bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutations in the SLAC1 anion channel slow stomatal opening and severely reduce K+ uptake channel activity via enhanced cytosolic [Ca2+] and increased Ca2+ sensitivity of K+ uptake channels
Authors: Laanemets Kristiina , Wang Yong‐Fei , Lindgren Ove , Wu Juyou , Nishimura Noriyuki , Lee Stephen , Caddell Daniel , Merilo Ebe , Brosche Mikael , Kilk Kalle , Soomets Ursel , Kangasjärvi Jaakko , Schroeder Julian I. , Kollist Hannes 
Published: November 2012

Summary

The Arabidopsis guard cell anion channel SLAC1 is essential for stomatal closure in response to various endogenous and environmental stimuli. Interestingly, here we reveal an unexpected impairment of slac1 alleles on stomatal opening.

We report that mutations in SLAC1 unexpectedly slow stomatal opening induced by light, low CO2 and elevated air humidity in intact plants and that this is caused by the severely reduced activity of inward K+ (K+in) channels in slac1 guard cells.

Expression of channels and transporters involved in stomatal opening showed small but significant reductions in transcript levels in slac1 guard cells; however, this was deemed insufficient to explain the severely impaired K+in channel activity in slac1. We further examined resting cytosolic Ca2+ concentration ([Ca2+]cyt) and K+in channel sensitivity to [Ca2+]cyt in slac1. These experiments showed higher resting [Ca2+]cyt in slac1 guard cells and that reducing [Ca2+]cyt to < 10 nM rapidly restored the activity of K+in channels in slac1 closer to wild‐type levels.

These findings demonstrate an unanticipated compensatory feedback control in plant stomatal regulation, which counteracts the impaired stomatal closing response of slac1, by down‐regulating stomatal opening mechanisms and implicates enhanced [Ca2+]cyt sensitivity priming as a mechanistic basis for the down‐regulated K+in channel activity.
Spatiotemporal Analysis of Cryptosporidium Species/Genotypes and Relationships with Other Zoonotic Pathogens in Surface Water from Mixed-Use Watersheds
Authors: Wilkes Graham , Ruecker Norma J. , Neumann Norman F. , Gannon Victor P. J. , Jokinen Cassandra , Sunohara Mark , Topp Edward , Pintar Katarina D. M. , Edge Thomas A. , Lapen David R. 
Published: November 2012

ABSTRACTNearly 690 raw surface water samples were collected during a 6-year period from multiple watersheds in the South Nation River basin, Ontario, Canada.Cryptosporidiumoocysts in water samples were enumerated, sequenced, and genotyped by detailed phylogenetic analysis. The resulting species and genotypes were assigned to broad, known host and human infection risk classes. Wildlife/unknown, livestock, avian, and human host classes occurred in 21, 13, 3, and <1% of sampled surface waters, respectively.Cryptosporidium andersoniwas the most commonly detected livestock species, while muskrat I and II genotypes were the most dominant wildlife genotypes. The presence ofGiardiaspp.,Salmonellaspp.,Campylobacterspp., andEscherichia coliO157:H7 was evaluated in all water samples. The greatest significant odds ratios (odds of pathogen presence when host class is present/odds of pathogen presence when host class is absent) forGiardiaspp.,Campylobacterspp., andSalmonellaspp. in water were associated, respectively, with livestock (odds ratio of 3.1), avian (4.3), and livestock (9.3) host classes. Classification and regression tree analyses (CART) were used to group generalized host and human infection risk classes on the basis of a broad range of environmental and land use variables while tracking cooccurrence of zoonotic pathogens in these groupings. The occurrence of livestock-associatedCryptosporidiumwas most strongly related to agricultural water pollution in the fall (conditions also associated with elevated odds ratios of other zoonotic pathogens occurring in water in relation to all sampling conditions), whereas wildlife/unknown sources ofCryptosporidiumwere geospatially associated with smaller watercourses where urban/rural development was relatively lower. Conditions that support wildlife may not necessarily increase overall human infection risks associated withCryptosporidiumsince mostCryptosporidiumgenotypes classed as wildlife in this study (e.g., muskrat I and II genotype) do not pose significant infection risks to humans. Consequently, from a human health perspective, land use practices in agricultural watersheds that create opportunities for wildlife to flourish should not be rejected solely on the basis of their potential to increase relative proportions of wildlife fecal contamination in surface water. The present study suggests that mitigating livestock fecal pollution in surface water in this region would likely reduce human infection risks associated withCryptosporidiumand other zoonotic pathogens.
Intracellular Free Iron and Its Potential Role in Ultrahigh-Pressure-Induced Inactivation of Escherichia coli
Authors: Yan Yuan , Waite-Cusic Joy G. , Kuppusamy Periannan , Yousef Ahmed E. 
Published: November 2012

ABSTRACT

Intracellular free iron of
Escherichia coli
was determined by whole-cell electron paramagnetic resonance spectrometry. Ultrahigh pressure (UHP) increased both intracellular free iron and cell lethality in a pressure-dose-dependent manner. The iron chelator 2,2′-dipyridyl protected cells against UHP treatments. A mutation that produced iron overload conditions sensitized
E. coli
to UHP treatment.
Chitin-Induced Gene Expression in Secondary Metabolic Pathways of Streptomyces coelicolor A3(2) Grown in Soil
Authors: Nazari Behnam , Kobayashi Michihiko , Saito Akihiro , Hassaninasab Azam , Miyashita Kiyotaka , Fujii Takeshi 
Published: November 2012

ABSTRACTMicroarray analyses revealed that the expression of genes for secondary metabolism together with that of primary metabolic genes was induced by chitin in autoclaved soil cultures ofStreptomyces coelicolorA3(2). The data also indicated that DasR was involved in the regulation of gene expression for chitin catabolism, secondary metabolism, and stress responses.
Quantification of Yeast and Bacterial Gene Transcripts in Retail Cheeses by Reverse Transcription-Quantitative PCR
Authors: Monnet Christophe , Straub Cécile , Castellote Jessie , Onesime Djamila , Bonnarme Pascal , Irlinger Françoise 
Published: November 2012

ABSTRACT

The cheese microbiota contributes to a large extent to the development of the typical color, flavor, and texture of the final product. Its composition is not well defined in most cases and varies from one cheese to another. The aim of the present study was to establish procedures for gene transcript quantification in cheeses by reverse transcription-quantitative PCR. Total RNA was extracted from five smear-ripened cheeses purchased on the retail market, using a method that does not involve prior separation of microbial cells. 16S rRNA and malate:quinone oxidoreductase gene transcripts of
Corynebacterium casei
,
Brevibacterium aurantiacum
, and
Arthrobacter arilaitensis
and 26S rRNA and beta tubulin gene transcripts of
Geotrichum candidum
and
Debaryomyces hansenii
could be detected and quantified in most of the samples. Three types of normalization were applied: against total RNA, against the amount of cheese, and against a reference gene. For the first two types of normalization, differences of reverse transcription efficiencies from one sample to another were taken into account by analysis of exogenous control mRNA. No good correlation was found between the abundances of target mRNA or rRNA transcripts and the viable cell concentration of the corresponding species. However, in most cases, no mRNA transcripts were detected for species that did not belong to the dominant species. The applications of gene expression measurement in cheeses containing an undefined microbiota, as well as issues concerning the strategy of normalization and the assessment of amplification specificity, are discussed.
Enhanced Gene Detection Assays for Fumarate-Adding Enzymes Allow Uncovering of Anaerobic Hydrocarbon Degraders in Terrestrial and Marine Systems
Authors: von Netzer Frederick , Pilloni Giovanni , Kleindienst Sara , Krüger Martin , Knittel Katrin , Gründger Friederike , Lueders Tillmann 
Published: November 2012

ABSTRACTThe detection of anaerobic hydrocarbon degrader populations via catabolic gene markers is important for the understanding of processes at contaminated sites. Fumarate-adding enzymes (FAEs; i.e., benzylsuccinate and alkylsuccinate synthases) have already been established as specific functional marker genes for anaerobic hydrocarbon degraders. Several recent studies based on pure cultures and laboratory enrichments have shown the existence of new and deeply branching FAE gene lineages, such as clostridial benzylsuccinate synthases and homologues, as well as naphthylmethylsuccinate synthases. However, established FAE gene detection assays were not designed to target these novel lineages, and consequently, their detectability in different environments remains obscure. Here, we present a new suite of parallel primer sets for detecting the comprehensive range of FAE markers known to date, including clostridial benzylsuccinate, naphthylmethylsuccinate, and alkylsuccinate synthases. It was not possible to develop one single assay spanning the complete diversity of FAE genes alone. The enhanced assays were tested with a range of hydrocarbon-degrading pure cultures, enrichments, and environmental samples of marine and terrestrial origin. They revealed the presence of several, partially unexpected FAE gene lineages not detected in these environments before: distinct deltaproteobacterial and also clostridialbssAhomologues as well as environmentalnmsAhomologues. These findings were backed up by dual-digest terminal restriction fragment length polymorphism diagnostics to identify FAE gene populations independently of sequencing. This allows rapid insights into intrinsic degrader populations and degradation potentials established in aromatic and aliphatic hydrocarbon-impacted environmental systems.
Persistence and Leaching Potential of Microorganisms and Mineral N in Animal Manure Applied to Intact Soil Columns
Authors: Amin M. G. Mostofa , Forslund Anita , Bui Xuan Thanh , Juhler René K. , Petersen Søren O. , Lægdsmand Mette 
Published: November 2012

ABSTRACTPathogens may reach agricultural soils through application of animal manure and thereby pose a risk of contaminating crops as well as surface and groundwater. Treatment and handling of manure for improved nutrient and odor management may also influence the amount and fate of manure-borne pathogens in the soil. A study was conducted to investigate the leaching potentials of a phage (Salmonella entericaserovar Typhimurium bacteriophage 28B) and two bacteria,Escherichia coliandEnterococcusspecies, in a liquid fraction of raw pig slurry obtained by solid-liquid separation of this slurry and in this liquid fraction after ozonation, when applied to intact soil columns by subsurface injection. We also compared leaching potentials of surface-applied and subsurface-injected raw slurry. The columns were exposed to irrigation events (3.5-h period at 10 mm h−1) after 1, 2, 3, and 4 weeks of incubation with collection of leachate. By the end of incubation, the distribution and survival of microorganisms in the soil of each treatment and in nonirrigated columns with injected raw slurry or liquid fraction were determined.E. coliin the leachates was quantified by both plate counts and quantitative PCR (qPCR) to assess the proportions of culturable and nonculturable (viable and nonviable) cells. Solid-liquid separation of slurry increased the redistribution in soil of contaminants in the liquid fraction compared to raw slurry, and the percent recovery ofE. coliandEnterococcusspecies was higher for the liquid fraction than for raw slurry after the four leaching events. The liquid fraction also resulted in more leaching of all contaminants exceptEnterococcusspecies than did raw slurry. Ozonation reducedE. colileaching only. Injection enhanced the leaching potential of the microorganisms investigated compared to surface application, probably because of a better survival with subsurface injection and a shorter leaching path.
Poly-γ-
d
-Glutamic Acid Capsule Interferes with Lytic Infection of Bacillus anthracis by B. anthracis-Specific Bacteriophages
Authors: Negus David , Burton Jane , Sweed Angela , Gryko Romuald , Taylor Peter W. 
Published: November 2012

ABSTRACT

The poly-γ-
d
-glutamic acid capsule of
Bacillus anthracis
is a barrier to infection by
B. anthracis
-specific bacteriophages. Capsule expression was found to completely inhibit lytic infection by γ phage, an observation supported by the demonstration that this phage does not elaborate a hydrolase that would facilitate penetration through the protective capsule outer layer.
Occurrence of Virulence Genes Associated with Diarrheagenic Pathotypes in Escherichia coli Isolates from Surface Water
Authors: Sidhu Jatinder P. S. , Ahmed Warish , Hodgers Leonie , Toze Simon 
Published: November 2012

ABSTRACT

Escherichia coli
isolates (
n
= 300) collected from six sites in subtropical Brisbane, Australia, prior to and after storm events were tested for the presence of 11 virulence genes (VGs) specific to diarrheagenic pathotypes. The presence of
eaeA
,
stx
1
,
stx
2
, and
ehxA
genes specific for the enterohemorrhagic
E. coli
(EHEC) pathotype was detected in 56%, 6%, 10%, and 13% of isolates, respectively. The VGs
astA
(69%) and
aggR
(29%), carried by enteroaggregative (EAEC) pathotypes, were frequently detected in
E. coli
isolates. The enteropathogenic
E. coli
(EPEC) gene
bfp
was detected in 24% of isolates. In addition, enteroinvasive
E. coli
(EIEC) VG
ipaH
was also detected in 14% of isolates. During dry periods, isolates belonging to the EAEC pathotype were most commonly detected (23%), followed by EHEC (11%) and EPEC (11%). Conversely, a more uniform prevalence of pathotypes, EPEC (14%), EAEC (12%), EIEC (10%), EHEC (7%), and ETEC (7%), was observed after the storm events. The results of this study highlight the widespread occurrence of potentially diarrheagenic pathotypes in the urban aquatic ecosystems. While the presence of VGs in
E. coli
isolates alone is insufficient to determine pathogenicity, the presence of diarrheagenic
E. coli
pathotypes in high frequency after the storm events could lead to increased health risks if untreated storm water were to be used for nonpotable purposes and recreational activities.
Cello-Oligosaccharide Oxidation Reveals Differences between Two Lytic Polysaccharide Monooxygenases (Family GH61) from Podospora anserina
Authors: Bey Mathieu , Zhou Simeng , Poidevin Laetitia , Henrissat Bernard , Coutinho Pedro M. , Berrin Jean-Guy , Sigoillot Jean-Claude 
Published: November 2012

ABSTRACT

The genome of the coprophilic ascomycete
Podospora anserina
encodes 33 different genes encoding copper-dependent lytic polysaccharide monooxygenases (LPMOs) from glycoside hydrolase family 61 (GH61). In this study, two of these enzymes (
P. anserina
GH61A [
Pa
GH61A] and
Pa
GH61B), which both harbored a family 1 carbohydrate binding module, were successfully produced in
Pichia pastoris
. Synergistic cooperation between
Pa
GH61A or
Pa
GH61B with the cellobiose dehydrogenase (CDH) of
Pycnoporus cinnabarinus
on cellulose resulted in the formation of oxidized and nonoxidized cello-oligosaccharides. A striking difference between
Pa
GH61A and
Pa
GH61B was observed through the identification of the products, among which were doubly and triply oxidized cellodextrins, which were released only by the combination of
Pa
GH61B with CDH. The mass spectrometry fragmentation patterns of these oxidized products could be consistent with oxidation at the C-6 position with a geminal diol group. The different properties of
Pa
GH61A and
Pa
GH61B and their effect on the interaction with CDH are discussed in regard to the proposed
in vivo
function of the CDH/GH61 enzyme system in oxidative cellulose hydrolysis.
Role of Cytosolic Glyceraldehyde-3-Phosphate Dehydrogenase in Visceral Organ Infection by Leishmania donovani
Authors: Zhang Wen-Wei , McCall Laura-Isobel , Matlashewski Greg 
Published: November 2012

ABSTRACT

The initial 7 steps of the glycolytic pathway from glucose to 3-phosphoglycerate are localized in the glycosomes in
Leishmania
, including step 6, catalyzed by the enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH). In
L. donovani
and
L. mexicana
, there exists a second GAPDH enzyme present in the cytosol that is absent in
L. braziliensis
and that has become a pseudogene in
L. major.
To investigate the role of the cytosolic GAPDH (cGAPDH), an
L. donovani
cGAPDH-null mutant was generated, and conversely, the functional
L. donovani
cGAPDH was introduced into
L. major
and the resulting engineered parasites were characterized. The
L. donovani
cGAPDH-null mutant was able to proliferate at the same rate as the wild-type parasite in glucose-deficient medium. However, in the presence of glucose, the
L. donovani
cGAPDH-null mutant consumed less glucose and proliferated more slowly than the wild-type parasite and displayed reduced infectivity in visceral organs of experimentally infected mice. This demonstrates that cGAPDH is functional in
L. donovani
and is required for survival in visceral organs. Restoration of cGAPDH activity in
L. major
, in contrast, had an adverse effect on
L. major
proliferation in glucose-containing medium, providing a possible explanation of why it has evolved into a pseudogene in
L. major
. This study indicates that there is a difference in glucose metabolism between
L. donovani
and
L. major
, and this may represent an important factor in the ability of
L. donovani
to cause visceral disease.
White-Opaque Switching of Candida albicans Allows Immune Evasion in an Environment-Dependent Fashion
Authors: Sasse Christoph , Hasenberg Mike , Weyler Michael , Gunzer Matthias , Morschhäuser Joachim 
Published: November 2012

ABSTRACTCandida albicansstrains that are homozygous at the mating type locus can spontaneously and reversibly switch from the normal yeast morphology (white) to an elongated cell type (opaque), which is the mating-competent form of the fungus. White-opaque switching also influences the ability ofC. albicansto colonize and proliferate in specific host niches and its susceptibility to host defense mechanisms. We used live imaging to observe the interaction of white and opaque cells with host phagocytic cells. For this purpose, we generated derivatives of the switching-competent strain WO-1 that express green fluorescent protein from a white-specific promoter and red fluorescent protein from an opaque-specific promoter or vice versa. When mixed populations of these differentially labeled white and opaque cells were incubated with human polymorphonuclear neutrophils (PMNs) on a glass slide, the neutrophils selectively phagocytosed and killed white cells, despite frequent physical interaction with opaque cells. White cells were attacked only after they started to form a germ tube, indicating that the suppression of filamentation in opaque cells saved them from recognition by the PMNs. In contrast to neutrophils, dendritic cells internalized white as well as opaque cells. However, when embedded in a collagen matrix, the PMNs also phagocytosed both white and opaque cells with similar efficiency. These results suggest that, depending on the environment, white-opaque switching enablesC. albicansto escape from specific host defense mechanisms.
Role of Pseudomonas aeruginosa Peptidoglycan-Associated Outer Membrane Proteins in Vesicle Formation
Authors: Wessel Aimee K. , Liew Jean , Kwon Taejoon , Marcotte Edward M. , Whiteley Marvin 
Published: November 2012

ABSTRACT

Gram-negative bacteria produce outer membrane vesicles (OMVs) that package and deliver proteins, small molecules, and DNA to prokaryotic and eukaryotic cells. The molecular details of OMV biogenesis have not been fully elucidated, but peptidoglycan-associated outer membrane proteins that tether the outer membrane to the underlying peptidoglycan have been shown to be critical for OMV formation in multiple
Enterobacteriaceae
. In this study, we demonstrate that the peptidoglycan-associated outer membrane proteins OprF and OprI, but not OprL, impact production of OMVs by the opportunistic pathogen
Pseudomonas aeruginosa
. Interestingly, OprF does not appear to be important for tethering the outer membrane to peptidoglycan but instead impacts OMV formation through modulation of the levels of the
Pseudomonas
quinolone signal (PQS), a quorum signal previously shown by our laboratory to be critical for OMV formation. Thus, the mechanism by which OprF impacts OMV formation is distinct from that for other peptidoglycan-associated outer membrane proteins, including OprI.
Gene Conservation among Endospore-Forming Bacteria Reveals Additional Sporulation Genes in Bacillus subtilis
Authors: Traag Bjorn A. , Pugliese Antonia , Eisen Jonathan A. , Losick Richard 
Published: November 2012

ABSTRACTThe capacity to form endospores is unique to certain members of the low-G+C group of Gram-positive bacteria (Firmicutes) and requires signature sporulation genes that are highly conserved across members of distantly related genera, such asClostridiumandBacillus. Using gene conservation among endospore-forming bacteria, we identified eight previously uncharacterized genes that are enriched among endospore-forming species. The expression of five of these genes was dependent on sporulation-specific transcription factors. Mutants of none of the genes exhibited a conspicuous defect in sporulation, but mutants of two,ylxYandylyA, were outcompeted by a wild-type strain under sporulation-inducing conditions, but not during growth. In contrast, aylmCmutant displayed a slight competitive advantage over the wild type specific to sporulation-inducing conditions. The phenotype of aylyAmutant was ascribed to a defect in spore germination efficiency. This work demonstrates the power of combining phylogenetic profiling with reverse genetics and gene-regulatory studies to identify unrecognized genes that contribute to a conserved developmental process.
The Bacillus subtilis Response Regulator Gene
degU
Is Positively Regulated by CcpA and by Catabolite-Repressed Synthesis of ClpC
Authors: Ishii Hiroshi , Tanaka Teruo , Ogura Mitsuo 
Published: November 2012

ABSTRACT

In
Bacillus subtilis
, the response regulator DegU and its cognate kinase, DegS, constitute a two-component system that regulates many cellular processes, including exoprotease production and genetic competence. Phosphorylated DegU (DegU-P) activates its own promoter and is degraded by the ClpCP protease. We observed induction of
degU
by glucose in sporulation medium. This was abolished in two mutants: the
ccpA
(catabolite control protein A) and
clpC
disruptants. Transcription of the promoter of the operon containing
clpC
(PclpC) decreased in the presence of glucose, and the disruption of
ccpA
resulted in derepression of PclpC. However, this was not directly mediated by CcpA, because we failed to detect binding of CcpA to PclpC. Glucose decreased the expression of
clpC
, leading to low cellular concentrations of the ClpCP protease. Thus,
degU
is induced through activation of autoregulation by a decrease in ClpCP-dependent proteolysis of DegU-P. An electrophoretic mobility shift assay showed that CcpA bound directly to the
degU
upstream region, indicating that CcpA activates
degU
through binding. The bound region was narrowed down to 27 bases, which contained a
cre
(
c
atabolite-
r
esponsive
e
lement) sequence with a low match to the
cre
consensus sequence. In a footprint analysis, CcpA specifically protected a region containing the
cre
sequence from DNase I digestion. The induction of
degU
by glucose showed complex regulation of the
degU
gene.