermidis
cultures, we found that oxygen negatively regulates biofilm development by influencing the activity of σ
B
. Under anaerobic conditions, increased σ
B
activity activates
icaADBC
, which encodes enzymes responsible for polysaccharide intercellular adhesin synthesis, by repressing transcription of the negative regulator
icaR
.
Phylogenetic Relationships of Yessotoxin-Producing Dinoflagellates, Based on the Large Subunit and Internal Transcribed Spacer Ribosomal DNA Domains
Authors: Howard Meredith D. A. , Smith G. Jason , Kudela Raphael M.
Published: November 2008

Yessotoxin (YTX) is a globally distributed marine toxin produced by some isolates of the dinoflagellate speciesProtoceratium reticulatum, Lingulodinium polyedrum, andGonyaulax spiniferawithin the order Gonyaulacales. The process of isolating cells and testing each isolate individually for YTX production during toxic blooms are labor intensive, and this impedes our ability to respond quickly to toxic blooms. In this study, we used molecular sequences from the large subunit and internal transcribed spacer genomic regions in the ribosomal operon of known YTX-producing dinoflagellates to determine if genetic differences exist among geographically distinct populations or between toxic and nontoxic isolates within species. In all analyses, all three YTX-producing species fell within the Gonyaulacales order in agreement with morphological taxonomy. Phylogenetic analyses of available rRNA gene sequences indicate that the capacity for YTX production appears to be confined to the order Gonyaulacales. These findings indicate that Gonyaulacoloid dinoflagellate species are the most likely to produce YTX and thus should be prioritized for YTX screening during events. Dinoflagellate species that fall outside of the Gonyaulacales order are unlikely to produce YTX. Although the rRNA operon offers multiple sequence domains to resolve species level diversification within this dinoflagellate order, these domains are not sufficiently variable to provide robust markers for YTX toxicity.
The Group III Two-Component Histidine Kinase of Filamentous Fungi Is Involved in the Fungicidal Activity of the Bacterial Polyketide Ambruticin
Authors: Dongo Anita , Bataillé-Simoneau Nelly , Campion Claire , Guillemette Thomas , Hamon Bruno , Iacomi-Vasilescu Béatrice , Katz Leonard , Simoneau Philippe
Published: November 2008

We have shown that the plant pathogen
Alternaria brassicicola
exhibited very high susceptibility to ambruticin VS4 and to a lesser extent to the phenylpyrrole fungicide fludioxonil. These compounds are both derived from natural bacterial metabolites with antifungal properties and are thought to exert their toxicity by interfering with osmoregulation in filamentous fungi. Disruption of the osmosensor group III histidine kinase gene Ab
NIK1
(for
A. brassicola
NIK1) resulted in high levels of resistance to ambruticin and fludioxonil, while a mutant isolate characterized by a single-amino-acid substitution in the HAMP domain of the kinase only exhibited moderate resistance. Moreover, the natural resistance of
Saccharomyces cerevisiae
to these antifungal molecules switched to sensitivity in strains expressing AbNIK1p. We also showed that exposure to fludioxonil and ambruticin resulted in abnormal phosphorylation of a Hog1-like mitogen-activated protein kinase (MAPK) in
A. brassicicola
. Parallel experiments carried out with wild-type and mutant isolates of
Neurospora crassa
revealed that, in this species, ambruticin susceptibility was dependent on the OS1-RRG1 branch of the phosphorelay pathway downstream of the OS2 MAPK cascade but independent of the yeast Skn7-like response regulator RRG2. These results show that the ability to synthesize a functional group III histidine kinase is a prerequisite for the expression of ambruticin and phenylpyrrole susceptibility in
A. brassicicola
and
N. crassa
and that, at least in the latter species, improper activation of the high-osmolarity glycerol-related pathway could explain their fungicidal properties.
Pseudomonas aeruginosa
-
Candida albicans
Interactions: Localization and Fungal Toxicity of a Phenazine Derivative
Authors: Gibson Jane , Sood Arpana , Hogan Deborah A.
Published: November 2008

Phenazines are redox-active small molecules that play significant roles in the interactions between pseudomonads and diverse eukaryotes, including fungi. When
Pseudomonas aeruginosa
and
Candida albicans
were cocultured on solid medium, a red pigmentation developed that was dependent on
P. aeruginosa
phenazine biosynthetic genes. Through a genetic screen in combination with biochemical experiments, it was found that a
P. aeruginosa
-produced precursor to pyocyanin, proposed to be 5-methyl-phenazinium-1-carboxylate (5MPCA), was necessary for the formation of the red pigmentation. The 5MPCA-derived pigment was found to accumulate exclusively within fungal cells, where it retained the ability to be reversibly oxidized and reduced, and its detection correlated with decreased fungal viability. Pyocyanin was not required for pigment formation or fungal killing. Spectral analyses showed that the partially purified pigment from within the fungus differed from aeruginosins A and B, two red phenazine derivatives formed late in
P. aeruginosa
cultures. The red pigment isolated from
C. albicans
that had been cocultured with
P. aeruginosa
was heterogeneous and difficult to release from fungal cells, suggesting its modification within the fungus. These findings suggest that intracellular targeting of some phenazines may contribute to their toxicity and that this strategy could be useful in developing new antifungals.
Correlation of Shiga Toxin Gene Frequency with Commonly Used Microbial Indicators of Recreational Water Quality
Authors: Smith Cody J. , Olszewski Adam M. , Mauro Steven A.
Published: November 2008

Shiga toxin (Stx) genes produce proteins that are pathogenic to humans, leading to severe gastrointestinal illness. This work focuses on examining the abundance and distribution of
stx
genes in relation to common microbial indicators in beach water and streams in the vicinity of Presque Isle State Park in Erie, PA. By use of quantitative PCR, the relative abundance levels of
stx
DNA in over 700 samples in the sampling area were determined. The results demonstrate that the abundance and distribution of
stx
genes are variable and do not correlate with the abundance of
Escherichia coli
bacteria, enterococci, or viral particles. These results suggest that microbial indicators of water quality are not adequate in predicting the occurrence of organisms that harbor
stx
genes and highlight the need for standardized pathogen-specific detection protocols for waters utilized for recreational swimming.
Synergistic Inactivation of Spores of ProteolyticClostridium botulinumStrains by High Pressure and Heat Is Strain and Product Dependent
Authors: Bull M. K. , Olivier S. A. , van Diepenbeek R. J. , Kormelink F. , Chapman B.
Published: November 2008

The combined high pressure and heat resistances of spores of five proteolyticClostridium botulinumstrains and of the nonpathogenic surrogate strainClostridium sporogenesPA3679 were compared with their heat-only resistances on the basis of equivalent accumulated thermal lethality, expressed as equivalent minutes at a reference temperature of 105°C (F105°C). Comparisons were made with three model (i.e., diluted) products, namely, 30% (wt/wt) Bolognese sauce, 50% (wt/wt) cream sauce, and rice water agar. Pressure was determined to act synergistically with heat during high-pressure thermal (HPT) processing forC. botulinumFRRB 2802 (NCTC 7273) andC. botulinumFRRB 2804 (NCTC 3805 and 62A) in the Bolognese and cream sauces and forC. botulinumFRRB 2807 (213B) in the Bolognese sauce only. No synergy was observed forC. botulinumFRRB 2803 (NCTC 2916) or FRRB 2806 (62A) orC. sporogenesFRRB 2790 (NCTC 8594 and PA3679) in any of the model products. No significant protective effect of pressure against spore inactivation was determined for anyClostridiumstrain in any product. Because synergy was not consistently observed among strains ofC. botulinumor among products, the prediction of inactivation ofC. botulinumspores by HPT sterilization (HPTS) for the present must assume a complete lack of synergy. Therefore, any HPTS process for low-acid shelf-stable foods must be at least thermally equivalent to an F0process of 2.8 min, in line with current good manufacturing practices. The results of this study suggest that the use ofC. sporogenesPA3679 as a surrogate organism may risk overestimating inactivation ofC. botulinumby HPT processing.
Quantitative PCR Monitoring of Antibiotic Resistance Genes and Bacterial Pathogens in Three European Artificial Groundwater Recharge Systems
Authors: Böckelmann Uta , Dörries Hans-Henno , Ayuso-Gabella M. Neus , Salgot de Marçay Miquel , Tandoi Valter , Levantesi Caterina , Masciopinto Costantino , Van Houtte Emmanuel , Szewzyk Ulrich , Wintgens Thomas , Grohmann Elisabeth
Published: November 2008

Aquifer recharge presents advantages for integrated water management in the anthropic cycle, namely, advanced treatment of reclaimed water and additional dilution of pollutants due to mixing with natural groundwater. Nevertheless, this practice represents a health and environmental hazard because of the presence of pathogenic microorganisms and chemical contaminants. To assess the quality of water extracted from recharged aquifers, the groundwater recharge systems in Torreele, Belgium, Sabadell, Spain, and Nardò, Italy, were investigated for fecal-contamination indicators, bacterial pathogens, and antibiotic resistance genes over the period of 1 year. Real-time quantitative PCR assays for
Helicobacter pylori, Yersinia enterocolitica
, and
Mycobacterium avium
subsp.
paratuberculosis
, human pathogens with long-time survival capacity in water, and for the resistance genes
ermB, mecA, blaSHV-5, ampC, tetO
, and
vanA
were adapted or developed for water samples differing in pollutant content. The resistance genes and pathogen concentrations were determined at five or six sampling points for each recharge system. In drinking and irrigation water, none of the pathogens were detected.
tetO
and
ermB
were found frequently in reclaimed water from Sabadell and Nardò.
mecA
was detected only once in reclaimed water from Sabadell. The three aquifer recharge systems demonstrated different capacities for removal of fecal contaminators and antibiotic resistance genes. Ultrafiltration and reverse osmosis in the Torreele plant proved to be very efficient barriers for the elimination of both contaminant types, whereas aquifer passage followed by UV treatment and chlorination at Sabadell and the fractured and permeable aquifer at Nardò posed only partial barriers for bacterial contaminants.
Characterization of Denitrification Gene Clusters of Soil Bacteria via a Metagenomic Approach
Authors: Demanèche Sandrine , Philippot Laurent , David Maude M. , Navarro Elisabeth , Vogel Timothy M. , Simonet Pascal
Published: November 2008

We characterized operons encoding enzymes involved in denitrification, a nitrogen-cycling process involved in nitrogen losses and greenhouse gas emission, using a metagenomic approach which combines molecular screening and pyrosequencing. Screening of 77,000 clones from a soil metagenomic library led to the identification and the subsequent characterization of nine denitrification gene clusters.
Silencing of Six Hydrophobins in
Cladosporium fulvum
: Complexities of Simultaneously Targeting Multiple Genes
Authors: Lacroix Hélène , Spanu Pietro D.
Published: November 2008

In this study, we have constructed and expressed inverted repeat chimeras from the first exons of the six known hydrophobins of the fungus
Cladosporium fulvum
, the causal agent of tomato leaf mold. We used quantitative PCR to measure specifically the expression levels of the hydrophobins. The targeted genes are silenced to different degrees, but we also detected clear changes in the expression levels of nontargeted genes. This work highlights the difficulties that are likely to be encountered when attempting to silence more than one gene in a multigene family.
Lacticin Q, a Lactococcal Bacteriocin, Causes High-Level Membrane Permeability in the Absence of Specific Receptors
Authors: Yoneyama Fuminori , Imura Yuichi , Ichimasa Shiro , Fujita Koji , Zendo Takeshi , Nakayama Jiro , Matsuzaki Katsumi , Sonomoto Kenji
Published: November 2008

To characterize the mode of action of lacticin Q (LnqQ), its membrane-permeabilizing activity was compared with that of nisin A because of the similar antimicrobial features of these compounds. Lipid II, the receptor for nisin A, was not required for LnqQ activity. LnqQ induced high-level membrane permeability in the absence of specific receptors.
Xylella fastidiosa
Afimbrial Adhesins Mediate Cell Transmission to Plants by Leafhopper Vectors
Authors: Killiny Nabil , Almeida Rodrigo P. P.
Published: November 2008

The interactions between the economically important plant-pathogenic bacterium
Xylella fastidiosa
and its leafhopper vectors are poorly characterized. We used different approaches to determine how
X. fastidiosa
cells interact with the cuticular surface of the foreguts of vectors. We demonstrate that
X. fastidiosa
binds to different polysaccharides with various affinities and that these interactions are mediated by cell surface carbohydrate-binding proteins. In addition, competition assays showed that
N
-acetylglucosamine inhibits bacterial adhesion to vector foregut extracts and intact wings, demonstrating that attachment to leafhopper surfaces is affected in the presence of specific polysaccharides. In vitro experiments with several
X. fastidiosa
knockout mutants indicated that hemagglutinin-like proteins are associated with cell adhesion to polysaccharides. These results were confirmed with biological experiments in which hemagglutinin-like protein mutants were transmitted to plants by vectors at lower rates than that of the wild type. Furthermore, although these mutants were defective in adhesion to the cuticle of vectors, their growth rate once attached to leafhoppers was similar to that of the wild type, suggesting that these proteins are important for initial adhesion of
X. fastidiosa
to leafhoppers. We propose that
X. fastidiosa
colonization of leafhopper vectors is a complex, stepwise process similar to the formation of biofilms on surfaces.
Complete Fermentation of Xylose and Methylglucuronoxylose Derived from Methylglucuronoxylan by
Enterobacter asburiae
Strain JDR-1
Authors: Bi Changhao , Rice John D. , Preston James F.
Published: November 2008

Acid pretreatment is commonly used to release pentoses from the hemicellulose fraction of cellulosic biomass for bioconversion. The predominant pentose in the hemicellulose fraction of hardwoods and crop residues is xylose in the polysaccharide methylglucuronoxylan, in which as many as one in six of the β-1,4-linked xylopyranose residues is substituted with α-1,2-linked 4-
O
-methylglucuronopyranose. Resistance of the α-1,2-methylglucuronosyl linkages to acid hydrolysis results in release of the aldobiuronate 4-
O
-methylglucuronoxylose, which is not fermented by bacterial biocatalysts currently used for bioconversion of hemicellulose.
Enterobacter asburiae
strain JDR-1, isolated from colonized hardwood (sweetgum), efficiently ferments both methylglucuronoxylose and xylose, producing predominantly ethanol and acetate.
13
C-nuclear magnetic resonance studies defined the Embden-Meyerhof pathway for metabolism of glucose and the pentose phosphate pathway for xylose metabolism. Rates of substrate utilization, product formation, and molar growth yields indicated methylglucuronoxylose is transported into the cell and hydrolyzed to release methanol, xylose, and hexauronate.
Enterobacter asburiae
strain JDR-1 is the first microorganism described that ferments methylglucuronoxylose generated along with xylose during the acid-mediated saccharification of hemicellulose. Genetic definition of the methylglucuronoxylose utilization pathway may allow metabolic engineering of established gram-negative bacterial biocatalysts for complete bioconversion of acid hydrolysates of methylglucuronoxylan. Alternatively,
Enterobacter asburiae
strain JDR-1 may be engineered for the efficient conversion of acid hydrolysates of hemicellulose to biofuels and chemical feedstocks.
Dual Role for the Tyrosine Decarboxylation Pathway inEnterococcus faeciumE17: Response to an Acid Challenge and Generation of a Proton Motive Force
Authors: Pereira C. I. , Matos D. , San Romão M. V. , Barreto Crespo M. T.
Published: November 2008

In this work we investigated the role of the tyrosine decarboxylation pathway in the response ofEnterococcus faeciumE17 cells to an acid challenge. It was found that 91% of the cells were able to remain viable in the presence of tyrosine when they were incubated for 3 h in a complex medium at pH 2.5. This effect was shown to be related to the tyrosine decarboxylation pathway. Therefore, the role of tyrosine decarboxylation in pH homeostasis was studied. The membrane potential and pH gradient, the parameters that compose the proton motive force (PMF), were measured at different pHs (pH 4.5 to 7). We obtained evidence showing that the tyrosine decarboxylation pathway generates a PMF composed of a pH gradient formed due to proton consumption in the decarboxylation reaction and by a membrane potential which results from electrogenic transport of tyrosine in exchange for the corresponding biogenic amine tyramine. The properties of the tyrosine transporter were also studied in this work by using whole cells and right-side-out vesicles. The results showed that the transporter catalyzes homologous tyrosine/tyrosine antiport, as well as electrogenic heterologous tyrosine-tyramine exchange. The tyrosine transporter had properties of a typical precursor-product exchanger operating in a proton motive decarboxylation pathway. Therefore, the tyrosine decarboxylation pathway contributes to an acid response mechanism inE. faeciumE17. This decarboxylation pathway gives the strain a competitive advantage in nutrient-depleted conditions, as well as in harsh acidic environments, and a better chance of survival, which contributes to higher cell counts in food fermentation products.
Bioinformatic and Expression Analyses of Genes Mediating Zinc Homeostasis inNostoc punctiforme
Authors: Hudek Lee , Rai L. C. , Freestone David , Michalczyk Agnes , Gibson Maria , Song Y. F. , Ackland M. Leigh
Published: November 2008

Zinc homeostasis was investigated inNostoc punctiforme. Cell tolerance to Zn2+over 14 days showed that ZnCl2levels above 22 μM significantly reduced cell viability. After 3 days in 22 μM ZnCl2, ca. 12% of the Zn2+was in an EDTA-resistant component, suggesting an intracellular localization. Zinquin fluorescence was detected within cells exposed to concentrations up to 37 μM relative to 0 μM treatment. Radiolabeled65Zn showed Zn2+uptake increased over a 3-day period, while efflux occurred more rapidly within a 3-h time period. Four putative genes involved in Zn2+uptake and efflux inN. punctiformewere identified: (i) the predicted Co/Zn/Cd cation transporter, putative CDF; (ii) the predicted divalent heavy-metal cation transporter, putative Zip; (iii) the ATPase component and Fe/Zn uptake regulation protein, putative Fur; and (iv) an ABC-type Mn/Zn transport system, putative zinc ZnuC, ZnuABC system component. Quantitative real-time PCR indicated the responsiveness of all four genes to 22 μM ZnCl2within 3 h, followed by a reduction to below basal levels after 24 h by putative ZIP, ZnuC, and Fur and a reduction to below basal level after 72 h by putative CDF efflux gene. These results demonstrate differential regulation of zinc transporters over time, indicating a role for them in zinc homeostasis inN. punctiforme.
Diversity and Seasonality of Bioluminescent
Vibrio cholerae
Populations in Chesapeake Bay
Authors: Zo Young-Gun , Chokesajjawatee Nipa , Grim Christopher , Arakawa Eiji , Watanabe Haruo , Colwell Rita R.
Published: November 2008

Association of luminescence with phenotypic and genotypic traits and with environmental parameters was determined for 278 strains of
Vibrio cholerae
isolated from the Chesapeake Bay during 1998 to 2000. Three clusters of luminescent strains (A, B, and C) and two nonluminescent clusters (X and Y) were identified among 180 clonal types.
V. cholerae
O1 strains isolated during pandemics and endemic cholera in the Ganges Delta were related to cluster Y. Heat-stable enterotoxin (encoded by
stn
) and the membrane protein associated with bile resistance (encoded by
ompU
) were found to be linked to luminescence in strains of cluster A. Succession from nonluminescent to luminescent populations of
V. cholerae
occurred during spring to midsummer. Occurrence of cluster A strains in water with neutral pH was contrasted with that of cluster Y strains in water with a pH of >8. Cluster A was found to be associated with a specific calanoid population cooccurring with cyclopoids. Cluster B was related to cluster Y, with its maximal prevalence at pH 8. Occurrence of cluster B strains was more frequent with warmer water temperatures and negatively correlated with maturity of the copepod community. It is concluded that each cluster of luminescent
V. cholerae
strains occupies a distinct ecological niche. Since the dynamics of these niche-specific subpopulations are associated with zooplankton community composition, the ecology of luminescent
V. cholerae
is concluded to be related to its interaction with copepods and related crustacean species.
Flavodiiron Protein from
Trichomonas vaginalis
Hydrogenosomes: the Terminal Oxygen Reductase
Authors: Smutná Tamara , Gonçalves Vera L. , Saraiva Lígia M. , Tachezy Jan , Teixeira Miguel , Hrdý Ivan
Published: November 2008

Trichomonas vaginalis
is one of a few eukaryotes that have been found to encode several homologues of flavodiiron proteins (FDPs). Widespread among anaerobic prokaryotes, these proteins are believed to function as oxygen and/or nitric oxide reductases to provide protection against oxidative/nitrosative stresses and host immune responses. One of the
T. vaginalis
FDP homologues is equipped with a hydrogenosomal targeting sequence and is expressed in the hydrogenosomes, oxygen-sensitive organelles that participate in carbohydrate metabolism and assemble iron-sulfur clusters. The bacterial homologues characterized thus far have been dimers or tetramers; the trichomonad protein is a dimer of identical 45-kDa subunits, each noncovalently binding one flavin mononucleotide. The protein reduces dioxygen to water but is unable to utilize nitric oxide as a substrate, similarly to its closest homologue from another human parasite
Giardia intestinalis
and related archaebacterial proteins.
T. vaginalis
FDP is able to accept electrons derived from pyruvate or NADH via ferredoxin and is proposed to play a role in the protection of hydrogenosomes against oxygen.
Trimeric Autotransporters ofHaemophilus parasuis: Generation of an Extensive Passenger Domain Repertoire Specific for Pathogenic Strains
Authors: Pina Sonia , Olvera Alex , Barceló Anna , Bensaid Albert
Published: November 2008

Haemophilus parasuisis the agent responsible for causing Glässer's disease, but little is known about the pathogenic determinants of this major pig disease. Here we describe, for the pathogenic strain Nagasaki, the molecular characterization of 13 trimeric autotransporters as assessed by the presence of YadA C-terminal translocator domains which were classified into three groups. All passenger domains possess motifs and repeats characteristic of adhesins, hemagglutinins, and invasins with various centrally located copies of collagen-like repeats. This domain architecture is shared with two trimeric autotransporter proteins ofH. somnus129Pt. Genomic comparison by microarray hybridization demonstrated homologies amongH. parasuisvirulent strains and high divergence with respect to nonvirulent strains. Therefore, these genes were namedvtaA(virulence-associatedtrimericautotransporters). The sequencing of 17 homologousvtaAgenes of different invasive strains highlighted an extensive mosaic structure. Based also on the presence of DNA uptake signal sequences within thevtaAgenes, we propose a mechanism of evolution by which gene duplication and the accumulation of mutations and recombinations, plus the lateral gene transfer of the passenger domain, led to the diversity of this multigene family. This study provides insights to help understand the tissue colonization and invasiveness characteristic ofH. parasuispathogenic strains.
Eicosapentaenoic Acid Plays a Beneficial Role in Membrane Organization and Cell Division of a Cold-Adapted Bacterium,Shewanella livingstonensisAc10
Authors: Kawamoto Jun , Kurihara Tatsuo , Yamamoto Kentaro , Nagayasu Makiko , Tani Yasushi , Mihara Hisaaki , Hosokawa Masashi , Baba Takeshi , Sato Satoshi B. , Esaki Nobuyoshi
Published: November 2008

Shewanella livingstonensisAc10, a psychrotrophic gram-negative bacterium isolated from Antarctic seawater, produces eicosapentaenoic acid (EPA) as a component of phospholipids at low temperatures. EPA constitutes about 5% of the total fatty acids of cells grown at 4°C. We found that five genes, termedorf2, orf5, orf6, orf7, andorf8, are specifically required for the synthesis of EPA by targeted disruption of the respective genes. The mutants lacking EPA showed significant growth retardation at 4°C but not at 18°C. Supplementation of a synthetic phosphatidylethanolamine that contained EPA at thesn-2 position complemented the growth defect. The EPA-less mutant became filamentous, and multiple nucleoids were observed in a single cell at 4°C, indicating that the mutant has a defect in cell division. Electron microscopy of the cells by high-pressure freezing and freeze-substitution revealed abnormal intracellular membranes in the EPA-less mutant at 4°C. We also found that the amounts of several membrane proteins were affected by the depletion of EPA. While polyunsaturated fatty acids are often considered to increase the fluidity of the hydrophobic membrane core, diffusion of a small hydrophobic molecule, pyrene, in the cell membranes and large unilamellar vesicles prepared from the lipid extracts was very similar between the EPA-less mutant and the parental strain. These results suggest that EPA inS. livingstonensisAc10 is not required for bulk bilayer fluidity but plays a beneficial role in membrane organization and cell division at low temperatures, possibly through specific interaction between EPA and proteins involved in these cellular processes.
Acid-Susceptible Mutants ofMycobacterium tuberculosisShare Hypersusceptibility to Cell Wall and Oxidative Stress and to the Host Environment
Authors: Vandal Omar H. , Roberts Julia A. , Odaira Toshiko , Schnappinger Dirk , Nathan Carl F. , Ehrt Sabine
Published: November 2008

Mycobacterium tuberculosiscan persist in macrophage phagosomes that acidify to a pH of ∼4.5 after activation of the macrophage with gamma interferon. How the bacterium resists the low pH of the acidified phagosome is incompletely understood. A screen of 10,100M. tuberculosistransposon mutants for mutants hypersensitive to pH 4.5 led to the discovery of 21 genes whose disruption attenuated survival ofM. tuberculosisat a low pH (41). Here, we show that acid-sensitiveM. tuberculosismutants with transposon insertions in Rv2136c, Rv2224c,ponA2, andlysXwere hypersensitive to antibiotics, sodium dodecyl sulfate, heat shock, and reactive oxygen and nitrogen intermediates, indicating that acid resistance can be associated with protection against other forms of stress. The Rv2136c mutant was impaired in intrabacterial pH homeostasis and unable to maintain a neutral intrabacterial pH in activated macrophages. The Rv2136c, Rv2224c, andponA2mutants were attenuated in mice, with the Rv2136c mutant displaying the most severe level of attenuation. Pathways utilized byM. tuberculosisfor acid resistance and intrabacterial pH maintenance are potential targets for chemotherapy.
Hydrogen Peroxide-Mediated Interference Competition by
Streptococcus pneumoniae
Has No Significant Effect on
Staphylococcus aureus
Nasal Colonization of Neonatal Rats
Authors: Margolis Elisa
Published: November 2008

It has been proposed that the relative scarcity of
Staphylococcus aureus
and
Streptococcus pneumoniae
cocolonization in the nasopharynxes of humans can be attributed to hydrogen peroxide-mediated interference competition. Previously it has been shown in vitro that H
2
O
2
produced by
S. pneumoniae
is bactericidal to
S. aureus
. To ascertain whether H
2
O
2
has this inhibitory effect in the nasal passages of neonatal rats, colonization experiments were performed with
S. aureus
and
S. pneumoniae
. The results of these experiments with neonatal rats are inconsistent with the hypothesis that hydrogen peroxide-mediated killing of
S. aureus
by
S. pneumoniae
is responsible for the relative scarcity of cocolonization by these bacteria. In mixed-inoculum colonization experiments and experiments where
S. aureus
invaded the nasopharynxes of rats with established
S. pneumoniae
populations, the density of
S. aureus
did not differ whether the
S. pneumoniae
strain was H
2
O
2
secreting or non-H
2
O
2
secreting (SpxB). Moreover, the advantage of catalase production by
S. aureus
in competition with a non-catalase-producing strain (KatA) during nasal colonization was no greater in the presence of H
2
O
2
-producing
S. pneumoniae
than in the presence of non-H
2
O
2
-producing
S. pneumoniae
.
Transforming DNA Uptake Gene Orthologs Do Not Mediate Spontaneous Plasmid Transformation in
Escherichia coli
Authors: Sun Dongchang , Zhang Xuewu , Wang Lingyu , Prudhomme Marc , Xie Zhixiong , Martin Bernard , Claverys Jean-Pierre
Published: November 2008

Spontaneous plasmid transformation of
Escherichia coli
occurs on nutrient-containing agar plates.
E. coli
has also been reported to use double-stranded DNA (dsDNA) as a carbon source. The mechanism(s) of entry of exogenous dsDNA that allows plasmid establishment or the use of DNA as a nutrient remain(s) unknown. To further characterize plasmid transformation, we first documented the stimulation of transformation by agar and agarose. We provide evidence that stimulation is not due to agar contributing a supplement of Ca
2+
, Fe
2+
, Mg
2+
, Mn
2+
, or Zn
2+
. Second, we undertook to inactivate the
E. coli
orthologues of
Haemophilus influenzae
components of the transformation machine that allows the uptake of single-stranded DNA (ssDNA) from exogenous dsDNA. The putative outer membrane channel protein (HofQ), transformation pseudopilus component (PpdD), and transmembrane pore (YcaI) are not required for plasmid transformation. We conclude that plasmid DNA does not enter
E. coli
cells as ssDNA. The finding that purified plasmid monomers transform
E. coli
with single-hit kinetics supports this conclusion; it establishes that a unique monomer molecule is sufficient to give rise to a transformant, which is not consistent with the reconstitution of an intact replicon through annealing of partially overlapping complementary ssDNA, taken up from two independent monomers. We therefore propose that plasmid transformation involves internalization of intact dsDNA molecules. Our data together, with previous reports that HofQ is required for the use of dsDNA as a carbon source, suggest the existence of two routes for DNA entry, at least across the outer membrane of
E. coli
.
Defects in the Error Prevention Oxidized Guanine System Potentiate Stationary-Phase Mutagenesis in
Bacillus subtilis
Authors: Vidales Luz E. , Cárdenas Lluvia C. , Robleto Eduardo , Yasbin Ronald E. , Pedraza-Reyes Mario
Published: November 2008

Previous studies showed that a
Bacillus subtilis
strain deficient in mismatch repair (MMR; encoded by the
mutSL
operon) promoted the production of stationary-phase-induced mutations. However, overexpression of the
mutSL
operon did not completely suppress this process, suggesting that additional DNA repair mechanisms are involved in the generation of stationary-phase-associated mutants in this bacterium. In agreement with this hypothesis, the results presented in this work revealed that starved
B. subtilis
cells lacking a functional error prevention GO (8-oxo-G) system (composed of YtkD, MutM, and YfhQ) had a dramatic propensity to increase the number of stationary-phase-induced revertants. These results strongly suggest that the occurrence of mutations is exacerbated by reactive oxygen species in nondividing cells of
B. subtilis
having an inactive GO system. Interestingly, overexpression of the MMR system significantly diminished the accumulation of mutations in cells deficient in the GO repair system during stationary phase. These results suggest that the MMR system plays a general role in correcting base mispairing induced by oxidative stress during stationary phase. Thus, the absence or depression of both the MMR and GO systems contributes to the production of stationary-phase mutants in
B. subtilis.
In conclusion, our results support the idea that oxidative stress is a mechanism that generates genetic diversity in starved cells of
B. subtilis
, promoting stationary-phase-induced mutagenesis in this soil microorganism.
Characterization of themyo-Inositol Utilization Island ofSalmonella entericaserovar Typhimurium
Authors: Kröger Carsten , Fuchs Thilo M.
Published: November 2008

Knockout mutation of STM4432 resulted in a growth-deficient phenotype ofSalmonella entericaserovar Typhimurium in the presence ofmyo-inositol (MI) as the sole carbon source. STM4432 is part of a 22.6-kb genomic island which spans STM4417 to STM4436 (genomic island 4417/4436) and is responsible for MI degradation. Genome comparison revealed the presence of this island in only sixSalmonellastrains and a high variability of theiolgene organization in gram-negative bacteria. Upon nonpolar deletion of 11 island loci, the genes involved in six enzymatic steps of the MI pathway were identified. The generation time ofS. entericaserovar Typhimurium in minimal medium with MI decreases with higher concentrations of this polyol. Reverse transcriptase PCR showed five separate transcriptional units encompassing the genesiolA-iolB,iolE-iolG1,iolC1-iolC2,iolD1-iolD2-iolG2, andiolI2-iolH. Luciferase reporter assays revealed a strong induction of their promoters in the presence of MI but not glucose. The main regulator, IolR, was identified due to a reduced lag phase of a strain mutated in STM4417 (iolR). Deletion ofiolRresulted in stimulation of theioloperons, indicating its negative effect on theiolgenes ofS. entericaserovar Typhimurium in rich medium at a transcriptional level. Bandshift assays demonstrated the binding of this putative repressor to promoter sequences ofiolA,iolC1, andiolD1. Binding of IolR to its own promoter and inducediolRexpression in an IolR-negative background demonstrate that its transcription is autoregulated. This is the first characterization of MI degradation in a gram-negative bacterium, revealing a complex transcriptional organization and regulation of theS. entericaserovar Typhimuriumiolgenes.
Dynamic Association of the Replication Initiator and Transcription Factor DnaA with theBacillus subtilisChromosome during Replication Stress
Authors: Breier Adam M. , Grossman Alan D.
Published: November 2008

DnaA functions as both a transcription factor and the replication initiator in bacteria. We characterized the DNA binding dynamics of DnaA on a genomic level. Based on cross-linking and chromatin immunoprecipitation data, DnaA binds at least 17 loci, 15 of which are regulated transcriptionally in response to inhibition of replication (replication stress). Six loci, each of which has a cluster of at least nine potential DnaA binding sites, had significant increases in binding by DnaA when replication was inhibited, indicating that the association of DnaA with at least some of its target sites is altered after replication stress. When replication resumed fromoriCafter inhibition of replication initiation, these high levels of binding decreased rapidly at origin-proximal and origin-distal regions, well before a replication fork could pass through each of the regulated regions. These findings indicate that there is rapid signaling to decrease activation of DnaA during replication and that interaction between DnaA bound at each site and the replication machinery is not required for regulation of DnaA activity in response to replication stress.
The BlcC (AttM) Lactonase ofAgrobacterium tumefaciensDoes Not Quench the Quorum-Sensing System That Regulates Ti Plasmid Conjugative Transfer
Authors: Khan Sharik R. , Farrand Stephen K.
Published: November 2008

The conjugative transfer ofAgrobacteriumplasmids is controlled by a quorum-sensing system consisting of TraR and its acyl-homoserine lactone (HSL) ligand. The acyl-HSL is essential for the TraR-mediated activation of the Ti plasmid Tra genes. Strains A6 and C58 ofAgrobacterium tumefaciensproduce a lactonase, BlcC (AttM), that can degrade the quormone, leading some to conclude that the enzyme quenches the quorum-sensing system. We tested this hypothesis by examining the effects of the mutation, induction, or mutational derepression ofblcCon the accumulation of acyl-HSL and on the conjugative competence of strain C58. The induction ofblcresulted in an 8- to 10-fold decrease in levels of extracellular acyl-HSL but in only a twofold decrease in intracellular quormone levels, a measure of the amount of active intracellular TraR. The induction or mutational derepression ofblcas well as a null mutation inblcChad no significant effect on the induction of or continued transfer of pTiC58 from donors in any stage of growth, including stationary phase. In matings performed in developing tumors, wild-type C58 transferred the Ti plasmid to recipients, yielding transconjugants by 14 to 21 days following infection.blcC-null donors yielded transconjugants 1 week earlier, but by the following week, transconjugants were recovered at numbers indistinguishable from those of the wild type. Donors mutationally derepressed forblcCyielded transconjugants in planta at numbers 10-fold lower than those for the wild type at weeks 2 and 3, but by week 4, the two donors showed no difference in recoverable transconjugants. We conclude that BlcC has no biologically significant effect on Ti plasmid transfer or its regulatory system.
CcpC-Dependent Regulation of Citrate Synthase Gene Expression inListeria monocytogenes
Authors: Mittal Meghna , Picossi Silvia , Sonenshein Abraham L.
Published: November 2008

Citrate synthase, the first and rate-limiting enzyme of the tricarboxylic acid branch of the Krebs cycle, was shown to be required for de novo synthesis of glutamate and glutamine inListeria monocytogenes. The citrate synthase (citZ) gene was found to be part of a complex operon with the upstream genes lmo1569 and lmo1568. The downstream isocitrate dehydrogenase (citC) gene appears to be part of the same operon as well. Two promoters were shown to drivecitZexpression, a distal promoter located upstream of lmo1569 and a proximal promoter located upstream of the lmo1568 gene. Transcription ofcitZfrom both promoters was regulated by CcpC by interaction with a single site; assays of transcription in vivo and assays of CcpC binding in vitro revealed that CcpC interacts with and represses the proximal promoter that drives expression of the lmo1568,citZ, andcitCgenes and, by binding to the same site, prevents read-through transcription from the distal, lmo1569 promoter. Expression of the lmo1568 operon was not affected by the carbon source but was repressed during growth in complex medium by addition of glutamine.
The Tail Sheath of Bacteriophage N4 Interacts with the
Escherichia coli
Receptor
Authors: McPartland Jennifer , Rothman-Denes Lucia B.
Published: November 2008

Unlike other characterized phages, the lytic coliphage N4 must inject the 360-kDa virion RNA polymerase (vRNAP), in addition to its 72-kbp genome, into the host for successful infection. The process of adsorption to the host sets up and elicits the necessary conformational changes in the virion to allow genome and vRNAP injection. Infection of suppressor and nonsuppressor strains,
Escherichia coli
W3350
supF
and
E. coli
W3350, with a mutant N4 isolate (N4am229) harboring an amber mutation in Orf65 yielded virions containing (N4gp65
+
) and lacking (N4gp65
−
) gp65, respectively. N4gp65
+
but not N4gp65
−
phage was able to adsorb to the host. Recombinant gp65 with a hexahistidine tag at the N terminus or hexahistidine and c-
myc
tags at the C terminus was able to complement N4gp65
−
virions in vivo and in vitro. Immunogold detection of gp65 in vivo complemented virions revealed its localization at the N4 tail. Finally, we show both in vitro and in vivo that gp65 interacts with the previously determined N4 outer membrane receptor, NfrA.
Structure and Composition of Ice Algal Assemblages from the Gulf of St. Lawrence, Magdalen Islands Area
Authors: Sève Michèle A. De , Dunbar Maxwell J.
Published: November 2008

Two types of ice algal assemblages were found in the Gulf of St. Lawrence: assemblages composed predominantly of pennate diatoms (abundance > 98.0%) and assemblages with a high abundance of centric diatoms (abundance > 46.2%). The first type is similar to Arctic landfast ice algal assemblages with the pennate diatoms Nitzschia cylindrus, N. polaris, and Navicula kariana as dominant species. The second type is similar to drifting ice algal assemblages previously described from the Gulf of St. Lawrence, with a percentage of centric diatom species > 46.2% due to the dominance of the planktonic diatom Thalassiosira nordenskioeldii. Species richness and the Shannon-Weaver index of diversity were low; density ranged from 104–106 × cells∙L−1 and was negatively correlated with percent centric diatoms. Results on the structure and the composition of the ice algal assemblages are related to ice type, i.e. landfast and drifting pack ice, and compared with ice algal assemblages from higher latitudes.
Variability, Spatial Patterns and Scales of Similarity in Size–Frequency Distributions of the Northern Shrimp (Pandalus borealis) and its Migrations in the Gulf of St. Lawrence
Authors: Simard Yvan , Savard Louise
Published: November 2008

The causes of high variability of length–frequency distributions (LFDs) of the northern shrimp in the Gulf of St. Lawerence were investigated with spatial statistics. The LFD is considered as a multivariate whose spatial structure was analyzed with cluster analysis, dissimilarity variograms and multivariate correlograms. Data were collected in 1984, 1985, and 1987 on the three main shrimp grounds: Sept-Iles, North-Anticosti, and Esquiman. The LFDs were spatially autocorrelated over a wide range of scales, and well-defined homogeneous assemblages were observed in each region every year. The autocorrelation signature revealed that the spatial organization resulted from large gradients, partially related to the topography of the shrimp grounds, which probably resulted from the ontogenic depth-migration of the shrimps. The specific mean length of cohorts consistently increased along the spatial gradients, up to about one-half of the annual growth increment. This was attributed to the fact that the migration routes passed through an increasing temperature gradient, which, directly or indirectly, accelerated their growth. Significant regional and interannual differences in the relative proportion of the modal components of LFDs were noted, and were ascribed to fluctuations in the success and distribution of recruitment and survivorship.
Seasonal Variations in the Smolt Characteristics of Juvenile Atlantic Salmon (Salmo salar) from Estuarine and Riverine Environments
Authors: Cunjak R. A. , Saunders R. L. , Chadwick E. M. P.
Published: November 2008

Smolt characteristics such as lipid-moisture dynamics, ATPase activity, salinity tolerance, and condition factor were determined for Atlantic salmon parr (Salmo salar) moving to, or residing in, estuaries of two rivers in eastern Canada. Lipid and water content and gill Na+K+-ATPase activity of these parr differed markedly from river-resident parr. ATPase activity, sex ratio, and condition factor indicated more similarity between estuarine parr and smolts. Estuarine parr were unable to tolerate high salinities in spring, summer, or autumn, but there was an indication of an autumnal increase in salinity tolerance which coincided with maximum levels in ATPase activity and a secondary downstream movement of parr and smolt-like salmon in the autumn. The data suggest that the largest estuarine parr are essentially presmolts which utilize the estuary as a rearing environment prior to subsequent emigration seaward when environmental conditions are again amenable to a reopening of the 'smolt window.' These observations also highlight some inadequacies in applying existing criteria for the smoking process and for modelling life histories of salmonids.
Cellulosic Biofuels
Authors: Carroll Andrew , Somerville Chris
Published: November 2008

The development of sustainable, low-carbon, liquid fuels from cellulosic biomass will require advances in many areas of science and engineering. This review describes the major topics of enquiry concerning cellulosic biofuels with an emphasis on those areas of research and development that include research problems of interest to plant biologists.
Sequential Flow Membraneless Microfluidic Fuel Cell with Porous Electrodes
Authors: Salloum Kamil S. , Hayes Joel R. , Friesen Cody , Posner Jonathan D.
Published: November 2008

A novel convective flow fuel cell with porous electrodes is described. In this fuel cell design, the fuel (formic acid in sulfuric acid) flows radially outward through a thin disc anode and across a gap to a ring shaped cathode. The oxidant (potassium permanganate in sulfuric acid) is introduced into the gap and advects radially outward through the cathode. This fuel cell differs from previous designs in that the reactants flow in series rather than in parallel. The flow velocity field is examined using microscale particle image velocimetry and shown to be nearly axisymmetric and steady. The results show that increasing the electrolyte concentration and flow rate reduce the cell Ohmic resistance and mass transport losses, resulting in larger peak power densities. Additionally, the fuel utilization decreased with higher flow rates, and increased with higher ionic strength solutions.