bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microarray-Based Characterization of Microbial Community Functional Structure and Heterogeneity in Marine Sediments from the Gulf of Mexico
Authors: Wu Liyou , Kellogg Laurie , Devol Allan H. , Tiedje James M. , Zhou Jizhong 
Published: May 2008

ABSTRACT

Marine sediments of coastal margins are important sites of carbon sequestration and nitrogen cycling. To determine the metabolic potential and structure of marine sediment microbial communities, two cores were collected each from the two stations (GMT at a depth of 200 m and GMS at 800 m) in the Gulf of Mexico, and six subsamples representing different depths were analyzed from each of these two cores using functional gene arrays containing ∼2,000 probes targeting genes involved in carbon fixation; organic carbon degradation; contaminant degradation; metal resistance; and nitrogen, sulfur, and phosphorous cycling. The geochemistry was highly variable for the sediments based on both site and depth. A total of 930 (47.1%) probes belonging to various functional gene categories showed significant hybridization with at least 1 of the 12 samples. The overall functional gene diversity of the samples from shallow depths was in general lower than those from deep depths at both stations. Also high microbial heterogeneity existed in these marine sediments. In general, the microbial community structure was more similar when the samples were spatially closer. The number of unique genes at GMT increased with depth, from 1.7% at 0.75 cm to 18.9% at 25 cm. The same trend occurred at GMS, from 1.2% at 0.25 cm to 15.2% at 16 cm. In addition, a broad diversity of geochemically important metabolic functional genes related to carbon degradation, nitrification, denitrification, nitrogen fixation, sulfur reduction, phosphorus utilization, contaminant degradation, and metal resistance were observed, implying that marine sediments could play important roles in biogeochemical cycling of carbon, nitrogen, phosphorus, sulfate, and various metals. Finally, the Mantel test revealed significant positive correlations between various specific functional genes and functional processes, and canonical correspondence analysis suggested that sediment depth, PO
4
3−
, NH
4
+
, Mn(II), porosity, and Si(OH)
4
might play major roles in shaping the microbial community structure in the marine sediments.
A PCR-Based Method for Monitoring
Legionella pneumophila
in Water Samples Detects Viable but Noncultivable Legionellae That Can Recover Their Cultivability
Authors: Dusserre Eric , Ginevra Christophe , Hallier-Soulier Sylvie , Vandenesch François , Festoc Gabriel , Etienne Jerome , Jarraud Sophie , Molmeret Maëlle 
Published: May 2008

ABSTRACT

Legionella pneumophila
is the causative agent of Legionnaires' disease. This bacterium is ubiquitous in aqueous environments and uses amoebae as an intracellular replicative niche. Real-time PCR has been developed for rapid detection of
Legionella
DNA in water samples. In addition to culturable bacteria, this method may also detect dead and viable but noncultivable (VBNC) legionellae. In order to understand the significance of positive PCR results in this setting, we prepared water samples containing known concentrations of
L. pneumophila
and analyzed them comparatively by means of conventional culture, real-time PCR, viability labeling, and immunodetection (solid-phase cytometry). We also examined the influence of chlorination on the results of the four methods. The different techniques yielded similar results for nonchlorinated water samples but not for chlorinated samples. After treatment for 24 h with 0.5 and 1 ppm chlorine, all cultures were negative, PCR and immunodetection showed about 10
6
genome units and bacteria/ml, and total-viable-count (TVC) labeling detected 10
5
and 10
2
metabolically active bacteria/ml, respectively. Thus, PCR also detected bacteria that were VBNC. The recoverability of VBNC forms was confirmed by 5 days of coculture with
Acanthamoeba polyphaga
. Therefore, some TVC-positive bacteria were potentially infective. These data show that
L. pneumophila
PCR detects not only culturable bacteria but also VBNC forms and dead bacterial DNA at low chlorine concentrations.
Genome-Wide Gene Expression Patterns and Growth Requirements Suggest thatPelobacter carbinolicusReduces Fe(III) Indirectly via Sulfide Production
Authors: Haveman Shelley A. , DiDonato Raymond J. , Villanueva Laura , Shelobolina Evgenya S. , Postier Bradley L. , Xu Bo , Liu Anna , Lovley Derek R. 
Published: May 2008

ABSTRACTAlthoughPelobacterspecies are closely related toGeobacterspecies, recent studies suggested thatPelobacter carbinolicusmay reduce Fe(III) via a different mechanism because it lacks the outer-surfacec-type cytochromes that are required for Fe(III) reduction byGeobacter sulfurreducens. Investigation into the mechanisms for Fe(III) reduction demonstrated thatP. carbinolicushad growth yields on both soluble and insoluble Fe(III) consistent with those of other Fe(III)-reducing bacteria. Comparison of whole-genome transcript levels during growth on Fe(III) versus fermentative growth demonstrated that the greatest apparent change in gene expression was an increase in transcript levels for four contiguous genes. These genes encode two putative periplasmic thioredoxins; a putative outer-membrane transport protein; and a putative NAD(FAD)-dependent dehydrogenase with homology to disulfide oxidoreductases in the N terminus, rhodanese (sulfurtransferase) in the center, and uncharacterized conserved proteins in the C terminus. UnlikeG. sulfurreducens, transcript levels for cytochrome genes did not increase inP. carbinolicusduring growth on Fe(III).P. carbinolicuscould use sulfate as the sole source of sulfur during fermentative growth, but required elemental sulfur or sulfide for growth on Fe(III). The increased expression of genes potentially involved in sulfur reduction, coupled with the requirement for sulfur or sulfide during growth on Fe(III), suggests thatP. carbinolicusreduces Fe(III) via an indirect mechanism in which (i) elemental sulfur is reduced to sulfide and (ii) the sulfide reduces Fe(III) with the regeneration of elemental sulfur. This contrasts with the direct reduction of Fe(III) that has been proposed forGeobacterspecies.
Leishmania
Adaptor Protein-1 Subunits Are Required for Normal Lysosome Traffic, Flagellum Biogenesis, Lipid Homeostasis, and Adaptation to Temperatures Encountered in the Mammalian Host
Authors: Vince James E. , Tull Dedreia L. , Spurck Timothy , Derby Merran C. , McFadden Geoffrey I. , Gleeson Paul A. , Gokool Suzanne , McConville Malcolm J. 
Published: May 2008

ABSTRACT

The adaptor protein-1 (AP-1) complex is involved in membrane transport between the Golgi apparatus and endosomes. In the protozoan parasite
Leishmania mexicana mexicana
, the AP-1 μ1 and σ1 subunits are not required for growth at 27°C but are essential for infectivity in the mammalian host. In this study, we have investigated the function of these AP-1 subunits in order to understand the molecular basis for this loss of virulence. The μ1 and σ1 subunits were localized to late Golgi and endosome membranes of the major parasite stages. Parasite mutants lacking either AP-1 subunit lacked obvious defects in Golgi structure, endocytosis, or exocytic transport. However, these mutants displayed reduced rates of endosome-to-lysosome transport and accumulated fragmented, sterol-rich lysosomes. Defects in flagellum biogenesis were also evident in nondividing promastigote stages, and this phenotype was exacerbated by inhibitors of sterol and sphingolipid biosynthesis. Furthermore, both AP-1 mutants were hypersensitive to elevated temperature and perturbations in membrane lipid composition. The pleiotropic requirements for AP-1 in membrane trafficking and temperature stress responses explain the loss of virulence of these mutants in the mammalian host.
SSD1
Is Integral to Host Defense Peptide Resistance in
Candida albicans
Authors: Gank Kimberly D. , Yeaman Michael R. , Kojima Satoshi , Yount Nannette Y. , Park Hyunsook , Edwards John E. , Filler Scott G. , Fu Yue 
Published: May 2008

ABSTRACT

Candida albicans
is usually a harmless human commensal. Because inflammatory responses are not normally induced by colonization, antimicrobial peptides are likely integral to first-line host defense against invasive candidiasis. Thus,
C. albicans
must have mechanisms to tolerate or circumvent molecular effectors of innate immunity and thereby colonize human tissues. Prior studies demonstrated that an antimicrobial peptide-resistant strain of
C. albicans
, 36082
R
, is hypervirulent in animal models versus its susceptible counterpart (36082
S
). The current study aimed to identify a genetic basis for antimicrobial peptide resistance in
C. albicans
. Screening of a
C. albicans
genomic library identified
SSD1
as capable of conferring peptide resistance to a susceptible surrogate,
Saccharomyces cerevisiae
. Sequencing confirmed that the predicted translation products of 36082
S
and 36082
R
SSD1
genes were identical. However, Northern analyses corroborated that
SSD1
is expressed at higher levels in 36082
R
than in 36082
S
. In isogenic backgrounds,
ssd1
Δ/
ssd1
Δ null mutants were significantly more susceptible to antimicrobial peptides than parental strains but had equivalent susceptibilities to nonpeptide stressors. Moreover,
SSD1
complementation of
ssd1
Δ/
ssd1
Δ mutants restored parental antimicrobial peptide resistance phenotypes, and overexpression of
SSD1
conferred enhanced peptide resistance. Consistent with these in vitro findings,
ssd1
null mutants were significantly less virulent in a murine model of disseminated candidiasis than were their parental or complemented strains. Collectively, these results indicate that
SSD1
is integral to
C. albicans
resistance to host defense peptides, a phenotype that appears to enhance the virulence of this organism in vivo.
Competitive and Cooperative Effects in Quorum-Sensing-Regulated Galactoglucan Biosynthesis in
Sinorhizobium meliloti
Authors: McIntosh Matthew , Krol Elizaveta , Becker Anke 
Published: May 2008

ABSTRACT

The symbiotic nitrogen-fixing bacterium
Sinorhizobium meliloti
possesses the Sin quorum-sensing system based on
N
-acyl homoserine lactones (AHLs) as signal molecules. The Sin system consists of SinI, the AHL synthase, and SinR, the LuxR-type regulator. This system regulates the expression of a multitude of
S. meliloti
genes through ExpR, another LuxR-type regulator. Analysis of the activity of the
sinI
promoter showed that the expression of
sinI
is dependent on
sinR
and enhanced by a combination of
expR
and Sin AHLs. The characterization of the ExpR binding site upstream of
sinI
and the identification of binding sites upstream of the galactoglucan biosynthesis genes
wgaA
(
expA1
) and
wgeA
(
expE1
) allowed the definition of a consensus sequence for these binding sites. Based on this consensus, two additional ExpR binding sites in the promoter regions of
exoI
and
exsH
, two genes related to the production of succinoglycan, were found. The specific binding of ExpR to the
wgaA
and
wgeA
promoters was enhanced in the presence of oxo-C
14
-HL. Positive regulation of the galactoglucan biosynthesis genes by ExpR was shown to be dependent on WggR (ExpG) and influenced by MucR, both of which are previously characterized regulators of these genes. Based on these results, a reworked model of the Sin-ExpR quorum-sensing regulation scheme of galactoglucan production in
S. meliloti
is suggested.
The
Campylobacter jejuni
Thiol Peroxidases Tpx and Bcp Both Contribute to Aerotolerance and Peroxide-Mediated Stress Resistance but Have Distinct Substrate Specificities
Authors: Atack John M. , Harvey Philippa , Jones Michael A. , Kelly David J. 
Published: May 2008

ABSTRACT

The microaerophilic food-borne pathogen
Campylobacter jejuni
experiences variable oxygen concentrations during its life cycle, especially during transitions between the external environment and the avian or mammalian gut. Single knockout mutations in either one of two related thiol peroxidase genes,
tpx
and
bcp
, resulted in normal microaerobic growth (10% [vol/vol] oxygen) but poorer growth than that of the wild type under high-aeration conditions (21% [vol/vol] oxygen). However, a
tpx/bcp
double mutant had a severe microaerobic growth defect and did not grow at high aeration in shake flasks. Although the single mutant strains were no more sensitive than the wild-type strains in disc diffusion assays with hydrogen peroxide, organic peroxides, superoxide, or nitrosative stress agents, in all cases the double mutant was hypersensitive. Quantitative cell viability and cellular lipid peroxidation assays indicated some increased sensitivity of the single
tpx
and
bcp
mutants to peroxide stress. Protein carbonylation studies revealed that the
tpx/bcp
double mutant had a higher degree of oxygen- and peroxide-induced oxidative protein damage than did either of the single mutants. An analysis of the peroxidase activity of the purified recombinant enzymes showed that, surprisingly, Tpx reduced only hydrogen peroxide as substrate, whereas Bcp also reduced organic peroxides. Immunoblotting of wild-type cell extracts with Tpx- or Bcp-specific antibodies showed increased abundance of both proteins under high aeration compared to that under microaerobic growth conditions. Taken together, the results suggest that Tpx and Bcp are partially redundant antioxidant enzymes that play an important role in protection of
C. jejuni
against oxygen-induced oxidative stress.
A Plasmid-Borne
Shewanella algae
Gene,
qnrA3
, and Its Possible Transfer In Vivo between
Kluyvera ascorbata
and
Klebsiella pneumoniae
Authors: Lascols Christine , Podglajen Isabelle , Verdet Charlotte , Gautier Valérie , Gutmann Laurent , Soussy Claude-James , Collatz Ekkehard , Cambau Emmanuelle 
Published: May 2008

ABSTRACT

The plasmid-borne quinolone resistance gene
qnrA1
is prevalent in multidrug-resistant
Enterobacteriaceae
. A chromosomally encoded homologue in
Shewanella algae
,
qnrA3
, has been described. We isolated two
qnrA3
-positive strains, one of
Klebsiella pneumoniae
(He96) and one of
Kluyvera ascorbata
(Kas96), from the feces of an immunocompromised outpatient. The
qnrA3
allele was identical to that of
S. algae
except for 5 nucleotides and differed from
qnrA1
by 29 nucleotides affecting three amino acids. The analysis of the
qnrA3
genetic environment showed that
qnrA3
was inserted downstream from an IS
CR1
element at a recombination crossover site described for other resistance genes, including
qnrA1
, and immediately upstream from IS
26
, a situation not described before. IS
26
preceded an incomplete class 1 integron which contained, among other genes,
aac
(
6
′)-
Ib-cr
, another transferable quinolone resistance gene, and the β-lactamase gene
bla
OXA-1/30
. The 10-kb fragment encompassing
qnrA3
was compared to previously described
qnrA1
-containing plasmids and multidrug-resistant plasmids; it shares identical sequences with pC15a, pHSH2, pQR1, pQKp311H, and pSAL-1 but with rearrangements, deletions, and mutations. Conjugal transfer of
qnrA3
was highly efficient (10
−2
) from
K. pneumoniae
He96 or
K. ascorbata
Kas96 to
Escherichia coli
J53 but less so (10
−5
) from either donor to a clinical strain of
Enterobacter cloacae
. This first description of a plasmid-borne copy and of the in vitro transfer of
qnrA3
is taken to illustrate its likely in vivo transfer from
S. algae
to the
Enterobacteriaceae
.
Opposite Effects of Mn2+and Zn2+on PsaR-Mediated Expression of the Virulence GenespcpA,prtA, andpsaBCAofStreptococcus pneumoniae
Authors: Kloosterman Tomas G. , Witwicki Robert M. , van der Kooi-Pol Magdalena M. , Bijlsma Jetta J. E. , Kuipers Oscar P. 
Published: May 2008

ABSTRACTHomeostasis of Zn2+and Mn2+is important for the physiology and virulence of the human pathogenStreptococcus pneumoniae. Here, transcriptome analysis was used to determine the response ofS. pneumoniaeD39 to a high concentration of Zn2+. Interestingly, virulence genes encoding the choline binding protein PcpA, the extracellular serine protease PrtA, and the Mn2+uptake system PsaBC(A) were strongly upregulated in the presence of Zn2+. Using random mutagenesis, a previously described Mn2+-responsive transcriptional repressor, PsaR, was found to mediate the observed Zn2+-dependent derepression. In addition, PsaR is also responsible for the Mn2+-dependent repression of these genes. Subsequently, we investigated how these opposite effects are mediated by the same regulator. In vitro binding of purified PsaR to theprtA,pcpA, andpsaBpromoters was stimulated by Mn2+, whereas Zn2+destroyed the interaction of PsaR with its target promoters. Mutational analysis of thepcpApromoter demonstrated the presence of a PsaR operator that mediates the transcriptional effects. In conclusion, PsaR is responsible for the counteracting effects of Mn2+and Zn2+on the expression of several virulence genes inS. pneumoniae, suggesting that the ratio of these metal ions exerts an important influence on pneumococcal pathogenesis.
Modulation of Hexa-Acyl Pyrophosphate Lipid A Population underEscherichia coliPhosphate (Pho) Regulon Activation
Authors: Lamarche Martin G. , Kim Sang-Hyun , Crépin Sébastien , Mourez Michael , Bertrand Nicolas , Bishop Russell E. , Dubreuil J. Daniel , Harel Josée 
Published: May 2008

ABSTRACTEnvironmental phosphate is an important signal for microorganism gene regulation, and it has recently been shown to trigger some key bacterial virulence mechanisms. In many bacteria, the Pho regulon is the major circuit involved in adaptation to phosphate limitation. The Pho regulon is controlled jointly by the two-component regulatory system PhoR/PhoB and by the phosphate-specific transport (Pst) system, which both belong to the Pho regulon. We showed that apstmutation results in virulence attenuation in extraintestinal pathogenicEscherichia coli(ExPEC) strains. Our results indicate that the bacterial cell surface of thepstmutants is altered. In this study, we show thatpstmutants of ExPEC strains display an increased sensitivity to different cationic antimicrobial peptides and vancomycin. Remarkably, the hexa-acylated 1-pyrophosphate form of lipid A is significantly less abundant inpstmutants. Among differentially expressed genes in thepstmutant,lpxTcoding for an enzyme that transfers a phosphoryl group to lipid A, forming the 1-diphosphate species, was found to be downregulated. Our results strongly suggest that the Pho regulon is involved in lipid A modifications, which could contribute to bacterial surface perturbations. Since the Pho regulon and the Pst system are conserved in many bacteria, such a lipid A modification mechanism could be widely distributed among gram-negative bacterial species.
The Role of Prophage for Genome Diversification within a Clonal Lineage ofLactobacillus johnsonii: Characterization of the Defective Prophage LJ771
Authors: Denou Emmanuel , Pridmore Raymond David , Ventura Marco , Pittet Anne-Cécile , Zwahlen Marie-Camille , Berger Bernard , Barretto Caroline , Panoff Jean-Michel , Brüssow Harald 
Published: May 2008

ABSTRACTTwo independent isolates of the gut commensalLactobacillus johnsoniiwere sequenced. These isolates belonged to the same clonal lineage and differed mainly by a 40.8-kb prophage, LJ771, belonging to the Sfi11 phage lineage. LJ771 shares close DNA sequence identity withLactobacillus gasseriprophages. LJ771 coexists as an integrated prophage and excised circular phage DNA, but phage DNA packaged into extracellular phage particles was not detected. Between the phage lysin gene andattRa likelymazE(“antitoxin”)/pemK(“toxin”) gene cassette was detected in LJ771 but not in theL. gasseriprophages. ExpressedpemKcould be cloned inEscherichia colionly together with themazEgene. LJ771 was shown to be highly stable and could be cured only by coexpression ofmazEfrom a plasmid. The prophage was integrated into the methionine sulfoxide reductase gene (msrA) and complemented the 5′ end of this gene, creating a protein with a slightly altered N-terminal sequence. The twoL. johnsoniistrains had identical in vitro growth and in vivo gut persistence phenotypes. Also, in an isogenic background, the presence of the prophage resulted in no growth disadvantage.
Impact of standardised reporting in adrenocortical carcinoma: a single centre clinicopathological review
Authors: Advani A , Vaikkakara S , Gill M S , Arun C S , Pearce S H , Ball S G , James R A , Lennard T W J , Bliss R D , Quinton R , Johnson S J 
Published: May 2008

Aims:Structured multicentre efforts are needed if the prognosis of adrenocortical carcinoma (ACC) is to be improved. Data collection may be enhanced through standardised histopathological reporting using criteria such as the recently published Royal College of Pathologists’ (UK) minimum dataset (MDS). This study aimed to perform a clinicopathological review of the adult patients treated at the Royal Victoria Infirmary, Newcastle upon Tyne, in the 10 years preceding the MDS.Methods:Case records were examined for all patients diagnosed with ACC between 1996 and 2006. Pathology was reviewed and compared with the Royal College of Pathologists’ MDS along with the original reports. A systematic evaluation of Ki-67 immunolabelling was also performed.Results:Eleven patients with ACC were diagnosed and treated. Histopathological reporting according to the MDS identified more features of malignancy than in the original reports (8.5±1.2 versus 5.1±0.8, p<0.02). The median number of microscopic criteria of malignancy was 7 (range 5–10), with ⩾5 features occurring in all cases. The most commonly observed features of malignancy were diffuse architecture, <25% clear cells, confluent necrosis, abnormal mitoses and mitotic count ⩾6 per 50 high-power fields. Capsular invasion and ⩾8 MDS criteria of malignancy were associated with a worse outcome (each p<0.01). Median Ki-67 index was 19.0% (range 3.7–44.1%) and was not apparently related to survival.Conclusions:Standardised criteria for histopathological reporting of ACC will improve the accuracy of data for cancer registration and may also assist in individual patient stratification. An elevated Ki-67 index is a feature of ACC, although it does not appear to predict individual patient survival.
Genetic variation in the diameter–height relationship in Scots pine (Pinus sylvestris)
Authors: Kroon Johan , Andersson Bengt , Mullin Tim J. 
Published: June 2008

Genetic parameters were estimated for the diameter–height (d-h) relationship and three other tree stem-form characteristics (total height, breast height diameter, and total tree volume) for data from 10 diallel progeny trials of Scots pine ( Pinus sylvestris L.), at about 30 years of age in Sweden. Linear mixed models were fit to the data, where adjustments for intertree competition and microsite heterogeneity were made by means of covariates in a nearest-neighbour analysis. The d-h relationship was analyzed with a covariate (tree height) adjusted model of diameter. Average estimates of the additive coefficient of variation and narrow-sense heritability for the d-h relationship were 7.4% and 0.22, respectively. Estimates of dominance were comparatively small (average dominance: phenotypic variance ratio of 0.04). The results indicate that there is scope to modify the d-h relationship by selection and breeding. Additive genetic correlations between the d-h relationship and height were negative, with a mean of –0.62. Selection for height would thus result in stems that are more slender than average, suggesting that tall trees allocate relatively more resources to height growth than to diameter growth. Selection based on height alone will negatively affect volume gain.