bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined Effects of Long-Living Chemical Species during Microbial Inactivation Using Atmospheric Plasma-Treated Water
Authors: Naïtali Murielle , Kamgang-Youbi Georges , Herry Jean-Marie , Bellon-Fontaine Marie-Noëlle , Brisset Jean-Louis 
Published: October 2010

ABSTRACT

Electrical discharges in humid air at atmospheric pressure (nonthermal quenched plasma) generate long-lived chemical species in water that are efficient for microbial decontamination. The major role of nitrites was evidenced together with a synergistic effect of nitrates and H
2
O
2
and matching acidification. Other possible active compounds are considered, e.g., peroxynitrous acid.
Identification ofMET10-932and Characterization as an Allele Reducing Hydrogen Sulfide Formation in Wine Strains ofSaccharomyces cerevisiae
Authors: Linderholm Angela , Dietzel Kevin , Hirst Marissa , Bisson Linda F. 
Published: October 2010

ABSTRACTA vineyard isolate of the yeastSaccharomyces cerevisiae, UCD932, was identified as a strain producing little or no detectable hydrogen sulfide during wine fermentation. Genetic analysis revealed that this trait segregated as a single genetic determinant. The gene also conferred a white colony phenotype on BiGGY agar (bismuth-glucose-glycine-yeast agar), which is thought to indicate low basal levels of sulfite reductase activity. However, this isolate does not display a requirement for S-containing amino acids, indicating that the sulfate reduction pathway is fully operational. Genetic crosses against known mutations conferring white colony color on BiGGY agar identified the gene leading to reduced H2S formation as an allele ofMET10(MET10-932), which encodes a catalytic subunit of sulfite reductase. Sequence analysis ofMET10-932revealed several corresponding amino acid differences in relation to laboratory strain S288C. Allele differences for other genes of the sulfate reduction pathway were also detected in UCD932. TheMET10allele of UCD932 was found to be unique in comparison to the sequences of several other vineyard isolates with differing levels of production of H2S. Replacing theMET10allele of high-H2S-producing strains withMET10-932prevented H2S formation by those strains. A single mutative change, corresponding to T662K, inMET10-932resulted in a loss of H2S production. The role of site 662 in sulfide reduction was further analyzed by changing the encoded amino acid at this position. A change back to threonine or to the conservative serine fully restored the H2S formation conferred by this allele. In addition to T662K, arginine, tryptophan, and glutamic acid substitutions similarly reduced sulfide formation.
Functional Gene Analysis Suggests Different Acetogen Populations in the Bovine Rumen and Tammar Wallaby Forestomach
Authors: Gagen Emma J. , Denman Stuart E. , Padmanabha Jagadish , Zadbuke Someshwar , Al Jassim Rafat , Morrison Mark , McSweeney Christopher S. 
Published: October 2010

ABSTRACT

Reductive acetogenesis via the acetyl coenzyme A (acetyl-CoA) pathway is an alternative hydrogen sink to methanogenesis in the rumen. Functional gene-based analysis is the ideal approach for investigating organisms capable of this metabolism (acetogens). However, existing tools targeting the formyltetrahydrofolate synthetase gene (
fhs
) are compromised by lack of specificity due to the involvement of formyltetrahydrofolate synthetase (FTHFS) in other pathways. Acetyl-CoA synthase (ACS) is unique to the acetyl-CoA pathway and, in the present study, acetyl-CoA synthase genes (
acsB
) were recovered from a range of acetogens to facilitate the design of
acsB
-specific PCR primers.
fhs
and
acsB
libraries were used to examine acetogen diversity in the bovine rumen and forestomach of the tammar wallaby (
Macropus eugenii
), a native Australian marsupial demonstrating foregut fermentation analogous to rumen fermentation but resulting in lower methane emissions. Novel, deduced amino acid sequences of
acsB
and
fhs
affiliated with the
Lachnospiraceae
in both ecosystems and the
Ruminococcaeae/Blautia
group in the rumen. FTHFS sequences that probably originated from nonacetogens were identified by low “homoacetogen similarity” scores based on analysis of FTHFS residues, and comprised a large proportion of FTHFS sequences from the tammar wallaby forestomach. A diversity of FTHFS and ACS sequences in both ecosystems clustered between the
Lachnospiraceae
and
Clostridiaceae
acetogens but without close sequences from cultured isolates. These sequences probably originated from novel acetogens. The community structures of the
acsB
and
fhs
libraries from the rumen and the tammar wallaby forestomach were different (LIBSHUFF,
P
< 0.001), and these differences may have significance for overall hydrogenotrophy in both ecosystems.
Glutaredoxins Grx4 and Grx3 of
Saccharomyces cerevisiae
Play a Role in Actin Dynamics through Their Trx Domains, Which Contributes to Oxidative Stress Resistance
Authors: Pujol-Carrion Nuria , de la Torre-Ruiz Maria Angeles 
Published: October 2010

ABSTRACT

Grx3 and Grx4 are two monothiol glutaredoxins of
Saccharomyces cerevisiae
that have previously been characterized as regulators of Aft1 localization and therefore of iron homeostasis. In this study, we present data showing that both Grx3 and Grx4 have new roles in actin cytoskeleton remodeling and in cellular defenses against oxidative stress caused by reactive oxygen species (ROS) accumulation. The Grx4 protein plays a unique role in the maintenance of actin cable integrity, which is independent of its role in the transcriptional regulation of Aft1. Grx3 plays an additive and redundant role, in combination with Grx4, in the organization of the actin cytoskeleton, both under normal conditions and in response to external oxidative stress. Each Grx3 and Grx4 protein contains a thioredoxin domain sequence (Trx), followed by a glutaredoxin domain (Grx). We performed functional analyses of each of the two domains and characterized different functions for them. Each of the two Grx domains plays a role in ROS detoxification and cell viability. However, the Trx domain of each Grx4 and Grx3 protein acts independently of its respective Grx domain in a novel function that involves the polarization of the actin cytoskeleton, which also determines cell resistance against oxidative conditions. Finally, we present experimental evidence demonstrating that Grx4 behaves as an antioxidant protein increasing cell survival under conditions of oxidative stress.
Limitations in Xylose-FermentingSaccharomyces cerevisiae, Made Evident through Comprehensive Metabolite Profiling and Thermodynamic Analysis
Authors: Klimacek Mario , Krahulec Stefan , Sauer Uwe , Nidetzky Bernd 
Published: October 2010

ABSTRACTLittle is known about how the general lack of efficiency with which recombinantSaccharomyces cerevisiaestrains utilize xylose affects the yeast metabolome. Quantitative metabolomics was therefore performed for two xylose-fermentingS. cerevisiaestrains, BP000 and BP10001, both engineered to produce xylose reductase (XR), NAD+-dependent xylitol dehydrogenase and xylulose kinase, and the corresponding wild-type strain CEN.PK 113-7D, which is not able to metabolize xylose. Contrary to BP000 expressing an NADPH-preferring XR, BP10001 expresses an NADH-preferring XR. An updated protocol of liquid chromatography/tandem mass spectrometry that was validated by applying internal13C-labeled metabolite standards was used to quantitatively determine intracellular pools of metabolites from the central carbon, energy, and redox metabolism and of eight amino acids. Metabolomic responses to different substrates, glucose (growth) or xylose (no growth), were analyzed for each strain. In BP000 and BP10001, flux through glycolysis was similarly reduced (∼27-fold) when xylose instead of glucose was metabolized. As a consequence, (i) most glycolytic metabolites were dramatically (≤120-fold) diluted and (ii) energy and anabolic reduction charges were affected due to decreased ATP/AMP ratios (3- to 4-fold) and reduced NADP+levels (∼3-fold), respectively. Contrary to that in BP000, the catabolic reduction charge was not altered in BP10001. This was due mainly to different utilization of NADH by XRs in BP000 (44%) and BP10001 (97%). Thermodynamic analysis complemented by enzyme kinetic considerations suggested that activities of pentose phosphate pathway enzymes and the pool of fructose-6-phosphate are potential factors limiting xylose utilization. Coenzyme and ATP pools did not rate limit flux through xylose pathway enzymes.
Antiviral Drug Resistance of Human Cytomegalovirus
Authors: Lurain Nell S. , Chou Sunwen 
Published: October 2010

SUMMARYThe study of human cytomegalovirus (HCMV) antiviral drug resistance has enhanced knowledge of the virological targets and the mechanisms of antiviral activity. The currently approved drugs, ganciclovir (GCV), foscarnet (FOS), and cidofovir (CDV), target the viral DNA polymerase. GCV anabolism also requires phosphorylation by the virus-encoded UL97 kinase. GCV resistance mutations have been identified in both genes, while FOS and CDV mutations occur only in the DNA polymerase gene. Confirmation of resistance mutations requires phenotypic analysis; however, phenotypic assays are too time-consuming for diagnostic purposes. Genotypic assays based on sequencing provide more rapid results but are dependent on prior validation by phenotypic methods. Reports from many laboratories have produced an evolving list of confirmed resistance mutations, although differences in interpretation have led to some confusion. Recombinant phenotyping methods performed in a few research laboratories have resolved some of the conflicting results. Treatment options for drug-resistant HCMV infections are complex and have not been subjected to controlled clinical trials, although consensus guidelines have been proposed. This review summarizes the virological and clinical data pertaining to HCMV antiviral drug resistance.
Role of Bacteria in Oncogenesis
Authors: Chang Alicia H. , Parsonnet Julie 
Published: October 2010

SUMMARYAlthough scientific knowledge in viral oncology has exploded in the 20th century, the role of bacteria as mediators of oncogenesis has been less well elucidated. Understanding bacterial carcinogenesis has become increasingly important as a possible means of cancer prevention. This review summarizes clinical, epidemiological, and experimental evidence as well as possible mechanisms of bacterial induction of or protection from malignancy.
Development, Characterization, and Application of Monoclonal Antibodies against Severe Acute Respiratory Syndrome Coronavirus Nucleocapsid Protein
Authors: Das Dipankar , Kammila Sriram , Suresh Mavanur R. 
Published: October 2010

ABSTRACT
Five monoclonal antibodies (MAbs) against recombinant nucleocapsid protein (NP) of severe acute respiratory syndrome (SARS)-causing coronavirus (CoV) were developed by hybridoma technology. Epitope mapping by Western blotting showed that these anti-SARS-CoV NP MAbs bind to distinct domains of NP. These anti-SARS-CoV NP MAbs, with their high specificity, are potentially ideal candidates for developing early and sensitive diagnostic assays for SARS-CoV.
Porcine Reproductive and Respiratory Syndrome Virus Infection at the Time of Porcine Circovirus Type 2 Vaccination Has No Impact on Vaccine Efficacy
Authors: Sinha A. , Shen H. G. , Schalk S. , Beach N. M. , Huang Y. W. , Halbur P. G. , Meng X. J. , Opriessnig T. 
Published: October 2010

ABSTRACTSeveral porcine circovirus type 2 (PCV2) vaccines are now commercially available and have been shown to be effective at decreasing the occurrence of porcine circovirus-associated disease (PCVAD). Many herds are coinfected with PCV2 and porcine reproductive and respiratory syndrome virus (PRRSV). Some producers and veterinarians are concerned that if pigs are vaccinated for PCV2 at or near the time that they are typically infected with PRRSV, the efficacy of the PCV2 vaccine will be compromised. The impact of PRRSV on PCV2 vaccination is unclear and has not been investigated under controlled conditions. The objective of the present study was to determine whether the presence of PRRSV viremia has an effect on the efficacy of commercial PCV2 vaccinations. Three-week-old PCV2-negative conventional pigs with passively derived anti-PCV2 antibodies were either vaccinated with one of three commercial PCV2 vaccines or left nonvaccinated. A portion of the pigs were infected with PRRSV 1 week prior to PCV2 vaccination. To determine vaccine efficacy, a PCV2 challenge was conducted at 8 weeks of age. PCV2 vaccination, regardless of PRRSV infection status at the time of vaccination, was similarly effective in inducing an anti-PCV2 IgG response in the presence of maternally derived immunity and in protecting the pigs from PCV2 challenge, as determined by a reduction in the level of PCV2 viremia and a reduction in the prevalence and amount of PCV2 antigen in lymphoid tissues in vaccinated pigs compared to nonvaccinated pigs. The results indicate that acute PRRSV infection at the time of PCV2 vaccination has no adverse effect on PCV2 vaccine efficacy.
The Vacuolar Ca
2+
Exchanger Vcx1 Is Involved in Calcineurin-Dependent Ca
2+
Tolerance and Virulence in Cryptococcus neoformans
Authors: Kmetzsch Lívia , Staats Charley Christian , Simon Elisa , Fonseca Fernanda L. , de Oliveira Débora L. , Sobrino Luna , Rodrigues Jéssica , Leal Ana Lusia , Nimrichter Leonardo , Rodrigues Márcio L. , Schrank Augusto , Vainstein Marilene Henning 
Published: October 2010

ABSTRACT

Cryptococcus neoformans
is an encapsulated yeast that causes a life-threatening meningoencephalitis in immunocompromised individuals. The ability to survive and proliferate at the human body temperature is an essential virulence attribute of this pathogen. This trait is controlled in part by the Ca
2+
-calcineurin pathway, which senses and utilizes cytosolic calcium for signaling. In the present study, the identification of the
C. neoformans
gene
VCX1
, which encodes a vacuolar calcium exchanger, is reported. The
VCX1
knockout results in hypersensitivity to the calcineurin inhibitor cyclosporine A at 35°C, but not at 30°C. Furthermore, high concentrations of CaCl
2
lead to growth inhibition of the
vcx1
mutant strain only in the presence of cyclosporine A, indicating that Vcx1 acts in parallel with calcineurin. The loss of
VCX1
does not influence cell wall integrity or capsule size but decreases secretion of the major capsular polysaccharide glucuronoxylomannan (GXM) in culture supernatants.Vcx1 also influences
C. neoformans
phagocytosis by murine macrophages and is required for full virulence in mice. Analysis of cellular distribution by confocal microscopy confirmed the vacuolar localization of Vcx1 in
C. neoformans
cells.
Colocalization of Amanitin and a Candidate Toxin-Processing Prolyl Oligopeptidase in Amanita Basidiocarps
Authors: Luo Hong , Hallen-Adams Heather E. , Scott-Craig John S. , Walton Jonathan D. 
Published: October 2010

ABSTRACT

Fungi in the basidiomycetous genus
Amanita
owe their high mammalian toxicity to the bicyclic octapeptide amatoxins such as α-amanitin. Amatoxins and the related phallotoxins (such as the heptapeptide phalloidin) are encoded by members of the “MSDIN” gene family and are synthesized on ribosomes as short (34- to 35-amino-acid) proproteins. Antiamanitin antibodies and confocal microscopy were used to determine the cellular and subcellular localizations of amanitin accumulation in basidiocarps (mushrooms) of the Eastern North American destroying angel (
Amanita bisporigera
). Consistent with previous studies, amanitin is present throughout the basidiocarp (stipe, pileus, lamellae, trama, and universal veil), but it is present in only a subset of cells within these tissues. Restriction of amanitin to certain cells is especially marked in the hymenium. Several lines of evidence implicate a specific prolyl oligopeptidase,
A. bisporigera
POPB (AbPOPB), in the initial processing of the amanitin and phallotoxin proproteins. The gene for AbPOPB is restricted taxonomically to the amatoxin-producing species of
Amanita
and is clustered in the genome with at least one expressed member of the MSDIN gene family. Immunologically, amanitin and AbPOPB show a high degree of colocalization, indicating that toxin biosynthesis and accumulation occur in the same cells and possibly in the same subcellular compartments.
Intracellular Acetyl Unit Transport in Fungal Carbon Metabolism
Authors: Strijbis Karin , Distel Ben 
Published: October 2010

ABSTRACT

Acetyl coenzyme A (acetyl-CoA) is a central metabolite in carbon and energy metabolism. Because of its amphiphilic nature and bulkiness, acetyl-CoA cannot readily traverse biological membranes. In fungi, two systems for acetyl unit transport have been identified: a shuttle dependent on the carrier carnitine and a (peroxisomal) citrate synthase-dependent pathway. In the carnitine-dependent pathway, carnitine acetyltransferases exchange the CoA group of acetyl-CoA for carnitine, thereby forming acetyl-carnitine, which can be transported between subcellular compartments. Citrate synthase catalyzes the condensation of oxaloacetate and acetyl-CoA to form citrate that can be transported over the membrane. Since essential metabolic pathways such as fatty acid β-oxidation, the tricarboxylic acid (TCA) cycle, and the glyoxylate cycle are physically separated into different organelles, shuttling of acetyl units is essential for growth of fungal species on various carbon sources such as fatty acids, ethanol, acetate, or citrate. In this review we summarize the current knowledge on the different systems of acetyl transport that are operational during alternative carbon metabolism, with special focus on two fungal species:
Saccharomyces cerevisiae
and
Candida albicans
.
HU Protein Affects Transcription of Surface Polysaccharide Synthesis Genes in
Porphyromonas gingivalis
Authors: Alberti-Segui Christine , Arndt Annette , Cugini Carla , Priyadarshini Richa , Davey Mary E. 
Published: October 2010

ABSTRACT

K-antigen capsule synthesis is an important virulence determinant of the oral anaerobe
Porphyromonas gingivalis
. We previously reported that the locus required for synthesis of this surface polysaccharide in strain W83 (TIGR identification PG0106 to PG0120) is transcribed as a large (∼16.7-kb) polycistronic message. Through sequence analysis, we have now identified a 77-bp inverted repeat located upstream (206 bp) of the start codon of PG0106 that is capable of forming a large hairpin structure. Further sequence analysis just upstream and downstream of the capsule synthesis genes revealed the presence of two genes oriented in the same direction as the operon that are predicted to encode DNA binding proteins: PG0104, which is highly similar (57%) to DNA topoisomerase III, and PG0121, which has high similarity (72%) to DNA binding protein HU (β-subunit). In this report, we show that these two genes, as well as the 77-bp inverted repeat region, are cotranscribed with the capsule synthesis genes, resulting in a large transcript that is ∼19.4 kb (based on annotation). We also show that a PG0121 recombinant protein is a nonspecific DNA binding protein with strong affinity to the hairpin structure,
in vitro
, and that transcript levels of the capsule synthesis genes are downregulated in a PG0121 deletion mutant. Furthermore, we show that this decrease in transcript levels corresponds to a decrease in the amount of polysaccharide produced. Interestingly, expression analysis of another polysaccharide synthesis locus (PG1136 to PG1143) encoding genes involved in synthesis of a surface-associated phosphorylated branched mannan (APS) indicated that this locus is also downregulated in the PG0121 mutant. Altogether our data indicate that HU protein modulates expression of surface polysaccharides in
P. gingivalis
strain W83.
Evolutionary Competitiveness of Two Natural Variants of the IncQ-Like Plasmids, pRAS3.1 and pRAS3.2
Authors: Loftie-Eaton Wesley , Rawlings Douglas E. 
Published: October 2010

ABSTRACT

Plasmids pRAS3.1 and pRAS3.2 are natural variants of the IncQ-2 plasmid family, that except for two differences, have identical plasmid backbones. Plasmid pRAS3.1 has four 22-bp iterons in its
oriV
region, while pRAS3.2 has only three 6-bp repeats and pRAS3.1 has five 6-bp repeats in the promoter region of the
mobB-mobA/repB
genes and pRAS3.2 has only four. In previous work, we showed that the overall effect of these differences was that when the plasmid was in an
Escherichia coli
host, the copy numbers of pRAS3.1 and pRAS3.2 were approximately 41 and 30, respectively. As pRAS3.1 and pRAS3.2 are likely to have arisen from the same ancestor, we addressed the question of whether one of the variants had an evolutionary advantage over the other. By constructing a set of identical plasmids with the number of 22-bp iterons varying from three to seven, it was found that plasmids with four or five iterons displaced plasmids with three iterons even though they had lower copy numbers. Furthermore, the metabolic load that the plasmids placed on
E. coli
host cells compared with plasmid-free cells increased with copy number from 10.9% at a copy number of 59 to 2.6% at a copy number of 15. Plasmid pRAS3.1 with four 22-bp iterons was able to displace pRAS3.2 with three iterons when both were coresident in the same host. However, the lower-copy-number pRAS3.2 placed 2.8% less of a metabolic burden on an
E. coli
host population, and therefore, pRAS3.2 has a competitive advantage over pRAS3.1 at the population level, as pRAS3.2-containing cells would be expected to outgrow pRAS3.1-containing cells.
pSymA-Dependent Mobilization of the
Sinorhizobium meliloti
pSymB Megaplasmid
Authors: Blanca-Ordóñez Helena , Oliva-García Juan J. , Pérez-Mendoza Daniel , Soto María J. , Olivares José , Sanjuán Juan , Nogales Joaquina 
Published: October 2010

ABSTRACT

Sinorhizobium meliloti
1021 carries two megaplasmids, pSymA of 1,354 kb and pSymB of 1,683 kb, which are essential in establishing symbiosis with its legume hosts and important for bacterial fitness in the rhizosphere. We have previously shown that pSymA is self-transmissible and that its conjugal functions are regulated by the transcriptional repressor RctA. Here, we show conjugal transfer of pSymB as an in
trans
mobilization event that requires the type IV secretion system encoded by pSymA. pSymB carries a functional
oriT
and an adjacent relaxase gene,
traA2
, that is also transcriptionally repressed by
rctA
. Both symbiotic megaplasmids would require the relaxase genes in
cis
with their respective
oriT
s to achieve the highest transfer efficiencies.
The
Escherichia coli
CRISPR System Protects from λ Lysogenization, Lysogens, and Prophage Induction
Authors: Edgar Rotem , Qimron Udi 
Published: October 2010

ABSTRACT
We show that phage lysogenization, lysogens, and prophage induction are all targeted by CRISPR. The results demonstrate that genomic DNA is not immune to the CRISPR system, that the CRISPR system does not require noncytoplasmic elements, and that the system protects from phages entering and exiting the lysogenic cycle.