bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complex Phenotypic and Genotypic Responses of
Listeria monocytogenes
Strains Exposed to the Class IIa Bacteriocin Sakacin P
Authors: Tessema Girum Tadesse , Møretrø Trond , Kohler Achim , Axelsson Lars , Naterstad Kristine 
Published: September 2009

ABSTRACT

Sakacin P is a class IIa bacteriocin that is active against the food-borne pathogen
Listeria monocytogenes
, and use of this compound as a biopreservative in foods has been suggested. In the present study, we characterized 30 spontaneous sakacin P-resistant mutants of
L. monocytogenes
obtained after single exposure to sakacin P. The frequency of development of sakacin P resistance for all strains was in the range from 10
−8
to 10
−9
. Using the 50% inhibitory concentration (IC
50
) of sakacin P, the strains could be grouped into strains with high levels of resistance (IC
50
, ≥10
4
ng ml
−1
) and strains with low levels of resistance (IC
50
, <10
4
ng ml
−1
). Resistant strains belonging to the same IC
50
group also had similar physiological and genetic characteristics. Generally, the resistant strains showed substantial variations in many parameters, such as differences in the stability of the acquired resistance to sakacin P, growth fitness, food-related stress tolerance, and biofilm-forming ability. Fourier transform infrared spectroscopy revealed differences between wild-type and resistant strains in polysaccharide, fatty acid, and, protein regions. A mannose-specific phosphotransferase (PTS) operon has been described for class IIa bacteriocin resistance, and the sakacin P-resistant strains displayed both up- and downregulation of the expression of the
mptA
gene encoding the PTS system. This is the first comprehensive study of the diversity of a large number of spontaneous resistant mutants obtained after one exposure to a class IIa bacteriocin, particularly to sakacin P. The great diversity among the resistant strains exposed to the same stress conditions suggests that there are different resistance mechanisms.
Identification of
Bacillus anthracis
by Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry and Artificial Neural Networks
Authors: Lasch Peter , Beyer Wolfgang , Nattermann Herbert , Stämmler Maren , Siegbrecht Enrico , Grunow Roland , Naumann Dieter 
Published: September 2009

ABSTRACT

This report demonstrates the applicability of a combination of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) and chemometrics for rapid and reliable identification of vegetative cells of the causative agent of anthrax,
Bacillus anthracis. Bacillus
cultures were prepared under standardized conditions and inactivated according to a recently developed MS-compatible inactivation protocol for highly pathogenic microorganisms. MALDI-TOF MS was then employed to collect spectra from the microbial samples and to build up a database of bacterial reference spectra. This database comprised mass peak profiles of 374 strains from
Bacillus
and related genera, among them 102 strains of
B. anthracis
and 121 strains of
B. cereus
. The information contained in the database was investigated by means of visual inspection of gel view representations, univariate
t
tests for biomarker identification, unsupervised hierarchical clustering, and artificial neural networks (ANNs). Analysis of gel views and independent
t
tests suggested
B. anthracis
- and
B. cereus
group-specific signals. For example, mass spectra of
B. anthracis
exhibited discriminating biomarkers at 4,606, 5,413, and 6,679 Da. A systematic search in proteomic databases allowed tentative assignment of some of the biomarkers to ribosomal protein or small acid-soluble proteins. Multivariate pattern analysis by unsupervised hierarchical cluster analysis further revealed a subproteome-based taxonomy of the genus
Bacillus
. Superior classification accuracy was achieved when supervised ANNs were employed. For the identification of
B. anthracis
, independent validation of optimized ANN models yielded a diagnostic sensitivity of 100% and a specificity of 100%.
Comparison of Point-of-Use Technologies for Emergency Disinfection of Sewage-Contaminated Drinking Water
Authors: McLennan S. Devin , Peterson Lauren A. , Rose Joan B. 
Published: September 2009

ABSTRACT

Four point-of-use disinfection technologies for treating sewage-contaminated well water were compared. Three systems, based on flocculant-disinfectant packets and
N
-halamine chlorine and bromine contact disinfectants, provided a range of 4.0 to >6.6 log
10
reductions (LR) of naturally occurring fecal indicator and heterotrophic bacteria and a range of 0.9 to >1.9 LR of coliphage.
Development of a Log-Quadratic Model To Describe Microbial Inactivation, Illustrated by Thermal Inactivation of
Clostridium botulinum
Authors: Stone G. , Chapman B. , Lovell D. 
Published: September 2009

ABSTRACT

In the commercial food industry, demonstration of microbiological safety and thermal process equivalence often involves a mathematical framework that assumes log-linear inactivation kinetics and invokes concepts of decimal reduction time (

D
T

),
z
values, and accumulated lethality. However, many microbes, particularly spores, exhibit inactivation kinetics that are not log linear. This has led to alternative modeling approaches, such as the biphasic and Weibull models, that relax strong log-linear assumptions. Using a statistical framework, we developed a novel log-quadratic model, which approximates the biphasic and Weibull models and provides additional physiological interpretability. As a statistical linear model, the log-quadratic model is relatively simple to fit and straightforwardly provides confidence intervals for its fitted values. It allows a

D
T

-like value to be derived, even from data that exhibit obvious “tailing.” We also showed how existing models of non-log-linear microbial inactivation, such as the Weibull model, can fit into a statistical linear model framework that dramatically simplifies their solution. We applied the log-quadratic model to thermal inactivation data for the spore-forming bacterium
Clostridium botulinum
and evaluated its merits compared with those of popular previously described approaches. The log-quadratic model was used as the basis of a secondary model that can capture the dependence of microbial inactivation kinetics on temperature. This model, in turn, was linked to models of spore inactivation of Sapru et al. and Rodriguez et al. that posit different physiological states for spores within a population. We believe that the log-quadratic model provides a useful framework in which to test vitalistic and mechanistic hypotheses of inactivation by thermal and other processes.
Identification and Classification ofbclGenes and Proteins ofBacillus cereusGroup Organisms and Their Application inBacillus anthracisDetection and Fingerprinting
Authors: Leski Tomasz A. , Caswell Clayton C. , Pawlowski Marcin , Klinke David J. , Bujnicki Janusz M. , Hart Sean J. , Lukomski Slawomir 
Published: September 2009

ABSTRACTTheBacillus cereusgroup includes three closely related species,B. anthracis,B. cereus, andB. thuringiensis, which form a highly homogeneous subdivision of the genusBacillus. One of these species,B. anthracis, has been identified as one of the most probable bacterial biowarfare agents. Here, we evaluate the sequence and length polymorphisms of theBacilluscollagen-like proteinbclgenes as a basis forB. anthracisdetection and fingerprinting. Five genes, designatedbclAtobclE, are present inB. anthracisstrains. Examination ofbclABCDEsequences identified polymorphisms inbclBalleles of theB. cereusgroup organisms. These sequence polymorphisms allowed specific detection ofB. anthracisstrains by PCR using both genomic DNA and purifiedBacillusspores in reactions. By exploiting the length variation of thebclalleles it was demonstrated that the combinedbclABCDEPCR products generate markedly different fingerprints for theB. anthracisAmes and Sterne strains. Moreover, we predict thatbclABCDElength polymorphism creates unique signatures forB. anthracisstrains, which facilitates identification of strains with specificity and confidence. Thus, we present a new diagnostic concept forB. anthracisdetection and fingerprinting, which can be used alone or in combination with previously established typing platforms.
Novel GH10 Xylanase, with a Fibronectin Type 3 Domain, from
Cellulosimicrobium
sp. Strain HY-13, a Bacterium in the Gut of
Eisenia fetida
Authors: Kim Do Young , Han Mi Kyoung , Park Doo-Sang , Lee Jong Suk , Oh Hyun-Woo , Shin Dong-Ha , Jeong Tae-Sook , Kim Sung Uk , Bae Kyung Sook , Son Kwang-Hee , Park Ho-Yong 
Published: September 2009

ABSTRACT

The gene encoding a novel modular xylanase from
Cellulosimicrobium
sp. strain HY-13 was identified and expressed in
Escherichia coli
, and its truncated gene product was characterized. The enzyme consisted of three distinct functional domains, an N-terminal catalytic GH10 domain, a fibronectin type 3 domain, and C-terminal carbohydrate-binding module 2.
Establishing Molecular Tools for Genetic Manipulation of the Pleuromutilin-Producing FungusClitopilus passeckerianus
Authors: Kilaru Sreedhar , Collins Catherine M. , Hartley Amanda J. , Bailey Andy M. , Foster Gary D. 
Published: September 2009

ABSTRACTWe describe efficient polyethylene glycol (PEG)-mediated andAgrobacterium-mediated transformation systems for a pharmaceutically important basidiomycete fungus,Clitopilus passeckerianus, which produces pleuromutilin, a diterpene antibiotic. Three dominant selectable marker systems based on hygromycin, phleomycin, and carboxin selection were used to study the feasibility of PEG-mediated transformation ofC. passeckerianus. The PEG-mediated transformation ofC. passeckerianusprotoplasts was successful and generated hygromycin-resistant transformants more efficiently than either phleomycin or carboxin resistance.Agrobacterium-mediated transformation with plasmid pBGgHg containinghphgene under the control of theAgaricus bisporus gpdIIpromoter led to hygromycin-resistant colonies and was successful when homogenized mycelium and fruiting body gill tissue were used as starting material. Southern blot analysis of transformants revealed the apparently random integration of the transforming DNA to be predominantly multiple copies for the PEG-mediated system and a single copy for theAgrobacterium-mediated system within the genome.C. passeckerianusactin and tubulin promoters were amplified from genomic DNA and proved successful in driving green fluorescent protein and DsRed expression inC. passeckerianus, but only when constructs contained a 5′ intron, demonstrating that the presence of an intron is prerequisite for efficient transgene expression. The feasibility of RNA interference-mediated gene silencing was investigated usinggfpas a target gene easily scored inC. passeckerianus. Upon transformation ofgfpantisense constructs into a highly fluorescent strain, transformants were recovered that exhibited either reduced or undetectable fluorescence. This was confirmed by Northern blotting showing depletion of the target mRNA levels. This demonstrated that gene silencing is a suitable tool for modulating gene expression inC. passeckerianus. The molecular tools developed in this study should facilitate studies aimed at gene isolation or characterization in this pharmaceutically important species.
Bacteria
,
Archaea
, and
Crenarchaeota
in the Epilimnion and Hypolimnion of a Deep Holo-Oligomictic Lake
Authors: Callieri Cristiana , Corno Gianluca , Caravati Emanuele , Rasconi Serena , Contesini Mario , Bertoni Roberto 
Published: September 2009

ABSTRACT

In a deep, subalpine holo-oligomictic lake, the relative abundance of
Archaea
and
Crenarchaeota
, but not that of
Bacteria
, increases significantly with depth and varies seasonally. Cell-specific prokaryotic productivity is homogeneous along the water column. The concept of active
Archaea
observed in the deep ocean can therefore be extended to a deep oxic lake.
Molecular Identification and Hidden Diversity of Novel
Daphnia
Parasites from European Lakes
Authors: Wolinska Justyna , Giessler Sabine , Koerner Henrike 
Published: September 2009

ABSTRACT

Parasites play important roles in local population dynamics and genetic structure. However, due to insufficient diagnostic tools, detailed host-parasite interactions may remain concealed by hidden parasite diversity in natural systems. Microscopic examination of 19 European lake
Daphnia
populations revealed the presence of three groups of parasites: fungi, microsporidia, and oomycetes. For most of these parasites no genetic markers have been described so far. Based on sequence similarities of the nuclear small-subunit and internal transcribed spacer (ITS) rRNA gene regions, one fungus, four microsporidian, and nine oomycete taxa were discovered in 147 infected
Daphnia
(and/or three other zooplankton crustaceans). Additionally, cloning of rRNA gene regions revealed parasite sequence variation within host individuals. This was most pronounced in the ITS region of one microsporidian taxon, where the within-host sequence variation ranged from 1.7% to 5.3% polymorphic sites for parasite isolates from 14 different geographical locations. Interestingly, the parasite isolates from close locations grouped together based on sequence similarities, suggesting that there was parasite dispersal. Taken together, the data obtained in this study revealed hidden diversity of parasite communities in
Daphnia
lake populations. Moreover, a higher level of resolution for identifying parasite strains makes it possible to test new hypotheses with respect to parasite dispersal, transmission routes, and coinfection.
Listeria monocytogenes
Attachment to and Detachment from Stainless Steel Surfaces in a Simulated Dairy Processing Environment
Authors: Poimenidou Sofia , Belessi Charalambia A. , Giaouris Efstathios D. , Gounadaki Antonia S. , Nychas George-John E. , Skandamis Panagiotis N. 
Published: September 2009

ABSTRACT

The presence of pathogens in dairy products is often associated with contamination via bacteria attached to food-processing equipment, especially from areas where cleaning/sanitation is difficult. In this study, the attachment of
Listeria monocytogenes
on stainless steel (SS), followed by detachment and growth in foods, was evaluated under conditions simulating a dairy processing environment. Initially, SS coupons were immersed in milk, vanilla custard, and yogurt inoculated with the pathogen (10
7
CFU/ml or CFU/g) and incubated at two temperatures (5 and 20°C) for 7 days. By the end of incubation, cells were mechanically detached from coupons and used to inoculate freshly pasteurized milk which was subsequently stored at 5°C for 20 days. The suspended cells in all three products in which SS coupons were immersed were also used to inoculate freshly pasteurized milk (5°C for 20 days). When SS coupons were immersed in milk, shorter lag phases were obtained for detached than for planktonically grown cells, regardless of the preincubation temperature (5 or 20°C). The opposite was observed when custard incubated at 20°C was used to prepare the two types of inocula. However, in this case, a significant increase in growth rate was also evident when the inoculum was derived from detached cells. In another parallel study, while
L. monocytogenes
was not detectable on SS coupons after 7 days of incubation (at 5°C) in inoculated yogurt, marked detachment and growth were observed when these coupons were subsequently transferred and incubated at 5°C in fresh milk or/and custard. Overall, the results obtained extend our knowledge on the risk related to contamination of dairy products with detached
L. monocytogenes
cells.
Improved Squalene Production via Modulation of the Methylerythritol 4-Phosphate Pathway and Heterologous Expression of Genes from
Streptomyces peucetius
ATCC 27952 in
Escherichia coli
Authors: Ghimire Gopal Prasad , Lee Hei Chan , Sohng Jae Kyung 
Published: September 2009

ABSTRACT

Putative hopanoid genes from
Streptomyces peucetius
were introduced into
Escherichia coli
to improve the production of squalene, an industrially important compound. High expression of
hopA
and
hopB
(encoding squalene/phytoene synthases) together with
hopD
(encoding farnesyl diphosphate synthase) yielded 4.1 mg/liter of squalene. This level was elevated to 11.8 mg/liter when there was also increased expression of
dxs
and
idi
,
E. coli
genes encoding 1-deoxy-
d
-xylulose 5-phosphate synthase and isopentenyl diphosphate isomerase.
Microbial Populations Responsive to Denitrification-Inducing Conditions in Rice Paddy Soil, as Revealed by Comparative 16S rRNA Gene Analysis
Authors: Ishii Satoshi , Yamamoto Michihiro , Kikuchi Mami , Oshima Kenshiro , Hattori Masahira , Otsuka Shigeto , Senoo Keishi 
Published: September 2009

ABSTRACT

Rice paddy soil has been shown to have strong denitrifying activity. However, the microbial populations responsible for nitrate respiration and denitrification have not been well characterized. In this study, we performed a clone library analysis of >1,000 clones of the nearly full-length 16S rRNA gene to characterize bacterial community structure in rice paddy soil. We also identified potential key players in nitrate respiration and denitrification by comparing the community structures of soils with strong denitrifying activity to those of soils without denitrifying activity. Clone library analysis showed that bacteria belonging to the phylum
Firmicutes
, including a unique
Symbiobacterium
clade, dominated the clones obtained in this study. Using the template match method, several operational taxonomic units (OTUs), most belonging to the orders
Burkholderiales
and
Rhodocyclales
, were identified as OTUs that were specifically enriched in the sample with strong denitrifying activity. Almost one-half of these OTUs were classified in the genus
Herbaspirillum
and appeared >10-fold more frequently in the soils with strong denitrifying activity than in the soils without denitrifying activity. Therefore, OTUs related to
Herbaspirillum
are potential key players in nitrate respiration and denitrification under the conditions used.
ATP-Dependent but Proton Gradient-Independent Polyphosphate-Synthesizing Activity in Extraradical Hyphae of an Arbuscular Mycorrhizal Fungus
Authors: Tani Chiharu , Ohtomo Ryo , Osaki Mitsuru , Kuga Yukari , Ezawa Tatsuhiro 
Published: September 2009

ABSTRACT

Arbuscular mycorrhizal (AM) fungi benefit their host plants by supplying phosphate obtained from the soil. Polyphosphate is thought to act as the key intermediate in this process, but little is currently understood about how polyphosphate is synthesized or translocated within arbuscular mycorrhizas.
Glomus
sp. strain HR1 was grown with marigold in a mesh bag compartment system, and extraradical hyphae were harvested and fractionated by density gradient centrifugation. Using this approach, three distinct layers were obtained: layers 1 and 2 were composed of amorphous and membranous materials, together with mitochondria, lipid bodies, and electron-opaque bodies, and layer 3 was composed mainly of partially broken hyphae and fragmented cell walls. The polyphosphate kinase/luciferase system, a highly sensitive polyphosphate detection method, enabled the detection of polyphosphate-synthesizing activity in layer 2 in the presence of ATP. This activity was inhibited by vanadate but not by bafilomycin A
1
or a protonophore, suggesting that ATP may not energize the reaction through H
+
-ATPase but may act as a direct substrate in the reaction. This report represents the first demonstration that AM fungi possess polyphosphate-synthesizing activity that is localized in the organelle fraction and not in the cytosol or at the plasma membrane.
Thermostable Cyanuric Acid Hydrolase from
Moorella thermoacetica
ATCC 39073
Authors: Li Qingyan , Seffernick Jennifer L. , Sadowsky Michael J. , Wackett Lawrence P. 
Published: September 2009

ABSTRACT

Cyanuric acid, a metabolic intermediate in the degradation of many
s
-triazine compounds, is further metabolized by cyanuric acid hydrolase. Cyanuric acid also accumulates in swimming pools due to the breakdown of the sanitizing agents di- and trichloroisocyanuric acid. Structurally stable cyanuric acid hydrolases are being considered for usage in pool water remediation. In this study, cyanuric acid hydrolase from the thermophile
Moorella thermoacetica
ATCC 39073 was cloned, expressed in
Escherichia coli
, and purified to homogeneity. The recombinant enzyme was found to have a broader temperature range and greater stability, at both elevated and low temperatures, than previously described cyanuric acid hydrolases. The enzyme had a narrow substrate specificity, acting only on cyanuric acid and
N
-methylisocyanuric acid. The
M. thermoacetica
enzyme did not require metals or other discernible cofactors for activity. Cyanuric acid hydrolase from
M. thermoacetica
is the most promising enzyme to use for cyanuric acid remediation applications.
Immortalized Human Brain Endothelial Cell Line HCMEC/D3 as a Model of the Blood-Brain Barrier Facilitates In Vitro Studies of Central Nervous System Infection by
Cryptococcus neoformans
Authors: Vu Kiem , Weksler Babette , Romero Ignacio , Couraud Pierre-Olivier , Gelli Angie 
Published: September 2009

ABSTRACT

Cryptococcus neoformans
cells must cross the blood-brain barrier prior to invading the central nervous system. Here we demonstrate that the immortalized human brain endothelial cell line HCMEC/D3 is a useful alternative to primary brain endothelial cells as a model of the blood-brain barrier for studies of central nervous system infection.
Zinc-Independent Folate Biosynthesis: Genetic, Biochemical, and Structural Investigations Reveal New Metal Dependence for GTP Cyclohydrolase IB
Authors: Sankaran Banumathi , Bonnett Shilah A. , Shah Kinjal , Gabriel Scott , Reddy Robert , Schimmel Paul , Rodionov Dmitry A. , de Crécy-Lagard Valérie , Helmann John D. , Iwata-Reuyl Dirk , Swairjo Manal A. 
Published: September 2009

ABSTRACT

GTP cyclohydrolase I (GCYH-I) is an essential Zn
2+
-dependent enzyme that catalyzes the first step of the de novo folate biosynthetic pathway in bacteria and plants, the 7-deazapurine biosynthetic pathway in
Bacteria
and
Archaea
, and the biopterin pathway in mammals. We recently reported the discovery of a new prokaryotic-specific GCYH-I (GCYH-IB) that displays no sequence identity to the canonical enzyme and is present in ∼25% of bacteria, the majority of which lack the canonical GCYH-I (renamed GCYH-IA). Genomic and genetic analyses indicate that in those organisms possessing both enzymes, e.g.,
Bacillus subtilis
, GCYH-IA and -IB are functionally redundant, but differentially expressed. Whereas GCYH-IA is constitutively expressed, GCYH-IB is expressed only under Zn
2+
-limiting conditions. These observations are consistent with the hypothesis that GCYH-IB functions to allow folate biosynthesis during Zn
2+
starvation. Here, we present biochemical and structural data showing that bacterial GCYH-IB, like GCYH-IA, belongs to the tunneling-fold (T-fold) superfamily. However, the GCYH-IA and -IB enzymes exhibit significant differences in global structure and active-site architecture. While GCYH-IA is a unimodular, homodecameric, Zn
2+
-dependent enzyme, GCYH-IB is a bimodular, homotetrameric enzyme activated by a variety of divalent cations. The structure of GCYH-IB and the broad metal dependence exhibited by this enzyme further underscore the mechanistic plasticity that is emerging for the T-fold superfamily. Notably, while humans possess the canonical GCYH-IA enzyme, many clinically important human pathogens possess only the GCYH-IB enzyme, suggesting that this enzyme is a potential new molecular target for antibacterial development.