bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of Effects of Compost Amendment and of Single-Strain Inoculation on Root Bacterial Communities of Young Cucumber Seedlings
Authors: Ofek Maya , Hadar Yitzhak , Minz Dror
Published: August 2009

Compost amendment and inoculations with specific microorganisms are fundamentally different soil treatment methods, commonly used in agriculture for the improvement of plant growth and health. Although distinct, both methods affect the rhizosphere and the plant roots. In the present study we used a 16S rRNA gene approach to achieve an overview of early consequences of these treatments on the assemblage of plant root bacterial communities. For this purpose, cucumber seedlings were grown, under controlled conditions, in perlite potting mix amended with biosolid compost or straw compost, or inoculated with
Streptomyces
spp. A uniform trend of response of root bacterial communities for all treatments was observed. Root bacterial density, measured as bacterial targets per plant
tef
gene by real-time PCR, was reduced in 31 to 67%. In addition, increased taxonomic diversity accompanied shifts in composition (α-diversity). The magnitude of change in these parameters relative to the perlite control varied between the different treatments but not in relation to the treatment method (compost amendments versus inoculations). Similarity between the compositions of root and of potting mix bacterial communities (β-diversity) was relatively unchanged. The abundance of
Oxalobacteraceae
was >50% of the total root bacterial community in the untreated perlite. Root domination by this group subsided >10-fold (straw compost) to >600-fold (
Streptomyces
sp. strain S1) after treatment. Thus, loss of dominance appears to be the major phenomenon underlining the response trend of the root bacterial communities.
Assessment of Shiga Toxin-ProducingEscherichia coliIsolates from Wildlife Meat as Potential Pathogens for Humans
Authors: Miko Angelika , Pries Karin , Haby Sabine , Steege Katja , Albrecht Nadine , Krause Gladys , Beutin Lothar
Published: August 2009

A total of 140 Shiga toxin-producingEscherichia coli(STEC) strains from wildlife meat (deer, wild boar, and hare) isolated in Germany between 1998 and 2006 were characterized with respect to their serotypes and virulence markers associated with human pathogenicity. The strains grouped into 38 serotypes, but eight O groups (21, 146, 128, 113, 22, 88, 6, and 91) and four H types (21, 28, 2, and 8) accounted for 71.4% and 75.7% of all STEC strains from game, respectively. Eighteen of the serotypes, including enterohemorrhagicE. coli(EHEC) O26:[H11] and O103:H2, were previously found to be associated with human illness. Genes linked to high-level virulence for humans (stx2,stx2d, andeae) were present in 46 (32.8%) STEC strains from game. Fifty-four STEC isolates from game belonged to serotypes which are frequently found in human patients (O103:H2, O26:H11, O113:H21, O91:H21, O128:H2, O146:H21, and O146:H28). These 54 STEC isolates were compared with 101 STEC isolates belonging to the same serotypes isolated from farm animals, from their food products, and from human patients. Within a given serotype, most STEC strains were similar with respect to theirstxgenotypes and other virulence attributes, regardless of origin. The 155 STEC strains were analyzed for genetic similarity by XbaI pulsed-field gel electrophoresis. O103:H2, O26:H11, O113:H21, O128:H2, and O146:H28 STEC isolates from game were 85 to 100% similar to STEC isolates of the same strains from human patients. By multilocus sequence typing, game EHEC O103:H2 strains were attributed to a clonal lineage associated with hemorrhagic diseases in humans. The results from our study indicate that game animals represent a reservoir for and a potential source of human pathogenic STEC and EHEC strains.
Diversity, Abundance, and Consistency of Microbial Oxygenase Expression and Biodegradation in a Shallow Contaminated Aquifer
Authors: Yagi Jane M. , Madsen Eugene L.
Published: August 2009

The diversity of Rieske dioxygenase genes and short-term temporal variability in the abundance of two selected dioxygenase gene sequences were examined in a naphthalene-rich, coal tar waste-contaminated subsurface study site. Using a previously published PCR-based approach (S. M. Ní Chadhain, R. S. Norman, K. V. Pesce, J. J. Kukor, and G. J. Zylstra, Appl. Environ. Microbiol. 72:4078-4087, 2006) a broad suite of genes was detected, ranging from dioxygenase sequences associated with
Rhodococcus
and
Sphingomonas
to 32 previously uncharacterized Rieske gene sequence clone groups. The
nag
genes appeared frequently (20% of the total) in two groundwater monitoring wells characterized by low (∼10
2
ppb; ∼1 μM) ambient concentrations of naphthalene. A quantitative competitive PCR assay was used to show that abundances of
nag
genes (and archetypal
nah
genes) fluctuated substantially over a 9-month period. To contrast short-term variation with long-term community stability, in situ community gene expression (dioxygenase mRNA) and biodegradation potential (community metabolism of naphthalene in microcosms) were compared to measurements from 6 years earlier. cDNA sequences amplified from total RNA extracts revealed that
nah-
and
nag
-type genes were expressed in situ, corresponding well with structural gene abundances. Despite evidence for short-term (9-month) shifts in dioxygenase gene copy number, agreement in field gene expression (dioxygenase mRNA) and biodegradation potential was observed in comparisons to equivalent assays performed 6 years earlier. Thus, stability in community biodegradation characteristics at the hemidecadal time frame has been documented for these subsurface microbial communities.
Afforestation Alters the Composition of Functional Genes in Soil and Biogeochemical Processes in South American Grasslands
Authors: Berthrong Sean T. , Schadt Christopher W. , Piñeiro Gervasio , Jackson Robert B.
Published: August 2009

Soil microbes are highly diverse and control most soil biogeochemical reactions. We examined how microbial functional genes and biogeochemical pools responded to the altered chemical inputs accompanying land use change. We examined paired native grasslands and adjacentEucalyptusplantations (previously grassland) in Uruguay, a region that lacked forests before European settlement. Along with measurements of soil carbon, nitrogen, and bacterial diversity, we analyzed functional genes using the GeoChip 2.0 microarray, which simultaneously quantified several thousand genes involved in soil carbon and nitrogen cycling. Plantations and grassland differed significantly in functional gene profiles, bacterial diversity, and biogeochemical pool sizes. Most grassland profiles were similar, but plantation profiles generally differed from those of grasslands due to differences in functional gene abundance across diverse taxa. Eucalypts decreased ammonification and N fixation functional genes by 11% and 7.9% (P< 0.01), which correlated with decreased microbial biomass N and more NH4+in plantation soils. Chitinase abundance decreased 7.8% in plantations compared to levels in grassland (P= 0.017), and C polymer-degrading genes decreased by 1.5% overall (P< 0.05), which likely contributed to 54% (P< 0.05) more C in undecomposed extractable soil pools and 27% less microbial C (P< 0.01) in plantation soils. In general, afforestation altered the abundance of many microbial functional genes, corresponding with changes in soil biogeochemistry, in part through altered abundance of overall functional gene types rather than simply through changes in specific taxa. Such changes in microbial functional genes correspond with altered C and N storage and have implications for long-term productivity in these soils.
ACC (1-Aminocyclopropane-1-Carboxylate) Deaminase Activity, a Widespread Trait in
Burkholderia
Species, and Its Growth-Promoting Effect on Tomato Plants
Authors: Onofre-Lemus Janette , Hernández-Lucas Ismael , Girard Lourdes , Caballero-Mellado Jesús
Published: August 2009

The genus
Burkholderia
includes pathogens of plants and animals and some human opportunistic pathogens, such as the
Burkholderia cepacia
complex (Bcc), but most species are nonpathogenic, plant associated, and rhizospheric or endophytic. Since rhizobacteria expressing ACC (1-aminocyclopropane-1-carboxylate) deaminase may enhance plant growth by lowering plant ethylene levels, in this work we investigated the presence of ACC deaminase activity and the
acdS
gene in 45 strains, most of which are plant associated, representing 20 well-known
Burkholderia
species. The results demonstrated that ACC deaminase activity is a widespread feature in the genus
Burkholderia
, since 18 species exhibited ACC deaminase activities in the range from 2 to 15 μmol of α-ketobutyrate/h/mg protein, which suggests that these species may be able to modulate ethylene levels and enhance plant growth. In these 18
Burkholderia
species the
acdS
gene sequences were highly conserved (76 to 99% identity). Phylogenetic analysis of
acdS
gene sequences in
Burkholderia
showed tight clustering of the Bcc species, which were clearly distinct from diazotrophic plant-associated
Burkholderia
species. In addition, an
acdS
knockout mutant of the N
2
-fixing bacterium
Burkholderia unamae
MTl-641
T
and a transcriptional
acdSp
-
gusA
fusion constructed in this strain showed that ACC deaminase could play an important role in promotion of the growth of tomato plants. The widespread ACC deaminase activity in
Burkholderia
species and the common association of these species with plants suggest that this genus could be a major contributor to plant growth under natural conditions.
Cryptic Lineages of the Genus
Escherichia
Authors: Walk Seth T. , Alm Elizabeth W. , Gordon David M. , Ram Jeffrey L. , Toranzos Gary A. , Tiedje James M. , Whittam Thomas S.
Published: August 2009

Extended multilocus sequence typing (MLST) analysis of atypical
Escherichia
isolates was used to identify five novel phylogenetic clades (CI to CV) among isolates from environmental, human, and animal sources. Analysis of individual housekeeping loci showed that
E. coli
and its sister clade, CI, remain largely indistinguishable and represent nascent evolutionary lineages. Conversely, clades of similar age (CIII and CIV) were found to be phylogenetically distinct. When all
Escherichia
lineages (named and unnamed) were evaluated, we found evidence that
E
scherichia fergusonii
has evolved at an accelerated rate compared to
E. coli
, CI, CIII, CIV, and CV, suggesting that this species is younger than estimated by the molecular clock method. Although the five novel clades were phylogenetically distinct, we were unable to identify a discriminating biochemical marker for all but one of them (CIII) with traditional phenotypic profiling. CIII had a statistically different phenotype from
E. coli
that resulted from the loss of sucrose and sorbitol fermentation and lysine utilization. The lack of phenotypic distinction has likely hindered the ability to differentiate these clades from typical
E. coli
, and so their ecological significance and importance for applied and clinical microbiology are yet to be determined. However, our sampling suggests that CIII, CIV, and CV represent environmentally adapted
Escherichia
lineages that may be more abundant outside the host gastrointestinal tract.
An Mrp-Like Cluster in the Halotolerant Cyanobacterium
Aphanothece halophytica
Functions as a Na
+
/H
+
Antiporter
Authors: Fukaya Fuminori , Promden Worrawat , Hibino Takashi , Tanaka Yoshito , Nakamura Tatsunosuke , Takabe Teruhiro
Published: August 2009

The
mrp
homolog gene cluster
mrpCD1D2EFGAB
(Ap-
mrp
) was found in a halotolerant cyanobacterium,
Aphanothece halophytica
, amplified, and expressed in
Escherichia coli
mutant TO114. Ap-
mrp
complemented the salt-sensitive phenotype of TO114 and exhibited Na
+
/H
+
and Li
+
/H
+
exchange activities, indicating that Ap-Mrp functions as a Na
+
/H
+
antiporter.
Versatile Dual-Technology System for Markerless Allele Replacement in
Burkholderia pseudomallei
Authors: López Carolina M. , Rholl Drew A. , Trunck Lily A. , Schweizer Herbert P.
Published: August 2009

Burkholderia pseudomallei
is the etiologic agent of melioidosis, a rare but serious tropical disease. In the United States, genetic research with this select agent bacterium is strictly regulated. Although several select agent compliant methods have been developed for allelic replacement, all of them suffer from some drawbacks, such as a need for specific host backgrounds or use of minimal media. Here we describe a versatile select agent compliant allele replacement system for
B. pseudomallei
based on a mobilizable vector, pEXKm5, which contains (i) a multiple cloning site within a
lacZ
α gene for facile cloning of recombinant DNA fragments, (ii) a constitutively expressed
gusA
indicator gene for visual detection of merodiploid formation and resolution, and (iii) elements required for resolution of merodiploids using either I-SceI homing endonuclease-stimulated recombination or
sacB-
based counterselection. The homing endonuclease-based allele replacement system is completed by pBADSce, which contains an
araC
-

P
BAD
-I

-
sceI
expression cassette for arabinose-inducible I-SceI expression and a temperature-sensitive pRO1600 replicon for facile plasmid curing. Complementing these systems is the improved Δ
asd Escherichia coli
mobilizer strain RHO3. This strain is susceptible to commonly used antibiotics and allows nutritional counterselection on rich media because of its diaminopimelic acid auxotrophy. The versatility of the I-SceI- and
sacB
-based methods afforded by pEXKm5 in conjunction with
E. coli
RHO3 was demonstrated by isolation of diverse deletion mutants in several clinical, environmental, and laboratory
B. pseudomallei
strains. Finally,
sacB
-based counterselection was employed to isolate a defined chromosomal
fabD
(Ts) allele that causes synthesis of a temperature-sensitive FabD, an essential fatty acid biosynthesis enzyme.
Recovery of Nonpathogenic Mutant Bacteria from Tumors Caused by Several
Agrobacterium tumefaciens
Strains: a Frequent Event?
Authors: Llop Pablo , Murillo Jesús , Lastra Beatriz , López María M.
Published: August 2009

We have evaluated the interaction that bacterial genotypes and plant hosts have with the loss of pathogenicity in tumors, using seven
Agrobacterium tumefaciens
strains inoculated on 12 herbaceous and woody hosts. We performed a screening of the agrobacteria present inside the tumors, looking for nonpathogenic strains, and found a high variability of those strains in this niche. To verify the origin of the putative nonpathogenic mutant bacteria, we applied an efficient, reproducible, and specific randomly amplified polymorphic DNA analysis method. In contrast with previous studies, we recovered a very small percentage (0.01%) of nonpathogenic strains that can be considered true mutants. Of 5,419 agrobacterial isolates examined, 662 were nonpathogenic in tomato, although only 7 (from pepper and tomato tumors induced by two
A. tumefaciens
strains) could be considered to derive from the inoculated strain. Six mutants were affected in the transferred DNA (T-DNA) region; one of them contained IS
426
inserted into the
iaaM
gene, whereas the whole T-DNA region was apparently deleted in three other mutants, and the virulence of the remaining two mutants was fully restored with the T-DNA genes as well. The plasmid profile was altered in six of the mutants, with changes in the size of the Ti plasmid or other plasmids and/or the acquisition of new plasmids. Our results also suggest that the frequent occurrence of nonpathogenic clones in the tumors is probably due to the preferential growth of nonpathogenic agrobacteria, of either endophytic or environmental origin, but different from the bacterial strain inducing the tumor.
Integrated Capture and Spectroscopic Detection of Viruses
Authors: Vargas Crystal A. , Wilhelm Allison A. , Williams Jeremy , Lucas Pierre , Reynolds Kelly A. , Riley Mark R.
Published: August 2009

The goal of this work is to develop an online monitoring scheme for detection of viruses in flowing drinking water. The approach applies an electrodeposition process that is similar to the use of charged membrane filters previously employed for collection of viruses from aqueous samples. In the present approach, charged materials are driven onto a robust optical sensing element which has high transparency to infrared light. A spectroscopic measurement is performed using the evanescent wave that penetrates no more than 1 μm from the surface of an infrared optical element in an attenuated total reflectance measurement scheme. The infrared measurement provides quantitative information on the amount and identity of material deposited from the water. Initial studies of this sensing scheme used proteins reversibly electrodeposited onto germanium chips. The results of those studies were applied to design a method for collection of viruses onto an attenuated total reflectance crystal. Spectral signatures can be discriminated between three types of protein and two viruses. There is the potential to remove deposited material by reversing the voltage polarity. This work demonstrates a novel and practical scheme for detection of viruses in water systems with potential application to near-continual, automated monitoring of municipal drinking water.
Development of a Single-Plasmid-Based Regulatable Gene Expression System for
Borrelia burgdorferi
Authors: Whetstine Christine R. , Slusser Joyce G. , Zückert Wolfram R.
Published: August 2009

We developed a single-plasmid-based regulatable protein expression system for
Borrelia burgdorferi
. Expression of a target gene is driven by P

ost

, a hybrid
B. burgdorferi ospA
-
tetO
promoter, from a recombinant
B. burgdorferi
plasmid constitutively expressing TetR. The system was tested using the green fluorescent protein (GFP) as a reporter. Under noninducing conditions, recombinant
B. burgdorferi
cells were nonfluorescent, no GFP protein was detected, and residual, small amounts of transcript were detectable only by reverse transcription-PCR but not by Northern blot hybridization. Upon induction with anhydrotetracycline, increasing levels of GFP transcript, protein, and fluorescence were observed. This tight and titratable promoter system will be invaluable for the study of essential borrelial proteins. Since target protein, operator, and repressor are carried by a single plasmid, the system's application is independent of a particular strain background.
A Unique 45-Amino-Acid Region in the Toprim Domain of
Plasmodium falciparum
Gyrase B Is Essential for Its Activity
Authors: Dar Ashraf , Prusty Dhaneswar , Mondal Neelima , Dhar Suman K.
Published: August 2009

DNA gyrase is the only topoisomerase that can introduce negative supercoils into the DNA at the cost of ATP hydrolysis. Some but not all the steps of the topoisomerization reaction are understood clearly for both eukaryotic topoII and DNA gyrase. This study is an attempt to understand whether the B subunit of DNA gyrase binds to DNA directly, which may be central to the stimulation of its ATPase activity essential for gyrase function. We have dissected the
Plasmodium falciparum
gyrase B (PfGyrB) subunit to identify a 45-amino-acid region in the toprim domain that is responsible for its intrinsic DNA binding activity, DNA-stimulated ATPase activity, and DNA cleavage. We find that DNA has to enter through the ATP-operated clamp of PfGyrB to gain access to the DNA binding region. Furthermore, the rate of ATP hydrolysis of PfGyrB increases significantly with increasing DNA length, suggesting a possible communication between the ATPase domain and the DNA binding region that can account for its optimal ATPase activity. These results not only highlight the mechanism of GyrB action in the deadly human parasite
P. falciparum
but also provide meaningful insights into the current mechanistic model of DNA transport by gyrase during the topoisomerization reaction.
Transcriptional Responses of
Candida albicans
to Epithelial and Endothelial Cells
Authors: Park Hyunsook , Liu Yaoping , Solis Norma , Spotkov Joshua , Hamaker Jessica , Blankenship Jill R. , Yeaman Michael R. , Mitchell Aaron P. , Liu Haoping , Filler Scott G.
Published: August 2009

Candida albicans
interacts with oral epithelial cells during oropharyngeal candidiasis and with vascular endothelial cells when it disseminates hematogenously. We set out to identify
C. albicans
genes that govern interactions with these host cells in vitro. The transcriptional response of
C. albicans
to the FaDu oral epithelial cell line and primary endothelial cells was determined by microarray analysis. Contact with epithelial cells caused a decrease in transcript levels of genes related to protein synthesis and adhesion, whereas contact with endothelial cells did not significantly influence any specific functional category of genes. Many genes whose transcripts were increased in response to either host cell had not been previously characterized. We constructed mutants with homozygous insertions in 22 of these uncharacterized genes to investigate their function during host-pathogen interaction. By this approach, we found that
YCK2
,
VPS51
, and
UEC1
are required for
C. albicans
to cause normal damage to epithelial cells and resist antimicrobial peptides.
YCK2
is also necessary for maintenance of cell polarity.
VPS51
is necessary for normal vacuole formation, resistance to multiple stressors, and induction of maximal endothelial cell damage.
UEC1
encodes a unique protein that is required for resistance to cell membrane stress. Therefore, some
C. albicans
genes whose transcripts are increased upon contact with epithelial or endothelial cells are required for the organism to damage these cells and withstand the stresses that it likely encounters during growth in the oropharynx and bloodstream.
Role of Ferroxidases in Iron Uptake and Virulence of
Cryptococcus neoformans
Authors: Jung Won Hee , Hu Guanggan , Kuo Wayne , Kronstad James W.
Published: August 2009

Iron acquisition is a critical aspect of the virulence of many pathogenic microbes, and iron limitation is an important defense mechanism for mammalian hosts. We are examining mechanisms of iron regulation and acquisition in the fungal pathogen
Cryptococcus neoformans
, and here, we characterize the roles of the ferroxidases Cfo1 and Cfo2. Cfo1 is required for the reductive iron uptake system that mediates the utilization of transferrin, an important iron source for
C. neoformans
during infection. The virulence of a
cfo1
mutant was attenuated in a mouse model of cryptococcosis, and the mutant also displayed increased sensitivities to the antifungal drugs fluconazole and amphotericin B. Wild-type levels of drug sensitivity were restored by the addition of exogenous heme, which suggested that reduced levels of intracellular iron may curtail heme levels and interfere with ergosterol biosynthesis. We constructed green fluorescent protein (GFP) fusion proteins and found elevated expression of Cfo1-GFP upon iron limitation, as well as localization of the fusion to the plasma membrane. Trafficking to this location was disrupted by a defect in the catalytic subunit of cyclic AMP-dependent protein kinase. This result is consistent with findings from studies indicating an influence of the kinase on the expression of protein-trafficking functions in
C. neoformans
.
The Transcription Factor Homolog CTF1 Regulates β-Oxidation in
Candida albicans
Authors: Ramírez Melissa A. , Lorenz Michael C.
Published: August 2009

Carbon starvation is one of the many stresses to which microbial pathogens are subjected while in the host. Pathways necessary for the utilization of alternative carbon sources, such as gluconeogenesis, the glyoxylate cycle, and β-oxidation of fatty acids, have been shown to be required for full virulence in several systems, including the fungal pathogen
Candida albicans
. We have investigated the regulatory network governing alternative carbon metabolism in this organism through characterization of transcriptional regulators identified based on the model fungi,
Saccharomyces cerevisiae
and
Aspergillus nidulans
.
C. albicans
has homologs of the ScCAT8/AnFacB and ScADR1/AnAmdX transcription factors that regulate induction of genes encoding the proteins of gluconeogenesis, the glyoxylate cycle, and ethanol utilization. Surprisingly,
C. albicans
mutants lacking
CAT8
or
ADR1
have no apparent phenotypes and do not regulate genes for key enzymes of these pathways. Fatty acid degradation and peroxisomal biogenesis are controlled by nonhomologous regulators, OAF1/PIP2 in
S. cerevisiae
and FarA/FarB in
A. nidulans
;
C. albicans
is missing OAF1 and PIP2 and, instead, has a single homolog of the Far proteins, CTF1. We have shown that
CTF1
is required for growth on lipids and for expression of genes necessary for β-oxidation, such as
FOX2
.
ctf1
Δ/
ctf1
Δ (
ctf1
Δ/Δ) strains do not, however, show the pleiotropic phenotypes observed for
fox2
Δ/Δ mutants. The
ctf1
Δ/Δ mutant confers a mild attenuation in virulence, like the
fox2
Δ/Δ mutant. Thus, phenotypic and genotypic observations highlight important differences in the regulatory network for alternative carbon metabolism in
C. albicans
compared to the paradigms developed in other model fungi.
Aneuploid Chromosomes Are Highly Unstable during DNA Transformation of
Candida albicans
Authors: Bouchonville Kelly , Forche Anja , Tang Karen E. S. , Selmecki Anna , Berman Judith
Published: August 2009

Candida albicans
strains tolerate aneuploidy, historically detected as karyotype alterations by pulsed-field gel electrophoresis and more recently revealed by array comparative genome hybridization, which provides a comprehensive and detailed description of gene copy number. Here, we first retrospectively analyzed 411 expression array experiments to predict the frequency of aneuploidy in different strains. As expected, significant levels of aneuploidy were seen in strains exposed to stress conditions, including UV light and/or sorbose treatment, as well as in strains that are resistant to antifungal drugs. More surprisingly, strains that underwent transformation with DNA displayed the highest frequency of chromosome copy number changes, with strains that were initially aneuploid exhibiting ∼3-fold more copy number changes than strains that were initially diploid. We then prospectively analyzed the effect of lithium acetate (LiOAc) transformation protocols on the stability of trisomic chromosomes. Consistent with the retrospective analysis, the proportion of karyotype changes was highly elevated in strains carrying aneuploid chromosomes. We then tested the hypothesis that stresses conferred by heat and/or LiOAc exposure promote chromosome number changes during DNA transformation procedures. Indeed, a short pulse of very high temperature caused frequent gains and losses of multiple chromosomes or chromosome segments. Furthermore, milder heat exposure over longer periods caused increased levels of loss of heterozygosity. Nonetheless, aneuploid chromosomes were also unstable when strains were transformed by electroporation, which does not include a heat shock step. Thus, aneuploid strains are particularly prone to undergo changes in chromosome number during the stresses of DNA transformation protocols.
Importance of Proteins Controlling Initiation of DNA Replication in the Growth of the High-Pressure-Loving Bacterium
Photobacterium profundum
SS9
Authors: El-Hajj Ziad W. , Tryfona Theodora , Allcock David J. , Hasan Fariha , Lauro Federico M. , Sawyer Lindsay , Bartlett Douglas H. , Ferguson Gail P.
Published: August 2009

The molecular mechanism(s) by which deep-sea bacteria grow optimally under high hydrostatic pressure at low temperatures is poorly understood. To gain further insight into the mechanism(s), a previous study screened transposon mutant libraries of the deep-sea bacterium
Photobacterium profundum
SS9 and identified mutants which exhibited alterations in growth at high pressure relative to that of the parent strain. Two of these mutants, FL23 (PBPRA3229::mini-Tn
10
) and FL28 (PBPRA1039::mini-Tn
10
), were found to have high-pressure sensitivity and enhanced-growth phenotypes, respectively. The PBPRA3229 and PBPRA1039 genes encode proteins which are highly similar to
Escherichia coli
DiaA, a positive regulator, and SeqA, a negative regulator, respectively, of the initiation of DNA replication. In this study, we investigated the hypothesis that PBPRA3229 and PBPRA1039 encode DiaA and SeqA homologs, respectively. Consistent with this, we determined that the plasmid-carried PBPRA3229 and PBPRA1039 genes restored synchrony to the initiation of DNA replication in
E. coli
mutants lacking DiaA and SeqA, respectively. Additionally, PBPRA3229 restored the cold sensitivity phenotype of an
E. coli dnaA
(Cs)
diaA
double mutant whereas PBPRA1039 suppressed the cold sensitivity phenotype of an
E. coli dnaA
(Cs) single mutant. Taken together, these findings show that the genes disrupted in FL23 and FL28 encode DiaA and SeqA homologs, respectively. Consequently, our findings add support to a model whereby high pressure affects the initiation of DNA replication in
P. profundum
SS9 and either the presence of a positive regulator (DiaA) or the removal of a negative regulator (SeqA) promotes growth under these conditions.
Tetracycline-Associated Transcriptional Regulation of Transfer Genes of the
Bacteroides
Conjugative Transposon CTnDOT
Authors: Jeters Robert T. , Wang Gui-Rong , Moon Kyung , Shoemaker Nadja B. , Salyers Abigail A.
Published: August 2009

Many human colonic
Bacteroides
spp. harbor a conjugative transposon, CTnDOT, which carries two antibiotic resistance genes,
tetQ
and
ermF
. A distinctive feature of CTnDOT is that its excision and transfer are stimulated by tetracycline. Regulation of the genes responsible for excision has been described previously. We provide here the first characterization of the regulation of CTnDOT transfer (
tra
) genes. Reverse transcription-PCR analysis of the region containing the
tra
genes showed that these genes are regulated at the transcriptional level. Surprisingly, increased production of
tra
gene mRNA in tetracycline-stimulated cells was mediated by the proteins encoded by the excision genes. Previous studies have shown that expression of the excision gene operon is controlled by the regulatory protein RteC. Accordingly, it was possible that RteC was also regulating
tra
gene expression and that the excision proteins were only accessory proteins. However, placing the excision gene operon under the control of a heterologous promoter showed that the excision proteins alone could activate
tra
gene expression and that RteC was not directly involved. We also found a second level of
tra
gene control. The transfer of CTnDOT was inhibited by a DNA segment that included only a portion of the 3′ end of one of the excision genes (
exc
). This segment contained a small open reading frame,
rteR
. By replacing the codons encoding the first two amino acids of the putative protein product of this open reading frame with stop codons, we showed that the
rteR
gene might encode a small regulatory RNA. RteR acted in
trans
to reduce the number of
tra
transcripts in a way that was independent of the excision proteins. The repressive effect of RteR was not the result of decreased stability of the
tra
mRNA. Instead, RteR appears to be modulating the level of
tra
gene expression in some more direct fashion. The complex regulatory system that controls and links the expression of CTnDOT excision and transfer genes may be designed to ensure stable maintenance of CTnDOT in nature by reducing the fitness toll it takes on the cell that harbors it.
Organophosphate Hydrolase in
Brevundimonas diminuta
Is Targeted to the Periplasmic Face of the Inner Membrane by the Twin Arginine Translocation Pathway
Authors: Gorla Purushotham , Pandey Jay Prakash , Parthasarathy Sunil , Merrick Mike , Siddavattam Dayananda
Published: August 2009

A twin arginine translocation (Tat) motif, involved in transport of folded proteins across the inner membrane, was identified in the signal peptide of the membrane-associated organophosphate hydrolase (OPH) of
Brevundimonas diminuta
. Expression of the precursor form of OPH carrying a C-terminal His tag in an
opd
-negative background and subsequent immunoblotting with anti-His antibodies showed that only the mature form of OPH associated with the membrane and that the precursor form of OPH was entirely found in the cytoplasm. When OPH was expressed without the signal peptide, most of it remained in the cytoplasm, where it was apparently correctly folded and showed activity comparable to that of the membrane-associated OPH encoded by the wild-type
opd
gene. Amino acid substitutions in the invariant arginine residues of the Tat signal peptide affected both the processing and localization of OPH, confirming a critical role for the Tat system in membrane targeting of OPH in
B. diminuta
. The localization of OPH to the periplasmic face of the inner membrane in
B. diminuta
was demonstrated by proteinase K treatment of spheroplasts and also by fluorescence-activated cell sorting analysis of cells expressing OPH-green fluorescent protein fusions with and without an SsrA tag that targets cytoplasmic proteins to the ClpXP protease.
Physical fitness levels among European adolescents: the HELENA study
Authors: Ortega F B , Artero E G , Ruiz J R , España-Romero V , Jiménez-Pavón D , Vicente-Rodriguez G , Moreno L A , Manios Y , Béghin L , Ottevaere C , Ciarapica D , Sarri K , Dietrich S , Blair S N , Kersting M , Molnar D , González-Gross M , Gutiérrez Á , Sjöström M , Castillo M J ,   on behalf of the HELENA study
Published: August 2009

Objective

To report sex- and age-specific physical fitness levels in European adolescents.

Methods

A sample of 3428 adolescents (1845 girls) aged 12.5–17.49 years from 10 European cities in Austria, Belgium, France, Germany, Greece (an inland city and an island city), Hungary, Italy, Spain and Sweden was assessed in the Healthy Lifestyle in Europe by Nutrition in Adolescence study between 2006 and 2008. The authors assessed muscular fitness, speed/agility, flexibility and cardiorespiratory fitness using nine different fitness tests: handgrip, bent arm hang, standing long jump, Bosco jumps (squat jump, counter movement jump and Abalakov jump), 4×10-m shuttle run, back-saver sit and reach and 20-m shuttle run tests.

Results

The authors derived sex- and age-specific normative values for physical fitness in the European adolescents using the LMS statistical method and expressed as tabulated percentiles from 10 to 100 and as smoothed centile curves (P5, P25, P50, P75and P95). The figures showed greater physical fitness in the boys, except for the flexibility test, and a trend towards increased physical fitness in the boys as their age increased, whereas the fitness levels in the girls were more stable across ages.

Conclusions

The normative values hereby provided will enable evaluation and correct interpretation of European adolescents' fitness status.
Contribution of free play towards physical activity guidelines for New Zealand primary school children aged 7–9 years
Authors: McGall S E , McGuigan M R , Nottle C
Published: August 2009

Objective

The objectives of this study were to investigate children's physical activity patterns to gain comparisons between home and school and to determine whether the current physical activity guidelines of 60 min of moderate to vigorous physical activity (MVPA) daily were being met.

Methods

Participants were recruited from two New Zealand primary schools (60 children, mean age (SD) 8.3 (0.7) years). Physical activity was measured for seven consecutive days using Actigraph accelerometers. Total activity and average counts were determined for school playtime, after school and weekends. Differences between average counts for these intervals were compared using the t statistic. Time and percentage of time spent were categorised into the activity thresholds: sedentary (<100), light (101–299), moderate (3000–5200) and vigorous (>5200). Total activity for each day was also determined.

Results

No child met the recommended 60 min of MVPA daily during the investigation. Compared to school playtime, activity counts were lower by 36% (CI 25% to 45.5%, p<0.001, effect size (ES)=−1.29) after school, 50.1% (CI 37% to 60.5%, p<0.001, ES=−2.01) on Saturday and 57.4% (CI 46.3% to 66.3%, p<0.001, ES=−2.47) on Sunday. Mean results showed children spent 91–96% of their time engaged in light or sedentary activities. Even during school playtime, where the children were most active, only 8 of 80 min were spent engaged in MVPA.

Conclusions

This study found activity levels were considerably lower than the recommended guidelines, and children were more active during school playtime compared to after school and weekends.
Diagnosis of conjunctivitis in primary care: comparison of two different culture procedures
Authors: Tellegen E , ter Riet G , Sloos J H , van Weert H C P M
Published: August 2009

Background:

In general practice, infectious conjunctivitis is a common and mostly (64%) self-limiting disorder. In case of an aberrant course or severe symptoms, a general practitioner may take a culture. Direct inoculation is considered the reference standard, but usually a swab is sent to a laboratory.

Objectives:

To compare the diagnostic performance of the swab, transported by surface mail with direct inoculation.

Methods:

19 general practitioners took two samples of the conjunctiva from 88 patients with symptoms suggestive of infectious conjunctivitis by rolling a cotton swab across the conjunctiva of the lower fornix. One swab was used to inoculate three agar plates directly, while the other was sent in a Stuart medium to the laboratory and inoculated at the time of arrival. The numbers of positive cultures of both methods were compared.

Results:

A pathogen was found in 31 of 88 samples (35% (95% CI 26 to 46)). Surprisingly, the number of positive cultures was higher for the Stuart medium (27/88) than for direct inoculation (23/88). The difference was 4.5% (90% CI 0 to 12, p = 0.388; one-sided McNemar test for paired proportions). In five of the 19 samples that were positive in both tests, the cultured pathogens were different.

Conclusions:

The Stuart medium detected more bacteria than direct inoculation. The lower 90% CI, testing non-inferiority at p = 0.05, indicates that it is unlikely that the Stuart medium misses any positive cultures compared with direct inoculation.
Flavoured cigarettes, sensation seeking and adolescents’ perceptions of cigarette brands
Authors: Manning K C , Kelly K J , Comello M L
Published: August 2009

Objectives:

This study examined the interactive effects of cigarette package flavour descriptors and sensation seeking on adolescents’ brand perceptions.

Methods:

High school students (n = 253) were randomly assigned to one of two experimental conditions and sequentially exposed to cigarette package illustrations for three different brands. In the flavour descriptor condition, the packages included a description of the cigarettes as “cherry”, while in the traditional descriptor condition the cigarette brands were described with common phrases found on tobacco packages such as “domestic blend.” Following exposure to each package participants’ hedonic beliefs, brand attitudes and trial intentions were assessed. Sensation seeking was also measured, and participants were categorised as lower or higher sensation seekers.

Results:

Across hedonic belief, brand attitude and trial intention measures, there were interactions between package descriptor condition and sensation seeking. These interactions revealed that among high (but not low) sensation seekers, exposure to cigarette packages including sweet flavour descriptors led to more favourable brand impressions than did exposure to packages with traditional descriptors.

Conclusions:

Among high sensation seeking youths, the appeal of cigarette brands is enhanced through the use of flavours and associated descriptions on product packaging.
The adoption of smoke-free hospital campuses in the United States
Authors: Williams S C , Hafner J M , Morton D J , Holm A L , Milberger S M , Koss R G , Loeb J M
Published: August 2009

Background:

The adoption of a smoke-free hospital campus policy is often a highly publicised local event. National media coverage suggests that the trend towards adopting these policies is growing, and this publicity can frequently lead hospital administrators to consider the adoption of such policies within their own institutions. Little is actually known, however, about the prevalence of these policies or their impact.

Objectives:

To determine the national prevalence of smoke-free hospital campus policies and the relation between these policies and performance on nationally standardised measures for smoking cessation counselling in US hospitals.

Methods:

4494 Joint Commission-accredited hospitals were invited to complete a web-based questionnaire assessing current smoking policies and future plans. Smoking cessation counselling rates were assessed through nationally standardised measures.

Results:

The 1916 hospitals responding to the survey (43%) were statistically similar to non-responders with respect to performance measure rates, smoking policies and demographic characteristics. Approximately 45% of responders reported an existing smoke-free hospital campus policy. With respect to demographics, higher proportions of smoke-free campus policies were reported in non-teaching and non-profit hospitals. Smoke-free campus hospitals were also more likely to provide smoking cessation counselling to patients with acute myocardial infarction, heart failure and pneumonia who smoke (p<0.001).

Conclusions:

By February 2008, 45% of US hospitals (up from approximately 3% in 1992) had adopted a smoke-free campus policy; another 15% reported actively pursuing the adoption of such a policy. By the end of 2009, it is likely that the majority of US hospitals will have a smoke-free campus.
TOPOLOGICAL PROPERTIES OF BANK NETWORKS: THE CASE OF BRAZIL
Authors: TABAK BENJAMIN M. , CAJUEIRO DANIEL O. , SERRA THIAGO R.
Published: August 2009

This paper investigates the topological properties of bank networks. We build the minimum spanning tree, which is based on the concept of ultrametricity, using the correlation matrix for a variety of banking variables. Empirical results suggest that the private and foreign banks tend to form clusters within the network. Furthermore, banks with different sizes are also strongly connected and tend to form clusters. These results are robust to the use of different variables to build the network, such as bank profitability, assets, equity, revenue and loans.
COMPARATIVE STUDY OF SEMICLASSICAL APPROACHES TO QUANTUM DYNAMICS
Authors: SCHUBERT G. , FILINOV V. S. , MATYASH K. , SCHNEIDER R. , FEHSKE H.
Published: August 2009

Quantum states can be described equivalently by density matrices, Wigner functions, or quantum tomograms. We analyze the accuracy and performance of three related semiclassical approaches to quantum dynamics, in particular with respect to their numerical implementation. As test cases, we consider the time evolution of Gaussian wave packets in different one-dimensional geometries, whereby tunneling, resonance, and anharmonicity effects are taken into account. The results and methods are benchmarked against an exact quantum mechanical treatment of the system, which is based on a highly efficient Chebyshev expansion technique of the time evolution operator.
PHASE TRANSITION IN A STOCHASTIC FOREST FIRE MODEL AND EFFECTS OF THE DEFINITION OF NEIGHBORHOOD
Authors: LICHTENEGGER KLAUS , SCHAPPACHER WILHELM
Published: August 2009

We present results on a stochastic forest fire model, where the influence of the neighbor trees is treated in a more realistic way than usual and the definition of neighborhood can be tuned by an additional parameter.

This model exhibits a surprisingly sharp phase transition which can be shifted by redefinition of neighborhood. The results can also be interpreted in terms of disease-spreading and are quite unsettling from the epidemiologist's point of view, since variation of one crucial parameter only by a few percent can result in the change from endemic to epidemic behavior.
INFLUENCE OF A SMALL FRACTION OF INDIVIDUALS WITH ENHANCED MUTATIONS ON A POPULATION GENETIC POOL
Authors: CEBRAT S. , STAUFFER D.
Published: August 2009

It has been observed that a higher mutation load could be introduced into the genomes of children conceived by assisted reproduction technology (fertilization in-vitro). This generates two effects — slightly higher mutational pressure on the whole genetic pool of population and inhomogeneity of mutation distributions in the genetic pool. Computer simulations of the Penna ageing model suggest that already a small fraction of births with enhanced number of new mutations can negatively influence the whole population.
PHASE TRANSITION IN THE GENOME EVOLUTION FAVORS NONRANDOM DISTRIBUTION OF GENES ON CHROMOSOMES
Authors: KOWALSKI JAKUB , WAGA WOJCIECH , ZAWIERTA MARTA , CEBRAT STANISŁAW
Published: August 2009

We have used the Monte Carlo-based computer models to show that selection pressure could affect the distribution of recombination hotspots along the chromosome. Close to the critical crossover rate, where genomes may switch between the Darwinian purifying selection or complementation of haplotypes, the distribution of recombination events and the force of selection exerted on genes affect the structure of chromosomes. The order of expression of genes and their location on chromosome may decide about the extinction or survival of competing populations.
STOCHASTIC RESONANCE IN A SINGLE-MODE LASER DRIVEN BY QUADRATIC COLORED PUMP NOISE AND QUANTUM NOISE WITH CROSS-CORRELATION BETWEEN REAL AND IMAGINARY PARTS OF NOISE
Authors: XU DE-SHENG , CAO LI , WU DA-JIN
Published: August 2009

Based on the single-mode laser noise model driven by quadratic colored pump noise and quantum noise with cross-correlation between real and imaginary parts of noise proposed in International Journal of Modern Physics B20, 5383 (2006) and Phys. Rev. E 73, 023802 (2006), the stochastic resonance (SR) of laser intensity is investigated by virtue of the linearized approximation. The analytic expression of signal-to-noise ratio (SNR) is calculated. It is found that the phenomena of stochastic resonance respectively exist in the curves of the SNR versus the noise cross-correlation coefficient λpand the SNR versus the pump parameter a, as well as the SNR versus the signal frequency [Formula: see text] for the model. It is shown that there are three different types of SR in the model: the conventional form of SR, the SR in the broad sense and the bona fide SR.
The road to Smith: how the Geological Society came to possess English geology
Authors: Knell Simon J.
Published: August 2009

The modern image of the Geological Society owes much to William Smith whom the Society used, in 1831, to claim ascendency over European rivals. At its birth, however, the Society pursued a science adopted from the Continent, which privileged field data and saw mineralogy and chemistry as the sciences of the Earth. The Society's birth mobilized the nation; its co-operative, mobile, investigative, subtly theoretical and didactic vigour materialized in the production of Greenough's geological map of England. Yet Smith's geology spread virus-like, converting the membership in various ways, some acknowledging Smith, others denying him. In possession of Smith's geology, and impressed by his publications, the Society men emerged from a philosophical wilderness, only to break out in a competitive fever to write an
Elements of Geology
. The Society's great supporter, John Farey, broke free, disillusioned and determined to destroy Greenough. Nevertheless, Greenough pushed forward with his map, competing directly with Smith and intent on surpassing him. However, following the development of a powerbase for his geology in Yorkshire, Smith rode into London to be crowned the father of a peculiarly English science. Smith's map now became the national icon of English geology, less than a decade after the Society had rendered it obsolete. Next to it, Greenough's map – the Society's ‘glory’ – symbolized the Society's co-operative spirit and political acumen, attributes no less important to the science's advance.