bluuebunny/crossref_metadata_2025_split huggingface dataset:
Demonstration of Allelic Exchange in the Slow-Growing Bacterium
Mycobacterium avium
subsp.
paratuberculosis
, and Generation of Mutants with Deletions at the
pknG, relA
, and
lsr2
Loci
Authors: Park Kun Taek , Dahl John L. , Bannantine John P. , Barletta Raúl G. , Ahn Jongsam , Allen Andrew J. , Hamilton Mary Jo , Davis William C. 
Published: January 2008

ABSTRACT

Mycobacterium avium
subsp.
paratuberculosis
is the causative pathogen of Johne's disease, a chronic inflammatory wasting disease in ruminants. This disease has been difficult to control because of the lack of an effective vaccine. To address this need, we adapted a specialized transduction system originally developed for
M. tuberculosis
and modified it to improve the efficiency of allelic exchange in order to generate site-directed mutations in preselected
M. avium
subsp.
paratuberculosis
genes. With our novel optimized method, the allelic exchange frequency was 78 to 100% and the transduction frequency was 1.1 × 10
−7
to 2.9 × 10
−7
. Three genes were selected for mutagenesis:
pknG
and
relA
, which are genes that are known to be important virulence factors in
M. tuberculosis
and
M. bovis
, and
lsr2
, a gene regulating lipid biosynthesis and antibiotic resistance. Mutants were successfully generated with a virulent strain of
M. avium
subsp.
paratuberculosis
(
M. avium
subsp.
paratuberculosis
K10) and with a recombinant K10 strain expressing the green fluorescent protein gene,
gfp
. The improved efficiency of disruption of selected genes in
M. avium
subsp.
paratuberculosis
should accelerate development of additional mutants for vaccine testing and functional studies.
Identification of Genes Affecting Hydrogen Sulfide Formation inSaccharomyces cerevisiae
Authors: Linderholm Angela L. , Findleton Carrie L. , Kumar Gagandeep , Hong Yeun , Bisson Linda F. 
Published: January 2008

ABSTRACTA screen of theSaccharomyces cerevisiaedeletion strain set was performed to identify genes affecting hydrogen sulfide (H2S) production. Mutants were screened using two assays: colony color on BiGGY agar, which detects the basal level of sulfite reductase activity, and production of H2S in a synthetic juice medium using lead acetate detection of free sulfide in the headspace. A total of 88 mutants produced darker colony colors than the parental strain, and 4 produced colonies significantly lighter in color. There was no correlation between the appearance of a dark colony color on BiGGY agar and H2S production in synthetic juice media. Sixteen null mutations were identified as leading to the production of increased levels of H2S in synthetic juice using the headspace analysis assay. All 16 mutants also produced H2S in actual juices. Five of these genes encode proteins involved in sulfur containing amino acid or precursor biosynthesis and are directly associated with the sulfate assimilation pathway. The remaining genes encode proteins involved in a variety of cellular activities, including cell membrane integrity, cell energy regulation and balance, or other metabolic functions. The levels of hydrogen sulfide production of each of the 16 strains varied in response to nutritional conditions. In most cases, creation of multiple deletions of the 16 mutations in the same strain did not lead to a further increase in H2S production, instead often resulting in decreased levels.
Teichoic Acid Glycosylation Mediated by
gtcA
Is Required for Phage Adsorption and Susceptibility of
Listeria monocytogenes
Serotype 4b
Authors: Cheng Ying , Promadej Nattawan , Kim Jae-Won , Kathariou S. 
Published: January 2008

ABSTRACT

An insertion mutant of
gtcA
, responsible for serotype-specific glycosylation of the cell wall teichoic acid in serotype 4b strains of
Listeria monocytogenes
, was also resistant to both
Listeria
genus- and serotype 4b-specific phages. The sugar substituents on teichoic acid appeared essential for the adsorption of phages A500 (serotype 4b specific) and A511 (
Listeria
genus specific) to serotype 4b
L. monocytogenes
.
Surface Response of Fluorine Polymer-Incorporated Resin Composites to Cariogenic Biofilm Adherence
Authors: Gyo Mariko , Nikaido Toru , Okada Koichi , Yamauchi Junichi , Tagami Junji , Matin Khairul 
Published: January 2008

ABSTRACT

Experimental resin composites with incorporated polytetrafluoroethylene (PTFE) particles were developed, which theoretically could improve the surface properties of the materials, including the inhibition of bacterial adherence. To assess the surface properties in relation to biofilm formation and detachment, 23.1% (wt/wt) linear PTFE particles (FL-30) and cross-linked PTFE particles (FC-30) were incorporated into pure resin composites. Pure PTFE plates and pure resin composites without PTFE (F-0) were used as control specimens. Sucrose-dependent
Streptococcus mutans
biofilms were formed on the specimen blocks inside an oral biofilm reactor for various time periods and analyzed with or without application of driving forces. In addition, water contact angles and surface roughness were measured. The water contact angles of FL-30 (61.2°) and FC-30 (65.8°) were larger than that of F-0 (48.5°). The largest contact angle (107°) was detected on pure PTFE plates. However, the surfaces of FL-30, FC-30, and pure PTFE plates were rougher than that of F-0. Although the surface properties of the materials differed in terms of contact angles and roughness, these factors seemed not to affect biofilm formation on the surfaces within 5 h. Pure PTFE plates harbored almost the same amounts of biofilm as F-0. However, when a very strong driving force was applied, it was clear that there were significantly smaller amounts of biofilms retained on pure PTFE plates, which showed contact angles much higher than those of the other materials. Hydrophobicity of the resin composite was improved by incorporation of PTFE fillers. However, surface resistance against biofilm formation was not improved.
Silver as a Residual Disinfectant To Prevent Biofilm Formation in Water Distribution Systems
Authors: Silvestry-Rodriguez Nadia , Bright Kelly R. , Slack Donald C. , Uhlmann Donald R. , Gerba Charles P. 
Published: January 2008

ABSTRACT
Biofilms can have deleterious effects on drinking water quality and may harbor pathogens. Experiments were conducted using 100 μg/liter silver to prevent biofilm formation in modified Robbins devices with polyvinyl chloride and stainless steel surfaces. No significant difference was observed on either surface between the silver treatment and the control.
Genetic Dissection of Tropodithietic Acid Biosynthesis by Marine Roseobacters
Authors: Geng Haifeng , Bruhn Jesper Bartholin , Nielsen Kristian F. , Gram Lone , Belas Robert 
Published: January 2008

ABSTRACT

The symbiotic association between the roseobacter
Silicibacter
sp. strain TM1040 and the dinoflagellate
Pfiesteria piscicida
involves bacterial chemotaxis to dinoflagellate-produced dimethylsulfoniopropionate (DMSP), DMSP demethylation, and ultimately a biofilm on the surface of the host. Biofilm formation is coincident with the production of an antibiotic and a yellow-brown pigment. In this report, we demonstrate that the antibiotic is a sulfur-containing compound, tropodithietic acid (TDA). Using random transposon insertion mutagenesis, 12 genes were identified as critical for TDA biosynthesis by the bacteria, and mutation in any one of these results in a loss of antibiotic activity (Tda
−
) and pigment production. Unexpectedly, six of the genes, referred to as
tdaA-F
, could not be found on the annotated TM1040 genome and were instead located on a previously unidentified plasmid (ca. 130 kb; pSTM3) that exhibited a low frequency of spontaneous loss. Homologs of
tdaA
and
tdaB
from
Silicibacter
sp. strain TM1040 were identified by mutagenesis in another TDA-producing roseobacter,
Phaeobacter
sp. strain 27-4, which also possesses two large plasmids (ca. 60 and ca. 70 kb, respectively), and
tda
genes were found by DNA-DNA hybridization in 88% of a diverse collection of nine roseobacters with known antibiotic activity. These data suggest that roseobacters may use a common pathway for TDA biosynthesis that involves plasmid-encoded proteins. Using metagenomic library databases and a bioinformatics approach, differences in the biogeographical distribution between the critical TDA synthesis genes were observed. The implications of these results to roseobacter survival and the interaction between TM1040 and its dinoflagellate host are discussed.
Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen
Pseudomonas aeruginosa
PAO1
Authors: Oberhardt Matthew A. , Puchałka Jacek , Fryer Kimberly E. , Martins dos Santos Vítor A. P. , Papin Jason A. 
Published: January 2008

ABSTRACT

Pseudomonas aeruginosa
is a major life-threatening opportunistic pathogen that commonly infects immunocompromised patients. This bacterium owes its success as a pathogen largely to its metabolic versatility and flexibility. A thorough understanding of
P. aeruginosa
's metabolism is thus pivotal for the design of effective intervention strategies. Here we aim to provide, through systems analysis, a basis for the characterization of the genome-scale properties of this pathogen's versatile metabolic network. To this end, we reconstructed a genome-scale metabolic network of
Pseudomonas aeruginosa
PAO1. This reconstruction accounts for 1,056 genes (19% of the genome), 1,030 proteins, and 883 reactions. Flux balance analysis was used to identify key features of
P. aeruginosa
metabolism, such as growth yield, under defined conditions and with defined knowledge gaps within the network. BIOLOG substrate oxidation data were used in model expansion, and a genome-scale transposon knockout set was compared against in silico knockout predictions to validate the model. Ultimately, this genome-scale model provides a basic modeling framework with which to explore the metabolism of
P. aeruginosa
in the context of its environmental and genetic constraints, thereby contributing to a more thorough understanding of the genotype-phenotype relationships in this resourceful and dangerous pathogen.
The Genome Sequence of the Tomato-Pathogenic ActinomyceteClavibacter michiganensissubsp.michiganensisNCPPB382 Reveals a Large Island Involved in Pathogenicity
Authors: Gartemann Karl-Heinz , Abt Birte , Bekel Thomas , Burger Annette , Engemann Jutta , Flügel Monika , Gaigalat Lars , Goesmann Alexander , Gräfen Ines , Kalinowski Jörn , Kaup Olaf , Kirchner Oliver , Krause Lutz , Linke Burkhard , McHardy Alice , Meyer Folker , Pohle Sandra , Rückert Christian , Schneiker Susanne , Zellermann Eva-Maria , Pühler Alfred , Eichenlaub Rudolf , Kaiser Olaf , Bartels Daniela 
Published: January 2008

ABSTRACTClavibacter michiganensissubsp.michiganensisis a plant-pathogenic actinomycete that causes bacterial wilt and canker of tomato. The nucleotide sequence of the genome of strain NCPPB382 was determined. The chromosome is circular, consists of 3.298 Mb, and has a high G+C content (72.6%). Annotation revealed 3,080 putative protein-encoding sequences; only 26 pseudogenes were detected. Tworrnoperons, 45 tRNAs, and three small stable RNA genes were found. The two circular plasmids, pCM1 (27.4 kbp) and pCM2 (70.0 kbp), which carry pathogenicity genes and thus are essential for virulence, have lower G+C contents (66.5 and 67.6%, respectively). In contrast to the genome of the closely related organismClavibacter michiganensissubsp.sepedonicus, the genome ofC. michiganensissubsp.michiganensislacks complete insertion elements and transposons. The 129-kbchp/tomAregion with a low G+C content near the chromosomal origin of replication was shown to be necessary for pathogenicity. This region contains numerous genes encoding proteins involved in uptake and metabolism of sugars and several serine proteases. There is evidence that single genes located in this region, especially genes encoding serine proteases, are required for efficient colonization of the host. AlthoughC. michiganensissubsp.michiganensisgrows mainly in the xylem of tomato plants, no evidence for pronounced genome reduction was found.C. michiganensissubsp.michiganensisseems to have as many transporters and regulators as typical soil-inhabiting bacteria. However, the apparent lack of a sulfate reduction pathway, which makesC. michiganensissubsp.michiganensisdependent on reduced sulfur compounds for growth, is probably the reason for the poor survival ofC. michiganensissubsp.michiganensisin soil.
Role of Periplasmic Trehalase in Uptake of Trehalose by the Thermophilic Bacterium
Rhodothermus marinus
Authors: Jorge Carla D. , Fonseca Luís L. , Boos Winfried , Santos Helena 
Published: January 2008

ABSTRACT

Trehalose uptake at 65°C in
Rhodothermus marinus
was characterized. The profile of trehalose uptake as a function of concentration showed two distinct types of saturation kinetics, and the analysis of the data was complicated by the activity of a periplasmic trehalase. The kinetic parameters of this enzyme determined in whole cells were as follows:

K
m

= 156 ± 11 μM and
V
max
= 21.2 ± 0.4 nmol/min/mg of total protein. Therefore, trehalose could be acted upon by this periplasmic activity, yielding glucose that subsequently entered the cell via the glucose uptake system, which was also characterized. To distinguish the several contributions in this intricate system, a mathematical model was developed that took into account the experimental kinetic parameters for trehalase, trehalose transport, glucose transport, competition data with trehalose, glucose, and palatinose, and measurements of glucose diffusion out of the periplasm. It was concluded that
R. marinus
has distinct transport systems for trehalose and glucose; moreover, the experimental data fit perfectly with a model considering a high-affinity, low-capacity transport system for trehalose (

K
m

= 0.11 ± 0.03 μM and
V
max
= 0.39 ± 0.02 nmol/min/mg of protein) and a glucose transporter with moderate affinity and capacity (

K
m

= 46 ± 3 μM and
V
max
= 48 ± 1 nmol/min/mg of protein). The contribution of the trehalose transporter is important only in trehalose-poor environments (trehalose concentrations up to 6 μM); at higher concentrations trehalose is assimilated primarily via trehalase and the glucose transport system. Trehalose uptake was constitutive, but the activity decreased 60% in response to osmotic stress. The nature of the trehalose transporter and the physiological relevance of these findings are discussed.
Molecular Characterization of the
Salmonella enterica
Serovar Typhi Vi-Typing Bacteriophage E1
Authors: Pickard Derek , Thomson Nicholas R. , Baker Stephen , Wain John , Pardo Mercedes , Goulding David , Hamlin Nancy , Choudhary Jyoti , Threfall John , Dougan Gordon 
Published: January 2008

ABSTRACT

Some bacteriophages target potentially pathogenic bacteria by exploiting surface-associated virulence factors as receptors. For example, phage have been identified that exhibit specificity for Vi capsule producing
Salmonella enterica
serovar Typhi. Here we have characterized the Vi-associated E1-typing bacteriophage using a number of molecular approaches. The absolute requirement for Vi capsule expression for infectivity was demonstrated using different Vi-negative
S. enterica
derivatives. The phage particles were shown to have an icosahedral head and a long noncontractile tail structure. The genome is 45,362 bp in length with defined capsid and tail regions that exhibit significant homology to the
S. enterica
transducing phage ES18. Mass spectrometry was used to confirm the presence of a number of hypothetical proteins in the Vi phage E1 particle and demonstrate that a number of phage proteins are modified posttranslationally. The genome of the Vi phage E1 is significantly related to other bacteriophages belonging to the same serovar Typhi phage-typing set, and we demonstrate a role for phage DNA modification in determining host specificity.
Transcriptome Analysis of Agmatine and Putrescine Catabolism inPseudomonas aeruginosaPAO1
Authors: Chou Han Ting , Kwon Dong-Hyeon , Hegazy Mohamed , Lu Chung-Dar 
Published: January 2008

ABSTRACTPolyamines (putrescine, spermidine, and spermine) are major organic polycations essential for a wide spectrum of cellular processes. The cells require mechanisms to maintain homeostasis of intracellular polyamines to prevent otherwise severe adverse effects. We performed a detailed transcriptome profile analysis ofPseudomonas aeruginosain response to agmatine and putrescine with an emphasis in polyamine catabolism. Agmatine serves as the precursor compound for putrescine (and hence spermidine and spermine), which was proposed to convert into 4-aminobutyrate (GABA) and succinate before entering the tricarboxylic acid cycle in support of cell growth, as the sole source of carbon and nitrogen. Two acetylpolyamine amidohydrolases, AphA and AphB, were found to be involved in the conversion of agmatine into putrescine. Enzymatic products of AphA were confirmed by mass spectrometry analysis. Interestingly, the alanine-pyruvate cycle was shown to be indispensable for polyamine utilization. The newly identifieddadRAXlocus encoding the regulator alanine transaminase and racemase coupled with SpuC, the major putrescine-pyruvate transaminase, were key components to maintaining alanine homeostasis. Corresponding mutant strains were severely hampered in polyamine utilization. On the other hand, an alternative γ-glutamylation pathway for the conversion of putrescine into GABA is present in some organisms. Subsequently, GabD, GabT, and PA5313 were identified for GABA utilization. The growth defect of the PA5313gabTdouble mutant in GABA suggested the importance of these two transaminases. The succinic-semialdehyde dehydrogenase activity of GabD and its induction by GABA were also demonstrated in vitro. Polyamine utilization in general was proven to be independent of the PhoPQ two-component system, even though a modest induction of this operon was induced by polyamines. Multiple potent catabolic pathways, as depicted in this study, could serve pivotal roles in the control of intracellular polyamine levels.
The Chaperone IpgC Copurifies with the Virulence Regulator MxiE
Authors: Pilonieta M. Carolina , Munson George P. 
Published: January 2008

ABSTRACT

The expression of a subset of
Shigella flexneri
virulence genes is dependent upon a cytoplasmic chaperone, IpgC, and an activator from the AraC/XylS family, MxiE. In this paper, we report that the chaperone forms a specific and stable heteromer with MxiE.
A 15-year prospective study of shift work and disability pension: Table 1
Authors: Tüchsen F , Christensen K B , Lund T , Feveile H 
Published: January 2008

Objective:To estimate the hazard ratio for disability pension associated with shift work.Methods:Cohorts of shift and day workers were identified in three waves of the Danish Work Environment Cohort Study and followed up for incidence of disability pension in a national register of social transfer payment. A total of 3980 female and 4025 male employees were included in the cohorts. Information about shift work status, age, smoking habits, body mass index and ergonomic work environment were updated according to responses in subsequent waves of the survey when possible. Respondents reporting shift work were classified as shift workers in the following waves as well. Respondents were followed in the register from the time of first interview and were censored at the time of their 60th birthday, emigration, death or end of follow-up (18 June 2006). The authors used the Cox proportional hazards model to estimate hazard ratios for incidence of disability pension and 95% confidence intervals.Results:The authors observed 253 new disability pensions among women and 173 among men during 56 903 and 57 886 person-years at risk respectively, Among women, shift work predicted disability after adjustment for age, general health and socioeconomic status HR 1.39 (95% CI 1.07 to 1.82). After further adjustment for body mass index, smoking habits, socioeconomic status and ergonomic exposures the association remained statistically significant HR 1.34 (95% CI 1.02 to 1.75). Shift work was not associated with disability among men.Conclusion:Shift work might be moderately associated with disability pension among women; however, more powerful studies are needed to establish the possible association.
Induction of Cancer Metastasis by Cyclophosphamide Pretreatment of Host Mice: An Opposite Effect of Chemotherapy
Authors: Yamauchi Kensuke , Yang Meng , Hayashi Katsuhiro , Jiang Ping , Yamamoto Norio , Tsuchiya Hiroyuki , Tomita Katsuro , Moossa Abdool R. , Bouvet Michael , Hoffman Robert M. 
Published: January 2008

Abstract
Although side effects of cancer chemotherapy are well known, “opposite effects” of chemotherapy that enhance the malignancy of the treated cancer are not well understood. In this report, we describe the induction of intravascular proliferation, extravasation, and colony formation by cancer cells, critical steps of metastasis, by pretreatment of host mice with the commonly used chemotherapy drug cyclophosphamide. In contrast, in the unpretreated mice, most cancer cells remained quiescent in vessels without extravasation. HT1080 human fibrosarcoma cells, labeled in the nucleus with green fluorescent protein and red fluorescent protein in the cytoplasm for imaging, were injected into the epigastric cranialis vein of nude mice. Twenty-four hours before cancer cell injection, cyclophosphamide was given i.p. Double-labeled cancer cells were imaged at the cellular level in live mice with the Olympus OV100 Small Animal Imaging System with variable magnification. Cyclophosphamide seems to interfere with a host process that inhibits intravascular proliferation, extravasation, and extravascular colony formation. Cyclophosphamide does not directly affect the cancer cells because cyclophosphamide has been cleared by the time the cancer cells were injected. This report shows an important unexpected “opposite effect” of chemotherapy that enhances critical steps in malignancy rather than inhibiting them, suggesting that certain current approaches to cancer chemotherapy should be modified. [Cancer Res 2008;68(2):516–20]