bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection for Cu-Tolerant Bacterial Communities with Altered Composition, but Unaltered Richness, via Long-Term Cu Exposure
Authors: Berg Jeanette , Brandt Kristian K. , Al-Soud Waleed A. , Holm Peter E. , Hansen Lars H. , Sørensen Søren J. , Nybroe Ole 
Published: August 2012

ABSTRACT

Toxic metal pollution affects the composition and metal tolerance of soil bacterial communities. However, there is virtually no knowledge concerning the responses of members of specific bacterial taxa (e.g., phyla or classes) to metal toxicity, and contradictory results have been obtained regarding the impact of metals on operational taxonomic unit (OTU) richness. We used tag-coded pyrosequencing of the 16S rRNA gene to elucidate the impacts of copper (Cu) on bacterial community composition and diversity within a well-described Cu gradient (20 to 3,537 μg g
−1
) stemming from industrial contamination with CuSO
4
more than 85 years ago. DNA sequence information was linked to analysis of pollution-induced community tolerance (PICT) to Cu, as determined by the [
3
H]leucine incorporation technique, and to chemical characterization of the soil. PICT was significantly correlated to bioavailable Cu, as determined by the results seen with a Cu-specific bioluminescent biosensor strain, demonstrating a specific community response to Cu. The relative abundances of members of several phyla or candidate phyla, including the
Proteobacteria
,
Bacteroidetes
,
Verrumicrobia
,
Chloroflexi
,
WS3
, and
Planctomycetes
, decreased with increasing bioavailable Cu, while members of the dominant phylum, the
Actinobacteria
, showed no response and members of the
Acidobacteria
showed a marked increase in abundance. Interestingly, changes in the relative abundances of classes frequently deviated from the responses of the phyla to which they belong. Despite the apparent Cu impacts on Cu resistance and community structure, bioavailable Cu levels did not show any correlation to bacterial OTU richness (97% similarity level). Our report highlights several bacterial taxa responding to Cu and thereby provides new guidelines for future studies aiming to explore the bacterial domain for members of metal-responding taxa.
Deletion of the Aspergillus flavus Orthologue of
A. nidulans fluG
Reduces Conidiation and Promotes Production of Sclerotia but Does Not Abolish Aflatoxin Biosynthesis
Authors: Chang Perng-Kuang , Scharfenstein Leslie L. , Mack Brian , Ehrlich Kenneth C. 
Published: August 2012

ABSTRACT

The
fluG
gene is a member of a family of genes required for conidiation and sterigmatocystin production in
Aspergillus nidulans
. We examined the role of the
Aspergillus flavus fluG
orthologue in asexual development and aflatoxin biosynthesis. Deletion of
fluG
in
A. flavus
yielded strains with an approximately 3-fold reduction in conidiation but a 30-fold increase in sclerotial formation when grown on potato dextrose agar in the dark. The concurrent developmental changes suggest that
A. flavus
FluG exerts opposite effects on a mutual signaling pathway for both processes. The altered conidial development was in part attributable to delayed expression of
brlA
, a gene controlling conidiophore formation. Unlike the loss of sterigmatocystin production by
A. nidulans fluG
deletion strains, aflatoxin biosynthesis was not affected by the
fluG
deletion in
A. flavus
. In
A. nidulans
, FluG was recently found to be involved in the formation of dehydroaustinol, a component of a diffusible signal of conidiation. Coculturing experiments did not show a similar diffusible meroterpenoid secondary metabolite produced by
A. flavus
. These results suggest that the function of
fluG
and the signaling pathways related to conidiation are different in the two related aspergilli.
Specific Fusion of β-1,4-Endoglucanase and β-1,4-Glucosidase Enhances Cellulolytic Activity and Helps in Channeling of Intermediates
Authors: Adlakha Nidhi , Sawant Sneha , Anil Annamma , Lali Arvind , Yazdani Syed Shams 
Published: August 2012

ABSTRACT

Identification and design of new cellulolytic enzymes with higher catalytic efficiency are a key factor in reducing the production cost of lignocellulosic bioalcohol. We report here identification of a novel β-glucosidase (Gluc1C) from
Paenibacillus
sp. strain MTCC 5639 and construction of bifunctional chimeric proteins based on Gluc1C and Endo5A, a β-1,4-endoglucanase isolated from MTCC 5639 earlier. The 448-amino-acid-long Gluc1C contained a GH superfamily 1 domain and hydrolyzed cellodextrin up to a five-sugar chain length, with highest efficiency toward cellobiose. Addition of Gluc1C improved the ability of Endo5A to release the reducing sugars from carboxymethyl cellulose. We therefore constructed six bifunctional chimeric proteins based on Endo5A and Gluc1C varying in the positions and sizes of linkers. One of the constructs, EG5, consisting of Endo5A-(G
4
S)
3
-Gluc1C, demonstrated 3.2- and 2-fold higher molar specific activities for β-glucosidase and endoglucanase, respectively, than Gluc1C and Endo5A alone. EG5 also showed 2-fold higher catalytic efficiency than individual recombinant enzymes. The thermal denaturation monitored by circular dichroism (CD) spectroscopy demonstrated that the fusion of Gluc1C with Endo5A resulted in increased thermostability of both domains by 5°C and 9°C, respectively. Comparative hydrolysis experiments done on alkali-treated rice straw and CMC indicated 2-fold higher release of product by EG5 than that by the physical mixture of Endo5A and Gluc1C, providing a rationale for channeling of intermediates. Addition of EG5 to a commercial enzyme preparation significantly enhanced release of reducing sugars from pretreated biomass, indicating its commercial applicability.
Recovery of Phenotypes Obtained by Adaptive Evolution through Inverse Metabolic Engineering
Authors: Hong Kuk-Ki , Nielsen Jens 
Published: August 2012

ABSTRACT

In a previous study, system level analysis of adaptively evolved yeast mutants showing improved galactose utilization revealed relevant mutations. The governing mutations were suggested to be in the Ras/PKA signaling pathway and ergosterol metabolism. Here, site-directed mutants having one of the mutations
RAS2

Lys77

,
RAS2

Tyr112

, and
ERG5

Pro370

were constructed and evaluated. The mutants were also combined with overexpression of
PGM2
, earlier proved as a beneficial target for galactose utilization. The constructed strains were analyzed for their gross phenotype, transcriptome and targeted metabolites, and the results were compared to those obtained from reference strains and the evolved strains. The
RAS2

Lys77

mutation resulted in the highest specific galactose uptake rate among all of the strains with an increased maximum specific growth rate on galactose. The
RAS2

Tyr112

mutation also improved the specific galactose uptake rate and also resulted in many transcriptional changes, including ergosterol metabolism. The
ERG5

Pro370

mutation only showed a small improvement, but when it was combined with
PGM2
overexpression, the phenotype was almost the same as that of the evolved mutants. Combination of the
RAS2
mutations with
PGM2
overexpression also led to a complete recovery of the adaptive phenotype in galactose utilization. Recovery of the gross phenotype by the reconstructed mutants was achieved with much fewer changes in the genome and transcriptome than for the evolved mutants. Our study demonstrates how the identification of specific mutations by systems biology can direct new metabolic engineering strategies for improving galactose utilization by yeast.
Depletion of Cryptosporidium parvum Oocysts from Contaminated Sewage by Using Freshwater Benthic Pearl Clams (Hyriopsis schlegeli)
Authors: Izumi Toshihiko , Yagita Kenji , Izumiyama Shinji , Endo Takuro , Itoh Yasoo 
Published: August 2012

ABSTRACT

The freshwater benthic pearl clam,
Hyriopsis schlegeli
, was experimentally exposed to
Cryptosporidium parvum
oocysts, and it was verified that the oocysts were eliminated predominantly via the fecal route, retaining their ability to infect cultured cells (HCT-8). The total fecal oocyst elimination rate was more than 90% within 5 days after exposure to the oocysts.
H. schlegeli
was able to survive in the final settling pond of a sewage plant for long periods, as confirmed by its pearl production. In the light of these findings, the clam was placed in the final settling pond in a trial to test its long-term efficacy in depleting oocysts contaminating the pond water. The number of clams placed was set to ensure a theoretical oocyst removal rate of around 50%, and the turbidity and the density of feed microbes in the overflow trough water of the pond were about 35% and 40 to 60% lower, respectively, than in the control water throughout the year. It was found that the clam feces containing oocysts were sufficiently heavy for them to settle to the bottom of the pond, despite the upward water flow. From these results, we concluded that efficient depletion of oocysts in the sewage water of small or midscale sewage treatment plants can be achieved by appropriate placement of
H. schlegeli
clams.
Terrestrial Runoff Controls the Bacterial Community Composition of Biofilms along a Water Quality Gradient in the Great Barrier Reef
Authors: Witt Verena , Wild Christian , Uthicke Sven 
Published: August 2012

ABSTRACT

16S rRNA gene molecular analysis elucidated the spatiotemporal distribution of bacterial biofilm communities along a water quality gradient. Multivariate statistics indicated that terrestrial runoff, in particular dissolved organic carbon and chlorophyll
a
concentrations, induced shifts of specific bacterial communities between locations and seasons, suggesting microbial biofilms could be suitable bioindicators for water quality.
Substrate Specificity of Thiamine Pyrophosphate-Dependent 2-Oxo-Acid Decarboxylases in Saccharomyces cerevisiae
Authors: Romagnoli Gabriele , Luttik Marijke A. H. , Kötter Peter , Pronk Jack T. , Daran Jean-Marc 
Published: August 2012

ABSTRACTFusel alcohols are precursors and contributors to flavor and aroma compounds in fermented beverages, and some are under investigation as biofuels. The decarboxylation of 2-oxo acids is a key step in the Ehrlich pathway for fusel alcohol production. InSaccharomyces cerevisiae, five genes share sequence similarity with genes encoding thiamine pyrophosphate-dependent 2-oxo-acid decarboxylases (2ODCs).PDC1,PDC5, andPDC6encode differentially regulated pyruvate decarboxylase isoenzymes;ARO10encodes a 2-oxo-acid decarboxylase with broad substrate specificity, andTHI3has not yet been shown to encode an active decarboxylase. Despite the importance of fusel alcohol production inS. cerevisiae, the substrate specificities of these five 2ODCs have not been systematically compared. When the five 2ODCs were individually overexpressed in apdc1Δpdc5Δpdc6Δaro10Δthi3Δ strain, only Pdc1, Pdc5, and Pdc6 catalyzed the decarboxylation of the linear-chain 2-oxo acids pyruvate, 2-oxo-butanoate, and 2-oxo-pentanoate in cell extracts. The presence of a Pdc isoenzyme was also required for the production ofn-propanol andn-butanol in cultures grown on threonine and norvaline, respectively, as nitrogen sources. These results demonstrate the importance of pyruvate decarboxylases in the natural production ofn-propanol andn-butanol byS. cerevisiae. No decarboxylation activity was found for Thi3 with any of the substrates tested. Only Aro10 and Pdc5 catalyzed the decarboxylation of the aromatic substrate phenylpyruvate, with Aro10 showing superior kinetic properties. Aro10, Pdc1, Pdc5, and Pdc6 exhibited activity with all branched-chain and sulfur-containing 2-oxo acids tested but with markedly different decarboxylation kinetics. The high affinity of Aro10 identified it as a key contributor to the production of branched-chain and sulfur-containing fusel alcohols.
Genetic Identification of a High-Affinity Ni Transporter and the Transcriptional Response to Ni Deprivation in Synechococcus sp. Strain WH8102
Authors: Dupont C. L. , Johnson D. A. , Phillippy K. , Paulsen I. T. , Brahamsha B. , Palenik B. 
Published: August 2012

ABSTRACTOne biological need for Ni in marine cyanobacteria stems from the utilization of the Ni metalloenzyme urease for the assimilation of urea as a nitrogen source. In many of the same cyanobacteria, includingSynechococcussp. strain WH8102, an additional and obligate nutrient requirement for Ni results from usage of a Ni superoxide dismutase (Ni-SOD), which is encoded bysodN. To better understand the effects of Ni deprivation on WH8102, parallel microarray-based analysis of gene expression and gene knockout experiments were conducted. The global transcriptional response to Ni deprivation depends upon the nitrogen source provided for growth; fewer than 1% of differentially expressed genes for Ni deprivation on ammonium or urea were concordantly expressed. Surprisingly, genes for putative Ni transporters, including one colocalized on the genome withsodN,sodT, were not induced despite an increase in Ni transport. Knockouts of the putative Ni transporter genesodTappeared to be lethal in WH8102, so the genes forsodTandsodNin WH8102 were interrupted with the gene for Fe-SOD,sodB, and its promoter fromSynechococcussp. strain WH7803. ThesodT::sodBexconjugants were unable to grow at low Ni concentrations, confirming that SodT is a Ni transporter. ThesodN::sodBexconjugants displayed higher growth rates at low Ni concentrations than did the wild type, presumably due to a relaxed competition between urease and Ni-SOD for Ni. BothsodT::sodBandsodN::sodBlines exhibited an impaired ability to grow at low Fe concentrations. We propose a posttranslational allosteric SodT regulation involving the binding of Ni to a histidine-rich intracellular protein loop.
Stable Carbon Isotope Fractionation by Methylotrophic Methanogenic Archaea
Authors: Penger Jörn , Conrad Ralf , Blaser Martin 
Published: August 2012

ABSTRACT

In natural environments methane is usually produced by aceticlastic and hydrogenotrophic methanogenic archaea. However, some methanogens can use C
1
compounds such as methanol as the substrate. To determine the contributions of individual substrates to methane production, the stable-isotope values of the substrates and the released methane are often used. Additional information can be obtained by using selective inhibitors (e.g., methyl fluoride, a selective inhibitor of acetoclastic methanogenesis). We studied stable carbon isotope fractionation during the conversion of methanol to methane in
Methanosarcina acetivorans
,
Methanosarcina barkeri
, and
Methanolobus zinderi
and generally found large fractionation factors (−83‰ to −72‰). We further tested whether methyl fluoride impairs methylotrophic methanogenesis. Our experiments showed that even though a slight inhibition occurred, the carbon isotope fractionation was not affected. Therefore, the production of isotopically light methane observed in the presence of methyl fluoride may be due to the strong fractionation by methylotrophic methanogens and not only by hydrogenotrophic methanogens as previously assumed.
Differences in the Fecal Concentrations and Genetic Diversities of Campylobacter jejuni Populations among Individual Cows in Two Dairy Herds
Authors: Rapp Delphine , Ross Colleen M. , Pleydell Eve J. , Muirhead Richard W. 
Published: August 2012

ABSTRACT

Dairy cows have been identified as common carriers of
Campylobacter jejuni
, which causes many of the human gastroenteritis cases reported worldwide. To design on-farm management practices that control the human infection sourced from dairy cows, the first step is to acquire an understanding of the excretion patterns of the cow reservoir. We monitored the same 35 cows from two dairy farms for
C. jejuni
excretion fortnightly for up to 12 months. The objective was to examine the concentration of
C. jejuni
and assess the genetic relationship of the
C. jejuni
populations excreted by individual cows. Significant differences (
P
< 0.01) in
C. jejuni
fecal concentration were observed among the 35 cows, with median concentrations that varied by up to 3.6 log
10
· g
−1
feces. A total of 36 different genotypes were identified from the 514 positive samples by using enterobacterial repetitive intergenic consensus (ERIC)-PCR. Although 22 of these genotypes were excreted by more than one cow, the analysis of frequencies and distribution of the genotypes by model-based statistics revealed a high degree of individuality in the
C. jejuni
population in each cow. The observed variation in the frequency of excretion of a genotype among cows and the analysis by multilocus sequence typing (MLST) of these genotypes suggest that excretion of
C. jejuni
in high numbers is due to a successful adaptation of a particular genotype to a particular cow's gut environment, but that animal-related factors render some individual cows resistant to colonization by particular genotypes. The reasons for differences in
C. jejuni
colonization of animals warrant further investigation.
Virioplankton Community Structure in Tunisian Solar Salterns
Authors: Boujelben Ines , Yarza Pablo , Almansa Cristina , Villamor Judith , Maalej Sami , Antón Josefa , Santos Fernando 
Published: August 2012

ABSTRACT

The microbial community inhabiting Sfax solar salterns on the east coast of Tunisia has been studied by means of different molecular and culture-dependent tools that have unveiled the presence of novel microbial groups as well as a community structure different from that of other coastal hypersaline environments. We have focused on the study of the viral assemblages of these salterns and their changes along the salinity gradient and over time. Viruses from three ponds (C4, M1, and TS) encompassing salinities from moderately hypersaline to saturated (around 14, 19, and 35%, respectively) were sampled in May and October 2009 and analyzed by transmission electron microscopy (TEM) and pulsed-field gel electrophoresis (PFGE). Additionally, for all three October samples and the May TS sample, viral metagenomic DNA was cloned in fosmids, end sequenced, and analyzed. Viral concentration, as well as virus-to-cell ratios, increased along the salinity gradient, with around 10
10
virus-like particles (VLPs)/ml in close-to-saturation ponds, which represents the highest viral concentration reported so far for aquatic systems. Four distinct morphologies could be observed with TEM (spherical, tailed, spindled, and filamentous) but with various proportions in the different samples. Metagenomic analyses indicated that every pond harbored a distinct viral assemblage whose G+C content could be roughly correlated with that of the active part of the microbial community that may have constituted the putative hosts. As previously reported for hypersaline metaviromes, most sequences did not have matches in the databases, although some were conserved among the Sfax metaviromes. BLASTx, BLASTp, and dinucleotide frequency analyses indicated that (i) factors additional to salinity could be structuring viral communities and (ii) every metavirome had unique gene contents and dinucleotide frequencies. Comparison with hypersaline metaviromes available in the databases indicated that the viral assemblages present in close-to-saturation environments located thousands of kilometers apart presented some common traits among them in spite of their differences regarding the putative hosts. A small core metavirome for close-to-saturation systems was found that contained 7 sequences of around 100 nucleotides (nt) whose function was not hinted at by
in silico
search results, although it most likely represents properties essential for hyperhalophilic viruses.
Effect of Grape Seed Extract on Human Norovirus GII.4 and Murine Norovirus 1 in Viral Suspensions, on Stainless Steel Discs, and in Lettuce Wash Water
Authors: Li Dan , Baert Leen , Zhang Dongsheng , Xia Ming , Zhong Weiming , Van Coillie Els , Jiang Xi , Uyttendaele Mieke 
Published: August 2012

ABSTRACT
The anti-norovirus (anti-NoV) effect of grape seed extract (GSE) was examined by plaque assay for murine norovirus 1 (MNV-1), cell-binding reverse transcription-PCR for human NoV GII.4, and saliva-binding enzyme-linked immunosorbent assay for human NoV GII.4 P particles, with or without the presence of interfering substances (dried milk and lettuce extract). GSE at 0.2 and 2 mg/ml was shown to reduce the infectivity of MNV-1 (>3-log PFU/ml) and the specific binding ability of NoV GII.4 to Caco-2 cells (>1-log genomic copies/ml), as well as of its P particles to salivary human histo-blood group antigen receptors (optical density at 450 nm of >0.8). These effects were decreased as increasing concentrations of dried milk (0.02 and 0.2%) or lettuce extract were added. Under an electron microscope, human NoV GII.4 virus-like particles showed inflation and deformation after treatment with GSE. Under conditions that simulated applications in the food industry, the anti-NoV effect of GSE using MNV-1 as a target organism was shown to be limited in surface disinfection (<1-log PFU/ml, analyzed in accordance with EN 13697:2001). However, a 1.5- to 2-log PFU/ml reduction in MNV-1 infectivity was noted when 2 mg of GSE/ml was used to sanitize water in the washing bath of fresh-cut lettuce, and this occurred regardless of the chemical oxygen demand (0 to 1,500 mg/ml) of the processing water.
The Tsetse Fly Obligate Mutualist Wigglesworthia morsitans Alters Gene Expression and Population Density via Exogenous Nutrient Provisioning
Authors: Snyder Anna K. , McLain Colin , Rio Rita V. M. 
Published: August 2012

ABSTRACT

The obligate mutualist
Wigglesworthia morsitans
provisions nutrients to tsetse flies. The symbiont's response to thiamine (B
1
) supplementation of blood meals, specifically towards the regulation of thiamine biosynthesis and population density, is described. Despite an ancient symbiosis and associated genome tailoring,
Wigglesworthia
responds to nutrient availability, potentially accommodating a decreased need.
Coselection of Cadmium and Benzalkonium Chloride Resistance in Conjugative Transfers from Nonpathogenic Listeria spp. to Other Listeriae
Authors: Katharios-Lanwermeyer S. , Rakic-Martinez M. , Elhanafi D. , Ratani S. , Tiedje J. M. , Kathariou S. 
Published: August 2012

ABSTRACT

Resistance to the quaternary ammonium disinfectant benzalkonium chloride (BC) may be an important contributor to the ability of
Listeria
spp. to persist in the processing plant environment. Although a plasmid-borne disinfectant resistance cassette (
bcrABC
) has been identified in
Listeria monocytogenes
, horizontal transfer of these genes has not been characterized. Nonpathogenic
Listeria
spp. such as
L. innocua
and
L. welshimeri
are more common than
L. monocytogenes
in food processing environments and may contribute to the dissemination of disinfectant resistance genes in listeriae, including
L. monocytogenes
. In this study, we investigated conjugative transfer of resistance to BC and to cadmium from nonpathogenic
Listeria
spp. to other nonpathogenic listeriae, as well as to
L. monocytogenes
. BC-resistant
L. welshimeri
and
L. innocua
harboring
bcrABC
, along with the cadmium resistance determinant
cadA2
, were able to transfer resistance to other nonpathogenic listeriae as well as to
L. monocytogenes
of diverse serotypes, including strains from the 2011 cantaloupe outbreak. Transfer among nonpathogenic
Listeria
spp. was noticeably higher at 25°C than at 37°C, whereas acquisition of resistance by
L. monocytogenes
was equally efficient at 25 and 37°C. When the nonpathogenic donors were resistant to both BC and cadmium, acquisition of cadmium resistance was an effective surrogate for transfer of resistance to BC, suggesting coselection between these resistance attributes. The results suggest that nonpathogenic
Listeria
spp. may behave as reservoirs for disinfectant and heavy metal resistance genes for other listeriae, including the pathogenic species
L. monocytogenes
.