bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial Colonization of Pellet Softening Reactors Used during Drinking Water Treatment
Authors: Hammes Frederik , Boon Nico , Vital Marius , Ross Petra , Magic-Knezev Aleksandra , Dignum Marco 
Published: December 2010

ABSTRACT

Pellet softening reactors are used in centralized and decentralized drinking water treatment plants for the removal of calcium (hardness) through chemically induced precipitation of calcite. This is accomplished in fluidized pellet reactors, where a strong base is added to the influent to increase the pH and facilitate the process of precipitation on an added seeding material. Here we describe for the first time the opportunistic bacterial colonization of the calcite pellets in a full-scale pellet softening reactor and the functional contribution of these colonizing bacteria to the overall drinking water treatment process. ATP analysis, advanced microscopy, and community fingerprinting with denaturing gradient gel electrophoretic (DGGE) analysis were used to characterize the biomass on the pellets, while assimilable organic carbon (AOC), dissolved organic carbon, and flow cytometric analysis were used to characterize the impact of the biological processes on drinking water quality. The data revealed pellet colonization at concentrations in excess of 500 ng of ATP/g of pellet and reactor biomass concentrations as high as 220 mg of ATP/m
3
of reactor, comprising a wide variety of different microorganisms. These organisms removed as much as 60% of AOC from the water during treatment, thus contributing toward the biological stabilization of the drinking water. Notably, only a small fraction (about 60,000 cells/ml) of the bacteria in the reactors was released into the effluent under normal conditions, while the majority of the bacteria colonizing the pellets were captured in the calcite structures of the pellets and were removed as a reusable product.
Functional Analysis of the Twin-Arginine Translocation Pathway in
Sodalis glossinidius
, a Bacterial Symbiont of the Tsetse Fly
Authors: De Vooght Linda , Caljon Guy , Coosemans Marc , Van Den Abbeele Jan 
Published: December 2010

ABSTRACT

This study demonstrates a functional twin-arginine (Tat) translocation pathway present in the tsetse fly symbiont
Sodalis glossinidius
and its potential to export active heterologous proteins to the periplasm. Functionality was demonstrated using green fluorescent protein (GFP) fused to the Tat signal peptide of
Escherichia coli
trimethylamine
N
-oxide reductase (TorA).
Recombination Can Cause Telomere Elongations as Well as Truncations Deep within Telomeres in Wild-Type Kluyveromyces lactis Cells
Authors: Bechard Laura H. , Jamieson Nathan , McEachern Michael J. 
Published: December 2010

ABSTRACT

In this study, we examined the role of recombination at the telomeres of the yeast
Kluyveromyces lactis
. We demonstrated that an abnormally long and mutationally tagged telomere was subject to high rates of telomere rapid deletion (TRD) that preferentially truncated the telomere to near-wild-type size. Unlike the case in
Saccharomyces cerevisiae
, however, there was not a great increase in TRD in meiosis. About half of mitotic TRD events were associated with deep turnover of telomeric repeats, suggesting that telomeres were often cleaved to well below normal length prior to being reextended by telomerase. Despite its high rate of TRD, the long telomere showed no increase in the rate of subtelomeric gene conversion, a highly sensitive test of telomere dysfunction. We also showed that the long telomere was subject to appreciable rates of becoming elongated substantially further through a recombinational mechanism that added additional tagged repeats. Finally, we showed that the deep turnover that occurs within normal-length telomeres was diminished in the absence of
RAD52
. Taken together, our results suggest that homologous recombination is a significant process acting on both abnormally long and normally sized telomeres in
K. lactis
.
Initial Cell Type Choice in Dictyostelium
Authors: Jang Wonhee , Gomer Richard H. 
Published: December 2010

ABSTRACT

Much remains to be understood about how a group of cells break symmetry and differentiate into distinct cell types. The simple eukaryote
Dictyostelium discoideum
is an excellent model system for studying questions such as cell type differentiation.
Dictyostelium
cells grow as single cells. When the cells starve, they aggregate to develop into a multicellular structure with only two main cell types: spore and stalk. There has been a longstanding controversy as to how a cell makes the initial choice of becoming a spore or stalk cell. In this review, we describe how the controversy arose and how a consensus developed around a model in which initial cell type choice in
Dictyostelium
is dependent on the cell cycle phase that a cell happens to be in at the time that it starves.
FAD Binding by ApbE Protein from
Salmonella enterica
: a New Class of FAD-Binding Proteins
Authors: Boyd Jeffery M. , Endrizzi James A. , Hamilton Trinity L. , Christopherson Melissa R. , Mulder David W. , Downs Diana M. , Peters John W. 
Published: December 2010

ABSTRACT

The periplasmic protein ApbE was identified through the analysis of several mutants defective in thiamine biosynthesis and was implicated as having a role in iron-sulfur cluster biosynthesis or repair. While mutations in
apbE
cause decreased activity of several iron-sulfur enzymes
in vivo
, the specific role of ApbE remains unknown. Members of the AbpE family include NosX and RnfF, which have been implicated in oxidation-reduction associated with nitrous oxide and nitrogen metabolism, respectively. In this work, we show that ApbE binds one FAD molecule per monomeric unit. The structure of ApbE in the presence of bound FAD reveals a new FAD-binding motif. Protein variants that are nonfunctional
in vivo
were generated by random and targeted mutagenesis. Each variant was substituted in the environment of the FAD and analyzed for FAD binding after reconstitution. The variant that altered a key tyrosine residue involved in FAD binding prevented reconstitution of the protein.
Spiral Architecture of the Nucleoid in
Bdellovibrio bacteriovorus
Authors: Butan Carmen , Hartnell Lisa M. , Fenton Andrew K. , Bliss Donald , Sockett R. Elizabeth , Subramaniam Sriram , Milne Jacqueline L. S. 
Published: December 2010

ABSTRACT

We present a cryo-electron tomographic analysis of the three-dimensional architecture of a strain of the Gram-negative bacterium
Bdellovibrio bacteriovorus
in which endogenous MreB2 was replaced with monomeric teal fluorescent protein (mTFP)-labeled MreB2. In contrast to wild-type
Bdellovibrio
cells that predominantly displayed a compact nucleoid region, cells expressing mTFP-labeled MreB2 displayed a twisted spiral organization of the nucleoid. The more open structure of the MreB2-mTFP nucleoids enabled clear
in situ
visualization of ribosomes decorating the periphery of the nucleoid. Ribosomes also bordered the edges of more compact nucleoids from both wild-type cells and mutant cells. Surprisingly, MreB2-mTFP localized to the interface between the spiral nucleoid and the cytoplasm, suggesting an intimate connection between nucleoid architecture and MreB arrangement. Further, in contrast to wild-type cells, where a single tight chemoreceptor cluster localizes close to the single polar flagellum, MreB2-mTFP cells often displayed extended chemoreceptor arrays present at one or both poles and displayed multiple or inaccurately positioned flagella. Our findings provide direct structural evidence for spiral organization of the bacterial nucleoid and suggest a possible role for MreB in regulation of nucleoid architecture and localization of the chemotaxis apparatus.
A Transcriptional Regulator and ABC Transporters Link Stress Tolerance, (p)ppGpp, and Genetic Competence in
Streptococcus mutans
Authors: Seaton Kinda , Ahn Sang-Joon , Sagstetter Ann M. , Burne Robert A. 
Published: December 2010

ABSTRACT

Streptococcus mutans
, a primary agent of dental caries, has three (p)ppGpp synthases: RelA, which is required for a mupirocin-induced stringent response; RelP, which produces (p)ppGpp during exponential growth and is regulated by the RelRS two-component system; and RelQ. Transcription of
relPRS
and a gene cluster (
SMu0835
to
SMu0837
) located immediately upstream was activated in cells grown with aeration and during a stringent response, respectively. Bioinformatic analysis predicted that
SMu0836
and
SMu0837
encode ABC exporters, which we designated
rcrPQ
(r
el
c
ompetence-
r
elated) genes, respectively.
SMu0835
(
rcrR
) encodes a MarR family transcriptional regulator. Reverse transcriptase PCR (RT-PCR) and quantitative RT-PCR analysis showed that RcrR functions as an autogenous negative regulator of the expression of the
rcrRPQ
operon. A mutant in which a polar insertion replaced the
SMu836
gene (Δ
836polar
) grew more slowly and had final yields that were lower than those of the wild-type strain. Likewise, the Δ
836polar
strain had an impaired capacity to form biofilms, grew poorly at pH 5.5, and was more sensitive to oxidative stressors. Optimal expression of
rcrPQ
required RelP and vice versa. Replacement of
rcrR
with a nonpolar antibiotic resistance marker (Δ
835np
), which leads to overexpression of
rcrPQ
, yielded a strain that was not transformable with exogenous DNA. Transcriptional analysis revealed that the expression of
comYA
and
comX
was dramatically altered in the Δ
835np
and Δ
836polar
mutants. Collectively, the data support the suggestion that the
rcrRPQ
gene products play a critical role in physiologic homeostasis and stress tolerance by linking (p)ppGpp metabolism, acid and oxidative stress tolerance, and genetic competence.
Genome-Wide Identification of
Mycobacterium tuberculosis
Exported Proteins with Roles in Intracellular Growth
Authors: McCann Jessica R. , McDonough Justin A. , Sullivan Jonathan Tabb , Feltcher Meghan E. , Braunstein Miriam 
Published: December 2010

ABSTRACT

The exported proteins of
Mycobacterium tuberculosis
that are localized at the bacterial cell surface or secreted into the environment are ideally situated to interact with host factors and to function in virulence. In this study, we constructed a novel β-lactamase reporter transposon and used it directly in
M. tuberculosis
for genome-wide identification of exported proteins. From 177 β-lactam-resistant transposon mutants, we identified 111 different exported proteins. The majority of these proteins have no known function, and for nearly half of the proteins, our demonstration that they are exported when fused to a β-lactamase reporter is the first experimental proof of their extracytoplasmic localization. The transposon mutants in our banked library were of further value as a collection of mutants lacking individual exported proteins. By individually testing each of 111 mutants for growth in macrophages, six attenuated mutants with insertions in
mce1A
,
mce1B
,
mce2F
,
rv0199
,
ctaC
, and
lppX
were identified. Given that much of the
M. tuberculosis
genome encodes proteins of unknown function, our library of mapped transposon mutants is a valuable resource for efforts in functional genomics. This work also demonstrates the power of a β-lactamase reporter transposon that could be applied similarly to other bacterial pathogens.
Complete Genome Sequence of
Mycoplasma hyopneumoniae
Strain 168
Authors: Liu Wei , Feng Zhixin , Fang Liurong , Zhou Zhemin , Li Qiang , Li Sha , Luo Rui , Wang Lei , Chen Huanchun , Shao Guoqing , Xiao Shaobo 
Published: December 2010

ABSTRACT

Mycoplasma hyopneumoniae
strain 168, a pathogenic strain prevalent in China, was isolated in 1974. Although this strain has been widespread for a long time, the genome sequence had not been determined. Here, we announce the complete genome sequence of
M. hyopneumoniae
strain 168.
Relating the Physical Properties of
Pseudomonas aeruginosa
Lipopolysaccharides to Virulence by Atomic Force Microscopy
Authors: Ivanov Ivan E. , Kintz Erica N. , Porter Laura A. , Goldberg Joanna B. , Burnham Nancy A. , Camesano Terri A. 
Published: December 2010

ABSTRACT

Lipopolysaccharides (LPS) are an important class of macromolecules that are components of the outer membrane of Gram-negative bacteria such as
Pseudomonas aeruginosa
.
P
.
aeruginosa
contains two different sugar chains, the homopolymer common antigen (A band) and the heteropolymer O antigen (B band), which impart serospecificity. The characteristics of LPS are generally assessed after isolation rather than in the context of whole bacteria. Here we used atomic force microscopy (AFM) to probe the physical properties of the LPS of
P
.
aeruginosa
strain PA103 (serogroup O11)
in situ
. This strain contains a mixture of long and very long polymers of O antigen, regulated by two different genes. For this analysis, we studied the wild-type strain and four mutants, ΔWzz1 (producing only very long LPS), ΔWzz2 (producing only long LPS), DΔM (with both the
wzz1
and
wzz2
genes deleted), and Wzy::GM (producing an LPS core oligosaccharide plus one unit of O antigen). Forces of adhesion between the LPS on these strains and the silicon nitride AFM tip were measured, and the Alexander and de Gennes model of steric repulsion between a flat surface and a polymer brush was used to calculate the LPS layer thickness (which we refer to as length), compressibility, and spacing between the individual molecules. LPS chains were longest for the wild-type strain and ΔWzz1, at 170.6 and 212.4 nm, respectively, and these values were not statistically significantly different from one another. Wzy::GM and DΔM have reduced LPS lengths, at 34.6 and 37.7 nm, respectively. Adhesion forces were not correlated with LPS length, but a relationship between adhesion force and bacterial pathogenicity was found in a mouse acute pneumonia model of infection. The adhesion forces with the AFM probe were lower for strains with LPS mutations, suggesting that the wild-type strain is optimized for maximal adhesion. Our research contributes to further understanding of the role of LPS in the adhesion and virulence of
P
.
aeruginosa
.
Silibinin Prevents Lung Tumorigenesis in Wild-Type but not in iNOS−/− Mice: Potential of Real-Time Micro-CT in Lung Cancer Chemoprevention Studies
Authors: Ramasamy Kumaraguruparan , Dwyer-Nield Lori D. , Serkova Natalie J. , Hasebroock Kendra M. , Tyagi Alpna , Raina Komal , Singh Rana P. , Malkinson Alvin M. , Agarwal Rajesh 
Published: December 2010

Abstract
Purpose: Sustained nitric oxide (NO) generation positively correlates with lung cancer development and progression. Herein, we genetically confirmed this role of iNOS and evaluated the chemopreventive efficacy of silibinin in carcinogen-treated B6/129 wild-type (WT) and iNOS−/− mice.
Experimental Design: Male B6/129-Nos2tm1Lau (iNOS−/−) and B6/129PF2 WT mice were injected i.p. with 1 mg/g body weight urethane once weekly for 7 consecutive weeks, followed by silibinin gavage (742 mg/kg body weight) for 5 d/wk for 18 weeks.
Results: Quantification of micro-CT data in real-time showed that silibinin significantly decreases urethane-induced tumor number and size in WT mice, consistent with measurements made ex vivo at study termination. Genetic ablation of iNOS decreased urethane-induced tumor multiplicity by 87% (P &lt; 0.001) compared to WT mice. Silibinin decreased tumor multiplicity by 71% (P &lt; 0.01) in WT mice, but did not show any such considerable effect in iNOS−/− mice. Tumors from WT mice expressed more iNOS (P &lt; 0.01) but almost similar eNOS and nNOS than those in silibinin-treated mice. In these tumors, silibinin moderately (P &lt; 0.01) inhibited cell proliferation but strongly (P &lt; 0.01) reduced the number of newly formed nestin-positive microvessels. Silibinin decreased VEGFR2 level, and STAT3 and NF-κB activation in tumors.
Conclusions: The lack of effect of silibinin in iNOS−/− mice suggests that silibinin exerts most of its chemopreventive and angiopreventive effects through its inhibition of iNOS expression in lung tumors. Our results support iNOS as a potential target for controlling lung cancer, and demonstrate the value of real-time noninvasive micro-CT imaging modality for evaluating the efficacy of lung cancer chemopreventive agents. Clin Cancer Res; 17(4); 1–9. ©2010 AACR.
MYC Amplification as a Prognostic Marker of Early-Stage Lung Adenocarcinoma Identified by Whole Genome Copy Number Analysis
Authors: Iwakawa Reika , Kohno Takashi , Kato Motohiro , Shiraishi Kouya , Tsuta Koji , Noguchi Masayuki , Ogawa Seishi , Yokota Jun 
Published: December 2010

Abstract
Purpose: Even in small-sized (≤2 cm in greatest dimension) and/or pathologic stage I lung adenocarcinoma (ADC), a considerable proportion of the patients will relapse within 5 years and show poor prognosis. The purpose of this study was to identify genetic alterations that define prognosis of patients with early-stage lung ADC.
Experimental Design: Regions of copy number alterations in 65 small-sized lung ADCs and 40 ADC cell lines were determined by using GeneChip Human Mapping 10-K and 250-K single-nucleotide polymorphism (SNP) arrays, respectively. A copy number assay based on real-time genomic PCR (RT-G-PCR) was done for 60 small-sized lung ADCs and 162 stage I lung ADCs.
Results: Several regions on chromosomes 5p, 7p, 8q, and 14q were frequently (&gt;10%) amplified in both small-sized ADCs and lung ADC cell lines. In particular, the MYC gene was mapped in the minimum common region at chromosome 8q24.21, and therefore was indicated to be a target of gene amplification in lung ADCs. MYC amplification correlated with poor prognosis (P = 0.031) of patients with small-sized ADCs. MYC amplification detected by SNP array analysis was well reproduced by RT-G-PCR analysis. Therefore, to investigate the utility of MYC amplification as a prognostic marker for early-stage lung ADCs, 162 stage I lung ADCs were subjected to the analysis. MYC amplification was associated with relapse-free survival in these patients (P = 0.013 by multivariate Cox proportional hazard model analysis).
Conclusions: These results strongly indicate that MYC amplification is a prognostic marker of patients with early-stage lung ADCs. Clin Cancer Res; 17(6); 1481–9. ©2010 AACR.
Hypoxia modulates the gene expression profile of immunoregulatory receptors in human mature dendritic cells: identification of TREM-1 as a novel hypoxic marker in vitro and in vivo
Authors: Bosco Maria Carla , Pierobon Daniele , Blengio Fabiola , Raggi Federica , Vanni Cristina , Gattorno Marco , Eva Alessandra , Novelli Francesco , Cappello Paola , Giovarelli Mirella , Varesio Luigi 
Published: December 2010

Abstract
Dendritic cells (DCs) are a heterogeneous group of professional antigen-presenting cells functioning as sentinels of the immune system and playing a key role in the initiation and amplification of innate and adaptive immune responses. DC development and functions are acquired during a complex differentiation and maturation process influenced by several factors present in the local milieu. A common feature at pathologic sites is represented by hypoxia, a condition of low pO2, which creates a unique microenvironment affecting cell phenotype and behavior. Little is known about the impact of hypoxia on the generation of mature DCs (mDCs). In this study, we identified by gene expression profiling a significant cluster of genes coding for immune-related cell surface receptors strongly up-regulated by hypoxia in monocyte-derived mDCs and characterized one of such receptors, TREM-1, as a new hypoxia-inducible gene in mDCs. TREM-1 associated with DAP12 in hypoxic mDCs, and its engagement elicited DAP12-linked signaling, resulting in ERK-1, Akt, and IκBα phosphorylation and proinflammatory cytokine and chemokine secretion. Finally, we provided the first evidence that TREM-1 is expressed on mDCs infiltrating the inflamed hypoxic joints of children affected by juvenile idiopathic arthritis, representing a new in vivo marker of hypoxic mDCs endowed with proinflammatory properties.
Management of RSV infections in adult recipients of hematopoietic stem cell transplantation
Authors: Shah Jharna N. , Chemaly Roy F. 
Published: December 2010

Abstract
Respiratory syncytial virus (RSV) is a common cause of seasonal respiratory viral infection in patients who have undergone hematopoietic stem cell transplantation. RSV usually presents as an upper respiratory tract infection in this patient population but may progress rapidly to lower respiratory tract infection. Available therapies that have been used for the treatment of RSV infections are limited to ribavirin, intravenous immunoglobulin, and palivizumab. The use of aerosolized ribavirin, alone or in combination with either palivizumab or intravenous immunoglobulin, remains controversial. In this comprehensive review, we present and discuss the available literature on management of RSV infections in adult hematopoietic stem cell transplantation recipients with a focus on therapeutic modalities and outcomes.
Pharmacokinetic, pharmacodynamic, and pharmacogenetic determinants of osteonecrosis in children with acute lymphoblastic leukemia
Authors: Kawedia Jitesh D. , Kaste Sue C. , Pei Deqing , Panetta John C. , Cai Xiangjun , Cheng Cheng , Neale Geoffrey , Howard Scott C. , Evans William E. , Pui Ching-Hon , Relling Mary V. 
Published: December 2010

AbstractOsteonecrosis is a severe glucocorticoid-induced complication of acute lymphoblastic leukemia treatment. We prospectively screened children (n = 364) with magnetic resonance imaging of hips and knees, regardless of symptoms; the cumulative incidence of any (grade 1-4) versus symptomatic (grade 2-4) osteonecrosis was 71.8% versus 17.6%, respectively. We investigated whether age, race, sex, acute lymphoblastic leukemia treatment arm, body mass, serum lipids, albumin and cortisol levels, dexamethasone pharmacokinetics, and genome-wide germline genetic polymorphisms were associated with symptomatic osteonecrosis. Age more than 10 years (odds ratio, = 4.85; 95% confidence interval, 2.5-9.2; P = .00001) and more intensive treatment (odds ratio = 2.5; 95% confidence interval, 1.2-4.9; P = .011) were risk factors and included as covariates in all analyses. Lower albumin (P = .05) and elevated cholesterol (P = .02) associated with symptomatic osteonecrosis, and severe (grade 3 or 4) osteonecrosis was linked to poor dexamethasone clearance (P = .0005). Adjusting for clinical features, polymorphisms of ACP1 (eg, rs12714403, P = 1.9 × 10−6, odds ratio = 5.6; 95% confidence interval, 2.7-11.3), which regulates lipid levels and osteoblast differentiation, were associated with risk of osteonecrosis as well as with lower albumin and higher cholesterol. Overall, older age, lower albumin, higher lipid levels, and dexamethasone exposure were associated with osteonecrosis and may be linked by inherited genomic variation.