bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Resolution Amplified Fragment Length Polymorphism Typing of Lactococcus lactis Strains Enables Identification of Genetic Markers for Subspecies-Related Phenotypes
Authors: Kütahya Oylum Erkus , Starrenburg Marjo J. C. , Rademaker Jan L. W. , Klaassen Corné H. W. , van Hylckama Vlieg Johan E. T. , Smid Eddy J. , Kleerebezem Michiel 
Published: June 2011

ABSTRACT

A high-resolution amplified fragment length polymorphism (AFLP) methodology was developed to achieve the delineation of closely related
Lactococcus lactis
strains. The differentiation depth of 24 enzyme-primer-nucleotide combinations was experimentally evaluated to maximize the number of polymorphisms. The resolution depth was confirmed by performing diversity analysis on 82
L. lactis
strains, including both closely and distantly related strains with dairy and nondairy origins. Strains clustered into two main genomic lineages of
L. lactis
subsp.
lactis
and
L. lactis
subsp.
cremoris
type-strain-like genotypes and a third novel genomic lineage rooted from the
L. lactis
subsp.
lactis
genomic lineage. Cluster differentiation was highly correlated with small-subunit rRNA homology and multilocus sequence analysis (MLSA) studies. Additionally, the selected enzyme-primer combination generated
L. lactis
subsp.
cremoris
phenotype-specific fragments irrespective of the genotype. These phenotype-specific markers allowed the differentiation of
L. lactis
subsp.
lactis
phenotype from
L. lactis
subsp.
cremoris
phenotype strains within the same
L. lactis
subsp.
cremoris
type-strain-like genomic lineage, illustrating the potential of AFLP for the generation of phenotype-linked genetic markers.
Biodiversity and Emerging Biogeography of the Neutrophilic Iron-Oxidizing Zetaproteobacteria
Authors: McAllister Sean M. , Davis Richard E. , McBeth Joyce M. , Tebo Bradley M. , Emerson David , Moyer Craig L. 
Published: June 2011

ABSTRACT

Members of the neutrophilic iron-oxidizing candidate class
Zetaproteobacteria
have predominantly been found at sites of microbially mediated iron oxidation in marine environments around the Pacific Ocean. Eighty-four full-length (>1,400-bp) and 48 partial-length
Zetaproteobacteria
small-subunit (SSU) rRNA gene sequences from five novel clone libraries, one novel
Zetaproteobacteria
isolate, and the GenBank database were analyzed to assess the biodiversity of this burgeoning class of the
Proteobacteria
and to investigate its biogeography between three major sampling regions in the Pacific Ocean: Loihi Seamount, the Southern Mariana Trough, and the Tonga Arc. Sequences were grouped into operational taxonomic units (OTUs) on the basis of a 97% minimum similarity. Of the 28 OTUs detected, 13 were found to be endemic to one of the three main sampling regions and 2 were ubiquitous throughout the Pacific Ocean. Additionally, two deeply rooted OTUs that potentially dominate communities of iron oxidizers originating in the deep subsurface were identified. Spatial autocorrelation analysis and analysis of molecular variance (AMOVA) showed that geographic distance played a significant role in the distribution of
Zetaproteobacteria
biodiversity, whereas environmental parameters, such as temperature, pH, or total Fe concentration, did not have a significant effect. These results, detected using the coarse resolution of the SSU rRNA gene, indicate that the
Zetaproteobacteria
have a strong biogeographic signal.
Advanced Multiplex PCR Assay for Differentiation of Brucella Species
Authors: Kang Sung-Il , Her Moon , Kim Jong Wan , Kim Ji-Yeon , Ko Kyung Yuk , Ha Yun-Mi , Jung Suk Chan 
Published: June 2011

ABSTRACT

Two new primer sets of a 766- and a 344-bp fragment were introduced into the conventional Bruce-ladder PCR assay. This novel multiplex PCR assay rapidly and concisely discriminates
Brucella canis
and
Brucella microti
from
Brucella suis
strains and also may differentiate all of the 10
Brucella
species.
Calicivirus Removal in a Membrane Bioreactor Wastewater Treatment Plant
Authors: Sima Laura C. , Schaeffer Julien , Le Saux Jean-Claude , Parnaudeau Sylvain , Elimelech Menachem , Le Guyader Françoise S. 
Published: June 2011

ABSTRACT

To evaluate membrane bioreactor wastewater treatment virus removal, a study was conducted in southwest France. Samples collected from plant influent, an aeration basin, membrane effluent, solid sludge, and effluent biweekly from October 2009 to June 2010 were analyzed for calicivirus (norovirus and sapovirus) by real-time reverse transcription-PCR (RT-PCR) using extraction controls to perform quantification. Adenovirus and
Escherichia coli
also were analyzed to compare removal efficiencies. In the influent, sapovirus was always present, while the norovirus concentration varied temporally, with the highest concentration being detected from February to May. All three human norovirus genogroups (GI, GII, and GIV) were detected in effluent, but GIV was never detected in effluent; GI and GII were detected in 50% of the samples but at low concentrations. In the effluent, sapovirus was identified only once. An adenovirus titer showing temporal variation in influent samples was identified only twice in effluent.
E. coli
was always below the limit of detection in the effluent. Overall, the removal of calicivirus varied from 3.3 to greater than 6.8 log units, with no difference between the two main genogroups. Our results also demonstrated that the viruses are blocked by the membrane in the treatment plant and are removed from the plant as solid sludge.
Role of Exopolysaccharides in Pseudomonas aeruginosa Biofilm Formation and Architecture
Authors: Ghafoor Aamir , Hay Iain D. , Rehm Bernd H. A. 
Published: June 2011

ABSTRACT

Pseudomonas aeruginosa
is an opportunistic human pathogen and has been established as a model organism to study bacterial biofilm formation. At least three exopolysaccharides (alginate, Psl, and Pel) contribute to the formation of biofilms in this organism. Here mutants deficient in the production of one or more of these polysaccharides were generated to investigate how these polymers interactively contribute to biofilm formation. Confocal laser scanning microscopy of biofilms formed in flow chambers showed that mutants deficient in alginate biosynthesis developed biofilms with a decreased proportion of viable cells than alginate-producing strains, indicating a role of alginate in viability of cells in biofilms. Alginate-deficient mutants showed enhanced extracellular DNA (eDNA)-containing surface structures impacting the biofilm architecture. PAO1 Δ
pslA
Δ
alg8
overproduced Pel, and eDNA showing meshwork-like structures presumably based on an interaction between both polymers were observed. The formation of characteristic mushroom-like structures required both Psl and alginate, whereas Pel appeared to play a role in biofilm cell density and/or the compactness of the biofilm. Mutants producing only alginate, i.e., mutants deficient in both Psl and Pel production, lost their ability to form biofilms. A lack of Psl enhanced the production of Pel, and the absence of Pel enhanced the production of alginate. The function of Psl in attachment was independent of alginate and Pel. A 30% decrease in Psl promoter activity in the alginate-overproducing MucA-negative mutant PDO300 suggested inverse regulation of both biosynthesis operons. Overall, this study demonstrated that the various exopolysaccharides and eDNA interactively contribute to the biofilm architecture of
P. aeruginosa
.
An Alkaline Phosphatase/Phosphodiesterase, PhoD, Induced by Salt Stress and Secreted Out of the Cells of Aphanothece halophytica, a Halotolerant Cyanobacterium
Authors: Kageyama Hakuto , Tripathi Keshawanand , Rai Ashwani K. , Cha-um Suriyan , Waditee-Sirisattha Rungaroon , Takabe Teruhiro 
Published: June 2011

ABSTRACT

Alkaline phosphatases (APases) are important enzymes in organophosphate utilization. Three prokaryotic APase gene families, PhoA, PhoX, and PhoD, are known; however, their functional characterization in cyanobacteria largely remains to be clarified. In this study, we cloned the
phoD
gene from a halotolerant cyanobacterium,
Aphanothece halophytica
(

phoD
Ap

). The deduced protein, PhoD

Ap

, contains Tat consensus motifs and a peptidase cleavage site at the N terminus. The PhoD

Ap

enzyme was activated by Ca
2+
and exhibited APase and phosphodiesterase (APDase) activities. Subcellular localization experiments revealed the secretion and processing of PhoD

Ap

in a transformed cyanobacterium. Expression of the

phoD
Ap

gene in
A. halophytica
cells was upregulated not only by phosphorus (P) starvation but also under salt stress conditions. Our results suggest that
A. halophytica
cells possess a PhoD that participates in the assimilation of P under salinity stress.
In VitroFermentation of Linear and α-1,2-Branched Dextrans by the Human Fecal Microbiota
Authors: Sarbini Shahrul R. , Kolida Sofia , Naeye Thierry , Einerhand Alexandra , Brison Yoann , Remaud-Simeon Magali , Monsan Pierre , Gibson Glenn R. , Rastall Robert A. 
Published: June 2011

ABSTRACTThe role of structure and molecular weight in fermentation selectivity in linear α-1,6 dextrans and dextrans with α-1,2 branching was investigated. Fermentation by gut bacteria was determined in anaerobic, pH-controlled fecal batch cultures after 36 h. Inulin (1%, wt/vol), which is a known prebiotic, was used as a control. Samples were obtained at 0, 10, 24, and 36 h of fermentation for bacterial enumeration by fluorescentin situhybridization and short-chain fatty acid analyses. The gas production of the substrate fermentation was investigated in non-pH-controlled, fecal batch culture tubes after 36 h. Linear and branched 1-kDa dextrans produced significant increases inBifidobacteriumpopulations. The degree of α-1,2 branching did not influence theBifidobacteriumpopulations; however, α-1,2 branching increased the dietary fiber content, implying a decrease in digestibility. Other measured bacteria were unaffected by the test substrates except for theBacteroides-Prevotellagroup, the growth levels of which were increased on inulin and 6- and 70-kDa dextrans, and theFaecalibacterium prausnitziigroup, the growth levels of which were decreased on inulin and 1-kDa dextrans. A considerable increase in short-chain fatty acid concentration was measured following the fermentation of all dextrans and inulin. Gas production rates were similar among all dextrans tested but were significantly slower than that for inulin. The linear 1-kDa dextran produced lower total gas and shorter time to attain maximal gas production compared to those of the 70-kDa dextran (branched) and inulin. These findings indicate that dextrans induce a selective effect on the gut flora, short-chain fatty acids, and gas production depending on their length.
The Transcriptional Response of Listeria monocytogenes during Adaptation to Growth on Lactate and Diacetate Includes Synergistic Changes That Increase Fermentative Acetoin Production
Authors: Stasiewicz Matthew J. , Wiedmann Martin , Bergholz Teresa M. 
Published: June 2011

ABSTRACT

The organic acids lactate and diacetate are commonly used in combination in ready-to-eat foods because they show synergistic ability to inhibit the growth of
Listeria monocytogenes
. Full-genome microarrays were used to investigate the synergistic transcriptomic responses of two
L. monocytogenes
strains, H7858 (serotype 4b) and F6854 (serotype 1/2a), to these two organic acids under conditions representing osmotic and cold stress encountered in foods. Strains were exposed to brain heart infusion (BHI) broth at 7°C with 4.65% water-phase (w.p.) NaCl at pH 6.1 with (i) 2% w.p. potassium lactate, (ii) 0.14% w.p. sodium diacetate, (iii) the combination of both at the same levels, or (iv) no organic acids as a control. RNA was extracted 8 h after exposure, during lag phase, to capture gene transcription changes during adaptation to the organic acid stress. Significant differential transcription of 1,041 genes in H7858 and 640 genes in F6854 was observed in at least one pair of the 4 different treatments. The effects of combined treatment with lactate and diacetate included (i) synergistic transcription differences for 474 and 209 genes in H7858 and F6854, respectively, (ii) differential transcription of genes encoding cation transporters and ABC transporters of metals, and (iii) altered metabolism, including induction of a nutrient-limiting stress response, reduction of menaquinone biosynthesis, and a shift from fermentative production of acetate and lactate to energetically less favorable, neutral acetoin. These data suggest that additional treatments that interfere with cellular energy generation processes could more efficiently inhibit the growth of
L. monocytogenes
.
Comparative Phenotypic and Molecular Genetic Profiling of Wild Lactococcus lactis subsp.
lactis
Strains of the L. lactis subsp.
lactis
and L. lactis subsp.
cremoris
Genotypes, Isolated from Starter-Free Cheeses Made of Raw Milk
Authors: Fernández Elena , Alegría Ángel , Delgado Susana , Martín M. Cruz , Mayo Baltasar 
Published: June 2011

ABSTRACT

Twenty
Lactococcus lactis
strains with an
L. lactis
subsp.
lactis
phenotype isolated from five traditional cheeses made of raw milk with no added starters belonging to the
L. lactis
subsp.
lactis
and
L. lactis
subsp.
cremoris
genotypes (
lactis
and
cremoris
genotypes, respectively; 10 strains each) were subjected to a series of phenotypic and genetic typing methods, with the aims of determining their phylogenetic relationships and suitability as starters. Pulsed-field gel electrophoresis (PFGE) analysis of intact genomes digested with SalI and SmaI proved that all strains were different except for three isolates of the
cremoris
genotype, which showed identical PFGE profiles. Multilocus sequence typing (MLST) analysis using internal sequences of seven loci (namely,
atpA
,
rpoA
,
pheS
,
pepN
,
bcaT
,
pepX
, and 16S rRNA gene) revealed considerable intergenotype nucleotide polymorphism, although deduced amino acid changes were scarce. Analysis of the MLST data for the present strains and others from other dairy and nondairy sources showed that all of them clustered into the
cremoris
or
lactis
genotype group, by using both independent and combined gene sequences. These two groups of strains also showed distinctive carbohydrate fermentation and enzyme activity profiles, with the strains in the
cremoris
group showing broader profiles. However, the profiles of resistance/susceptibility to 16 antibiotics were very similar, showing no atypical resistance, except for tetracycline resistance in three identical
cremoris
genotype isolates. The numbers and concentrations of volatile compounds produced in milk by the strains belonging to these two groups were clearly different, with the
cremoris
genotype strains producing higher concentrations of more branched-chain, derived compounds. Together, the present results support the idea that the
lactis
and
cremoris
genotypes of phenotypic
Lactococcus lactis
subsp.
lactis
actually represent true subspecies. Some strains of the two subspecies in this study appear to be good starter candidates.
Development of a Method for Markerless Gene Deletion in Pseudomonas putida
Authors: Graf Nadja , Altenbuchner Josef 
Published: June 2011

ABSTRACT

We developed a negative counterselection system for
Pseudomonas putida
based on uracil phosphoribosyltransferase (UPRTase) and sensitivity against the antimetabolite 5-fluorouracil (5-FU). We constructed a
P. putida
strain that is resistant to 5-FU and constructed vectors for the deletion of the surface adhesion protein gene, the flagellum biosynthesis operon, and two endonuclease genes. The genes were efficiently disrupted and left a markerless chromosomal in-frame deletion.
Analysis of Insertion Sequences in Thermophilic Cyanobacteria: Exploring the Mechanisms of Establishing, Maintaining, and Withstanding High Insertion Sequence Abundance
Authors: Nelson William C. , Wollerman Lori , Bhaya Devaki , Heidelberg John F. 
Published: June 2011

ABSTRACT

Insertion sequences (ISs) are simple mobile genetic elements capable of relocating within a genome. Through this transposition activity, they are known to create mutations which are mostly deleterious to the cell, although occasionally they are beneficial. Two closely related isolates of thermophilic
Synechococcus
species from hot spring microbial mats are known to harbor a large number of diverse ISs. To explore the mechanism of IS acquisition within natural populations and survival in the face of high IS abundance, we examined IS content and location in natural populations of
Synechococcus
by comparing metagenomic data to the genomes of fully sequenced cultured isolates. The observed IS distribution in the metagenome was equivalent to the distribution in the isolates, indicating that the cultured isolates are appropriate models for the environmental population. High sequence conservation between IS families shared between the two isolates suggests that ISs are able to move between individuals within populations and between species via lateral gene transfer, consistent with models for IS family accumulation. Most IS families show evidence of recent activity, and interruption of critical genes in some individuals was observed, demonstrating that transposition is an ongoing mutational force in the populations.
Addition of Genes for Cellobiase and Pectinolytic Activity in Escherichia coli for Fuel Ethanol Production from Pectin-Rich Lignocellulosic Biomass
Authors: Edwards Meredith C. , Henriksen Emily DeCrescenzo , Yomano Lorraine P. , Gardner Brian C. , Sharma Lekh N. , Ingram Lonnie O. , Doran Peterson Joy 
Published: June 2011

ABSTRACT

Ethanologenic
Escherichia coli
strain KO11 was sequentially engineered to contain the
Klebsiella oxytoca
cellobiose phosphotransferase genes (
casAB
) as well as a pectate lyase (
pelE
) from
Erwinia chrysanthemi
, yielding strains LY40A (
casAB
) and JP07 (
casAB
pelE
), respectively. To obtain an effective secretion of PelE, the Sec-dependent pathway
out
genes from
E. chrysanthemi
were provided on a cosmid to strain JP07 to construct strain JP07C. Finally, oligogalacturonide lyase (
ogl
) from
E. chrysanthemi
was added to produce strain JP08C.
E. coli
strains LY40A, JP07, JP07C, and JP08C possessed significant cellobiase activity in cell lysates, while only strains JP07C and JP08C demonstrated extracellular pectate lyase activity. Fermentations conducted by using a mixture of pure sugars representative of the composition of sugar beet pulp (SBP) showed that strains LY40A, JP07, JP07C, and JP08C were able to ferment cellobiose, resulting in increased ethanol production from 15 to 45% in comparison to that of KO11. Fermentations with SBP at very low fungal enzyme loads during saccharification revealed significantly higher levels of ethanol production for LY40A, JP07C, and JP08C than for KO11. JP07C ethanol yields were not considerably higher than those of LY40A; however, oligogalacturonide polymerization studies showed an increased breakdown of biomass to small-chain (degree of polymerization, ≤6) oligogalacturonides. JP08C achieved a further breakdown of polygalacturonate to monomeric sugars, resulting in a 164% increase in ethanol yields compared to those of KO11. The addition of commercial pectin methylesterase (PME) further increased JP08C ethanol production compared to that of LY40A by demethylating the pectin for enzymatic attack by pectin-degrading enzymes.
Identification and Characterization of Genes Required for Cell-to-Cell Fusion in Neurospora crassa
Authors: Fu Ci , Iyer Priyadarshini , Herkal Amrita , Abdullah Julia , Stout Angela , Free Stephen J. 
Published: June 2011

ABSTRACT

A screening procedure was used to identify cell fusion (hyphal anastomosis) mutants in the
Neurospora crassa
single gene deletion library. Mutants with alterations in 24 cell fusion genes required for cell fusion between conidial anastomosis tubes (CATs) were identified and characterized. The cell fusion genes identified included 14 genes that are likely to function in signal transduction pathways needed for cell fusion to occur (
mik-1
,
mek-1
,
mak-1
,
nrc-1
,
mek-2
,
mak-2
,
rac-1
,
pp2A
,
so/ham-1
,
ham-2
,
ham-3
,
ham-5
,
ham-9
, and
mob3
). The screening experiments also identified four transcription factors that are required for cell fusion (
adv-1
,
ada-3
,
rco-1
, and
snf5
). Three genes encoding proteins likely to be involved in the process of vesicular trafficking were also identified as needed for cell fusion during the screening (
amph-1
,
ham-10
,
pkr1
). Three of the genes identified by the screening procedure,
ham-6
,
ham-7
, and
ham-8
, encode proteins that might function in mediating the plasma membrane fusion event. Three of the putative signal transduction proteins, three of the transcription factors, the three putative vesicular trafficking proteins, and the three proteins that might function in mediating cell fusion had not been identified previously as required for cell fusion.
Genomic Characterization of Neoparamoeba pemaquidensis (Amoebozoa) and Its Kinetoplastid Endosymbiont
Authors: Tanifuji Goro , Kim Eunsoo , Onodera Naoko T. , Gibeault Rebecca , Dlutek Marlena , Cawthorn Richard J. , Fiala Ivan , Lukeš Julius , Greenwood Spencer J. , Archibald John M. 
Published: June 2011

ABSTRACT

We have performed a genomic characterization of a kinetoplastid protist living within the amoebozoan
Neoparamoeba pemaquidensis
. The genome of this “
Ichthyobodo
-related organism” was found to be unexpectedly large, with at least 11 chromosomes between 1.0 and 3.5 Mbp and a total genome size of at least 25 Mbp.
The Quorum-Sensing Molecules Farnesol/Homoserine Lactone and Dodecanol Operate via Distinct Modes of Action in Candida albicans
Authors: Hall Rebecca A. , Turner Kara J. , Chaloupka James , Cottier Fabien , De Sordi Luisa , Sanglard Dominique , Levin Lonny R. , Buck Jochen , Mühlschlegel Fritz A. 
Published: June 2011

ABSTRACT

Living as a commensal,
Candida albicans
must adapt and respond to environmental cues generated by the mammalian host and by microbes comprising the natural flora. These signals have opposing effects on
C. albicans
, with host cues promoting the yeast-to-hyphal transition and bacteria-derived quorum-sensing molecules inhibiting hyphal development. Hyphal development is regulated through modulation of the cyclic AMP (cAMP)/protein kinase A (PKA) signaling pathway, and it has been postulated that quorum-sensing molecules can affect filamentation by inhibiting the cAMP pathway. Here, we show that both farnesol and 3-oxo-C
12
-homoserine lactone, a quorum-sensing molecule secreted by
Pseudomonas aeruginosa
, block hyphal development by affecting cAMP signaling; they both directly inhibited the activity of the
Candida
adenylyl cyclase, Cyr1p. In contrast, the 12-carbon alcohol dodecanol appeared to modulate hyphal development and the cAMP signaling pathway without directly affecting the activity of Cyr1p. Instead, we show that dodecanol exerted its effects through a mechanism involving the
C. albicans
hyphal repressor, Sfl1p. Deletion of
SFL1
did not affect the response to farnesol but did interfere with the response to dodecanol. Therefore, quorum sensing in
C. albicans
is mediated via multiple mechanisms of action. Interestingly, our experiments raise the possibility that the
Burkholderia cenocepacia
diffusible signal factor, BDSF, also mediates its effects via Sfl1p, suggesting that dodecanol's mode of action, but not farnesol or 3-oxo-C
12
-homoserine lactone, may be used by other quorum-sensing molecules.