bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Liquid- and Fog-Based Application of Sterilox Hypochlorous Acid Solution for Surface Inactivation of Human Norovirus
Authors: Park Geun Woo , Boston Deyanna M. , Kase Julie A. , Sampson Mark N. , Sobsey Mark D. 
Published: May 2007

ABSTRACT

Noroviruses (NVs) are the most frequent cause of outbreaks of gastroenteritis in common settings, with surface-mediated transfer via contact with fecally contaminated surfaces implicated in exposure. NVs are environmentally stable and persistent and have a low infectious dose. Several disinfectants have been evaluated for efficacy to control viruses on surfaces, but the toxicity and potential damage to treated materials limits their applicability. Sterilox hypochlorous acid (HOCl) solution (HAS) has shown broad-spectrum antimicrobial activity while being suitable for general use. The objectives of this study were to evaluate the efficacy of HAS to reduce NV both in aqueous suspensions and on inanimate carriers. HOCl was further tested as a fog to decontaminate large spaces. HOCl effectiveness was evaluated using nonculturable human NV measured by reverse transcriptase PCR (RT-PCR) and two surrogate viruses, coliphage MS2 and murine NV, that were detected by both infectivity and RT-PCR. Exposing virus-contaminated carriers of ceramic tile (porous) and stainless steel (nonporous) to 20 to 200 ppm of HOCl solution resulted in ≥99.9% (≥3 log
10
) reductions of both infectivity and RNA titers of tested viruses within 10 min of exposure time. HOCl fogged in a confined space reduced the infectivity and RNA titers of NV, murine NV, and MS2 on these carriers by at least 99.9% (3 log
10
), regardless of carrier location and orientation. We conclude that HOCl solution as a liquid or fog is likely to be effective in disinfecting common settings to reduce NV exposures and thereby control virus spread via fomites.
Self-Formed Adaptor PCR: a Simple and Efficient Method for Chromosome Walking
Authors: Wang Shiming , He Jian , Cui Zhongli , Li Shunpeng 
Published: May 2007

ABSTRACT
We developed a self-formed adaptor PCR (termed SEFA PCR) which can be used for chromosome walking. Most of the amplified flanking sequences were longer than 2.0 kb, and some were as long as 6.0 kb. SEFA PCR is simple and efficient and should have broad applications in the isolation of unknown sequences in complex genomes.
Isolation of Key Methanogens for Global Methane Emission from Rice Paddy Fields: a Novel Isolate Affiliated with the Clone Cluster Rice Cluster I
Authors: Sakai Sanae , Imachi Hiroyuki , Sekiguchi Yuji , Ohashi Akiyoshi , Harada Hideki , Kamagata Yoichi 
Published: May 2007

ABSTRACTDespite the fact that rice paddy fields (RPFs) are contributing 10 to 25% of global methane emissions, the organisms responsible for methane production in RPFs have remained uncultivated and thus uncharacterized. Here we report the isolation of a methanogen (strain SANAE) belonging to an abundant and ubiquitous group of methanogens called rice cluster I (RC-I) previously identified as an ecologically important microbial component via culture-independent analyses. To enrich the RC-I methanogens from rice paddy samples, we attempted to mimic the in situ conditions of RC-I on the basis of the idea that methanogens in such ecosystems should thrive by receiving low concentrations of substrate (H2) continuously provided by heterotrophic H2-producing bacteria. For this purpose, we developed a coculture method using an indirect substrate (propionate) in defined medium and a propionate-oxidizing, H2-producing syntroph,Syntrophobacter fumaroxidans, as the H2supplier. By doing so, we significantly enriched the RC-I methanogens and eventually obtained a methanogen within the RC-I group in pure culture. This is the first report on the isolation of a methanogen within RC-I.
Protein Arginine Methylation in
Candida albicans
: Role in Nuclear Transport
Authors: McBride Anne E. , Zurita-Lopez Cecilia , Regis Anthony , Blum Emily , Conboy Ana , Elf Shannon , Clarke Steven 
Published: May 2007

ABSTRACT

Protein arginine methylation plays a key role in numerous eukaryotic processes, such as protein transport and signal transduction. In
Candida albicans
, two candidate protein arginine methyltransferases (PRMTs) have been identified from the genome sequencing project. Based on sequence comparison,
C. albicans
candidate PRMTs display similarity to
Saccharomyces cerevisiae
Hmt1 and Rmt2. Here we demonstrate functional homology of Hmt1 between
C. albicans
and
S. cerevisiae
: CaHmt1 supports growth of
S. cerevisiae
strains that require Hmt1, and CaHmt1 methylates Npl3, a major Hmt1 substrate, in
S. cerevisiae
. In
C. albicans
strains lacking CaHmt1, asymmetric dimethylarginine and ω-monomethylarginine levels are significantly decreased, indicating that Hmt1 is the major
C. albicans
type I PRMT1. Given the known effects of type I PRMTs on nuclear transport of RNA-binding proteins, we tested whether Hmt1 affects nuclear transport of a putative Npl3 ortholog in
C. albicans
. CaNpl3 allows partial growth of
S. cerevisiae npl3
Δ strains, but its arginine-glycine-rich C terminus can fully substitute for that of ScNpl3 and also directs methylation-sensitive association with ScNpl3. Expression of green fluorescent protein-tagged CaNpl3 proteins in
C. albicans
strains with and without CaHmt1 provides evidence for CaHmt1 facilitating export of CaNpl3 in this fungus. We have also identified the
C. albicans
Rmt2, a type IV fungus- and plant-specific PRMT, by amino acid analysis of an
rmt2
Δ/
rmt2
Δ strain, as well as biochemical evidence for additional cryptic PRMTs.
Phosphatidylinositol 4-Kinase III-β Is Required for Golgi Maintenance and Cytokinesis in
Trypanosoma brucei
Authors: Rodgers Melissa J. , Albanesi Joseph P. , Phillips Margaret A. 
Published: May 2007

ABSTRACT

The parasitic protozoan
Trypanosoma brucei
contains two type III phosphatidylinositol 4-kinases (α and β). We have cloned the gene encoding the
T. brucei
type III phosphatidylinositol 4-kinase β (TbPI4KIII-β), expressed the protein in COS-7 cells, and confirmed that the protein catalyzes the phosphorylation of phosphatidylinositol. Depletion of TbPI4KIII-β in procyclic
T. brucei
by RNA interference (RNAi) resulted in inhibition of cell growth and a distorted cellular morphology. RNAi cells had a distorted Golgi apparatus, and lysosomal and flagellar pocket proteins were mislocalized. Ultrastructural analysis revealed the internal accumulation of a heterogeneous population of vesicles, abnormal positioning of organelles, and a loss of cell polarity. Scanning electron microcopy revealed a twisted phenotype, and dividing cells often exhibited a detached daughter flagellum and lacked a cleavage furrow. Cell cycle analysis confirmed that cells depleted of TbPI4KIII-β have a postmitotic cytokinesis block that occurs after a single round of mitosis, suggestive of a specific cell cycle block. In summary, TbPI4KIII-β is an essential protein in procyclic
T. brucei
, required for maintenance of Golgi structure, protein trafficking, normal cellular shape, and cytokinesis.
Transgene-Induced Silencing of the Zoosporogenesis-Specific
NIFC
Gene Cluster of
Phytophthora infestans
Involves Chromatin Alterations
Authors: Judelson Howard S. , Tani Shuji 
Published: May 2007

ABSTRACT

Clustered within the genome of the oomycete phytopathogen
Phytophthora infestans
are four genes encoding spore-specific nuclear LIM interactor-interacting factors (NIF proteins, a type of transcriptional regulator) that are moderately conserved in DNA sequence.
NIFC1
,
NIFC2
, and
NIFC3
are zoosporogenesis-induced and grouped within 4 kb, and 20 kb away resides a sporulation-induced form,
NIFS
. To test the function of the
NIFC
family, plasmids expressing full-length hairpin constructs of
NIFC1
or
NIFC2
were stably transformed into
P. infestans.
This triggered silencing of the cognate gene in about one-third of transformants, and all three
NIFC
genes were usually cosilenced. However,
NIFS
escaped silencing despite its high sequence similarity to the
NIFC
genes. Silencing of the three
NIFC
genes impaired zoospore cyst germination by 60% but did not affect other aspects of the life cycle. Silencing was transcriptional based on nuclear run-on assays and associated with tighter chromatin packing based on nuclease accessibility experiments. The chromatin alterations extended a few hundred nucleotides beyond the boundaries of the transcribed region of the
NIFC
cluster and were not associated with increased DNA methylation. A plasmid expressing a short hairpin RNA having sequence similarity only to
NIFC1
silenced both that gene and an adjacent member of the gene cluster, likely due to the expansion of a heterochromatic domain from the targeted locus. These data help illuminate the mechanism of silencing in
Phytophthora
and suggest that caution should be used when interpreting silencing experiments involving closely spaced genes.
The
Fusarium verticillioides FUM
Gene Cluster Encodes a Zn(II)2Cys6 Protein That Affects
FUM
Gene Expression and Fumonisin Production
Authors: Brown Daren W. , Butchko Robert A. E. , Busman Mark , Proctor Robert H. 
Published: May 2007

ABSTRACT

Fumonisins are mycotoxins produced by some
Fusarium
species and can contaminate maize or maize products. Ingestion of fumonisins is associated with diseases, including cancer and neural tube defects, in humans and animals. In fungi, genes involved in the synthesis of mycotoxins and other secondary metabolites are often located adjacent to each other in gene clusters. Such genes can encode structural enzymes, regulatory proteins, and/or proteins that provide self-protection. The fumonisin biosynthetic gene cluster includes 16 genes, none of which appear to play a role in regulation. In this study, we identified a previously undescribed gene (
FUM21
) located adjacent to the fumonisin polyketide synthase gene,
FUM1
. The presence of a Zn(II)2Cys6 DNA-binding domain in the predicted protein suggested that
FUM21
was involved in transcriptional regulation.
FUM21
deletion (Δ
fum21
) mutants produce little to no fumonisin in cracked maize cultures but some
FUM1
and
FUM8
transcripts in a liquid GYAM medium. Complementation of a Δ
fum21
mutant with a wild-type copy of the gene restored fumonisin production. Analysis of
FUM21
cDNAs identified four alternative splice forms (ASFs), and microarray analysis indicated the ASFs were differentially expressed. Based on these data, we present a model for how
FUM21
ASFs may regulate fumonisin biosynthesis.
Dual Regulation of the
Bacillus subtilis
Regulon Comprising the
lmrAB
and
yxaGH
Operons and
yxaF
Gene by Two Transcriptional Repressors, LmrA and YxaF, in Response to Flavonoids
Authors: Hirooka Kazutake , Kunikane Satoshi , Matsuoka Hiroshi , Yoshida Ken-Ichi , Kumamoto Kanako , Tojo Shigeo , Fujita Yasutaro 
Published: May 2007

ABSTRACT

Bacillus subtilis
LmrA is known to be a repressor that regulates the
lmrAB
and
yxaGH
operons;
lmrB
and
yxaG
encode a multidrug resistance pump and quercetin 2,3-dioxygenase, respectively. DNase I footprinting analysis revealed that LmrA and YxaF, which are paralogous to each other, bind specifically to almost the same
cis
sequences, LmrA/YxaF boxes, located in the promoter regions of the
lmrAB
operon, the
yxaF
gene, and the
yxaGH
operon for their repression and containing a consensus sequence of AWTATAtagaNYGgTCTA, where W, Y, and N stand for A or T, C or T, and any base, respectively (three-out-of-four match [in lowercase type]). Gel retardation analysis indicated that out of the eight flavonoids tested, quercetin, fisetin, and catechin are most inhibitory for LmrA to DNA binding, whereas quercetin, fisetin, tamarixetin, and galangin are most inhibitory for YxaF. Also, YxaF bound most tightly to the tandem LmrA/YxaF boxes in the
yxaGH
promoter region. The
lacZ
fusion experiments essentially supported the above-mentioned in vitro results, except that galangin did not activate the
lmrAB
and
yxaGH
promoters, probably due to its poor incorporation into cells. Thus, the LmrA/YxaF regulon presumably comprising the
lmrAB
operon, the
yxaF
gene, and the
yxaGH
operon is induced in response to certain flavonoids. The in vivo experiments to examine the regulation of the synthesis of the reporter β-galactosidase and quercetin 2,3-dioxgenase as well as that of multidrug resistance suggested that LmrA represses the
lmrAB
and
yxaGH
operons but that YxaF represses
yxaGH
more preferentially.
Delineation of the
Salmonella enterica
Serovar Typhimurium HilA Regulon through Genome-Wide Location and Transcript Analysis
Authors: Thijs Inge M. V. , De Keersmaecker Sigrid C. J. , Fadda Abeer , Engelen Kristof , Zhao Hui , McClelland Michael , Marchal Kathleen , Vanderleyden Jos 
Published: May 2007

ABSTRACT

The
Salmonella enterica
serovar Typhimurium HilA protein is the key regulator for the invasion of epithelial cells. By a combination of genome-wide location and transcript analysis, the HilA-dependent regulon has been delineated. Under invasion-inducing conditions, HilA binds to most of the known target genes and a number of new target genes. The
sopB
,
sopE
, and
sopA
genes, encoding effector proteins secreted by the type III secretion system on
Salmonella
pathogenicity island 1 (SPI-1), were identified as being both bound by HilA and differentially regulated in an HilA mutant. This suggests a cooperative role for HilA and InvF in the regulation of SPI-1-secreted effectors. Also,
siiA
, the first gene of SPI-4, is both bound by HilA and differentially regulated in an HilA mutant, thus linking this pathogenicity island to the invasion key regulator. Finally, the interactions of HilA with the SPI-2 secretion system gene
ssaH
and the flagellar gene
flhD
imply a repressor function for HilA under invasion-inducing conditions.
Deletion and Substitution Analysis of theEscherichia coliTonB Q160 Region
Authors: Vakharia-Rao Hema , Kastead Kyle A. , Savenkova Marina I. , Bulathsinghala Charles M. , Postle Kathleen 
Published: May 2007

ABSTRACTThe active transport of iron siderophores and vitamin B12across the outer membrane (OM) ofEscherichia colirequires OM transporters and the potential energy of the cytoplasmic membrane (CM) proton gradient and CM proteins TonB, ExbB, and ExbD. A region at the amino terminus of the transporter, called the TonB box, directly interacts with TonB Q160 region residues. R158 and R166 in the TonB Q160 region were proposed to play important roles in cocrystal structures of the TonB carboxy terminus with OM transporters BtuB and FhuA. In contrast to predictions based on the crystal structures, none of the single, double, or triple alanyl substitutions at arginyl residues significantly decreased TonB activity. Even the quadruple R154A R158A R166A R171A mutant TonB still retained 30% of wild-type activity. Up to five residues centered on TonB Q160 could be deleted without inactivating TonB or preventing its association with the OM. TonB mutant proteins with nested deletions of 7, 9, or 11 residues centered on TonB Q160 were inactive and appeared never to have associated with the OM. Because the 7-residue-deletion mutant protein (TonBΔ7, lacking residues S157 to Y163) could still form disulfide-linked dimers when combined with W213C or F202C in the TonB carboxy terminus, the TonBΔ7 deletion did not prevent necessary energy-dependent conformational changes that occur in the CM. Thus, it appeared that initial contact with the OM is made through TonB residues S157 to Y163. It is hypothesized that the TonB Q160 region may be part of a large disordered region required to span the periplasm and contact an OM transporter.
Convergent Peripheral Pathways Catalyze Initial Glucose Catabolism inPseudomonas putida: Genomic and Flux Analysis
Authors: del Castillo Teresa , Ramos Juan L. , Rodríguez-Herva José J. , Fuhrer Tobias , Sauer Uwe , Duque Estrella 
Published: May 2007

ABSTRACTIn this study, we show that glucose catabolism inPseudomonas putidaoccurs through the simultaneous operation of three pathways that converge at the level of 6-phosphogluconate, which is metabolized by the Edd and Eda Entner/Doudoroff enzymes to central metabolites. When glucose enters the periplasmic space through specific OprB porins, it can either be internalized into the cytoplasm or be oxidized to gluconate. Glucose is transported to the cytoplasm in a process mediated by an ABC uptake system encoded by open reading frames PP1015 to PP1018 and is then phosphorylated by glucokinase (encoded by theglkgene) and converted by glucose-6-phosphate dehydrogenase (encoded by thezwfgenes) to 6-phosphogluconate. Gluconate in the periplasm can be transported into the cytoplasm and subsequently phosphorylated by gluconokinase to 6-phosphogluconate or oxidized to 2-ketogluconate, which is transported to the cytoplasm, and subsequently phosphorylated and reduced to 6-phosphogluconate. In the wild-type strain, glucose was consumed at a rate of around 6 mmol g−1h−1, which allowed a growth rate of 0.58 h−1and a biomass yield of 0.44 g/g carbon used. Flux analysis of13C-labeled glucose revealed that, in the Krebs cycle, most of the oxalacetate fraction was produced by the pyruvate shunt rather than by the direct oxidation of malate by malate dehydrogenase. Enzymatic and microarray assays revealed that the enzymes, regulators, and transport systems of the three peripheral glucose pathways were induced in response to glucose in the outer medium. We generated a series of isogenic mutants in one or more of the steps of all three pathways and found that, although all three functioned simultaneously, the glucokinase pathway and the 2-ketogluconate loop were quantitatively more important than the direct phosphorylation of gluconate. In physical terms, glucose catabolism genes were organized in a series of clusters scattered along the chromosome. Within each of the clusters, genes encoding porins, transporters, enzymes, and regulators formed operons, suggesting that genes in each cluster coevolved. Theglkgene encoding glucokinase was located in an operon with theeddgene, whereas thezwf-1gene, encoding glucose-6-phosphate dehydrogenase, formed an operon with theedagene. Therefore, the enzymes of the glucokinase pathway and those of the Entner-Doudoroff pathway are physically linked and induced simultaneously. It can therefore be concluded that the glucokinase pathway is a sine qua non condition forP. putidato grow with glucose.
Silencing Essential Protein Secretion in
Mycobacterium smegmatis
by Using Tetracycline Repressors
Authors: Guo Xinzheng V. , Monteleone Mercedes , Klotzsche Marcus , Kamionka Annette , Hillen Wolfgang , Braunstein Miriam , Ehrt Sabine , Schnappinger Dirk 
Published: May 2007

ABSTRACT

Many processes that are essential for mycobacterial growth are poorly understood. To facilitate genetic analyses of such processes in mycobacteria, we and others have developed regulated expression systems that are repressed by a tetracycline repressor (TetR) and induced with tetracyclines, permitting the construction of conditional mutants of essential genes. A disadvantage of these systems is that tetracyclines function as transcriptional inducers and have to be removed to initiate gene silencing. Recently, reverse TetR mutants were identified that require tetracyclines as corepressors. Here, we report that one of these mutants, TetR r1.7, allows efficient repression of
lacZ
expression in
Mycobacterium smegmatis
in the presence but not the absence of anhydrotetracycline (atc). TetR and TetR r1.7 also allowed efficient silencing of the essential
secA1
gene, as demonstrated by inhibition of the growth of a conditional mutant and dose-dependent depletion of the SecA1 protein after the removal or addition, respectively, of atc. The kinetics of SecA1 depletion were similar with TetR and TetR r1.7. To test whether silencing of
secA1
could help identify substrates of the general secretion pathway, we analyzed the main porin of
M. smegmatis
, MspA. This showed that the amount of cell envelope-associated MspA decreased more than 90-fold after
secA1
silencing. We thus demonstrated that TetR r1.7 allows the construction of conditional mycobacterial mutants in which the expression of an essential gene can be efficiently silenced by the addition of atc and that gene silencing permits the identification of candidate substrates of mycobacterial secretion systems.
Mutagenesis and Molecular Modeling Reveal Three Key Extracellular Loops of the Membrane Receptor HasR That Are Involved in Hemophore HasA Binding
Authors: Barjon Clément , Wecker Karine , Izadi-Pruneyre Nadia , Delepelaire Philippe 
Published: May 2007

ABSTRACT
On the basis of the three-dimensional model of the heme/hemophore TonB-dependent outer membrane receptor HasR, mutants with six-residue deletions in the 11 putative extracellular loops were generated. Although all mutants continued to be active TonB-dependent heme transporters, mutations in three loops abolished hemophore HasA binding both in vivo and in vitro.
The Two Carboxylases of
Corynebacterium glutamicum
Essential for Fatty Acid and Mycolic Acid Synthesis
Authors: Gande Roland , Dover Lynn G. , Krumbach Karin , Besra Gurdyal S. , Sahm Hermann , Oikawa Tadao , Eggeling Lothar 
Published: May 2007

ABSTRACT

The suborder
Corynebacterianeae
comprises bacteria like
Mycobacterium tuberculosis
and
Corynebacterium glutamicum
, and these bacteria contain in addition to the linear fatty acids, unique α-branched β-hydroxy fatty acids, called mycolic acids. Whereas acetyl-coenzyme A (CoA) carboxylase activity is required to provide malonyl-CoA for fatty acid synthesis, a new type of carboxylase is apparently additionally present in these bacteria. It activates the α-carbon of a linear fatty acid by carboxylation, thus enabling its decarboxylative condensation with a second fatty acid to afford mycolic acid synthesis. We now show that the acetyl-CoA carboxylase of
C. glutamicum
consists of the biotinylated α-subunit AccBC, the β-subunit AccD1, and the small peptide AccE of 8.9 kDa, forming an active complex of approximately 812,000 Da. The carboxylase involved in mycolic acid synthesis is made up of the two highly similar β-subunits AccD2 and AccD3 and of AccBC and AccE, the latter two identical to the subunits of the acetyl-CoA carboxylase complex. Since AccD2 and AccD3 orthologues are present in all
Corynebacterianeae
, these polypeptides are vital for mycolic acid synthesis forming the unique hydrophobic outer layer of these bacteria, and we speculate that the two β-subunits present serve to lend specificity to this unique large multienzyme complex.
A Robust Species Tree for the
Alphaproteobacteria
Authors: Williams Kelly P. , Sobral Bruno W. , Dickerman Allan W. 
Published: May 2007

ABSTRACT

The branching order and coherence of the alphaproteobacterial orders have not been well established, and not all studies have agreed that mitochondria arose from within the
Rickettsiales
. A species tree for 72 alphaproteobacteria was produced from a concatenation of alignments for 104 well-behaved protein families. Coherence was upheld for four of the five orders with current standing that were represented here by more than one species. However, the family
Hyphomonadaceae
was split from the other
Rhodobacterales
, forming an expanded group with
Caulobacterales
that also included
Parvularcula
. The three earliest-branching alphaproteobacterial orders were the
Rickettsiales
, followed by the
Rhodospirillales
and then the
Sphingomonadales
. The principal uncertainty is whether the expanded
Caulobacterales
group is more closely associated with the
Rhodobacterales
or the
Rhizobiales
. The mitochondrial branch was placed within the
Rickettsiales
as a sister to the combined
Anaplasmataceae
and
Rickettsiaceae
, all subtended by the
Pelagibacter
branch.
Pelagibacter
genes will serve as useful additions to the bacterial outgroup in future evolutionary studies of mitochondrial genes, including those that have transferred to the eukaryotic nucleus.