bluuebunny/crossref_metadata_2025 huggingface dataset:
Comment on "An Association Between the Kinship and Fertility of Human Couples"
Authors: Labouriau Rodrigo , Amorim António
Published: December 2008

Helgason
et al
. (Reports, 8 February 2008, p. 813) reported a positive association between kinship and fertility in the Icelandic population. We point out that the data further suggest that fertility initially increases with kinship and then decays. This is supported by another large study on the Danish population suggesting a superposition of effects of inbreeding and outbreeding depression on human fertility.
Response to Comments on "An Association Between the Kinship and Fertility of Human Couples"
Authors: Helgason Agnar , Pálsson Snæbjörn , Guðbjartsson Daníel F. , Kristjánsson Þórður , Stefánsson Kári
Published: December 2008

Analyses of 137,844 Icelandic couples born between 1800 and 1965 reveal a monotonic drop in fertility with increasing marital radius (distance between the birthplaces of spouses). Marital radius was moderately correlated with kinship between spouses. This correlation was strongest during the peak of urbanization (1875 to 1925) but very weak after 1950. These results raise doubts about the use of marital radius as a proxy for kinship in contemporary human populations.
Mechanism of Threading a Polymer Through a Macrocyclic Ring
Authors: Deutman Alexander B. C. , Monnereau Cyrille , Elemans Johannes A. A. W. , Ercolani Gianfranco , Nolte Roeland J. M. , Rowan Alan E.
Published: December 2008

The translocation of biopolymers through pores and channels plays a fundamental role in numerous biological processes. We describe here the mechanism of the threading of a series of polymer chains through a synthetic macrocycle, which mimics these natural processes. The threading of polymers involves a kinetically favorable “entron” effect, which is associated with the initial filling of the cavity by the end of the polymer. A preassociation between the outside of the macrocycle and the polymer induces a process in which the polymer end loops back into the cavity of the macrocycle. This looping mechanism results in accelerated threading rates and unidirectional motion and is reminiscent of the protein translocation through membrane pores.
Collective Reactivity of Molecular Chains Self-Assembled on a Surface
Authors: Maksymovych Peter , Sorescu Dan C. , Jordan Kenneth D. , Yates John T.
Published: December 2008

Self-assembly of molecules on surfaces is a route toward not only creating structures, but also engineering chemical reactivity afforded by the intermolecular interactions. Dimethyldisulfide (CH
3
SSCH
3
) molecules self-assemble into linear chains on single-crystal gold surfaces. Injecting low-energy electrons into individual molecules in the self-assembled structures with the tip of a scanning tunneling microscope led to a propagating chemical reaction along the molecular chain as sulfur–sulfur bonds were broken and then reformed to produce new CH
3
SSCH
3
molecules. Theoretical and experimental evidence supports a mechanism involving electron attachment followed by dissociation of a CH
3
SSCH
3
molecule and initiation of a chain reaction by one or both of the resulting CH
3
S intermediates.
Shock Metamorphism of Bosumtwi Impact Crater Rocks, Shock Attenuation, and Uplift Formation
Authors: Ferrière Ludovic , Koeberl Christian , Ivanov Boris A. , Reimold Wolf Uwe
Published: December 2008

Shock wave attenuation rate and formation of central uplifts are not precisely constrained for moderately sized complex impact structures. The distribution of shock metamorphism in drilled basement rocks from the 10.5-kilometer-diameter Bosumtwi crater, and results of numerical modeling of inelastic rock deformation and modification processes during uplift, constrained with petrographic data, allowed reconstruction of the pre-impact position of the drilled rocks and revealed a shock attenuation by ∼5 gigapascals in the uppermost 200 meters of the central uplift. The proportion of shocked quartz grains and the average number of planar deformation feature sets per grain provide a sensitive indication of minor changes in shock pressure. The results further imply that for moderately sized craters the rise of the central uplift is dominated by brittle failure.
Germ Cell-Intrinsic and -Extrinsic Factors Govern Meiotic Initiation in Mouse Embryos
Authors: Lin Yanfeng , Gill Mark E. , Koubova Jana , Page David C.
Published: December 2008

Retinoic acid (RA) is an essential extrinsic inducer of meiotic initiation in mammalian germ cells. However, RA acts too widely in mammalian development to account, by itself, for the cell-type and temporal specificity of meiotic initiation. We considered parallels to yeast, in which extrinsic and intrinsic factors combine to restrict meiotic initiation. We demonstrate that, in mouse embryos, extrinsic and intrinsic factors together regulate meiotic initiation. The mouse RNA-binding protein DAZL, which is expressed by postmigratory germ cells, is a key intrinsic factor, enabling those cells to initiate meiosis in response to RA. Within a brief developmental window,
Dazl
-expressing germ cells in both XX and XY embryos actively acquire the ability to interpret RA as a meiosis-inducing signal.
Yes We Can! Choose Science in Autism
Authors: Lord Catherine
Published: December 2008

Autism's False Prophets
. Bad Science, Risky Medicine, and the Search for a Cure.
By Paul A. Offit
. Columbia University Press, New York, 2008. 322 pp. $24.95, £14.95. ISBN 9780231146364.

Presenting a strong case against claims that autism is caused by childhood vaccines, Offit also discusses why the antivaccine movement has attracted support.
Pharmacodynamics of Tigecycline against Phenotypically Diverse
Staphylococcus aureus
Isolates in a Murine Thigh Model
Authors: Crandon Jared L. , Banevicius Mary Anne , Nicolau David P.
Published: December 2008

Tigecycline is a currently marketed antimicrobial agent with activity against resistant gram-positive cocci, including methicillin-resistant
Staphylococcus aureus
(MRSA). Despite the proven efficacy of tigecycline in the treatment of infections caused by these pathogens, questions remain as to the exposure-response relationship best associated with its efficacy. The purpose of this study was to define this relationship against seven distinct
S. aureus
isolates by using a neutropenic murine thigh model. Single-dose pharmacokinetics were evaluated, and free drug exposures were calculated after determination of protein binding. Doses of 1.56 to 400 mg/kg of body weight divided 1 to 8 times daily were administered against two methicillin-susceptible
S. aureus
isolates, two hospital-associated MRSA (HA-MRSA) isolates, and three community-associated (CA-MRSA) isolates. Tigecycline pharmacokinetics were best described by a two-compartment model, with a mean half-life of 9.9 h. Protein binding was dose dependent (range, 92.9 to 81.2%). MICs were 0.25 μg/ml for all isolates, except for HA-MRSA 56 (MIC, 0.5 μg/ml) and CA-MRSA 156 (MIC, 0.125 μg/ml). Tigecycline displayed efficacy against all isolates, producing maximum decreases in log
10
numbers of CFU/ml of 1.8 to 2.3 from 0-h controls. Mean correlation coefficients for free-drug (
f
) concentration exposures derived from the parameters
fT
>MIC (the percentage of time during which the concentration of
f
remains above the MIC),
fC
max
/MIC (the ratio of the maximum concentration of
f
to the MIC), and
f
AUC/MIC (the ratio of the area under the concentration-time curve of
f
to the MIC) were 0.622, 0.812, and 0.958, respectively. Values for the mean effective exposure index at 80% (EI
80
) and 50% (EI
50
) for
f
AUC/MIC were 5.4 μg/ml (range, 2.8 to 13 μg/ml) and 2.6 μg/ml (range, 0.6 to 5.1 μg/ml), respectively. Experiments with nonneutropenic mice infected with CA-MRSA 156 resulted in maximum kill at all
f
AUC/MIC exposures tested (1.8 to 8.8 μg/ml). The
f
AUC/MIC ratio is the pharmacodynamic parameter most predictive of tigecycline efficacy. Furthermore, the presence of a functioning immune system markedly reduces the required exposure.
Carbapenem Resistance among
Pseudomonas aeruginosa
Strains from India: Evidence for Nationwide Endemicity of Multiple Metallo-β-Lactamase Clones (VIM-2, -5, -6, and -11 and the Newly Characterized VIM-18)
Authors: Castanheira Mariana , Bell Jan M. , Turnidge John D. , Mathai Dillip , Jones Ronald N.
Published: December 2008

Among 57 metallo-β-lactamase (MβL)-producing
Pseudomonas
spp. detected in India during 2006, five
bla
VIM
genes were found, including a newly characterized
bla
VIM
gene.
Pseudomonas aeruginosa
strains were clustered in 33 ribotypes with clones found in multiple hospitals. Several types of
bla
VIM-2
-carrying integrons were detected. The newly characterized variant VIM-18 showed a 4-amino-acid deletion compared to other VIM variants. In this study, we show that VIM-producing
Pseudomonas
spp. were highly prevalent in India with a great diversity of
bla
VIM
types and MβL-carrying integrons.
In Vitro Antimicrobial Activity of a New Cephalosporin, Ceftaroline, and Determination of Quality Control Ranges for MIC Testing
Authors: Brown Steven D. , Traczewski Maria M.
Published: December 2008

The spectrum of activity of ceftaroline was evaluated against 1,247 bacterial isolates representing 44 different species or phenotypic groups. For the majority of species, the activity of ceftaroline was comparable or superior to that of ceftriaxone. MIC and/or disk diffusion quality control ranges of ceftaroline were determined for five standard ATCC reference strains.
Antiretroviral Concentrations in Breast-Feeding Infants of Mothers Receiving Highly Active Antiretroviral Therapy
Authors: Mirochnick Mark , Thomas Timothy , Capparelli Edmund , Zeh Clement , Holland Diane , Masaba Rose , Odhiambo Prisca , Fowler Mary Glenn , Weidle Paul J. , Thigpen Michael C.
Published: December 2008

There are limited data describing the concentrations of zidovudine, lamivudine, and nevirapine in nursing infants as a result of transfer via breast milk. The Kisumu Breastfeeding Study is a phase IIb open-label trial of prenatal, intrapartum, and postpartum maternal treatment with zidovudine, lamivudine, and nevirapine from 34 weeks of gestation to 6 months postpartum. In a pharmacokinetic substudy, maternal plasma, breast milk, and infant dried blood spots were collected for drug assay on the day of delivery and at 2, 6, 14, and 24 weeks after delivery. Sixty-seven mother-infant pairs were enrolled. The median concentrations in breast milk of zidovudine, lamivudine, and nevirapine during the study period were 14 ng/ml, 1,214 ng/ml, and 4,546 ng/ml, respectively. Zidovudine was not detectable in any infant plasma samples obtained after the day of delivery, while the median concentrations in infant plasma samples from postpartum weeks 2, 6, and 14 were 67 ng/ml, 32 ng/ml, and 24 ng/ml for lamivudine and 987 ng/ml, 1,032 ng/ml, and 734 ng/ml for nevirapine, respectively. Therefore, lamivudine and nevirapine, but not zidovudine, are transferred to infants via breast milk in biologically significant concentrations. The extent and effect of infant drug exposure via breast milk must be well understood in order to evaluate the benefits and risks of maternal antiretroviral use during lactation.
SC29EK, a Peptide Fusion Inhibitor with Enhanced α-Helicity, Inhibits Replication of Human Immunodeficiency Virus Type 1 Mutants Resistant to Enfuvirtide
Authors: Naito Takeshi , Izumi Kazuki , Kodama Eiichi , Sakagami Yasuko , Kajiwara Keiko , Nishikawa Hiroki , Watanabe Kentaro , Sarafianos Stefan G. , Oishi Shinya , Fujii Nobutaka , Matsuoka Masao
Published: December 2008

Peptides derived from the α-helical domains of human immunodeficiency virus (HIV) type 1 (HIV-1) gp41 inhibit HIV-1 fusion to the cell membrane. Enfuvirtide (T-20) is a peptide-based drug that targets the step of HIV fusion, and as such, it effectively suppresses the replication of HIV-1 strains that are either wild type or resistant to multiple reverse transcriptase and/or protease inhibitors. However, HIV-1 variants with T-20 resistance have emerged; therefore, the development of new and potent inhibitors is urgently needed. We have developed a novel HIV fusion inhibitor, SC34EK, which is a gp41-derived 34-amino-acid peptide with glutamate (E) and lysine (K) substitutions on its solvent-accessible site that stabilize its α-helicity. Importantly, SC34EK effectively inhibits the replication of T-20-resistant HIV-1 strains as well as wild-type HIV-1. In this report, we introduce SC29EK, a 29-amino-acid peptide that is a shorter variant of SC34EK. SC29EK blocked the replication of T-20-resistant HIV-1 strains and maintained antiviral activity even in the presence of high serum concentrations (up to 50%). Circular dichroism analysis revealed that the α-helicity of SC29EK was well maintained, while that of the parental peptide, C29, which showed moderate and reduced inhibition of wild-type and T-20-resistant HIV-1 strains, was lower. Our results show that the α-helicity in a peptide-based fusion inhibitor is a key factor for activity and enables the design of short peptide inhibitors with improved pharmacological properties.
Antimicrobial Activity of Prulifloxacin Tested against a Worldwide Collection of Gastroenteritis-Producing Pathogens, Including Those Causing Traveler's Diarrhea
Authors: Fritsche Thomas R. , Biedenbach Douglas J. , Jones Ronald N.
Published: December 2008

Prulifloxacin, the prodrug of ulifloxacin (active component), is a newer fluoroquinolone with broad activity against enteric and nonenteric gram-negative bacilli. Ulifloxacin and other oral comparator agents were tested for activity against 582 gastroenteritis strains from global surveillance studies. Ulifloxacin was highly active against
Escherichia coli
,
Salmonella
spp.,
Shigella
spp.,
Yersinia
spp.,
Vibrio
spp.,
Aeromonas
spp., and
Plesiomonas
spp. (MIC
50
s and MIC
90
s, ≤0.03 μg/ml and ≤0.06 μg/ml, respectively). Only rare
Aeromonas
spp.,
Campylobacter
spp., and
E. coli
displayed elevated MIC results (≥4 μg/ml). Ciprofloxacin exhibited similar activity but was two- to fourfold less potent. Presently approved for clinical use in certain European countries and Japan, ulifloxacin was the most active of the antimicrobial agents tested against these gastroenteritis-causing pathogens.
Bronchopulmonary Disposition of Micafungin in Healthy Adult Volunteers
Authors: Nicasio Anthony M. , Tessier Pamela R. , Nicolau David P. , Knauft R. Fredrick , Russomanno John , Shore Eric , Kuti Joseph L.
Published: December 2008

By way of bronchoscopy and bronchoalveolar lavage, intrapulmonary steady-state concentrations of micafungin administered at 150 mg daily to 15 healthy volunteers were determined at 4, 12, and 24 h after the third dose. The micafungin disposition was predominantly intracellular, with approximately 106% penetration into alveolar macrophages and 5% penetration into epithelial lining fluid.
Role of
proP
and
proU
in Betaine Uptake by
Yersinia enterocolitica
under Cold and Osmotic Stress Conditions
Authors: Annamalai Thirunavukkarasu , Venkitanarayanan Kumar
Published: December 2008

Yersinia enterocolitica
is a food-borne pathogen with the ability to grow at cold temperatures and tolerate high osmolarity. The bacterium tolerates osmotic stress by intracellular accumulation of osmolytes, such as betaine. The
proP
gene and
proU
operon of
Y. enterocolitica
were sequenced, and single (ProP
−
ProU
+
and ProP
+
ProU
−
) and double (ProP
−
ProU
−
) mutants were generated. Upon exposure to osmotic or chill stress, the single and double mutants demonstrated a reduction in betaine uptake compared to that in the wild type, suggesting that
proP
and
proU
play a role in betaine uptake during osmotic and chill stress responses of
Y. enterocolitica
.
Temporal Dynamics of South End Tidal Creek (Sapelo Island, Georgia) Bacterial Communities
Authors: Kara Emily , Shade Ashley
Published: December 2008

Bacterial community dynamics in South End tidal creek, Sapelo Island, GA, were studied over a 74-h, five-tidal-cycle period. Observations were made hourly for the first consecutive 24 hours, every 3 hours on the second day, and every 6 hours on the third day. Tide most strongly influenced bacterial community composition (high-tide versus low-tide community analysis of similarities,
R
= 0.41,
P
< 0.03). Dissolved oxygen concentration and conductivity were important proximate drivers. However, after accounting for tide and environmental variables colinear with tide, cumulative time became more important in describing community variation. In-stream physical processes, including particulate suspension and sedimentation, may explain tide-associated trends in the bacterial community composition observed.
Diversity and Stratification of Archaea in a Hypersaline Microbial Mat
Authors: Robertson Charles E. , Spear John R. , Harris J. Kirk , Pace Norman R.
Published: December 2008

The Guerrero Negro (GN) hypersaline microbial mats have become one focus for biogeochemical studies of stratified ecosystems. The GN mats are found beneath several of a series of ponds of increasing salinity that make up a solar saltern fed from Pacific Ocean water pumped from the Laguna Ojo de Liebre near GN, Baja California Sur, Mexico. Molecular surveys of the laminated photosynthetic microbial mat below the fourth pond in the series identified an enormous diversity of bacteria in the mat, but archaea have received little attention. To determine the bulk contribution of archaeal phylotypes to the pond 4 study site, we determined the phylogenetic distribution of archaeal rRNA gene sequences in PCR libraries based on nominally universal primers. The ratios of bacterial/archaeal/eukaryotic rRNA genes, 90%/9%/1%, suggest that the archaeal contribution to the metabolic activities of the mat may be significant. To explore the distribution of archaea in the mat, sequences derived using archaeon-specific PCR primers were surveyed in 10 strata of the 6-cm-thick mat. The diversity of archaea overall was substantial albeit less than the diversity observed previously for bacteria. Archaeal diversity, mainly euryarchaeotes, was highest in the uppermost 2 to 3 mm of the mat and decreased rapidly with depth, where crenarchaeotes dominated. Only 3% of the sequences were specifically related to known organisms including methanogens. While some mat archaeal clades corresponded with known chemical gradients, others did not, which is likely explained by heretofore-unrecognized gradients. Some clades did not segregate by depth in the mat, indicating broad metabolic repertoires, undersampling, or both.
Molecular Ecology of
Listeria monocytogenes
: Evidence for a Reservoir in Milking Equipment on a Dairy Farm
Authors: Latorre Alejandra A. , Van Kessel Jo Ann S. , Karns Jeffrey S. , Zurakowski Michael J. , Pradhan Abani K. , Zadoks Ruth N. , Boor Kathryn J. , Schukken Ynte H.
Published: December 2008

A longitudinal study aimed to detect
Listeria monocytogenes
on a New York State dairy farm was conducted between February 2004 and July 2007. Fecal samples were collected every 6 months from all lactating cows. Approximately 20 environmental samples were obtained every 3 months. Bulk tank milk samples and in-line milk filter samples were obtained weekly. Samples from milking equipment and the milking parlor environment were obtained in May 2007. Fifty-one of 715 fecal samples (7.1%) and 22 of 303 environmental samples (7.3%) were positive for
L. monocytogenes
. A total of 73 of 108 in-line milk filter samples (67.6%) and 34 of 172 bulk tank milk samples (19.7%) were positive for
L. monocytogenes. Listeria monocytogenes
was isolated from 6 of 40 (15%) sampling sites in the milking parlor and milking equipment. In-line milk filter samples had a greater proportion of
L. monocytogenes
than did bulk tank milk samples (
P
< 0.05) and samples from other sources (
P
< 0.05). The proportion of
L. monocytogenes
-positive samples was greater among bulk tank milk samples than among fecal or environmental samples (
P
< 0.05). Analysis of 60 isolates by pulsed-field gel electrophoresis (PFGE) yielded 23 PFGE types after digestion with AscI and ApaI endonucleases. Three PFGE types of
L. monocytogenes
were repeatedly found in longitudinally collected samples from bulk tank milk and in-line milk filters.
Pichia anomalaDBVPG 3003 Secretes a Ubiquitin-Like Protein That Has Antimicrobial Activity
Authors: De Ingeniis Jessica , Raffaelli Nadia , Ciani Maurizio , Mannazzu Ilaria
Published: December 2008

The yeast strainPichia anomalaDBVPG 3003 secretes a killer toxin (Pikt) that has antifungal activity againstBrettanomyces/Dekkerasp. yeasts. Pikt interacts with β-1,6-glucan, consistent with binding to the cell wall of sensitive targets. In contrast to that of toxin K1, secreted bySaccharomyces cerevisiae, Pikt killer activity is not mediated by an increase in membrane permeability. Purification of the toxin yielded a homogeneous protein of about 8 kDa, which showed a marked similarity to ubiquitin in terms of molecular mass and N-terminal sequences. Pikt is also specifically recognized by anti-bovine ubiquitin antibodies and, similar to ubiquitin-like peptides, is not absorbed by DEAE-cellulose. However, Pikt differs from ubiquitin in its sensitivity to proteolytic enzymes. Therefore, Pikt appears to be a novel ubiquitin-like peptide that has killer activity.
Telomere Organization in the Ligninolytic Basidiomycete
Pleurotus ostreatus
Authors: Pérez Gúmer , Pangilinan Jasmyn , Pisabarro Antonio G. , Ramírez Lucía
Published: December 2008

Telomeres are structural and functional chromosome regions that are essential for the cell cycle to proceed normally. They are, however, difficult to map genetically and to identify in genome-wide sequence programs because of their structure and repetitive nature. We studied the telomeric and subtelomeric organization in the basidiomycete
Pleurotus ostreatus
using a combination of molecular and bioinformatics tools that permitted us to determine 19 out of the 22 telomeres expected in this fungus. The telomeric repeating unit in
P. ostreatus
is TTAGGG, and the numbers of repetitions of this unit range between 25 and 150. The mapping of the telomere restriction fragments to linkage groups 6 and 7 revealed polymorphisms compatible with those observed by pulsed field gel electrophoresis separation of the corresponding chromosomes. The subtelomeric regions in
Pleurotus
contain genes similar to those described in other eukaryotic systems. The presence of a cluster of laccase genes in chromosome 6 and a bipartite structure containing a Het-related protein and an alcohol dehydrogenase are especially relevant; this bipartite structure is characteristic of the Pezizomycotina fungi
Neurospora crassa
and
Aspergillus terreus
. As far as we know, this is the first report describing the presence of such structures in basidiomycetes and the location of a laccase gene cluster in the subtelomeric region, where, among others, species-specific genes allowing the organism to adapt rapidly to the environment usually map.
Role of the Hya Hydrogenase in Recycling of Anaerobically Produced H
2
in
Salmonella enterica
Serovar Typhimurium
Authors: Zbell Andrea L. , Maier Robert J.
Published: December 2008

Double and triple uptake-type hydrogenase mutants were used to determine which hydrogenase recycles fermentatively produced hydrogen. The Δ
hyb
Δ
hya
and Δ
hyd
Δ
hya
double mutants evolved H
2
at rates similar to that of the triple mutant strain, so Hya alone oxidizes the bulk of H
2
produced during fermentation. When only Hya was present, no hydrogen production was observed in nutrient-limited medium. H
2
uptake assays showed that Hya can oxidize both exogenously added H
2
and formate hydrogen lyase-evolved H
2
anaerobically. Even after anaerobic growth, all three uptake-type hydrogenases could function in the presence of oxygen, including using O
2
as a terminal acceptor.
Targeted Engineering of the Antibacterial Peptide Apidaecin, Based on an In Vivo Monitoring Assay System
Authors: Taguchi Seiichi , Mita Kensuke , Ichinohe Kenta , Hashimoto Shigeki
Published: December 2008

Seven mutant forms of the antibacterial peptide apidaecin with increased activity were created by combinatorial mutagenesis targeted to the three N-terminal amino acid residues that had previously been identified as a nonessential region. An in vitro MIC assay revealed that the amino acid substitutions in the functionally variable region were effective in improving differential activity toward the four gram-negative bacteria tested, while a gram-positive bacterium was unaffected.
Poultry-Associated
Salmonella enterica
subsp.
enterica
Serovar 4,12:d:− Reveals High Clonality and a Distinct Pathogenicity Gene Repertoire
Authors: Huehn Stephan , Bunge Cornelia , Junker Ernst , Helmuth Reiner , Malorny Burkhard
Published: December 2008

A European baseline survey during the years 2005 and 2006 has revealed that the monophasic
Salmonella enterica
subsp.
enterica
serovar 4,12:d:− was, with a prevalence of 23.6%, the most frequently isolated serovar in German broiler flocks. In Denmark and the United Kingdom, its serovar prevalences were 15.15% and 2.8%, respectively. Although poultry is a major source of human salmonellosis, serovar 4,12:d:− is rarely isolated in humans (approximately 0.09% per year). Molecular typing studies using pulsed-field gel electrophoresis and DNA microarray analysis show that the serovar is highly clonal and lacks genes with known contributions to pathogenicity. In contrast to other poultry-associated serovars, all strains were susceptible to 17 antimicrobial agents tested and did not encode any resistance determinant. Furthermore, serovar 4,12:d:− lacked the genes involved in galactonate metabolism and in the glycolysis and glyconeogenesis important for energy production in the cells. The conclusion of the study is that serovar 4,12:d:− seems to be primarily adapted to broilers and therefore causes only rare infections in humans.
Iron Requirement for Mn(II) Oxidation by
Leptothrix discophora
SS-1
Authors: El Gheriany Iman A. , Bocioaga Daniela , Hay Anthony G. , Ghiorse William C. , Shuler Michael L. , Lion Leonard W.
Published: December 2008

A common form of biocatalysis of Mn(II) oxidation results in the formation of biogenic Mn(III, IV) oxides and is a key reaction in the geochemical cycling of Mn. In this study, we grew the model Mn(II)-oxidizing bacterium
Leptothrix discophora
SS-1 in media with limited iron (0.1 μM iron/5.8 mM pyruvate) and sufficient iron (0.2 μM iron/5.8 mM pyruvate). The influence of iron on the rate of extracellular Mn(II) oxidation was evaluated. Cultures in which cell growth was limited by iron exhibited reduced abilities to oxidize Mn(II) compared to cultures in medium with sufficient iron. While the extracellular Mn(II)-oxidizing factor (MOF) is thought to be a putative multicopper oxidase, Mn(II) oxidation in the presence of zero added Cu(II) was detected and the decrease in the observed Mn(II) oxidation rate in iron-limited cultures was not relieved when the medium was supplemented with Cu(II). The decline of Mn(II) oxidation under iron-limited conditions was not accompanied by siderophore production and is unlikely to be an artifact of siderophore complex formation with Mn(III). The temporal variations in
mofA
gene transcript levels under conditions of limited and abundant iron were similar, indicating that iron limitation did not interfere with the transcription of the
mofA
gene. Our quantitative PCR results provide a step forward in understanding the regulation of Mn(II) oxidation. The mechanistic role of iron in Mn(II) oxidation is uncertain; the data are consistent with a direct requirement for iron as a component of the MOF or an indirect effect of iron resulting from the limitation of one of many cellular functions requiring iron.
Physicochemical Basis for the Inhibitory Effects of Organic and Inorganic Salts on the Growth of
Pectobacterium carotovorum
subsp.
carotovorum
and
Pectobacterium atrosepticum
Authors: Yaganza Elian-Simplice , Tweddell Russell J. , Arul Joseph
Published: December 2008

Twenty-one salts were tested for their effects on the growth of
Pectobacterium carotovorum
subsp.
carotovorum
and
Pectobacterium atrosepticum
. In liquid medium, 11 salts (0.2 M) exhibited strong inhibition of bacterial growth. The inhibitory action of salts relates to the water-ionizing capacity and the lipophilicity of their constituent ions.
DNA Sequencing and Homologous Expression of a Small Peptide Conferring Immunity to Gassericin A, a Circular Bacteriocin Produced by
Lactobacillus gasseri
LA39
Authors: Kawai Yasushi , Kusnadi Joni , Kemperman Rober , Kok Jan , Ito Yoshiyuki , Endo Mikiko , Arakawa Kensuke , Uchida Hideaki , Nishimura Junko , Kitazawa Haruki , Saito Tadao
Published: December 2008

Gassericin A, produced by
Lactobacillus gasseri
LA39, is a hydrophobic circular bacteriocin. The DNA region surrounding the gassericin A structural gene,
gaaA
, was sequenced, and seven open reading frames (ORFs) of 3.5 kbp (
gaaBCADITE
) were found with possible functions in gassericin A production, secretion, and immunity. The deduced products of the five consecutive ORFs
gaaADITE
have homology to those of genes involved in butyrivibriocin AR10 production, although the genetic arrangements are different in the two circular bacteriocin genes. GaaI is a small, positively charged hydrophobic peptide of 53 amino acids containing a putative transmembrane segment. Heterologous expression and homologous expression of GaaI in
Lactococcus lactis
subsp.
cremoris
MG1363 and
L. gasseri
JCM1131
T
, respectively, were studied. GaaI-expressing strains exhibited at least sevenfold-higher resistance to gassericin A than corresponding control strains, indicating that
gaaI
encodes an immunity peptide for gassericin A. Comparison of GaaI to peptides with similar characteristics found in the circular bacteriocin gene loci is discussed.
Anaerobic Biodegradation of
n
-Hexadecane by a Nitrate-Reducing Consortium
Authors: Callaghan Amy V. , Tierney Meghan , Phelps Craig D. , Young L. Y.
Published: December 2008

Nitrate-reducing enrichments, amended with
n
-hexadecane, were established with petroleum-contaminated sediment from Onondaga Lake. Cultures were serially diluted to yield a sediment-free consortium. Clone libraries and denaturing gradient gel electrophoresis analysis of 16S rRNA gene community PCR products indicated the presence of uncultured alpha- and betaproteobacteria similar to those detected in contaminated, denitrifying environments. Cultures were incubated with H
34
-hexadecane, fully deuterated hexadecane (
d
34
-hexadecane), or H
34
-hexadecane and NaH
13
CO
3
. Gas chromatography-mass spectrometry analysis of silylated metabolites resulted in the identification of [H
29
]pentadecanoic acid, [H
25
]tridecanoic acid, [1-
13
C]pentadecanoic acid, [3-
13
C]heptadecanoic acid, [3-
13
C]10-methylheptadecanoic acid, and
d
27
-pentadecanoic,
d
25
-, and
d
2
4
-tridecanoic acids. The identification of these metabolites suggests a carbon addition at the C-3 position of hexadecane, with subsequent β-oxidation and transformation reactions (chain elongation and C-10 methylation) that predominantly produce fatty acids with odd numbers of carbons. Mineralization of [1-
14
C]hexadecane was demonstrated based on the recovery of
14
CO
2
in active cultures.
Capsule Polysaccharide Conjugate Vaccine against Diarrheal Disease Caused by
Campylobacter jejuni
Authors: Monteiro Mario A. , Baqar Shahida , Hall Eric R. , Chen Yu-Han , Porter Chad K. , Bentzel David E. , Applebee Lisa , Guerry Patricia
Published: December 2008

The capsule polysaccharide (CPS) of
Campylobacter jejuni
is one of the few identified virulence determinants of this important human pathogen. Since CPS conjugate vaccines have been so effective against other mucosal pathogens, we evaluated this approach using CPSs from two strains of
C. jejuni
, 81-176 (HS23 and HS36 serotype complex) and CG8486 (HS4 serotype complex). The CPSs of 81-176 and CG8486 were independently linked to the carrier protein CRM
197
by reductive amination between an aldehyde(s), strategically created at the nonreducing end of each CPS, and accessible amines of CRM
197
. In both cases, the CPS:CRM
197
ratio used was 2:1 by weight. Mass spectrometry and gel electrophoresis showed that on average, each glycoconjugate preparation contained, at least in part, two to five CPSs attached to one CRM
197
. When administered subcutaneously to mice, these vaccines elicited robust immune responses and significantly reduced the disease following intranasal challenge with the homologous strains of
C. jejuni
. The CPS
81-176
-CRM
197
vaccine also provided 100% protection against diarrhea in the New World monkey
Aotus nancymaae
following orogastric challenge with
C. jejuni
81-176.
Essential Role of the SycP Chaperone in Type III Secretion of the YspP Effector
Authors: Matsumoto Hiroyuki , Young Glenn M.
Published: December 2008

The Ysa type III secretion (T3S) system enhances gastrointestinal infection byYersinia enterocoliticabv. 1B. One effector protein targeted into host cells is YspP, a protein tyrosine phosphatase. It was determined in this study that the secretion of YspP requires a chaperone, SycP. Genetic analysis showed that deletion ofsycPcompletely abolished the secretion of YspP without affecting the secretion of other Ysps by the Ysa T3S system. Analysis of the secretion and translocation signals of YspP defined the first 73 amino acids to form the minimal region of YspP necessary to promote secretion and translocation by the Ysa T3S system. Function of the YspP secretion/translocation signals was dependent on SycP. Curiously, when YspP was constitutively expressed inY. enterocoliticabv. 1B, it was recognized and secreted by the Ysc T3S system and the flagellar T3S system. In these cases, the first 21 amino acids were sufficient to promote secretion, and while SycP did enhance secretion, it was not essential. However, neither the Ysc T3S system nor the flagellar T3S system translocated YspP into mammalian cells. This supports a model where SycP confers secretion/translocation specificities for YspP by the Ysa T3S system. A series of biochemical approaches further established that SycP specifically interacts with YspP and protected YspP degradation in the cell prior to secretion. Collectively, the evidence suggests that YspP secretion by the Ysa T3S system is a posttranslational event.
Social Interactions and Distribution of
Bacillus subtilis
Pherotypes at Microscale
Authors: Stefanic Polonca , Mandic-Mulec Ines
Published: December 2008

Bacillus subtilis
strains communicate through the
comQXPA
quorum sensing (QS) system, which regulates genes expressed during early stationary phase. A high polymorphism of
comQXP
′ loci was found in closely related strains isolated from desert soil samples separated by distances ranging from meters to kilometers. The observed polymorphism comprised four communication groups (pherotypes), such that strains belonging to the same pherotype exchanged information efficiently but strains from different pherotypes failed to communicate. To determine whether the same level of polymorphism in the
comQXP
′ QS system could be detected at microscale,
B. subtilis
isolates were obtained from two separate 1-cm
3
soil samples, which were progressively divided into smaller sections. Cross-activation studies using pherotype-responsive reporter strains indicated the same number of communication pherotypes at microscale as previously determined at macroscale. Sequencing of the housekeeping gene
gyrA
and the QS
comQ
gene confirmed different evolutionary rates of these genes. Furthermore, an asymmetric communication response was detected inside the two pherotype clusters, suggesting continuous evolution of the QS system and possible development of new languages. To our knowledge, this is the first microscale study demonstrating the presence of different QS languages among isolates of one species, and the implications of this microscale diversity for microbial interactions are discussed.
Three
Mycobacterium tuberculosis
Rel Toxin-Antitoxin Modules Inhibit Mycobacterial Growth and Are Expressed in Infected Human Macrophages
Authors: Korch Shaleen B. , Contreras Heidi , Clark-Curtiss Josephine E.
Published: December 2008

Mycobacterium tuberculosis
protein pairs Rv1246c-Rv1247c, Rv2865-Rv2866, and Rv3357-Rv3358, here named RelBE, RelFG, and RelJK, respectively, were identified based on homology to the
Escherichia coli
RelBE toxin:antitoxin (TA) module. In this study, we have characterized each Rel protein pair and have established that they are functional TA modules. Overexpression of individual
M. tuberculosis rel
toxin genes
relE
,
relG
, and
relK
induced growth arrest in
Mycobacterium smegmatis
; a phenotype that was completely reversible by expression of their cognate antitoxin genes,
relB
,
relF
, and
relJ
, respectively. We also provide evidence that RelB and RelE interact directly, both in vitro and in vivo. Analysis of the genetic organization and regulation established that
relBE
,
relFG
, and
relJK
form bicistronic operons that are cotranscribed and autoregulated, in a manner unlike typical TA modules. RelB and RelF act as transcriptional activators, inducing expression of their respective promoters. However, RelBE, RelFG, and RelJK (together) repress expression to basal levels of activity, while RelJ represses promoter activity altogether. Finally, we have determined that all six
rel
genes are expressed in broth-grown
M. tuberculosis
, whereas
relE
,
relF
, and
relK
are expressed during infection of human macrophages. This is the first demonstration of
M. tuberculosis
expressing TA modules in broth culture and during infection of human macrophages.
Analysis of ColE1 MbeC Unveils an Extended Ribbon-Helix-Helix Family of Nicking Accessory Proteins
Authors: Varsaki Athanasia , Moncalián Gabriel , del Pilar Garcillán-Barcia Maria , Drainas Constantin , de la Cruz Fernando
Published: December 2008

MbeC is a 13-kDa ColE1-encoded protein required for efficient mobilization of ColE1, a plasmid widely used in cloning vector technology. MbeC protein was purified and used for in vitro DNA binding, which showed that it binds specifically double-stranded DNA (dsDNA) containing the ColE1
oriT
. Amino acid sequence comparison and secondary structure prediction imply that MbeC is related to the ribbon-helix-helix (RHH) protein family. Alignment with RHH members pointed to a conserved arginine (R13 in MbeC) that was mutated to alanine. The mutant MbeC(R13A) was unable to bind either single-stranded DNA or dsDNA. Limited proteolysis fragmented MbeC in two stable folding domains: the N-terminal domain, which contains the RHH motif, and the C-terminal domain, which comprises a signature shared by nicking accessory proteins. The results indicate that MbeC plays a similar role in conjugation as TraY and TrwA of plasmids F and R388, respectively. Thus, it appears that an extended, possibly universal mechanism of DNA conjugative processing exists, in which
oriT
-processing is carried out by relaxases assisted by homologous nicking accessory proteins. This mechanism seems to be shared by all major conjugative systems analyzed thus far.
Role of Conjugative Elements in the Evolution of the Multidrug-Resistant Pandemic CloneStreptococcus pneumoniaeSpain23FST81
Authors: Croucher Nicholas J. , Walker Danielle , Romero Patricia , Lennard Nicola , Paterson Gavin K. , Bason Nathalie C. , Mitchell Andrea M. , Quail Michael A. , Andrew Peter W. , Parkhill Julian , Bentley Stephen D. , Mitchell Tim J.
Published: December 2008

Streptococcus pneumoniaeis a human commensal and pathogen able to cause a variety of diseases that annually result in over a million deaths worldwide. TheS. pneumoniaeSpain23Fsequence type 81 lineage was among the first recognized pandemic clones and was responsible for almost 40% of penicillin-resistant pneumococcal infections in the United States in the late 1990s. Analysis of the chromosome sequence of a representative strain, and comparison with other available genomes, indicates roles for integrative and conjugative elements in the evolution of pneumococci and, more particularly, the emergence of the multidrug-resistant Spain 23F ST81 lineage. A number of recently acquired loci within the chromosome appear to encode proteins involved in the production of, or immunity to, antimicrobial compounds, which may contribute to the proficiency of this strain at nasopharyngeal colonization. However, further sequencing of other pandemic clones will be required to establish whether there are any general attributes shared by these strains that are responsible for their international success.
Regulation of Expression of the Region 3 Promoter of theEscherichia coliK5 Capsule Gene Cluster Involves H-NS, SlyA, and a Large 5′ Untranslated Region
Authors: Xue Peng , Corbett David , Goldrick Marie , Naylor Clare , Roberts Ian S.
Published: December 2008

Escherichia coligroup 2 capsule gene clusters are temperature regulated, being expressed at 37°C but not at 20°C. Expression is regulated at the level of transcription by two convergent promoters, PR1 and PR3. In this paper, we show that regulation of transcription from PR3 involves a number of novel features including H-NS, SlyA, and a large 741-bp 5′ untranslated region (UTR). H-NS represses transcription from PR3 at 20°C and binds both 5′ and 3′ of the transcription start site. The 3′ downstream regulatory element (DRE) was essential for temperature-dependent H-NS repression. At 37°C, SlyA activates transcription independent of H-NS but maximal transcription requires H-NS. The UTR is present between the transcription start site and the first gene in the operon,kpsM. We demonstrate that the UTR, as well as containing the H-NS DRE, functions to moderate the extent of transcription that reacheskpsMand allows the binding of antitermination factor RfaH.
Characterization of theEscherichia coliO157:H7 Sakai GadE Regulon
Authors: Kailasan Vanaja Sivapriya , Bergholz Teresa M. , Whittam Thomas S.
Published: December 2008

Integrating laterally acquired virulence genes into the backbone regulatory network is important for the pathogenesis ofEscherichia coliO157:H7, which has captured many virulence genes through horizontal transfer during evolution. GadE is an essential transcriptional activator of the glutamate decarboxylase (GAD) system, the most efficient acid resistance (AR) mechanism inE. coli. The full contribution of GadE to the AR and virulence ofE. coliO157:H7 remains largely unknown. We inactivatedgadEinE. coliO157:H7 Sakai and compared global transcription profiles of the mutant with that of the wild type in the exponential and stationary phases of growth. Inactivation ofgadEsignificantly altered the expression of 60 genes independently of the growth phase and of 122 genes in a growth phase-dependent manner. Inactivation ofgadEmarkedly downregulated the expression ofgadA, gadB, andgadCand of many acid fitness island genes. Nineteen genes encoded on the locus of enterocyte effacement (LEE), includingler, showed a significant increase in expression upongadEinactivation. Inactivation oflerin the ΔgadEstrain reversed the effect ofgadEdeletion on LEE expression, indicating that Ler is necessary for LEE repression by GadE. GadE is also involved in downregulation of LEE expression under conditions of moderately acidic pH. Characterization of AR of the ΔgadEstrain revealed that GadE is indispensable for a functional GAD system and for survival ofE. coliO157:H7 in a simulated gastric environment. Altogether, these data indicate that GadE is critical for the AR ofE. coliO157:H7 and that it plays an important role in virulence by downregulating expression of LEE.
TtgV Represses Two Different Promoters by Recognizing Different Sequences
Authors: Fillet Sandy , Vélez Marisela , Lu Duo , Zhang Xiaodong , Gallegos María-Trinidad , Ramos Juan L.
Published: December 2008

Expression of the multidrug efflux pumpttgDEFandttgGHIoperons is modulated in vivo mainly by the TtgV repressor. TtgV is a multidrug recognition repressor that exhibits a DNA binding domain with a long interaction helix comprising residues 47 to 64. The pattern of expression of the two pumps is different inPseudomonas putida: in the absence of effectors, the promoter for thettgDgene is silent, whereas thettgGgene is expressed at a high basal level. This correlates with the fact that TtgV exhibits a higher affinity for thettgDoperator (KD= 10 ± 1 nM) than for thettgG(KD= 19 ± 1 nM) operator. Sequence analysis revealed that both operators are 40% identical, and mutational analysis of thettgDandttgGoperators combined with electrophoretic mobility shift assays and in vivo expression analysis suggests that TtgV recognizes an inverted repeat with a high degree of palindromicity around the central axis. We generated a collection of alanine substitution mutants with substitutions between residues 47 and 64 of TtgV. The results of extensive combinations of promoter variants with these TtgV alanine substitution mutants revealed that TtgV modulates expression fromttgDandttgGpromoters through the recognition of both common and different sequences in the two promoters. In this regard, we found that TtgV mutants at residues 48, 50, 53, 54, 60, and 61 failed to bindttgGbut recognized thettgDoperator. TtgV residues R47, R52, L57, and T49 are critical for binding to both operators. Based on three-dimensional models, we propose that these residues contact nucleotides within the major groove of DNA.
Complete Genome Sequence of the Anaerobic, Protein-Degrading Hyperthermophilic Crenarchaeon
Desulfurococcus kamchatkensis
Authors: Ravin Nikolai V. , Mardanov Andrey V. , Beletsky Alexey V. , Kublanov Ilya V. , Kolganova Tatiana V. , Lebedinsky Alexander V. , Chernyh Nikolai A. , Bonch-Osmolovskaya Elizaveta A. , Skryabin Konstantin G.
Published: December 2008

Desulfurococcus kamchatkensis
is an anaerobic organotrophic hyperthermophilic crenarchaeon isolated from a terrestrial hot spring. Its genome consists of a single circular chromosome of 1,365,223 bp with no extrachromosomal elements. A total of 1,474 protein-encoding genes were annotated, among which 205 are exclusive for
D. kamchatkensis
. The search for a replication origin site revealed a single region coinciding with a global extreme of the nucleotide composition disparity curve and containing a set of crenarchaeon-type origin recognition boxes. Unlike in most archaea, two genes encoding homologs of the eukaryotic initiator proteins Orc1 and Cdc6 are located distantly from this site. A number of mobile elements are present in the genome, including seven transposons representing IS
607
and IS
200
/IS
605
families and multiple copies of miniature inverted repeat transposable elements. Two large clusters of regularly interspaced repeats are present; none of the spacer sequences matches known archaeal extrachromosomal elements, except one spacer matches the sequence of a resident gene of
D. kamchatkensis
. Many of the predicted metabolic enzymes are associated with the fermentation of peptides and sugars, including more than 30 peptidases with diverse specificities, a number of polysaccharide degradation enzymes, and many transporters. Consistently, the genome encodes both enzymes of the modified Embden-Meyerhof pathway of glucose oxidation and a set of enzymes needed for gluconeogenesis. The genome structure and content reflect the organism's nutritionally diverse, competitive natural environment, which is periodically invaded by viruses and other mobile elements.