bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial Distribution of Bacterial Colonies in a Model Cheese
Authors: Jeanson S. , Chadœuf J. , Madec M. N. , Aly S. , Floury J. , Brocklehurst T. F. , Lortal S. 
Published: December 2010

ABSTRACT

In most ripened cheeses, bacteria are responsible for the ripening process. Immobilized in the cheese matrix, they grow as colonies. Therefore, their distribution as well as the distance between them are of major importance for ripening steps since metabolites diffuse within the cheese matrix. No data are available to date about the spatial distribution of bacterial colonies in cheese. This is the first study to model the distribution of bacterial colonies in a food-type matrix using nondestructive techniques. We compared (i) the mean theoretical three-dimensional (3D) distances between colonies calculated on the basis of inoculation levels and considering colony distribution to be random and (ii) experimental measurements using confocal microscopy photographs of fluorescent colonies of a
Lactococcus lactis
strain producing green fluorescent protein (GFP) inoculated, at different levels, into a model cheese made by ultrafiltration (UF). Enumerations showed that the final numbers of cells were identical whatever the inoculation level (10
4
to 10
7
CFU/g). Bacterial colonies were shown to be randomly distributed, fitting Poisson's model. The initial inoculation level strongly influenced the mean distances between colonies (from 25 μm to 250 μm) and also their mean diameters. The lower the inoculation level, the larger the colonies were and the further away from each other. Multiplying the inoculation level by 50 multiplied the interfacial area of exchange with the cheese matrix by 7 for the same cell biomass. We finally suggested that final cell numbers should be discussed together with inoculation levels to take into account the distribution and, consequently, the interfacial area of colonies, which can have a significant influence on the cheese-ripening process on a microscopic scale.
Bacterial Communities Associated with the Lichen Symbiosis
Authors: Bates Scott T. , Cropsey Garrett W. G. , Caporaso J. Gregory , Knight Rob , Fierer Noah 
Published: December 2010

ABSTRACT

Lichens are commonly described as a mutualistic symbiosis between fungi and “algae” (
Chlorophyta
or
Cyanobacteria
); however, they also have internal bacterial communities. Recent research suggests that lichen-associated microbes are an integral component of lichen thalli and that the classical view of this symbiotic relationship should be expanded to include bacteria. However, we still have a limited understanding of the phylogenetic structure of these communities and their variability across lichen species. To address these knowledge gaps, we used bar-coded pyrosequencing to survey the bacterial communities associated with lichens. Bacterial sequences obtained from four lichen species at multiple locations on rock outcrops suggested that each lichen species harbored a distinct community and that all communities were dominated by
Alphaproteobacteria
. Across all samples, we recovered numerous bacterial phylotypes that were closely related to sequences isolated from lichens in prior investigations, including those from a lichen-associated
Rhizobiales
lineage (LAR1; putative N
2
fixers). LAR1-related phylotypes were relatively abundant and were found in all four lichen species, and many sequences closely related to other known N
2
fixers (e.g.,
Azospirillum
,
Bradyrhizobium
, and
Frankia
) were recovered. Our findings confirm the presence of highly structured bacterial communities within lichens and provide additional evidence that these bacteria may serve distinct functional roles within lichen symbioses.
The Mode of Cell Wall Growth in Selected Archaea Is Similar to the General Mode of Cell Wall Growth in Bacteria as Revealed by Fluorescent Dye Analysis
Authors: Wirth Reinhard , Bellack Annett , Bertl Markus , Bilek Yvonne , Heimerl Thomas , Herzog Bastian , Leisner Madeleine , Probst Alexander , Rachel Reinhard , Sarbu Christina , Schopf Simone , Wanner Gerhard 
Published: December 2010

ABSTRACT

The surfaces of 8 bacterial and 23 archaeal species, including many hyperthermophilic
Archaea
, could be stained using succinimidyl esters of fluorescent dyes. This allowed us for the first time to analyze the mode of cell wall growth in
Archaea
by subculturing stained cells. The data obtained show that incorporation of new cell wall material in
Archaea
follows the pattern observed for
Bacteria
: in the coccoid species
Pyrococcus furiosus
incorporation was in the region of septum formation while for the rod-shaped species
Methanopyrus kandleri
and
Methanothermus sociabilis
, a diffuse incorporation of cell wall material over the cell length was observed. Cell surface appendages like fimbriae/pili, fibers, or flagella were detectable by fluorescence staining only in a very few cases although their presence was proven by electron microscopy. Our data in addition prove that Alexa Fluor dyes can be used for
in situ
analyses at temperatures up to 100°C.
New Insights into the Lpt Machinery for Lipopolysaccharide Transport to the Cell Surface: LptA-LptC Interaction and LptA Stability as Sensors of a Properly Assembled Transenvelope Complex
Authors: Sperandeo Paola , Villa Riccardo , Martorana Alessandra M. , Šamalikova Maria , Grandori Rita , Dehò Gianni , Polissi Alessandra 
Published: December 2010

ABSTRACT

Lipopolysaccharide (LPS) is a major glycolipid present in the outer membrane (OM) of Gram-negative bacteria. The peculiar permeability barrier of the OM is due to the presence of LPS at the outer leaflet of this membrane that prevents many toxic compounds from entering the cell. In
Escherichia coli
LPS synthesized inside the cell is first translocated over the inner membrane (IM) by the essential MsbA flippase; then, seven essential Lpt proteins located in the IM (LptBCDF), in the periplasm (LptA), and in the OM (LptDE) are responsible for LPS transport across the periplasmic space and its assembly at the cell surface. The Lpt proteins constitute a transenvelope complex spanning IM and OM that appears to operate as a single device. We show here that
in vivo
LptA and LptC physically interact, forming a stable complex and, based on the analysis of loss-of-function mutations in LptC, we suggest that the C-terminal region of LptC is implicated in LptA binding. Moreover, we show that defects in Lpt components of either IM or OM result in LptA degradation; thus, LptA abundance in the cell appears to be a marker of properly bridged IM and OM. Collectively, our data support the recently proposed transenvelope model for LPS transport.
A Novel
cdsAB
Operon Is Involved in the Uptake of
l
-Cysteine and Participates in the Pathogenesis of
Yersinia ruckeri
Authors: Méndez Jessica , Reimundo Pilar , Pérez-Pascual David , Navais Roberto , Gómez Esther , Guijarro José A. 
Published: December 2010

ABSTRACT

Application of
in vivo
expression technology (IVET) to
Yersinia ruckeri
, an important fish pathogen, allowed the identification of two adjacent genes that represent a novel bacterial system involved in the uptake and degradation of
l
-cysteine. Analysis of the translational products of both genes showed permease domains (open reading frame 1 [ORF1]) and amino acid position identities (ORF2) with the
l
-cysteine desulfidase from
Methanocaldococcus jannaschii
, a new type of enzyme involved in the breakdown of
l
-cysteine. The operon was named
cdsAB
(cysteine desulfidase) and is found widely in anaerobic and facultative bacteria.
cdsAB
promoter analysis using
lacZY
gene fusion showed highest induction in the presence of
l
-cysteine. Two
cdsA
and
cdsB
mutant strains were generated. The limited toxic effect and the low utilization of
l
-cysteine observed in the
cdsA
mutant, together with radiolabeled experiments, strongly suggested that CdsA is an
l
-cysteine permease. Fifty percent lethal dose (LD
50
) and competence index experiments showed that both the
cdsA
and
cdsB
loci were involved in the pathogenesis of the bacteria. In conclusion, this study has shown for the first time in bacteria the existence of an
l
-cysteine uptake system that together with an additional
l
-cysteine desulfidase-encoding gene constitutes a novel operon involved in bacterial virulence.
Antibiotics and UV Radiation Induce Competence for Natural Transformation inLegionella pneumophila
Authors: Charpentier Xavier , Kay Elisabeth , Schneider Dominique , Shuman Howard A. 
Published: December 2010

ABSTRACTNatural transformation by competence is a major mechanism of horizontal gene transfer in bacteria. Competence is defined as the genetically programmed physiological state that enables bacteria to actively take up DNA from the environment. The conditions that signal competence development are multiple and elusive, complicating the understanding of its evolutionary significance. We used expression of the competence genecomEAas a reporter of competence development and screened several hundred molecules for their ability to induce competence in the freshwater living pathogenLegionella pneumophila. We found thatcomEAexpression is induced by chronic exposure to genotoxic molecules such as mitomycin C and antibiotics of the fluoroquinolone family. These results indicated that, inL. pneumophila, competence may be a response to genotoxic stress. Sunlight-emitted UV light represents a major source of genotoxic stress in the environment and we found that exposure to UV radiation effectively induces competence development. For the first time, we show that genetic exchanges by natural transformation occur within an UV-stressed population. Genotoxic stress induces the RecA-dependent SOS response in many bacteria. However, genetic and phenotypic evidence suggest thatL. pneumophilalacks a prototypic SOS response and competence development in response to genotoxic stress is RecA independent. Our results strengthen the hypothesis that competence may have evolved as a DNA damage response in SOS-deficient bacteria. This parasexual response to DNA damage may have enabledL. pneumophilato acquire and propagate foreign genes, contributing to the emergence of this human pathogen.
Labeling and Enzyme Studies of the Central Carbon Metabolism in
Metallosphaera sedula
Authors: Estelmann Sebastian , Hügler Michael , Eisenreich Wolfgang , Werner Katharina , Berg Ivan A. , Ramos-Vera W. Hugo , Say Rafael F. , Kockelkorn Daniel , Gad′on Nasser , Fuchs Georg 
Published: December 2010

ABSTRACT

Metallosphaera sedula
(
Sulfolobales
,
Crenarchaeota
) uses the 3-hydroxypropionate/4-hydroxybutyrate cycle for autotrophic carbon fixation. In this pathway, acetyl-coenzyme A (CoA) and succinyl-CoA are the only intermediates that can be considered common to the central carbon metabolism. We addressed the question of which intermediate of the cycle most biosynthetic routes branch off. We labeled autotrophically growing cells by using 4-hydroxy[1-
14
C]butyrate and [1,4-
13
C
1
]succinate, respectively, as precursors for biosynthesis. The labeling patterns of protein-derived amino acids verified the operation of the proposed carbon fixation cycle, in which 4-hydroxybutyrate is converted to two molecules of acetyl-CoA. The results also showed that major biosynthetic flux does not occur via acetyl-CoA, except for the formation of building blocks that are directly derived from acetyl-CoA. Notably, acetyl-CoA is not assimilated via reductive carboxylation to pyruvate. Rather, our data suggest that the majority of anabolic precursors are derived from succinyl-CoA, which is removed from the cycle via oxidation to malate and oxaloacetate. These C
4
intermediates yield pyruvate and phosphoenolpyruvate (PEP). Enzyme activities that are required for forming intermediates from succinyl-CoA were detected, including enzymes catalyzing gluconeogenesis from PEP. This study completes the picture of the central carbon metabolism in autotrophic
Sulfolobales
by connecting the autotrophic carbon fixation cycle to the formation of central carbon precursor metabolites.
Escherichia coli
Dihydropyrimidine Dehydrogenase Is a Novel NAD-Dependent Heterotetramer Essential for the Production of 5,6-Dihydrouracil
Authors: Hidese Ryota , Mihara Hisaaki , Kurihara Tatsuo , Esaki Nobuyoshi 
Published: December 2010

ABSTRACT

The reductive pyrimidine catabolic pathway is absent in
Escherichia coli
. However, the bacterium contains an enzyme homologous to mammalian dihydropyrimidine dehydrogenase. Here, we show that
E. coli
dihydropyrimidine dehydrogenase is the first member of a novel NADH-dependent subclass of iron-sulfur flavoenzymes catalyzing the conversion of uracil to 5,6-dihydrouracil
in vivo
.
SigG Does Not Control Gene Expression in Response to DNA Damage in
Mycobacterium tuberculosis
H37Rv
Authors: Smollett Katherine L. , Dawson Lisa F. , Davis Elaine O. 
Published: December 2010

ABSTRACT

Expression of the
Mycobacterium tuberculosis sigG
sigma factor was induced by a variety of DNA-damaging agents, but inactivation of
sigG
did not affect induction of gene expression or bacterial survival under these conditions. Therefore, SigG does not control the DNA repair response of
M. tuberculosis
H37Rv.
Requirement of the
agr
Locus for Colony Spreading of
Staphylococcus aureus
Authors: Tsompanidou Eleni , Sibbald Mark J. J. B. , Chlebowicz Monika A. , Dreisbach Annette , Back Jaap Willem , van Dijl Jan Maarten , Buist Girbe , Denham Emma L. 
Published: December 2010

ABSTRACT

The important human pathogen
Staphylococcus aureus
is known to spread on soft agar plates. Here, we show that colony spreading of
S. aureus
involves the
agr
quorum-sensing system. This finding can be related to the
agr
-dependent expression of biosurfactants, such as phenol-soluble modulins, suggesting a connection between spreading motility and virulence.
CpG island methylator phenotype of cell-cycle regulators associated with TNM stage and poor prognosis in patients with oesophageal squamous cell carcinoma
Authors: Ling Yang , Huang Guoliang , Fan Lieying , Wei Lixin , Zhu Jing , Liu Yongping , Zhu Changtai , Zhang Changsong 
Published: December 2010

AimsCpG island methylator phenotype (CIMP) involves the targeting of multiple genes by promoter hypermethylation, and the cell-cycle regulatory proteins often change in human neoplasms. To gain insight into the role of epigenetic aberration of cell-cycle regulator genes in oesophagus squamous cell carcinoma (ESCC), the authors determined the hypermethylation profile in ESCC.MethodsThe promoter methylation status of nine cell-cycle regulator genes was examined in 50 ESCC, 50 dysplastic tissues and 50 normal epithelial tissues by methylation-specific PCR.ResultsThe frequency of promoter methylation was 52% forp14, 44% forp15, 50% forp16, 56% forp21, 38% forp27, 8% forp53, 42% forp57, 36% forp73, and 44% forRB1of 50 ESCC. CIMP+ was detected in 54% (27/50) of ESCC and 8% (4/50) of dysplastic tissues; no CIMP+ was present in normal epithelial tissues (p<0.001). The results show that promoter methylation ofp14,p15,p16,p21,p27,p57andp73was far more common in ESCC samples with CIMP+ than those with CIMP−. A significant difference between CIMP status and TNM stage and metastasis was found in ESCC (p<0.05). Patients with ESCC with CIMP+ had poorer 4-year survival than those with CIMP−.ConclusionsThe results suggest that CIMP of a subset of cell-cycle regulatory genes has an important role in the pathogenesis and progression of ESCC.
Oral contraceptive and hormone replacement therapy in women with cerebral aneurysms
Authors: Chen Michael , Ouyang Bichun , Goldstein-Smith Lindsay , Feldman Lisa 
Published: December 2010

BackgroundIt is well known that cerebral aneurysms occur more frequently in women, with numerous studies suggesting a role for hormones in aneurysm pathogenesis. Estrogen promotes normal physiologic vascular endothelial function but also fluctuates during the menstrual cycle and drops significantly at menopause.MethodsA retrospective, case control study was conducted to determine if exogenous estrogen use, which stabilizes estradiol levels, had any association with the presence of cerebral aneurysms. 60 women with intradural cerebral aneurysms were interviewed about their basic medical and female reproductive health histories, including oral contraceptive pill and hormone replacement therapy use and duration of use. This information was compared with the same data collected from women in the general public, as represented by 4682 women contacted through random digit phone dialing in the National Institute of Child Health and Human Development sponsored Contraceptive and Reproductive Experiences Study, published in 2002.ResultsMultivariate logistic regression showed a significant association between a lower rate of oral contraceptive (OR 2.1, CI 1.17 to 3.81; p=0.01) and hormone replacement therapy (OR 3.09, CI 1.54 to 6.22; p=0.002) use and the presence of a cerebral aneurysm.ConclusionThese data suggest that exposure to exogenous estrogen agents in women is associated with a lower frequency of cerebral aneurysms.
Modeling of low-cement extruded curb of concrete-faced rockfill dam
Authors: Zhang Ga , Zhang Jian-Min 
Published: December 2010

As the key structure of a practical construction technique, the low-cement extruded curb has been widely used in recent concrete-faced rockfill dams (CFRDs). The extruded curb exhibits significant interactions with the neighboring gravels and with the face slab. These interactions were investigated using element tests, and a new model was proposed. This model is composed of three parts: (i) the equivalent slab that is described using an ideal elastoplasticity model, (ii) the equivalent interface between the curb and the gravel cushion layer that is described using an elastoplasticity damage model, and (iii) the interface between the curb and the face slab that is described using a modified ideal elastoplasticity model. This model was verified via a two-dimensional numerical simulation of an ideal CFRD to capture the main behavior of the extruded curb with interactions between the extruded curb and the neighboring soil – face slab, employing a significantly smaller number of elements and a shorter calculation than direct simulation. The model was used to perform a three-dimensional stress–displacement analysis of the Bakun CFRD (205 m in height), and the results showed that the extruded curb causes a change in the stress of the face slab.
Nm23-H1 Indirectly Promotes the Survival of Acute Myeloid Leukemia Blast Cells by Binding to More Mature Components of the Leukemic Clone
Authors: Lilly Andrew J. , Khanim Farhat L. , Hayden Rachel E. , Luong Quang T. , Drayson Mark T. , Bunce Christopher M. 
Published: December 2010

Abstract
Nm23-H1 plays complex roles in the development of diverse cancers including breast carcinoma, high-grade lymphomas, and acute myeloid leukemia (AML). In the case of AML and lymphomas, serum Nm23-H1 protein is elevated with the highest levels correlating with poorest prognosis. A recent study identified that this association is most likely causal in AML and that Nm23-H1 acts as an AML cell survival factor. In this study, we report heterogeneity in the ability of AML samples to bind and respond to Nm23-H1, and we offer evidence that binding is essential for improved survival. Further, we show that the subset of AMLs that bind Nm23-H1 do not do so through the putative Nm23-H1 receptor MUC1*. Although rNm23-H1 promoted the survival of the most primitive blasts within responding AMLs, it was not these cells that actually bound the protein. Instead, rNm23-H1 bound to more mature CD34lo/CD34− and CD11b+ cells, revealing an indirect survival benefit of Nm23-H1 on primitive blasts. In support of this finding, the survival of purified blast cells was enhanced by medium conditioned by more mature cells from the clone that had been stimulated by rNm23-H1. Levels of interleukin 1β (IL1β) and IL6 in rNm23-H1 conditioned medium mirrored the potency of the conditioned media to promote blast cell survival. Furthermore, Nm23-H1 expression was significantly associated with IL1β and IL6 expression in primary uncultured AML samples. These findings have implications for the role of Nm23-H1 in AML and its use as a prognostic marker. Additionally, they offer the first evidence of novel cross-talk between cell populations within the tumor clone. Cancer Res; 71(3); 1177–86. ©2010 AACR.
Using a Stem Cell–Based Signature to Guide Therapeutic Selection in Cancer
Authors: Shats Igor , Gatza Michael L. , Chang Jeffrey T. , Mori Seiichi , Wang Jialiang , Rich Jeremy , Nevins Joseph R. 
Published: December 2010

AbstractGiven the very substantial heterogeneity of most human cancers, it is likely that most cancer therapeutics will be active in only a small fraction of any population of patients. As such, the development of new therapeutics, coupled with methods to match a therapy with the individual patient, will be critical to achieving significant gains in disease outcome. One such opportunity is the use of expression signatures to identify key oncogenic phenotypes that can serve not only as biomarkers but also as a means of identifying therapeutic compounds that might specifically target these phenotypes. Given the potential importance of targeting tumors exhibiting a stem-like phenotype, we have developed an expression signature that reflects common biological aspects of various stem-like characteristics. The consensus stemness ranking (CSR) signature is upregulated in cancer stem cell–enriched samples at advanced tumor stages and is associated with poor prognosis in multiple cancer types. Using two independent computational approaches we utilized the CSR signature to identify clinically useful compounds that could target the CSR phenotype. In vitro assays confirmed selectivity of several predicted compounds including topoisomerase inhibitors and resveratrol towards breast cancer cell lines that exhibit a high-CSR phenotype. Importantly, the CSR signature could predict clinical response of breast cancer patients to a neoadjuvant regimen that included a CSR-specific agent. Collectively, these results suggest therapeutic opportunities to target the CSR phenotype in a relevant cohort of cancer patients. Cancer Res; 71(5); 1772–80. ©2010 AACR.
Activation of NF-κB by TMPRSS2/ERG Fusion Isoforms through Toll-Like Receptor-4
Authors: Wang Jianghua , Cai Yi , Shao Long-jiang , Siddiqui Javed , Palanisamy Nallasivam , Li Rile , Ren Chengxi , Ayala Gustavo , Ittmann Michael 
Published: December 2010

Abstract
The TMPRSS2/ERG (T/E) fusion gene is present and thought to be an oncogenic driver of approximately half of all prostate cancers. Fusion of the androgen-regulated TMPRSS2 promoter to the ERG oncogene results in constitutive high level expression of ERG which promotes prostate cancer invasion and proliferation. Here, we report the characterization of multiple alternatively spliced T/E fusion gene isoforms which have differential effects on invasion and proliferation. We found that T/E fusion gene isoforms differentially increase NF-κB–mediated transcription, which may explain in part the differences in biological activities of the T/E fusion isoforms. This increased activity is due to phosphorylation of NF-κB p65 on Ser536. Tissue microarray immunochemistry revealed that p65 phospho-Ser536 is present in the majority of prostate cancers where it is associated with ERG protein expression. The T/E fusion gene isoforms differentially increase expression of a number of NF-κB associated genes including PAR1, CCL2, FOS, TLR3, and TLR4 (Toll-like receptor). TLR4 activation is known to promote p65 Ser536 phosphorylation and knockdown of TLR4 with shRNA decreases Ser536 phosphorylation in T/E fusion gene expressing cells. TLR4 can be activated by proteins in the tumor microenvironment and lipopolysacharide from Gram (−) bacteria. Our findings suggest that bacterial infection of the prostate and/or endogenous microenvironment proteins may promote progression of high-grade prostatic intraepithelial neoplasia and/or prostate cancers that express the T/E fusion gene, where the NF-κB pathway might be targeted as a rational therapeutic approach. Cancer Res; 71(4); 1325–33. ©2010 AACR.