bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of a Novel Metagenome-Derived 6-Phospho-β-Glucosidase from Black Liquor Sediment
Authors: Yang Chunyu , Niu Yu , Li Chunfang , Zhu Deyu , Wang Wei , Liu Xinqiang , Cheng Bin , Ma Cuiqing , Xu Ping 
Published: January 2013

ABSTRACT

The enzyme 6-phospho-β-glucosidase is an important member of the glycoside hydrolase family 1 (GH1). However, its catalytic mechanisms, especially the key residues determining substrate specificity and affinity, are poorly understood. A metagenome-derived gene sequence, encoding a novel 6-phospho-β-glucosidase designated Pbgl25-217, was isolated and characterized. The optimal conditions for enzymatic activity were 37ï¿½C and pH 7; Ca
2+
, Mg
2+
, and Mn
2+
stabilized the activity of Pbgl25-217, whereas Ni
2+
, Fe
2+
, Zn
2+
, Cu
2+
, and Fe
3+
inhibited its activity. The

K
m

and
V
max
of Pbgl25-217 were 4.8 mM and 1,987.0 U mg
−1
, respectively. Seven conserved residues were recognized by multiple alignments and were tested by site-directed mutagenesis for their functions in substrate recognition and catalytic reaction. The results suggest that residues S427, Lys435, and Tyr437 act as “gatekeepers” in a phosphate-binding loop and play important roles in phosphate recognition. This functional identification may provide insights into the specificity of 6-phospho-β-glycosidases in GH1 and be useful for designing further directed evolution.
Effects of Temperature and pH on Reduction of Bacteria in a Point-of-Use Drinking Water Treatment Product for Emergency Relief
Authors: Marois-Fiset Jean-Thomas , Carabin Anne , Lavoie Audrey , Dorea Caetano C. 
Published: January 2013

ABSTRACT

The effects of temperature and pH on the water treatment performance of a point-of-use (POU) coagulant/disinfectant product were evaluated. Cold temperatures (∼5ï¿½C) reduced the bactericidal efficiency of the product with regard to
Escherichia coli
and total coliform log
10
reductions.
Development of a Continuous Bioconversion System Using a Thermophilic Whole-Cell Biocatalyst
Authors: Ninh Pham Huynh , Honda Kohsuke , Yokohigashi Yukako , Okano Kenji , Omasa Takeshi , Ohtake Hisao 
Published: January 2013

ABSTRACT

The heat treatment of recombinant mesophilic cells having heterologous thermophilic enzymes results in the denaturation of indigenous mesophilic enzymes and the elimination of undesired side reactions; therefore, highly selective whole-cell catalysts comparable to purified enzymes can be readily prepared. However, the thermolysis of host cells leads to the heat-induced leakage of thermophilic enzymes, which are produced as soluble proteins, limiting the exploitation of their excellent stability in repeated and continuous reactions. In this study,
Escherichia coli
cells having the thermophilic fumarase from
Thermus thermophilus
(
Tt
FTA) were treated with glutaraldehyde to prevent the heat-induced leakage of the enzyme, and the resulting cells were used as a whole-cell catalyst in repeated and continuous reactions. Interestingly, although electron microscopic observations revealed that the cellular structure of glutaraldehyde-treated
E. coli
was not apparently changed by the heat treatment, the membrane permeability of the heated cells to relatively small molecules (up to at least 3 kDa) was significantly improved. By applying the glutaraldehyde-treated
E. coli
having
Tt
FTA to a continuous reactor equipped with a cell-separation membrane filter, the enzymatic hydration of fumarate to malate could be operated for more than 600 min with a molar conversion yield of 60% or higher.
In Situ
Determination of Clostridium Endospore Membrane Fluidity during Pressure-Assisted Thermal Processing in Combination with Nisin or Reutericyclin
Authors: Hofstetter S. , Winter R. , McMullen L. M. , Gï¿½nzle M. G. 
Published: January 2013

ABSTRACT
This study determined the membrane fluidity of clostridial endospores during treatment with heat and pressure with nisin or reutericyclin. Heating (90ï¿½C) reduced laurdan (6-dodecanoyl-2-dimethylaminonaphthalene) general polarization, corresponding to membrane fluidization. Pressure (200 MPa) stabilized membrane order. Reutericyclin and nisin exhibit divergent effects on heat- and pressure-induced spore inactivation and membrane fluidity.
Bifunctional Gene Cluster
lnqBCDEF
Mediates Bacteriocin Production and Immunity with Differential Genetic Requirements
Authors: Iwatani Shun , Horikiri Yuko , Zendo Takeshi , Nakayama Jiro , Sonomoto Kenji 
Published: January 2013

ABSTRACT

A comprehensive gene disruption of lacticin Q biosynthetic cluster
lnqQBCDEF
was carried out. The results demonstrated the necessity of the complete set of
lnqQBCDEF
for lacticin Q production, whereas immunity was flexible, with LnqEF (ABC transporter) being essential for and LnqBCD partially contributing to immunity.
Rates of Species Accumulation and Taxonomic Diversification during Phototrophic Biofilm Development Are Controlled by both Nutrient Supply and Current Velocity
Authors: Larson Chad A. , Passy Sophia I. 
Published: January 2013

ABSTRACTThe accumulation of new and taxonomically diverse species is a marked feature of community development, but the role of the environment in this process is not well understood. To address this problem, we subjected periphyton in laboratory streams to low (10-cm ï¿½ s−1), high (30-cm ï¿½ s−1), and variable (9- to 32-cm ï¿½ s−1) current velocity and low- versus high-nutrient inputs. We examined how current velocity and resource supply constrained (i) the rates of species accumulation, a measure of temporal beta-diversity, and (ii) the rates of diversification of higher taxonomic categories, defined here as the rate of higher taxon richness increase with the increase of species richness. Temporal biofilm dynamics were controlled by a strong nutrient-current interaction. Nutrients accelerated the rates of accumulation of new species, when flow velocity was not too stressful. Species were more taxonomically diverse under variable than under low-flow conditions, indicating that flow heterogeneity increased the niche diversity in the high-nutrient treatments. Conversely, the lower diversification rates under high- than under low-nutrient conditions at low velocity are explained with finer resource partitioning among species, belonging to a limited number of related genera. The overall low rates of diversification in high-current treatments suggest that the ability to withstand current stress was conserved within closely related species. Temporal heterogeneity of disturbance has been shown to promote species richness, but here we further demonstrate that it also affects two other components of biodiversity, i.e., temporal beta-diversity and diversification rate. Therefore, management efforts for preserving the inherent temporal heterogeneity of natural ecosystems will have detectable positive effects on biodiversity.
Cloning of a Novel Nicotine Oxidase Gene from Pseudomonas sp. Strain HZN6 Whose Product Nonenantioselectively Degrades Nicotine to Pseudooxynicotine
Authors: Qiu Jiguo , Ma Yun , Zhang Jing , Wen Yuezhong , Liu Weiping 
Published: January 2013

ABSTRACT

Pseudomonas
sp. strain HZN6 utilizes nicotine as its sole source of carbon, nitrogen, and energy. However, its catabolic mechanism has not been elucidated. In this study, self-formed adaptor PCR was performed to amplify the upstream sequence of the pseudooxynicotine amine oxidase gene. A 1,437-bp open reading frame (designated
nox
) was found to encode a nicotine oxidase (NOX) that shows 30% amino acid sequence identity with 6-hydroxy-l-nicotine oxidase from
Arthrobacter nicotinovorans
. The
nox
gene was cloned into a broad-host-range cloning vector and transferred into the non-nicotine-degrading bacteria
Escherichia coli
DH5α (DH-nox) and
Pseudomonas putida
KT2440 (KT-nox). The transconjugant KT-nox obtained nicotine degradation ability and yielded an equimolar amount of pseudooxynicotine, while DH-nox did not. Reverse transcription-PCR showed that the
nox
gene is expressed in both DH5α and KT2440, suggesting that additional factors required for nicotine degradation are present in a
Pseudomonas
strain(s), but not in
E. coli
. The mutant of strain HZN6 with
nox
disrupted lost the ability to degrade nicotine, but not pseudooxynicotine. These results suggested that the
nox
gene is responsible for the first step of nicotine degradation. The (
RS
)-nicotine degradation results showed that the two enantiomers were degraded at approximately the same rate, indicating that NOX does not show chiral selectivity. Site-directed mutagenesis revealed that both the conserved flavin adenine dinucleotide (FAD)-binding GXGXXG motif and His456 are essential for nicotine degradation activity.
Persistence of the 2009 Pandemic Influenza A (H1N1) Virus on N95 Respirators
Authors: Coulliette A. D. , Perry K. A. , Edwards J. R. , Noble-Wang J. A. 
Published: January 2013

ABSTRACT

In the United States, the 2009 pandemic influenza A (H1N1) virus (pH1N1) infected almost 20% of the population and caused >200,000 hospitalizations and >10,000 deaths from April 2009 to April 2010. On 24 April 2009, the CDC posted interim guidance on infection control measures in health care settings explicitly for pH1N1 and recommended using filtering face respirators (FFRs) when in close contact with a suspected- or confirmed-to-be-infected individual, particularly when performing aerosol-generating procedures. The persistence and infectivity of pH1N1 were evaluated on FFRs, specifically N95 respirators, under various conditions of absolute humidity (AH) (4.1 ï¿½ 10
5
mPa, 6.5 ï¿½ 10
5
mPa, and 14.6 ï¿½ 10
5
mPa), sample matrices (2% fetal bovine serum [FBS], 5 mg/ml mucin, and viral medium), and times (4, 12, 24, 48, 72, and 144 h). pH1N1 was distributed onto N95 coupons (3.8 to 4.2 cm
2
) and extracted by a vortex-centrifugation-filtration process, and the ability of the remaining virus to replicate was quantified using an enzyme-linked immunosorbent assay (ELISA) to determine the log
10
concentration of the infectious virus per coupon. Overall, pH1N1 remained infectious for 6 days, with an approximately 1-log
10
loss of virus concentrations over this time period. Time and AH both affected virus survival. We found significantly higher (
P
≤ 0.01) reductions in virus concentrations at time points beyond 24 to 72 h (−0.52-log
10
reduction) and 144 h (−0.74) at AHs of 6.5 ï¿½ 10
5
mPa (−0.53) and 14.6 ï¿½ 10
5
mPa (−0.47). This research supports discarding respirators after close contact with a person with suspected or confirmed influenza infection due to the virus's demonstrated ability to persist and remain infectious.
Inactivation of Pathogens in Feces by Desiccation and Urea Treatment for Application in Urine-Diverting Dry Toilets
Authors: Magri Maria Elisa , Philippi Luiz Sï¿½rgio , Vinnerï¿½s Bjï¿½rn 
Published: January 2013

ABSTRACTEcological sanitation technologies can be effective in providing health and environmental pollution control if they can efficiently reduce the pathogenicity of microorganisms carried in fecal material to safe levels. This study evaluated the sanitizing effects of different additives for dry treatment of feces from urine-diverting dry toilets, based on inactivation ofEnterococcus faecalis,Salmonella entericaserovar Typhimurium, bacteriophages MS2 and ΦX, andAscaris suum. The additives, ash (A) and oyster shell (O) in different amounts and urea (U) to optimize the process, were compared with no additive, solely urea, and sawdust as controls (C) and were covered ([x%O:A]) or uncovered (x%O:A). The main inactivation factors found were desiccation, ammonia content, and pH.S.Typhimurium andE. faecaliswere more affected by the ammonia content. A combination of neutral to high pH and desiccation was most effective for inactivation of MS2, and desiccation was most effective for inactivation of ΦX andA. suum. The inactivation rate was modeled for all combinations studied. The most promising treatments were [150%O:A+U], 150%O:A+U, and 150%O:A. According to the models, these could inactivate, for example, 7 log10units of all bacteria and bacteriophages within 83, 125, and 183 days, respectively. The inactivation ofA. suumwas modeled, albeit the measured decay in egg viability was low.
Dual Roles of Pseudomonas aeruginosa AlgE in Secretion of the Virulence Factor Alginate and Formation of the Secretion Complex
Authors: Rehman Zahid U. , Rehm Bernd H. A. 
Published: January 2013

ABSTRACT

AlgE is a monomeric 18-stranded β-barrel protein required for secretion of the extracellular polysaccharide alginate in
Pseudomonas aeruginosa
. To assess the molecular mechanism of alginate secretion, AlgE was subjected to site-specific and FLAG epitope insertion mutagenesis. Except for β-strands 6 and 10, epitope insertions into the transmembrane β-strands abolished localization of AlgE to the outer membrane. Interestingly, an epitope insertion into β-strand 10 produced alginate and was only detectable in outer membranes isolated from cells grown on solid media. The deletion of nine C-terminal amino acid residues destabilized AlgE. Replacement of amino acids that constitute the highly electropositive pore constriction showed that individual amino acid residues have a specific function in alginate secretion. Two of the triple mutants (K47E+R353A+R459E and R74E+R362A+R459E) severely reduced alginate production. Mutual stability analysis using the
algE
deletion mutant PDO300Δ
algE
(miniCTX) showed the periplasmic alginate biosynthesis proteins AlgK and AlgX were completely destabilized, while the copy number of the inner membrane c-di-GMP receptor Alg44 was reduced. Chromosomal integration of
algE
restored AlgK, AlgX, and Alg44, providing evidence for a multiprotein complex that spans the cell envelope. Periplasmic turn 4 of AlgE was identified as an important region for maintaining the stability of the putative multiprotein complex.
Uniformity of Glycyl Bridge Lengths in the Mature Cell Walls of Fem Mutants of Methicillin-Resistant Staphylococcus aureus
Authors: Sharif Shasad , Kim Sung Joon , Labischinski Harald , Chen Jiawei , Schaefer Jacob 
Published: January 2013

ABSTRACT

Peptidoglycan (PG) composition in intact cells of methicillin-resistant
Staphylococcus aureus
(MRSA) and its isogenic Fem mutants has been characterized by measuring the glycine content of PG bridge structures by solid-state nuclear magnetic resonance (NMR). The glycine content estimated from integrated intensities (rather than peak heights) in the cell walls of whole cells was increased by approximately 30% for the FemA mutant and was reduced by 25% for the FemB mutant relative to expected values for homogeneous structures. In contrast, the expected compositions were observed in isolated cell walls of the same mutants. For FemA mutant whole cells, the increase was due to the presence of triglycyl bridge PG units (confirmed directly by mass spectrometric analysis), which constituted 10% of the total PG. These species were coalesced in some sort of a lattice or aggregate with spatial proximity to other PG bridges. This result suggests that the triglycyl-bridged PG units form a PG-like structure that is not incorporated into the mature cell wall.
Localization of FtsZ in Helicobacter pylori and Consequences for Cell Division
Authors: Specht Mara , Dempwolff Felix , Schätzle Sarah , Thomann Ralf , Waidner Barbara 
Published: January 2013

ABSTRACT

Of the various kinds of cell division, the most common mode is binary fission, the division of a cell into two morphologically identical daughter cells. However, in the case of asymmetric cell division,
Caulobacter crescentus
produces two morphologically and functionally distinct cell types. Here, we have studied cell cycle progression of the human pathogen
Helicobacter pylori
using a functional green fluorescent protein (GFP) fusion of FtsZ protein and membrane staining. In small cells, representing newly divided cells, FtsZ localizes to a single cell pole. During the cell cycle, spiral intermediates are formed until an FtsZ ring is positioned with very little precision, such that central as well as acentral rings can be observed. Daughter cells showed considerably different sizes, suggesting that
H. pylori
divides asymmetrically. Fluorescence recovery after photobleaching (FRAP) analyses demonstrate that the
H. pylori
FtsZ ring is about as dynamic as that of
Escherichia coli
but that polar assemblies show less turnover. Strikingly, our results demonstrate that
H. pylori
cell division follows a different route from that in
E. coli
and
Bacillus subtilis.
It is also different from that in
C. crescentus
, where cytokinesis regulation proteins like MipZ play a role. Therefore, this report provides the first cell-biological analysis of FtsZ dynamics in the human pathogen
H. pylori
and even in epsilonproteobacteria to our knowledge. In addition, analysis of the filament architecture of
H. pylori
and
E. coli
FtsZ filaments in the heterologous system of
Drosophila melanogaster
S2 Schneider cells revealed that both have different filamentation properties
in vivo
, suggesting a unique intrinsic characteristic of each protein.
Xenocin Export by the Flagellar Type III Pathway in Xenorhabdus nematophila
Authors: Singh Preeti , Park Dongjin , Forst Steven , Banerjee Nirupama 
Published: January 2013

ABSTRACT

The xenocin operon of
Xenorhabdus nematophila
consists of
xciA
and
ximB
genes encoding a 64-kDa xenocin and 42-kDa immunity protein to kill competing microbes in the insect larva. The catalytic domain of xenocin has RNase activity and is responsible for its cytotoxicity. Under SOS conditions, xenocin is produced with immunity protein as a complex. Here, we show that xenocin and immunity protein complex are exported through the flagellar type III system of
X. nematophila
. Secretion of xenocin complex was abolished in an
flhA
strain but not in an
fliC
strain. The xenocin operon is not linked to the flagellar operon transcriptionally. The immunity protein is produced alone from a second, constitutive promoter and is targeted to the periplasm in a flagellum-independent manner. For stable expression of xenocin, coexpression of immunity protein was necessary. To examine the role of immunity protein in xenocin export, an enzymatically inactive protein was produced by site-directed mutagenesis in the active site of the catalytic domain. Toxicity was abolished in D535A and H538A variants of xenocin, which were expressed alone without an immunity domain and secreted in the culture supernatant through flagellar export. Secretion of xenocin through the flagellar pathway has important implications in the evolutionary success of
X. nematophila
.
IntDOT Interactions with Core Sites during Integrative Recombination
Authors: Laprise Jennifer , Yoneji Sumiko , Gardner Jeffrey F. 
Published: January 2013

ABSTRACT

Integrative and conjugative elements (ICEs), formerly called conjugative transposons, have been implicated in the proliferation of antibiotic resistance genes. CTnDOT is an extensively studied ICE found in
Bacteroides
spp. In addition to carrying resistance genes to both erythromycin and tetracycline, CTnDOT carries a gene that encodes a tyrosine recombinase called IntDOT that catalyzes integration into and excision out of the bacterial host chromosome. CTnDOT integrates into one of several known
attB
sites in the bacterial chromosome that consists of a pair of inverted repeat core sites called B and B′ in
attB
. The
attDOT
site contains the core sites and D and D′. These sites flank the overlap regions where strand exchanges occur. A notable feature of all known
attB
sites is the conservation of the B core site sequence, which is also found in the D core site of
attDOT
. In this study, we used a mutational analysis to establish the importance of this conserved sequence for integration and characterize the interaction of IntDOT with individual base pairs. We identified important T-A base pairs at position −5 in the B and D core sites and position +5 in the poorly conserved B′ core site that are important for integrative recombination. Base analog studies suggest that IntDOT may make specific contacts with the A residues in the major groove at positions −5 and +5. IntDOT interaction with the A at position −5 in the B core site is required for the first strand exchange.
YfdW and YfdU Are Required for Oxalate-Induced Acid Tolerance in Escherichia coli K-12
Authors: Fontenot Elise M. , Ezelle Karen E. , Gabreski Lauren N. , Giglio Eleanor R. , McAfee John M. , Mills Alexandria C. , Qureshi Maryam N. , Salmon Kristin M. , Toyota Cory G. 
Published: January 2013

ABSTRACTEscherichia colihas several mechanisms for surviving low-pH stress. We report that oxalic acid, a small-chain organic acid (SCOA), induces a moderate acid tolerance response (ATR) in two ways. Adaptation ofE. coliK-12 at pH 5.5 with 50 mM oxalate and inclusion of 25 mM oxalate in pH 3.0 minimal challenge medium separately conferred protection, with 67% ± 7% and 87% ± 17% survival after 2 h, respectively. The combination of oxalate adaptation and oxalate supplementation in the challenge medium resulted in increased survival over adaptation or oxalate in the challenge medium alone. The enzymes YfdW, a formyl coenzyme A (CoA) transferase, and YfdU, an oxalyl-CoA decarboxylase, are required for the adaptation effect but not during challenge. Unlike other SCOAs, this oxalate ATR is not a part of the RpoS regulon but appears to be linked to the signal protein GadE. We theorize that this oxalate ATR could enhance the pathogenesis of virulentE. coliconsumed with oxalate-containing foods like spinach.
Aeromonas hydrophila Lateral Flagellar Gene Transcriptional Hierarchy
Authors: Wilhelms Markus , Gonzalez Victor , Tomás Juan M. , Merino Susana 
Published: January 2013

ABSTRACT

Aeromonas hydrophila
AH-3 lateral flagella are not assembled when bacteria grow in liquid media; however, lateral flagellar genes are transcribed. Our results indicate that
A. hydrophila
lateral flagellar genes are transcribed at three levels (class I to III genes) and share some similarities with, but have many important differences from, genes of
Vibrio parahaemolyticus
.
A. hydrophila
lateral flagellum class I gene transcription is σ
70
dependent, which is consistent with the fact that lateral flagellum is constitutively transcribed, in contrast to the characteristics of
V. parahaemolyticus.
The fact that multiple genes are included in class I highlights that lateral flagellar genes are less hierarchically transcribed than polar flagellum genes. The
A. hydrophila lafK
-
fliEJ
L
gene cluster (where the subscript L distinguishes genes for lateral flagella from those for polar flagella) is exclusively from class I and is in
V. parahaemolyticus
class I and II. Furthermore, the
A. hydrophila flgAMN
L
cluster is not transcribed from the σ
54
/LafK-dependent promoter and does not contain class II genes. Here, we propose a gene transcriptional hierarchy for the
A. hydrophila
lateral flagella.