bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intracellular Copper Accumulation Enhances the Growth ofKineococcus radiotoleransduring Chronic Irradiation
Authors: Bagwell C. E. , Milliken C. E. , Ghoshroy S. , Blom D. A. 
Published: January 2008

ABSTRACTThe actinobacteriumKineococcus radiotoleransis highly resistant to ionizing radiation, desiccation, and oxidative stress, though the underlying biochemical mechanisms are unknown. The purpose of this study was to explore a possible linkage between the uptake of transition metals and extreme resistance to ionizing radiation and oxidative stress. The effects of six different divalent cationic metals on growth were examined in the absence of ionizing radiation. None of the metals tested were stimulatory, though cobalt was inhibitory to growth. In contrast, copper supplementation dramatically increased colony formation during chronic irradiation.K. radiotoleransexhibited specific uptake and intracellular accumulation of copper, compared to only a weak response to both iron and manganese supplementation. Copper accumulation sensitized cells to hydrogen peroxide. Acute-irradiation-induced DNA damage levels were similar in the copper-loaded culture and the age-synchronized no-copper control culture, though low-molecular-weight DNA was more persistent during postirradiation recovery in the Cu-loaded culture. Still, the estimated times for genome restoration differed by only 2 h between treatments. While we cannot discount the possibility that copper fulfills an unexpectedly important biochemical role in a low-radioactivity environment,K. radiotoleranshas a high capacity for intracellular copper sequestration and presumably efficiently coordinated oxidative stress defenses and detoxification systems, which confers cross-protection from the damaging effects of ionizing radiation.
Metagenomics: Read Length Matters
Authors: Wommack K. Eric , Bhavsar Jaysheel , Ravel Jacques 
Published: January 2008

ABSTRACT
Obtaining an unbiased view of the phylogenetic composition and functional diversity within a microbial community is one central objective of metagenomic analysis. New technologies, such as 454 pyrosequencing, have dramatically reduced sequencing costs, to a level where metagenomic analysis may become a viable alternative to more-focused assessments of the phylogenetic (e.g., 16S rRNA genes) and functional diversity of microbial communities. To determine whether the short (∼100 to 200 bp) sequence reads obtained from pyrosequencing are appropriate for the phylogenetic and functional characterization of microbial communities, the results of BLAST and COG analyses were compared for long (∼750 bp) and randomly derived short reads from each of two microbial and one virioplankton metagenome libraries. Overall, BLASTX searches against the GenBank nr database found far fewer homologs within the short-sequence libraries. This was especially pronounced for a Chesapeake Bay virioplankton metagenome library. Increasing the short-read sampling depth or the length of derived short reads (up to 400 bp) did not completely resolve the discrepancy in BLASTX homolog detection. Only in cases where the long-read sequence had a close homolog (low BLAST E-score) did the derived short-read sequence also find a significant homolog. Thus, more-distant homologs of microbial and viral genes are not detected by short-read sequences. Among COG hits, derived short reads sampled at a depth of two short reads per long read missed up to 72% of the COG hits found using long reads. Noting the current limitation in computational approaches for the analysis of short sequences, the use of short-read-length libraries does not appear to be an appropriate tool for the metagenomic characterization of microbial communities.
Amyloid-Like Adhesins Produced by Floc-Forming and Filamentous Bacteria in Activated Sludge
Authors: Larsen Poul , Nielsen Jeppe Lund , Otzen Daniel , Nielsen Per Halkjær 
Published: January 2008

ABSTRACT

Amyloid proteins (fimbriae or other microbial surface-associated structures) are expressed by many types of bacteria, not yet identified, in biofilms from various habitats, where they likely are of key importance to biofilm formation and biofilm properties. As these amyloids are potentially of great importance to the floc properties in activated sludge wastewater treatment plants (WWTP), the abundance of amyloid adhesins in activated sludge flocs from different WWTP and the identity of bacteria producing these were investigated. Amyloid adhesins were quantified using a combination of conformationally specific antibodies targeting amyloid fibrils, propidium iodide to target all fixed bacterial cells, confocal laser scanning microscopy, and digital image analysis. The biovolume fraction containing amyloid adhesins ranged from 10 to 40% in activated sludge from 10 different WWTP. The identity of bacteria producing amyloid adhesins was determined using fluorescence in situ hybridization with oligonucleotide probes in combination with antibodies or thioflavin T staining. Among the microcolony-forming bacteria, amyloids were primarily detected among
Alpha
- and
Betaproteobacteria
and
Actinobacteria
. A more detailed analysis revealed that many denitrifiers (from
Thauera, Azoarcus, Zoogloea
, and
Aquaspirillum
-related organisms) and
Actinobacteria
-related polyphosphate-accumulating organisms most likely produced amyloid adhesins, whereas nitrifiers did not. Many filamentous bacteria also expressed amyloid adhesins, including several
Alphaproteobacteria
(e.g.,
Meganema perideroedes
), some
Betaproteobacteria (e.g
.,
Aquaspirillum
-related filaments),
Gammaproteobacteria
(
Thiothrix
),
Bacteroidetes, Chloroflexi
(e.g., Eikelboom type 1851), and some foam-forming
Actinobacteria
(e.g.,
Gordonia amarae
). The results show that amyloid adhesins were an abundant component of activated sludge extracellular polymeric substances and seem to have unexpected, divers functions.
Role of the MexAB-OprM Efflux Pump of
Pseudomonas aeruginosa
in Tolerance to Tea Tree (
Melaleuca alternifolia
) Oil and Its Monoterpene Components Terpinen-4-ol, 1,8-Cineole, and α-Terpineol
Authors: Papadopoulos Chelsea J. , Carson Christine F. , Chang Barbara J. , Riley Thomas V. 
Published: January 2008

ABSTRACT

Using a series of efflux mutants of
Pseudomonas aeruginosa
, the MexAB-OprM pump was identified as contributing to this organism's tolerance to the antimicrobial agent tea tree (
Melaleuca alternifolia
) oil and its monoterpene components terpinen-4-ol, 1,8-cineole, and α-terpineol. These data show that a multidrug efflux system of
P. aeruginosa
can extrude monoterpenes and related alcohols.
Quantification of the Detrimental Effect of a Single Primer-Template Mismatch by Real-Time PCR Using the 16S rRNA Gene as an Example
Authors: Bru D. , Martin-Laurent F. , Philippot L. 
Published: January 2008

ABSTRACT
We investigated the effects of internal primer-template mismatches on the efficiency of PCR amplification using the 16S rRNA gene as the model template DNA. We observed that the presence of a single mismatch in the second half of the primer extension sequence can result in an underestimation of up to 1,000-fold of the gene copy number, depending on the primer and position of the mismatch.
Phylogenetic Characterization and Prevalence of “
Spirobacillus cienkowskii
,” a Red-Pigmented, Spiral-Shaped Bacterial Pathogen of Freshwater
Daphnia
Species
Authors: Rodrigues Jorge L. M. , Duffy Meghan A. , Tessier Alan J. , Ebert Dieter , Mouton Laurence , Schmidt Thomas M. 
Published: January 2008

ABSTRACT

Microscopic examination of the hemolymph from diseased daphniids in 17 lakes in southwestern Michigan and five rock pools in southern Finland revealed the presence of tightly coiled bacteria that bore striking similarities to the drawings of a morphologically unique pathogen, “
Spirobacillus cienkowskii
,” first described by Elya Metchnikoff more than 100 years ago. The uncultivated microbe was identified as a deeply branching member of the
Deltaproteobacteria
through phylogenetic analyses of two conserved genes: the 16S rRNA-encoding gene (
rrs
) and the β-subunit of topoisomerase (
gyrB
). Fluorescence in situ hybridization confirmed that the rRNA gene sequence originated from bacteria with the tightly coiled morphology. Microscopy and PCR amplification with pathogen-specific primers confirmed infections by this bacterium in four species of
Daphnia
:
Daphnia dentifera, D. magna, D. pulicaria
, and
D. retrocurva
. Extensive field surveys reveal that this bacterium is widespread geographically and able to infect many different cladoceran species. In a survey of populations of
D. dentifera
in lakes in Michigan, we found the bacterium in 17 of 18 populations studied. In these populations, 0 to 12% of the individuals were infected, with an average of 3% during mid-summer and early autumn. Infections were less common in rock pool populations of
D. magna
in southern Finland, where the pathogen was found in 5 of 137 populations. The broad geographic distribution, wide host range, and high virulence of
S. cienkowskii
suggest it plays an important role in the ecology and evolution of daphniids.
Functional Analysis of the
Mycobacterium tuberculosis
FAD-Dependent Thymidylate Synthase, ThyX, Reveals New Amino Acid Residues Contributing to an Extended ThyX Motif
Authors: Ulmer Jonathan E. , Boum Yap , Thouvenel Christopher D. , Myllykallio Hannu , Sibley Carol Hopkins 
Published: January 2008

ABSTRACT

A novel FAD-dependent thymidylate synthase, ThyX, is present in a variety of eubacteria and archaea, including the mycobacteria. A short motif found in all
thyX
genes, RHRX
7-8
S, has been identified. The three-dimensional structure of the
Mycobacterium tuberculosis
ThyX enzyme has been solved. Building upon this information, we used directed mutagenesis to produce 67 mutants of the
M. tuberculosis thyX
gene. Each enzyme was assayed to determine its ability to complement the defect in thymidine biosynthesis in a Δ
thyA
strain of
Escherichia coli
. Enzymes from selected strains were then tested in vitro for their ability to catalyze the oxidation of NADPH and the release of a proton from position 5 of the pyrimidine ring of dUMP. The results defined an extended motif of amino acids essential to enzyme activity in
M. tuberculosis
(Y44X
24
H69
X
25
R95HRX
7
S105
XRYX
90
R199 [with the underlined histidine acting as the catalytic residue and the underlined serine as the nucleophile]) and provided insight into the ThyX reaction mechanism. ThyX is found in a variety of bacterial pathogens but is absent in humans, which depend upon an unrelated thymidylate synthase, ThyA. Therefore, ThyX is a potential target for development of antibacterial drugs.
Borrelia burgdorferi
Uniquely Regulates Its Motility Genes and Has an Intricate Flagellar Hook-Basal Body Structure
Authors: Sal Melanie S. , Li Chunhao , Motalab M. A. , Shibata Satoshi , Aizawa Shin-Ichi , Charon Nyles W. 
Published: January 2008

ABSTRACT

Borrelia burgdorferi
is a flat-wave, motile spirochete that causes Lyme disease. Motility is provided by periplasmic flagella (PFs) located between the cell cylinder and an outer membrane sheath. The structure of these PFs, which are composed of a basal body, a hook, and a filament, is similar to the structure of flagella of other bacteria. To determine if hook formation influences flagellin gene transcription in
B. burgdorferi
, we inactivated the hook structural gene
flgE
by targeted mutagenesis. In many bacteria, completion of the hook structure serves as a checkpoint for transcriptional control of flagellum synthesis and other chemotaxis and motility genes. Specifically, the hook allows secretion of the anti-sigma factor FlgM and concomitant late gene transcription promoted by σ
28
. However, the control of
B. burgdorferi
PF synthesis differs from the control of flagellum synthesis in other bacteria; the gene encoding σ
28
is not present in the genome of
B. burgdorferi
, nor are any σ
28
promoter recognition sequences associated with the motility genes. We found that
B. burgdorferi flgE
mutants lacked PFs, were rod shaped, and were nonmotile, which substantiates previous evidence that PFs are involved in both cell morphology and motility. Although most motility and chemotaxis gene products accumulated at wild-type levels in the absence of FlgE, mutant cells had markedly decreased levels of the flagellar filament proteins FlaA and FlaB. Further analyses showed that the reduction in the levels of flagellin proteins in the spirochetes lacking FlgE was mediated at the posttranscriptional level. Taken together, our results indicate that in
B. burgdorferi
, the completion of the hook does not serve as a checkpoint for transcriptional regulation of flagellum synthesis. In addition, we also present evidence that the hook protein in
B. burgdorferi
forms a high-molecular-weight complex and that formation of this complex occurs in the periplasmic space.
The Response Regulator CpxR Directly Regulates Expression of SeveralLegionella pneumophila icm/dotComponents as Well as New Translocated Substrates
Authors: Altman Efrat , Segal Gil 
Published: January 2008

ABSTRACTLegionella pneumophilahas been shown to utilize theicm/dottype IV secretion system for pathogenesis. This system was shown to be composed oficm/dotcomplex components and accessory proteins, as well as a large number of translocated substrates. Bioinformatic analysis of the regulatory regions of all the genes revealed that severalicm/dotgenes, as well as two genes encodingicm/dottranslocated substrates, contain the conserved CpxR regulatory element, a regulator that has been shown previously to control the expression of theicmRgene. An experimental analysis, which included a comparison of gene expression in aL. pneumophilawild-type strain and gene expression in acpxRdeletion mutant, construction of mutants with mutations in the CpxR conserved regulatory elements, controlled expression studies, and mobility shift assays, demonstrated the direct relationship between the CpxR regulator and the expression of the genes. Furthermore, genomic analysis identified nine additional genes that contain a putative CpxR regulatory element; five of these genes (twolegAgenes and threeceggenes) were suggested previously to be putativeicm/dottranslocated substrates. The threeceggenes identified, which were shown previously to contain a putative PmrA regulatory element, were found here to be regulated by both CpxR and PmrA. The other six genes (twolegAgenes and four new genes products were found to be regulated by CpxR. Moreover, using the CyaA translocation assay, these nine gene products were found to be translocated into host cells in an Icm/Dot-dependent manner. Our results establish that the CpxR regulator is a fundamental regulator of theicm/dottype IV secretion system inL. pneumophila.
Regulation of Type IV Secretion Apparatus Genes during
Ehrlichia chaffeensis
Intracellular Development by a Previously Unidentified Protein
Authors: Cheng Zhihui , Wang Xueqi , Rikihisa Yasuko 
Published: January 2008

ABSTRACT

The type IV secretion (T4S) system is critical for the virulence of several pathogens. In the rickettsial pathogen
Ehrlichia chaffeensis
, the
virBD
genes are split into two operons, the
virB3
-
virB6
(preceded by
sodB
) and
virB8
-
virD4
operons. Between these two operons, there are duplications of
virB4
,
virB8
, and
virB9
. In this study we found that transcription of all five loci was downregulated prior to the release of
E. chaffeensis
from host THP-1 cells and was upregulated at the initiation of exponential growth. Electrophoretic mobility shift assays revealed an
E. chaffeensis
-encoded protein that specifically bound to the promoter regions upstream of the
virBD
loci. The protein was purified from the bacterial lysate by affinity chromatography using a biotinylated promoter region upstream of
sodB
. Mass spectrometry identified the protein as an
E. chaffeensis
12.3-kDa hypothetical protein, which was designated EcxR. Recombinant EcxR bound to the promoter regions upstream of five individual
virBD
loci. EcxR also activated transcription of all five
virBD
loci in
lacZ
reporter constructs. The expression of
ecxR
was positively autoregulated by EcxR. These results suggest that the five
virBD
loci are coordinately regulated by EcxR to allow developmental stage-specific expression of the T4S system in
E. chaffeensis.
A shift toward harmonics for high-frequency calling shown with phylogenetic study of frequency spectra in Eneopterinae crickets (Orthoptera, Grylloidea, Eneopteridae)
Authors: Robillard Tony , Grandcolas Philippe , Desutter-Grandcolas Laure 
Published: January 2008

Dominant frequency is an important feature of cricket song, as it can be used for species recognition and mate choice. The dominant frequency usually ranges from 2 to 8 kHz and corresponds to the fundamental frequency of the song. In preliminary studies we documented high-frequency songs in the subfamily Eneopterinae. To analyse this phenomenon further, we investigate the spectral properties of these cricket songs. Based on the analysis of the frequency spectra in reference to phylogeny, we show that a shift of dominant frequency from the fundamental toward the second or the third harmonic of the song occurred in the Lebinthini tribe. In this clade the upper harmonics (second or third) become the most powerful frequencies of the song. From an evolutionary point of view, we document a case of convergence toward high-frequency calling between species of Eneoptera Burmeister, 1838, which emit alternatively low and high fundamental frequencies, and the Lebinthini, which emit high frequencies using upper harmonics. Functional hypotheses are discussed to explain how these high frequencies could be produced.
AML1 mutations induced MDS and MDS/AML in a mouse BMT model
Authors: Watanabe-Okochi Naoko , Kitaura Jiro , Ono Ryoichi , Harada Hironori , Harada Yuka , Komeno Yukiko , Nakajima Hideaki , Nosaka Tetsuya , Inaba Toshiya , Kitamura Toshio 
Published: January 2008

Abstract
Myelodysplastic syndrome (MDS) is a hematopoietic stem-cell disorder characterized by trilineage dysplasia and susceptibility to acute myelogenous leukemia (AML). Analysis of molecular basis of MDS has been hampered by the heterogeneity of the disease. Recently, mutations of the transcription factor AML1/RUNX1 have been identified in 15% to 40% of MDS–refractory anemia with excess of blasts (RAEB) and MDS/AML. We performed mouse bone marrow transplantation (BMT) using bone marrow cells transduced with the AML1 mutants. Most mice developed MDS and MDS/AML-like symptoms within 4 to 13 months after BMT. Interestingly, among integration sites identified, Evi1 seemed to collaborate with an AML1 mutant harboring a point mutation in the Runt homology domain (D171N) to induce MDS/AML with an identical phenotype characterized by marked hepatosplenomegaly, myeloid dysplasia, leukocytosis, and biphenotypic surface markers. Collaboration between AML1-D171N and Evi1 was confirmed by a BMT model where coexpression of AML1-D171N and Evi1 induced acute leukemia of the same phenotype with much shorter latencies. On the other hand, a C-terminal truncated AML1 mutant (S291fsX300) induced pancytopenia with erythroid dysplasia in transplanted mice, followed by progression to MDS-RAEB or MDS/AML. Thus, we have developed a useful mouse model of MDS/AML that should help in the understanding of the molecular basis of MDS and the progression of MDS to overt leukemia.
Identification of genetic polymorphisms associated with risk for pulmonary hypertension in sickle cell disease
Authors: Ashley-Koch Allison E. , Elliott Laine , Kail Melanie E. , De Castro Laura M. , Jonassaint Jude , Jackson Terry L. , Price Jennifer , Ataga Kenneth I. , Levesque Marc C. , Weinberg J. Brice , Orringer Eugene P. , Collins Ann , Vance Jeffery M. , Telen Marilyn J. 
Published: January 2008

AbstractUp to 30% of adult patients with sickle cell disease (SCD) will develop pulmonary hypertension (pHTN), a complication associated with significant morbidity and mortality. To identify genetic factors that contribute to risk for pHTN in SCD, we performed association analysis with 297 single nucleotide polymorphisms (SNPs) in 49 candidate genes in patients with sickle cell anemia (Hb SS) who had been screened for pHTN by echocardiography (n = 111). Evidence of association was primarily identified for genes in the TGFβ superfamily, including activin A receptor, type II–like 1 (ACVRL1), bone morphogenetic protein receptor 2 (BMPR2), and bone morphogenetic protein 6 (BMP6). The association of pHTN with ACVRL1 and BMPR2 corroborates the previous association of these genes with primary pHTN. Moreover, genes in the TGFβ pathway have been independently implicated in risk for several sickle cell complications, suggesting that this gene pathway is important in overall sickle cell pathophysiology. Genetic variation in the β-1 adrenergic receptor (ADRB1) was also associated with pHTN in our dataset. A multiple regression model, which included age and baseline hemoglobin as covariates, retained SNPs in ACVRL1, BMP6, and ADRB1 as independently contributing to pHTN risk. These findings may offer new promise for identifying patients at risk for pHTN, developing new therapeutic targets, and reducing the occurrence of this life-threatening SCD complication.
Internal tandem duplication of FLT3 (FLT3/ITD) induces increased ROS production, DNA damage, and misrepair: implications for poor prognosis in AML
Authors: Sallmyr Annahita , Fan Jinshui , Datta Kamal , Kim Kyu-Tae , Grosu Dan , Shapiro Paul , Small Donald , Rassool Feyruz 
Published: January 2008

AbstractActivating mutations of the FMS-like tyrosine kinase-3 (FLT3) receptor occur in approximately 30% of acute myeloid leukemia (AML) patients and, at least for internal tandem duplication (ITD) mutations, are associated with poor prognosis. FLT3 mutations trigger downstream signaling pathways including RAS-MAP/AKT kinases and signal transducer and activator of transcription-5 (STAT5). We find that FLT3/ITD mutations start a cycle of genomic instability whereby increased reactive oxygen species (ROS) production leads to increased DNA double-strand breaks (DSBs) and repair errors that may explain aggressive AML in FLT3/ITD patients. Cell lines transfected with FLT3/ITD and FLT3/ITD-positive AML cell lines and primary cells demonstrate increased ROS. Increased ROS levels appear to be produced via STAT5 signaling and activation of RAC1, an essential component of ROS-producing NADPH oxidases. A direct association of RAC1-GTP binding to phosphorylated STAT5 (pSTAT5) provides a possible mechanism for ROS generation. A FLT3 inhibitor blocked increased ROS in FLT3/ITD cells resulting in decreased DSB and increased repair efficiency and fidelity. Our study suggests that the aggressiveness of the disease and poor prognosis of AML patients with FLT3/ITD mutations could be the result of increased genomic instability that is driven by higher endogenous ROS, increased DNA damage, and decreased end-joining fidelity.