bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strain/Species-Specific Probe Design for Microbial Identification Microarrays
Authors: Tu Qichao , He Zhili , Deng Ye , Zhou Jizhong 
Published: June 2013

ABSTRACT

Specific identification of microorganisms in the environment is important but challenging, especially at the species/strain level. Here, we have developed a novel
k
-mer-based approach to select strain/species-specific probes for microbial identification with diagnostic microarrays. Application of this approach to human microbiome genomes showed that multiple (≥10 probes per strain) strain-specific 50-mer oligonucleotide probes could be designed for 2,012 of 3,421 bacterial strains of the human microbiome, and species-specific probes could be designed for most of the other strains. The method can also be used to select strain/species-specific probes for sequenced genomes in any environments, such as soil and water.
Shiga Toxin 2-Encoding Bacteriophages in Human Fecal Samples from Healthy Individuals
Authors: Martinez-Castillo Alexandre , Quirós Pablo , Navarro Ferran , Miró Elisenda , Muniesa Maite 
Published: June 2013

ABSTRACTShiga toxin-converting bacteriophages (Stx phages) carry thestxgene and convert nonpathogenic bacterial strains into Shiga toxin-producing bacteria. Previous studies have shown that high densities of free and infectious Stx phages are found in environments polluted with feces and also in food samples. Taken together, these two findings suggest that Stx phages could be excreted through feces, but this has not been tested to date. In this study, we purified Stx phages from 100 fecal samples from 100 healthy individuals showing no enteric symptoms. The phages retrieved from each sample were then quantified by quantitative PCR (qPCR). In total, 62% of the samples carried Stx phages, with an average value of 2.6 × 104Stx phages/g. This result confirms the excretion of free Stx phages by healthy humans. Moreover, the Stx phages from feces were able to propagate in enrichment cultures ofstx-negativeEscherichia coli(strains C600 and O157:H7) and inShigella sonnei, indicating that at least a fraction of the Stx phages present were infective. Plaque blot hybridization revealed lysis by Stx phages from feces. Our results confirm the presence of infectious free Stx phages in feces from healthy persons, possibly explaining the environmental prevalence observed in previous studies. It cannot be ruled out, therefore, that some positivestxresults obtained during the molecular diagnosis of Shiga toxin-producingEscherichia coli(STEC)-related diseases using stool samples are due to the presence of Stx phages.
Induction of Biofilm Formation in the Betaproteobacterium Burkholderia unamae CK43B Exposed to Exogenous Indole and Gallic Acid
Authors: Kim Dongyeop , Sitepu Irnayuli R. , Hashidoko Yasuyuki 
Published: June 2013

ABSTRACT

Burkholderia unamae
CK43B, a member of the
Betaproteobacteria
that was isolated from the rhizosphere of a
Shorea balangeran
sapling in a tropical peat swamp forest, produces neither indole nor extracellular polymeric substances associated with biofilm formation. When cultured in a modified Winogradsky's medium supplemented with up to 1.7 mM indole,
B. unamae
CK43B maintains its planktonic state by cell swelling and effectively degrades exogenous indole. However, in medium supplemented with 1.7 mM exogenous indole and 1.0 mM gallic acid,
B. unamae
CK43B produced extracellular polymeric substances and formed a biofilm. The concentration indicated above of gallic acid alone had no effect on either the growth or the differentiation of
B. unamae
CK43B cells above a certain concentration threshold, whereas it inhibited indole degradation by
B. unamae
CK43B to 3-hydroxyindoxyl. In addition, coculture of
B. unamae
CK43B with indole-producing
Escherichia coli
in nutrient-rich Luria-Bertani medium supplemented with 1.0 mM gallic acid led to the formation of mixed cell aggregates. The viability and active growth of
B. unamae
CK43B cells in a coculture system with
Escherichia coli
were evidenced by fluorescence
in situ
hybridization. Our data thus suggest that indole facilitates intergenus communication between indole-producing gammaproteobacteria and some indole-degrading bacteria, particularly in gallic acid-rich environments.
The Microcosm Mediates the Persistence of Shiga Toxin-Producing Escherichia coli in Freshwater Ecosystems
Authors: Mauro Steven A. , Opalko Hannah , Lindsay Kyle , Colon Michael P. , Koudelka Gerald B. 
Published: June 2013

ABSTRACT

Water is a major route for infection of humans by exotoxin-producing bacteria, including Shiga toxin-producing
Escherichia coli
(STEC). While STEC has the potential to be present in nearly every type of water source, its distribution is sporadic, and an understanding of factors that govern its emergence and persistence within water is lacking. In this study, we examined the influence of microbe content on STEC persistence in freshwater. We found that depletion of microbes in the water leads to a considerable increase in the persistence of STEC, an effect that can be mitigated by adding grazing protists to the water. STEC strains appear to be more resistant to the impact of grazing protists than
E. coli
strains that lack the Shiga toxin (
stx
) gene. Our results demonstrate that the microcosm can dramatically influence the persistence of STEC in aquatic ecosystems and that the overall impact by microbes on STEC strains is fundamentally different from that of non-STEC strains of bacteria. Overall, these results provide insight into why STEC and possibly other exotoxin-producing bacterial pathogens display such variability in abundance, distribution, and persistence in aquatic ecosystems.
Draft Genome Sequences of Mycoplasma auris and Mycoplasma yeatsii, Two Species of the Ear Canal of
Caprinae
Authors: Dordet-Frisoni Emilie , Baranowski Eric , Barré Aurélien , Blanchard Alain , Breton Marc , Couture Carole , Dupuy Virginie , Gaurivaud Patrice , Jacob Daniel , Lemaitre Claire , Manso-Silván Lucía , Nikolski Macha , Nouvel Laurent-Xavier , Poumarat François , Sirand-Pugnet Pascal , Thébault Patricia , Theil Sébastien , Thiaucourt François , Citti Christine , Tardy Florence 
Published: June 2013

ABSTRACT

We report here the draft genome sequences of
Mycoplasma auris
and
Mycoplasma yeatsii
, two species commonly isolated from the external ear canal of
Caprinae
.
Has the Bacterial Biphenyl Catabolic Pathway Evolved Primarily To Degrade Biphenyl? The Diphenylmethane Case
Authors: Pham Thi Thanh My , Sylvestre Michel 
Published: June 2013

ABSTRACT

In this work, we have compared the ability of
Pandoraea pnomenusa
B356 and of
Burkholderia xenovorans
LB400 to metabolize diphenylmethane and benzophenone, two biphenyl analogs in which the phenyl rings are bonded to a single carbon. Both chemicals are of environmental concern.
P. pnomenusa
B356 grew well on diphenylmethane. On the basis of growth kinetics analyses, diphenylmethane and biphenyl were shown to induce the same catabolic pathway. The profile of metabolites produced during growth of strain B356 on diphenylmethane was the same as the one produced by isolated enzymes of the biphenyl catabolic pathway acting individually or in coupled reactions. The biphenyl dioxygenase oxidizes diphenylmethane to 3-benzylcyclohexa-3,5-diene-1,2-diol very efficiently, and ultimately this metabolite is transformed to phenylacetic acid, which is further metabolized by a lower pathway. Strain B356 was also able to cometabolize benzophenone through its biphenyl pathway, although in this case, this substrate was unable to induce the biphenyl catabolic pathway and the degradation was incomplete, with accumulation of 2-hydroxy-6,7-dioxo-7-phenylheptanoic acid. Unlike strain B356,
B. xenovorans
LB400 did not grow on diphenylmethane. Its biphenyl pathway enzymes metabolized diphenylmethane, but they poorly metabolize benzophenone. The fact that the biphenyl catabolic pathway of strain B356 metabolized diphenylmethane and benzophenone more efficiently than that of strain LB400 brings us to postulate that in strain B356, this pathway evolved divergently to serve other functions not related to biphenyl degradation.
Length Control of the Flagellar Hook in a Temperature-Sensitive
flgE
Mutant of Salmonella enterica Serovar Typhimurium
Authors: Uchida Kaoru , Dono Kohei , Aizawa Shin-Ichi 
Published: June 2013

ABSTRACT

The flagellar hook is a short, curved, extracellular structure located between the basal body and the filament. The hook is composed of the FlgE protein. In this study, we analyzed flagellum assembly in a temperature-sensitive
flgE
mutant of
Salmonella enterica
serovar Typhimurium. When the mutant cells were grown at 30°C, they produced flagella of a normal length (71% of the population) and short hooks without filaments (26%). At 37°C, 70% of the basal bodies lacked hooks, and intact flagella made up only 6% of the population. Mutant cells secreted monomeric FlgE in abundance at 37°C, suggesting that the mutant FlgE protein might be defective in polymerization at higher temperatures. The average length of the hooks in intact filaments was 55 nm, whereas after acid treatment, it was 45 nm. SDS-PAGE analysis of the hook-basal body showed that HAP1 was missing in the mutant but not in the wild type. We concluded that hook length in the mutant is controlled in the same way as in the wild type, but the hook appeared short after acid treatment due to the lack of HAP1. We also learned that the true length of the hook is possibly 45 nm, not 55 nm, as has been believed.
The Escherichia coli CydX Protein Is a Member of the CydAB Cytochrome
bd
Oxidase Complex and Is Required for Cytochrome
bd
Oxidase Activity
Authors: VanOrsdel Caitlin E. , Bhatt Shantanu , Allen Rondine J. , Brenner Evan P. , Hobson Jessica J. , Jamil Aqsa , Haynes Brittany M. , Genson Allyson M. , Hemm Matthew R. 
Published: June 2013

ABSTRACT

Cytochrome
bd
oxidase operons from more than 50 species of bacteria contain a short gene encoding a small protein that ranges from ∼30 to 50 amino acids and is predicted to localize to the cell membrane. Although cytochrome
bd
oxidases have been studied for more than 70 years, little is known about the role of this small protein, denoted CydX, in oxidase activity. Here we report that
Escherichia coli
mutants lacking CydX exhibit phenotypes associated with reduced oxidase activity. In addition, cell membrane extracts from Δ
cydX
mutant strains have reduced oxidase activity
in vitro
. Consistent with data showing that CydX is required for cytochrome
bd
oxidase activity, copurification experiments indicate that CydX interacts with the CydAB cytochrome
bd
oxidase complex. Together, these data support the hypothesis that CydX is a subunit of the CydAB cytochrome
bd
oxidase complex that is required for complex activity. The results of mutation analysis of CydX suggest that few individual amino acids in the small protein are essential for function, at least in the context of protein overexpression. In addition, the results of analysis of the paralogous small transmembrane protein AppX show that the two proteins could have some overlapping functionality in the cell and that both have the potential to interact with the CydAB complex.
Numbers of Individual Nutrient Germinant Receptors and Other Germination Proteins in Spores of Bacillus subtilis
Authors: Stewart Kerry-Ann V. , Setlow Peter 
Published: June 2013

ABSTRACT

Germination of dormant
Bacillus subtilis
spores with specific nutrient germinants is dependent on a number of inner membrane (IM) proteins, including (i) the GerA, GerB, and GerK germinant receptors (GRs) that respond to nutrient germinants; (ii) the GerD protein, essential for optimal GR function; and (iii) SpoVA proteins, essential for the release of the spore-specific molecule dipicolinic acid (DPA) during spore germination. Levels of GR A and C subunit proteins, GerD, and SpoVAD in wild-type spores were determined by Western blot analysis of spore fractions or total disrupted spores by comparison with known amounts of purified proteins. Surprisingly, after disruption of decoated
B. subtilis
spores with lysozyme and fractionation, ∼90% of IM fatty acids and GR subunits remained with the spores' insoluble integument fraction, indicating that yields of purified IM are low. The total lysate from disrupted wild-type spores contained ∼2,500 total GRs/spore: GerAA and GerAC subunits each at ∼1,100 molecules/spore and GerBC and GerKA subunits each at ∼700 molecules/spore. Levels of the GerBA subunit determined previously were also predicted to be ∼700 molecules/spore. These results indicate that the A/C subunit stoichiometry in GRs is most likely 1:1, with GerA being the most abundant GR. GerD and SpoVAD levels were ∼3,500 and ∼6,500 molecules/spore, respectively. These values will be helpful in formulating mathematic models of spore germination kinetics as well as setting lower limits on the size of the GR-GerD complex in the spores' IM, termed the germinosome.
Regulation of the
ald
Gene Encoding Alanine Dehydrogenase by AldR in Mycobacterium smegmatis
Authors: Jeong Ji-A , Baek Eun-Young , Kim Si Wouk , Choi Jong-Soon , Oh Jeong-Il 
Published: June 2013

ABSTRACT

The regulatory gene
aldR
was identified 95 bp upstream of the
ald
gene encoding
l
-alanine dehydrogenase in
Mycobacterium smegmatis
. The AldR protein shows sequence similarity to the regulatory proteins of the Lrp/AsnC family. Using an
aldR
deletion mutant, we demonstrated that AldR serves as both activator and repressor for the regulation of
ald
gene expression, depending on the presence or absence of
l
-alanine. The purified AldR protein exists as a homodimer in the absence of
l
-alanine, while it adopts the quaternary structure of a homohexamer in the presence of
l
-alanine. The binding affinity of AldR for the
ald
control region was shown to be increased significantly by
l
-alanine. Two AldR binding sites (O1 and O2) with the consensus sequence GA-N
2
-ATC-N
2
-TC and one putative AldR binding site with the sequence GA-N
2
-GTT-N
2
-TC were identified upstream of the
ald
gene. Alanine and cysteine were demonstrated to be the effector molecules directly involved in the induction of
ald
expression. The cellular level of
l
-alanine was shown to be increased in
M. smegmatis
cells grown under hypoxic conditions, and the hypoxic induction of
ald
expression appears to be mediated by AldR, which senses the intracellular level of alanine.
Phage-Encoded Inhibitor of Staphylococcus aureus Transcription Exerts Context-Dependent Effects on Promoter Function in a Modified Escherichia coli-Based Transcription System
Authors: Montero-Diez Cristina , Deighan Padraig , Osmundson Joseph , Darst Seth A. , Hochschild Ann 
Published: June 2013

ABSTRACT

Promoter recognition in bacteria is mediated primarily by the σ subunit of RNA polymerase (RNAP), which makes sequence-specific contacts with the promoter −10 and −35 elements in the context of the RNAP holoenzyme. However, the RNAP α subunit can also contribute to promoter recognition by making sequence-specific contacts with upstream (UP) elements that are associated with a subset of promoters, including the rRNA promoters. In
Escherichia coli
, these interactions between the RNAP α subunit (its C-terminal domain [CTD], in particular) and UP element DNA result in significant stimulation of rRNA transcription. Among the many cellular and bacteriophage-encoded regulators of transcription initiation that have been functionally dissected, most exert their effects via a direct interaction with either the σ or the α subunit. An unusual example is provided by a phage-encoded inhibitor of RNA synthesis in
Staphylococcus aureus
. This protein, phage G1 gp67, which binds tightly to σ in the context of the
S. aureus
RNAP holoenzyme, has recently been shown to exert selective effects on transcription by inhibiting the function of the α subunit CTD (αCTD). Here we report the development of a gp67-responsive
E. coli
-based transcription system. We examine transcription
in vitro
from promoters that do or do not carry the UP element associated with a well-characterized
E. coli
rRNA promoter. Our findings indicate that the αCTD can increase promoter activity significantly even in the absence of an UP element. We also find that gp67 can exert αCTD-dependent or αCTD-independent effects on transcription depending on the particular promoter, indicating that the mechanism of gp67 action is context dependent.
Quorum Sensing Regulatory Cascades Control Vibrio fluvialis Pathogenesis
Authors: Wang Yunduan , Wang Hui , Liang Weili , Hay Amanda J. , Zhong Zengtao , Kan Biao , Zhu Jun 
Published: June 2013

ABSTRACT

Quorum sensing (QS) is a process by which individual bacteria are able to communicate with one another, thereby enabling the population as a whole to coordinate gene regulation and subsequent phenotypic outcomes. Communication is accomplished through production and detection of small molecules in the extracellular milieu. In many bacteria, particularly
Vibrio
species, multiple QS systems result in multiple signals, as well as cross talk between systems. In this study, we identify two QS systems in the halophilic enteric pathogen
Vibrio fluvialis
: one acyl-homoserine lactone (AHL) based and one CAI-1/AI-2 based. We show that a LuxI homolog, VfqI, primarily produces 3-oxo-C10-HSL, which is sensed by a LuxR homolog, VfqR. VfqR-AHL is required to activate
vfqI
expression and autorepress
vfqR
expression. In addition, we have shown that similar to that in
V. cholerae
and
V. harveyi
,
V. fluvialis
produces CAI-1 and AI-2 signal molecules to activate the expression of a
V. cholerae
HapR homolog through LuxO. Although VfqR-AHL does not regulate
hapR
expression, HapR can repress
vfqR
transcription. Furthermore, we found that QS in
V. fluvialis
positively regulates production of two potential virulence factors, an extracellular protease and hemolysin. QS also affects cytotoxic activity against epithelial tissue cultures. These data suggest that
V. fluvialis
integrates QS regulatory pathways to play important physiological roles in pathogenesis.
Personhood within the context of sedation at the end of life in Singapore
Authors: Radha Krishna Lalit Kumar 
Published: June 2013

The concept of personhood is critical to the provision of holistic, patient-centred, palliative care yet no common definition of this term exists. Some characterise personhood by the presence of consciousness-related features such as self-awareness while others deem personhood present by virtue of Divine endowment or as a result of one's social relations. Efforts to appropriately delineate this concept come under scrutiny following suggestions that patients rendered deeply and irreversibly unconscious lack personhood and ought to be considered ‘dead’.This case report studies the views of a family caring for a deeply sedated terminally ill patient, to appropriately site local views of personhood within the context of sedation at the end of life. The resultant Ring Theory of Personhood dispenses with concerns that personhood is solely dependent upon consciousness and distances sedative treatments of last resort such as continuous deep sedation from euthanasia.
Impact from point-of-care devices on emergency department patient processing times compared with central laboratory testing of blood samples: a randomised controlled trial and cost-effectiveness analysis
Authors: Asha Stephen Edward , Chan Adam Chiu Fat , Walter Elizabeth , Kelly Patrick J , Morton Rachael L , Ajami Allan , Wilson Roger Denis , Honneyman Daniel 
Published: June 2013

ObjectiveTo determine if time to disposition decisions for emergency department (ED) patients can be reduced when blood tests are processed using point-of-care (POC) devices and to conduct a cost-effectiveness analysis of POC compared with laboratory testing.MethodsThis randomised trial enrolled adults suspected of an acute coronary syndrome or presenting with conditions considered to only require blood tests available by POC. Participants were randomised to have blood tests processed by POC or laboratory. Outcomes measured were time to disposition decision and ED length-of-stay (LOS). The cost-effectiveness analysis calculated the total and mean costs per ED presentation, as well as total and mean benefits in time saved to disposition decision.ResultsThere were 410 POC participants and 401 controls. The mean times to a disposition decision for POC versus controls were 3.24 and 3.50 h respectively, a difference of 7.6% (95% CI 0.4% to 14.3%, p=0.04), and 4.32 and 4.52 h respectively for ED LOS, a difference of 4.4% (95% CI −2.7% to 11.0%, p=0.21). Improved processing time was greatest for participants enrolled by senior staff with a reduction in time to disposition decision of 19.1% (95% CI 7.3% to 29.4%, p<0.01) and ED LOS of 15.6% (95% CI 4.9% to 25.2%, p=0.01). Mean pathology costs were $12 higher in the POC group (95% CI $7 to $18) and the incremental cost-effectiveness ratio was $113 per hour saved in time to disposition decision for POC compared with standard laboratory testing.ConclusionsSmall improvements in disposition decision time were achieved with POC testing for a moderate increase in cost. Greatest benefit may be achieved when POC is targeted to senior medical staff.
Temporary Solitaire stent neck remodeling in the coiling of ruptured aneurysms
Authors: Almekhlafi Mohammed A , Hockley Aaron , Wong John H , Goyal Mayank 
Published: June 2013

BackgroundStent-assisted coiling is a commonly adopted technique employed in the coiling of broader-based aneurysms. It avoids flow arrest and the risk of vessel rupture associated with balloon-assisted coiling. However, there is a risk of stent thrombosis with the corollary risk of stroke during and after the procedure. Antiplatelet agents are used to mitigate this risk but raise a secondary concern of hemorrhagic complications, particularly with ruptured aneurysm where further interventions such as ventriculostomy occur not infrequently. Stent removal after coil embolization would eliminate the risk of post-procedure stent thromboembolic complications and alleviate the need for continuing antiplatelet therapy.MethodsA prospectively maintained endovascular database was searched to identify patients who underwent stent-assisted coil embolization followed by stent retrieval and removal. The clinical and technical aspects of the cases were obtained in addition to the procedural outcomes.ResultsThree cases were identified where the use of the fully resheathable Solitaire AB Neurovascular Remodeling Device permitted the coiling of broad-based aneurysms with subsequent retrieval and removal of the stent. All patients presented with subarachnoid hemorrhage and received aspirin prior to the procedure. Two patients did not require antiplatelet therapy after the procedure. No coil herniation or thromboembolic events were encountered.ConclusionsStent retrieval and removal can be done safely in selected cases at the end of stent-assisted coil embolization using the Solitaire AB device. This technique avoids the need for continuing antiplatelet therapy, which can be particularly important in the setting of acute subarachnoid hemorrhage.