bluuebunny/crossref_metadata_2025_split huggingface dataset:
Promotion of Mn(II) Oxidation and Remediation of Coal Mine Drainage in Passive Treatment Systems by Diverse Fungal and Bacterial Communities
Authors: Santelli Cara M. , Pfister Donald H. , Lazarus Dana , Sun Lu , Burgos William D. , Hansel Colleen M. 
Published: May 2010

ABSTRACTBiologically active, passive treatment systems are commonly employed for removing high concentrations of dissolved Mn(II) from coal mine drainage (CMD). Studies of microbial communities contributing to Mn attenuation through the oxidation of Mn(II) to sparingly soluble Mn(III/IV) oxide minerals, however, have been sparse to date. This study reveals a diverse community of Mn(II)-oxidizing fungi and bacteria existing in several CMD treatment systems.
Parallel Analyses of
Alexandrium catenella
Cell Concentrations and Shellfish Toxicity in the Puget Sound
Authors: Dyhrman Sonya T. , Haley Sheean T. , Borchert Jerry A. , Lona Bob , Kollars Nicole , Erdner Deana L. 
Published: May 2010

ABSTRACT

Alexandrium catenella
is widespread in western North America and produces a suite of potent neurotoxins that cause paralytic shellfish poisoning (PSP) in humans and have deleterious impacts on public health and economic resources. There are seasonal PSP-related closures of recreational and commercial shellfisheries in the Puget Sound, but the factors that influence cell distribution, abundance, and relationship to paralytic shellfish toxins (PSTs) in this system are poorly described. Here, a quantitative PCR assay was used to detect
A. catenella
cells in parallel with state shellfish toxicity testing during the 2006 bloom season at 41 sites from April through October. Over 500,000
A. catenella
cells liter
−1
were detected at several stations, with two main pulses of cells driving cell distribution, one in June and the other in August. PSTs over the closure limit of 80 μg of PST 100 per g of shellfish tissue were detected at 26 of the 41 sites. Comparison of cell numbers and PST data shows that shellfish toxicity is preceded by an increase in
A. catenella
cells in 71% of cases. However, cells were also observed in the absence of PSTs in shellfish, highlighting the complex relationship between
A. catenella
and the resulting shellfish toxicity. These data provide important information on the dynamics of
A. catenella
cells in the Puget Sound and are a first step toward assessing the utility of plankton monitoring to augment shellfish toxicity testing in this system.
The Transcription Factor StuA Regulates Central Carbon Metabolism, Mycotoxin Production, and Effector Gene Expression in the Wheat Pathogen Stagonospora nodorum
Authors: IpCho Simon V. S. , Tan Kar-Chun , Koh Geraldine , Gummer Joel , Oliver Richard P. , Trengove Robert D. , Solomon Peter S. 
Published: May 2010

ABSTRACT

The
Stagonospora nodorum
StuA transcription factor gene
SnStuA
was identified by homology searching in the genome of the wheat pathogen
Stagonospora nodorum
. Gene expression analysis revealed that
SnStuA
transcript abundance increased throughout infection and
in vitro
growth to peak during sporulation. To investigate its role, the gene was deleted by homologous recombination. The growth of the resulting mutants was retarded on glucose compared to the wild-type growth, and the mutants also failed to sporulate. Glutamate as a sole carbon source restored the growth rate defect observed on glucose, although sporulation remained impaired. The
SnstuA
strains were essentially nonpathogenic, with only minor growth observed around the point of inoculation. The role of
SnstuA
was investigated using metabolomics, which revealed that this gene's product played a key role in regulating central carbon metabolism, with glycolysis, the TCA cycle, and amino acid synthesis all affected in the mutants. SnStuA was also found to positively regulate the synthesis of the mycotoxin alternariol. Gene expression studies on the recently identified effectors in
Stagonospora nodorum
found that SnStuA was a positive regulator of
SnTox3
but was not required for the expression of
ToxA
. This study has uncovered a multitude of novel regulatory targets of
SnStuA
and has highlighted the critical role of this gene product in the pathogenicity of
Stagonospora nodorum
.
ATP-Citrate Lyase Is Required for Production of Cytosolic Acetyl Coenzyme A and Development in Aspergillus nidulans
Authors: Hynes Michael J. , Murray Sandra L. 
Published: May 2010

ABSTRACT

Acetyl coenzyme A (CoA) is a central metabolite in carbon and energy metabolism and in the biosynthesis of cellular molecules. A source of cytoplasmic acetyl-CoA is essential for the production of fatty acids and sterols and for protein acetylation, including histone acetylation in the nucleus. In
Saccharomyces cerevisiae
and
Candida albicans
acetyl-CoA is produced from acetate by cytoplasmic acetyl-CoA synthetase, while in plants and animals acetyl-CoA is derived from citrate via ATP-citrate lyase. In the filamentous ascomycete
Aspergillus nidulans
, tandem divergently transcribed genes (
aclA
and
aclB
) encode the subunits of ATP-citrate lyase, and we have deleted these genes. Growth is greatly diminished on carbon sources that do not result in cytoplasmic acetyl-CoA, such as glucose and proline, while growth is not affected on carbon sources that result in the production of cytoplasmic acetyl-CoA, such as acetate and ethanol. Addition of acetate restores growth on glucose or proline, and this is dependent on
facA
, which encodes cytoplasmic acetyl-CoA synthetase, but not on the regulatory gene
facB
. Transcription of
aclA
and
aclB
is repressed by growth on acetate or ethanol. Loss of ATP-citrate lyase results in severe developmental effects, with the production of asexual spores (conidia) being greatly reduced and a complete absence of sexual development. This is in contrast to
Sordaria macrospora
, in which fruiting body formation is initiated but maturation is defective in an ATP-citrate lyase mutant. Addition of acetate does not repair these defects, indicating a specific requirement for high levels of cytoplasmic acetyl-CoA during differentiation. Complementation in heterokaryons between
aclA
and
aclB
deletions for all phenotypes indicates that the tandem gene arrangement is not essential.
The Conjugation-Specific Die5 Protein Is Required for Development of the Somatic Nucleus in both Paramecium and Tetrahymena
Authors: Matsuda Atsushi , Shieh Annie Wan-Yi , Chalker Douglas L. , Forney James D. 
Published: May 2010

ABSTRACT

Development in ciliated protozoa involves extensive genome reorganization within differentiating macronuclei, which shapes the somatic genome of the next vegetative generation. Major events of macronuclear differentiation include excision of internal eliminated sequences (IESs), chromosome fragmentation, and genome amplification. Proteins required for these events include those with homology throughout eukaryotes as well as proteins apparently unique to ciliates. In this study, we identified the ciliate-specific
D
efective in
I
ES
E
xcision 5 (
DIE5
) genes of
Paramecium tetraurelia
(
PtDIE5
) and
Tetrahymena thermophila
(
TtDIE5
) as orthologs that encode nuclear proteins expressed exclusively during development. Abrogation of PtDie5 protein (PtDie5p) function by RNA interference (RNAi)-mediated silencing or TtDie5p by gene disruption resulted in the failure of developing macronuclei to differentiate into new somatic nuclei.
Tetrahymena
Δ
DIE5
cells arrested late in development and failed to complete genome amplification, whereas RNAi-treated
Paramecium
cells highly amplified new macronuclear DNA before the failure in differentiation, findings that highlight clear differences in the biology of these distantly related species. Nevertheless, IES excision and chromosome fragmentation failed to occur in either ciliate, which strongly supports that Die5p is a critical player in these processes. In
Tetrahymena
, loss of zygotic expression during development was sufficient to block nuclear differentiation. This observation, together with the finding that knockdown of Die5p in
Paramecium
still allows genome amplification, indicates that this protein acts late in macronuclear development. Even though DNA rearrangements in these two ciliates look to be quite distinct, analysis of
DIE5
establishes the action of a conserved mechanism within the genome reorganization pathway.
Structure-Activity Analysis of thePseudomonasQuinolone Signal Molecule
Authors: Hodgkinson James , Bowden Steven D. , Galloway Warren R. J. D. , Spring David R. , Welch Martin 
Published: May 2010

ABSTRACTWe synthesized a range of PQS (Pseudomonasquinolone signal; 2-heptyl-3-hydroxy-4(1H)-quinolone) analogues and tested them for their ability to stimulate MvfR-dependentpqsAtranscription, MvfR-independent pyoverdine production, and membrane vesicle production. The structure-activity profile of the PQS analogues was different for each of these phenotypes. Certain inactive PQS analogues were also found to strongly synergize PQS-dependent pyoverdine production.
Comparative Analysis of Sequence Periodicity among Prokaryotic Genomes Points to Differences in Nucleoid Structure and a Relationship to Gene Expression
Authors: Mrázek Jan 
Published: May 2010

ABSTRACT
Regular spacing of short runs of A or T nucleotides in DNA sequences with a period close to the helical period of the DNA double helix has been associated with intrinsic DNA bending and nucleosome positioning in eukaryotes. Analogous periodic signals were also observed in prokaryotic genomes. While the exact role of this periodicity in prokaryotes is not known, it has been proposed to facilitate the DNA packaging in the prokaryotic nucleoid and/or to promote negative or positive supercoiling. We developed a methodology for assessments of intragenomic heterogeneity of these periodic patterns and applied it in analysis of 1,025 prokaryotic chromosomes. This technique allows more detailed analysis of sequence periodicity than previous methods where sequence periodicity was assessed in an integral form across the whole chromosome. We found that most genomes have the periodic signal confined to several chromosomal segments while most of the chromosome lacks a strong sequence periodicity. Moreover, there are significant differences among different prokaryotes in both the intensity and persistency of sequence periodicity related to DNA curvature. We proffer that the prokaryotic nucleoid consists of relatively rigid sections stabilized by short intrinsically bent DNA segments and characterized by locally strong periodic patterns alternating with regions featuring a weak periodic signal, which presumably permits higher structural flexibility. This model applies to most bacteria and archaea. In genomes with an exceptionally persistent periodic signal, highly expressed genes tend to concentrate in aperiodic sections, suggesting that structural heterogeneity of the nucleoid is related to local differences in transcriptional activity.
Regulation of High-Affinity Iron Acquisition Homologues in the Tsetse Fly SymbiontSodalis glossinidius
Authors: Runyen-Janecky Laura J. , Brown Alexandria N. , Ott Brittany , Tujuba Haddis G. , Rio Rita V. M. 
Published: May 2010

ABSTRACTSodalis glossinidiusis a facultative intracellular bacterium that is a secondary symbiont of the tsetse fly (Diptera: Glossinidae). Since studies with other facultative intracellular bacteria have shown that high-affinity iron acquisition genes are upregulatedin vivo, we investigated the regulation of severalSodalisgenes that encode putative iron acquisition systems. These genes, SG1538 (hemT) and SG1516 (sitA), are homologous to genes encoding periplasmic heme and iron/manganese transporters, respectively.hemTpromoter- andsitApromoter-gfpfusions were constructed, and in bothEscherichia coliandSodalisbackgrounds, expression levels of these fusions were higher when the bacteria were grown in iron-limiting media than when the bacteria were grown in iron-replete media. TheSodalispromoters were tested for iron regulation in anE. colistrain that lacks thefurgene, which encodes the iron-responsive transcriptional repressor Fur. Expression of the promoter-gfpfusions in theE. coli furmutant was constitutively high in both iron-replete and iron-deplete media, and addition of eitherShigella flexneri furorSodalis furto a plasmid restored normal regulation. ASodalis furmutant was constructed by intron mutagenesis, and semiquantitative reverse transcription-PCR (RT-PCR) showed that iron repression ofsitAexpression was also abolished in this strain.In vivoexpression analysis showed thathemTandsitAare expressed whenSodalisis within tsetse fly hosts, suggesting a biological role for these genes whenSodalisis within the tsetse fly.
Variation inStreptococcus pyogenesNAD+Glycohydrolase Is Associated with Tissue Tropism
Authors: Riddle David J. , Bessen Debra E. , Caparon Michael G. 
Published: May 2010

ABSTRACTStreptococcus pyogenesis an important pathogen that causes a variety of diseases. The most common infections involve the throat (pharyngitis) or skin (impetigo); however, the factors that determine tissue tropism and severity are incompletely understood. TheS. pyogenesNAD+glycohydrolase (SPN) is a virulence factor that has been implicated in contributing to the pathogenesis of severe infections. However, the role of SPN in determining the bacterium's tissue tropism has not been evaluated. In this report, we examine the sequences ofspnand its endogenous inhibitorifsfrom a worldwide collection ofS. pyogenesstrains. Analysis of average pairwise nucleotide diversity, average number of nucleotide differences, and ratio of nonsynonymous to synonymous substitutions revealed significant diversity inspnandifs. Application of established models of molecular evolution shows that SPN is evolving under positive selection and diverging into NAD+glycohydrolase (NADase)-active and -inactive subtypes. Additionally, the NADase-inactive SPN subtypes maintain the characteristics of a functional gene whileifsbecomes a pseudogene. Thus, NADase-inactive SPN continues to evolve under functional constraint. Furthermore, NADase activity did not correlate with invasive disease in our collection but was associated with tissue tropism. The ability to cause infection at both the pharynx and the skin (“generalist” strains) is correlated with NADase-active SPN, while the preference for causing infection at either the throat or the skin (“specialist” strains) is associated with NADase-inactive SPN. These findings suggest that SPN has a NADase-independent function and prompt a reevaluation of the role of SPN in streptococcal pathogenesis.
ThePseudomonas aeruginosaVfr Regulator Controls Global Virulence Factor Expression through Cyclic AMP-Dependent and -Independent Mechanisms
Authors: Fuchs Erin L. , Brutinel Evan D. , Jones Adriana K. , Fulcher Nanette B. , Urbanowski Mark L. , Yahr Timothy L. , Wolfgang Matthew C. 
Published: May 2010

ABSTRACTVfr is a global regulator of virulence factor expression in the human pathogenPseudomonas aeruginosa. Although indirect evidence suggests that Vfr activity is controlled by cyclic AMP (cAMP), it has been hypothesized that the putative cAMP binding pocket of Vfr may accommodate additional cyclic nucleotides. In this study, we used two different approaches to generate apo-Vfr and examined its ability to bind a representative set of virulence gene promoters in the absence and presence of different allosteric effectors. Of the cyclic nucleotides tested, only cAMP was able to restore DNA binding activity to apo-Vfr. In contrast, cGMP was capable of inhibiting cAMP-Vfr DNA binding. Further, we demonstrate thatvfrexpression is autoregulated and cAMP dependent and involves Vfr binding to a previously unidentified site within thevfrpromoter region. Using a combination ofin vitroandin vivoapproaches, we show that cAMP is required for Vfr-dependent regulation of a specific subset of virulence genes. In contrast, we discovered that Vfr controls expression of thelasRpromoter in a cAMP-independent manner. In summary, our data support a model in which Vfr controls virulence gene expression by distinct (cAMP-dependent and -independent) mechanisms, which may allowP. aeruginosato fine-tune its virulence program in response to specific host cues or environments.
The LysR-Type Transcriptional Regulator QseD Alters Type Three Secretion in Enterohemorrhagic
Escherichia coli
and Motility in K-12
Escherichia coli
Authors: Habdas Benjamin J. , Smart Jennifer , Kaper James B. , Sperandio Vanessa 
Published: May 2010

ABSTRACT

Enterohemorrhagic
Escherichia coli
(EHEC) O157:H7 responds to the host-produced epinephrine and norepinephrine, and bacterially produced autoinducer 3 (AI-3), through two-component systems. Further integration of multiple regulatory signaling networks, involving regulators such as the LysR-type transcriptional regulator (LTTR) QseA, promotes effective regulation of virulence factors. These include the production of flagella, a phage-encoded Shiga toxin, and genes within the locus of enterocyte effacement (LEE) responsible for attaching and effacing (AE) lesion formation. Here, we describe a new member of this signaling cascade, an LTTR heretofore renamed QseD (quorum-sensing
E. coli
regulator D). QseD is present in all enterobacteria but exists almost exclusively in O157:H7 isolates as a helix-turn-helix (HTH) truncated isoform. This “short” isoform (sQseD) is still able to regulate gene expression through a different mechanism than the full-length K-12
E. coli
“long” QseD isoform (lQseD). The EHEC Δ
qseD
mutant exhibits increased expression of all LEE operons and deregulation of AE lesion formation. The loss of
qseD
in EHEC does not affect motility, but the K-12 Δ
qseD
mutant is hypermotile. While the lQseD directly binds to the
ler
promoter, encoding the LEE master regulator, to repress LEE transcription, the sQseD isoform does not. LTTRs bind to DNA as tetramers, and these data suggest that sQseD regulates
ler
by forming heterotetramers with another LTTR. The LTTRs known to regulate LEE transcription, QseA and LrhA, do not interact with sQseD, suggesting that sQseD acts as a dominant-negative partner with a yet-unidentified LTTR.
Absence of the Inhibitory G-Protein Gα
i2
Predisposes to Ventricular Cardiac Arrhythmia
Authors: Zuberi Zia , Nobles Muriel , Sebastian Sonia , Dyson Alex , Lim Shiang Y. , Breckenridge Ross , Birnbaumer Lutz , Tinker Andrew 
Published: May 2010

Background—
We explored the role that inhibitory heterotrimeric G-proteins play in ventricular arrhythmia.

Methods and Results—

Mice with global genetic deletion of Gα
i2
[Gα
i2
(−/−)] were studied and found, based on telemetry, to have a prolonged QT interval on surface ECG when awake. In vivo electrophysiology studies revealed that the Gα
i2
(−/−) mice have a reduced ventricular effective refractory period and a predisposition to ventricular tachycardia when challenged with programmed electrical stimulation. Neither control nor combined global deletion of Gα
i1
and Gα
i3
mice showed these abnormalities. There was no evidence for structural heart disease at this time point in the Gα
i2
(−/−) mice as assessed by cardiac histology and echocardiography. The absence of Gα
i2
thus leads to a primary electrical abnormality, and we explored the basis for this finding. With patch clamping, single isolated ventricular cells showed that Gα
i2
(−/−) mice had a prolonged ventricular action potential duration (APD) but steeper action potential shortening as the diastolic interval was reduced in restitution studies. Gene expression studies showed increased expression of L-type Ca
2+
channel subunits, and patch clamping revealed an increase in these currents in Gα
i2
(−/−) mice. There were no changes in K
+
currents.

Conclusions—

The absence of inhibitory G-protein signaling mediated through Gα
i2
is a substrate for ventricular arrhythmias.
Evaluation of Left Ventricular Dyssynchrony by Onset of Active Myocardial Force Generation
Authors: Russell Kristoffer , Opdahl Anders , Remme Espen W. , Gjesdal Ola , Skulstad Helge , Kongsgaard Erik , Edvardsen Thor , Smiseth Otto A. 
Published: May 2010

Background—
Better clinical tools for measuring left ventricular electrical dyssynchrony are needed. The present study investigates if onset of active myocardial force generation (AFG) may serve as a measure of electrical dyssynchrony.

Methods and Results—

In anesthetized dogs, we evaluated left ventricular mechanical dyssynchrony by 2 different approaches. First, we measured timing of peak myocardial shortening velocity and strain. Second, we measured the first sign of tension development by onset AFG as defined by the myocardial pressure-segment length loop upward shift from its passive-elastic state. Electrical dyssynchrony was measured by intramyocardial electromyograms (IM-EMG). Dyssynchrony was quantified as peak intersegment time difference and as standard deviation of timing for 6 to 8 myocardial segments. During baseline, reduced preload and myocardial ischemia shortening velocity and strain indicated segmental mechanical heterogeneity, whereas onset AFG and onset R in IM-EMG indicated synchronous activation of all segments. After induction of left bundle-branch block, all methods indicated dyssynchrony. Peak intersegment time difference for shortening velocity and strain showed weak correlations (
r
=0.17 and 0.16) and weak agreements (mean differences, −48±27 ms and −28±27 ms, respectively) with IM-EMG. Onset AFG by pressure-segment length loops, however, correlated well with IM-EMG (
r
=0.93), and agreement was good (mean difference, −0.6±6.8 ms). Results were similar for standard deviation of timing. Onset AFG from pressure-strain analysis by echocardiography showed accuracy similar to sonomicrometry.

Conclusions—
Onset AFG was an accurate marker of myocardial electrical activation and was superior to shortening velocity and strain. Identification of electrical dyssynchrony by onset AFG may be feasible clinically using left ventricular pressure-strain analysis.