bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antimicrobial Actions of Degraded and Native Chitosan against Spoilage Organisms in Laboratory Media and Foods
Authors: Rhoades J. , Roller S. 
Published: April 2009

ABSTRACT
The objective of this study was to determine whether chitosan (poly-β-1,4-glucosamine) and hydrolysates of chitosan can be used as novel preservatives in foods. Chitosan was hydrolyzed by using oxidative-reductive degradation, crude papaya latex, and lysozyme. Mild hydrolysis of chitosan resulted in improved microbial inactivation in saline and greater inhibition of growth of several spoilage yeasts in laboratory media, but highly degraded products of chitosan exhibited no antimicrobial activity. In pasteurized apple-elderflower juice stored at 7°C, addition of 0.3 g of chitosan per liter eliminated yeasts entirely for the duration of the experiment (13 days), while the total counts and the lactic acid bacterial counts increased at a slower rate than they increased in the control. Addition of 0.3 or 1.0 g of chitosan per kg had no effect on the microbial flora of houmous, a chickpea dip; in the presence of 5.0 g of chitosan per kg, bacterial growth but not yeast growth was substantially reduced compared with growth in control dip stored at 7°C for 6 days. Improved antimicrobial potency of chitosan hydrolysates like that observed in the saline and laboratory medium experiments was not observed in juice and dip experiments. We concluded that native chitosan has potential for use as a preservative in certain types of food but that the increase in antimicrobial activity that occurs following partial hydrolysis is too small to justify the extra processing involved.
A New Chemolithoautotrophic Arsenite-Oxidizing Bacterium Isolated from a Gold Mine: Phylogenetic, Physiological, and Preliminary Biochemical Studies
Authors: Santini Joanne M. , Sly Lindsay I. , Schnagl Roger D. , Macy Joan M. 
Published: April 2009

ABSTRACT

A previously unknown chemolithoautotrophic arsenite-oxidizing bacterium has been isolated from a gold mine in the Northern Territory of Australia. The organism, designated NT-26, was found to be a gram-negative motile rod with two subterminal flagella. In a minimal medium containing only arsenite as the electron donor (5 mM), oxygen as the electron acceptor, and carbon dioxide-bicarbonate as the carbon source, the doubling time for chemolithoautotrophic growth was 7.6 h. Arsenite oxidation was found to be catalyzed by a periplasmic arsenite oxidase (optimum pH, 5.5). Based upon 16S rDNA phylogenetic sequence analysis, NT-26 belongs to the
Agrobacterium/Rhizobium
branch of the α-
Proteobacteria
and may represent a new species. This recently discovered organism is the most rapidly growing chemolithoautotrophic arsenite oxidizer known.
Multiparametric Flow Cytometry and Cell Sorting for the Assessment of Viable, Injured, and Dead Bifidobacterium Cells during Bile Salt Stress
Authors: Amor Kaouther Ben , Breeuwer Pieter , Verbaarschot Patrick , Rombouts Frank M. , Akkermans Antoon D. L. , De Vos Willem M. , Abee Tjakko 
Published: April 2009

ABSTRACT

Using a flow cytometry-based approach, we assessed the viability of
Bifidobacterium lactis
DSM 10140 and
Bifidobacterium adolescentis
DSM 20083 during exposure to bile salt stress. Carboxyfluorescein diacetate (cFDA), propidium iodide (PI), and oxonol [DiBAC
4
(3)] were used to monitor esterase activity, membrane integrity, and membrane potential, respectively, as indicators of bacterial viability. Single staining with these probes rapidly and noticeably reflected the behavior of the two strains during stress exposure. However, the flow cytometry results tended to overestimate the viability of the two strains compared to plate counts, which appeared to be related to the nonculturability of a fraction of the population as a result of sublethal injury caused by bile salts. When the cells were simultaneously stained with cFDA and PI, flow cytometry and cell sorting revealed a striking physiological heterogeneity within the stressed bifidobacterium population. Three subpopulations could be identified based on their differential uptake of the probes: cF-stained, cF and PI double-stained, and PI-stained subpopulations, representing viable, injured, and dead cells, respectively. Following sorting and recovery, a significant fraction of the double-stained subpopulation (40%) could resume growth on agar plates. Our results show that in situ assessment of the physiological activity of stressed bifidobacteria using multiparameter flow cytometry and cell sorting may provide a powerful and sensitive tool for assessment of the viability and stability of probiotics.
Utilization of Ganglioside-Degrading
Paenibacillus
sp. Strain TS12 for Production of Glucosylceramide
Authors: Sumida Tomomi , Sueyoshi Noriyuki , Ito Makoto 
Published: April 2009

ABSTRACT

Gangliosides, sialic acid-containing glycosphingolipids, are membrane constituents of vertebrates and are known to have important roles in cellular differentiation, adhesion, and recognition. We report here the isolation of a bacterium capable of degrading gangliotetraose-series gangliosides and a new method for the production of glucosylceramide with this bacterium. GM1a ganglioside was found to be sequentially degraded by
Paenibacillus
sp. strain TS12, which was isolated from soil, as follows: GM1a → asialo GM1 → asialo GM2 → lactosylceramide → glucosylceramide. TS12 was found to produce a series of ganglioside-degrading enzymes, such as sialidases, β-galactosidases, and β-hexosaminidases. TS12 also produced β-glucosidases, but glucosylceramide was somewhat resistant to the bacterial enzyme under the conditions used. Taking advantage of the specificity, we developed a new method for the production of glucosylceramide using TS12 as a biocatalyst. The method involves the conversion of crude bovine brain gangliosides to glucosylceramide by coculture with TS12 and purification of the product by chromatography with Wakogel C-300 HG.
The Murein Hydrolase of the Bacteriophage φ3626 Dual Lysis System Is Active against All Tested
Clostridium perfringens
Strains
Authors: Zimmer Markus , Vukov Natǎsa , Scherer Siegfried , Loessner Martin J. 
Published: April 2009

ABSTRACT

Clostridium perfringens
commonly occurs in food and feed, can produce an enterotoxin frequently implicated in food-borne disease, and has a substantial negative impact on the poultry industry. As a step towards new approaches for control of this organism, we investigated the cell wall lysis system of
C. perfringens
bacteriophage φ3626, whose dual lysis gene cassette consists of a holin gene and an endolysin gene. Hol3626 has two membrane-spanning domains (MSDs) and is a group II holin. A positively charged beta turn between the two MSDs suggests that both the amino terminus and the carboxy terminus of Hol3626 might be located outside the cell membrane, a very unusual holin topology. Holin function was experimentally demonstrated by using the ability of the holin to complement a deletion of the heterologous phage λ
S
holin in λΔSthf. The endolysin gene
ply3626
was cloned in
Escherichia coli
. However, protein synthesis occurred only when bacteria were supplemented with rare tRNA
Arg
and tRNA
Ile
genes. Formation of inclusion bodies could be avoided by drastically lowering the expression level. Amino-terminal modification by a six-histidine tag did not affect enzyme activity and enabled purification by metal chelate affinity chromatography. Ply3626 has an N-terminal amidase domain and a unique C-terminal portion, which might be responsible for the specific lytic range of the enzyme. All 48 tested strains of
C. perfringens
were sensitive to the murein hydrolase, whereas other clostridia and bacteria belonging to other genera were generally not affected. This highly specific activity towards
C. perfringens
might be useful for novel biocontrol measures in food, feed, and complex microbial communities.
Development of 16S rRNA-Gene-Targeted Group-Specific Primers for the Detection and Identification of Predominant Bacteria in Human Feces
Authors: Matsuki Takahiro , Watanabe Koichi , Fujimoto Junji , Miyamoto Yukiko , Takada Toshihiko , Matsumoto Kazumasa , Oyaizu Hiroshi , Tanaka Ryuichiro 
Published: April 2009

ABSTRACT

For the detection and identification of predominant bacteria in human feces, 16S rRNA-gene-targeted group-specific primers for the
Bacteroides fragilis
group
, Bifidobacterium,
the
Clostridium coccoides
group, and
Prevotella
were designed and evaluated. The specificity of these primers was confirmed by using DNA extracted from 90 species that are commonly found in the human intestinal microflora. The group-specific primers were then used for identification of 300 isolates from feces of six healthy volunteers. The isolates were clearly identified as 117 isolates of the
B. fragilis
group, 22 isolates of
Bifidobacterium
, 65 isolates of the
C. coccoides
group, and 17 isolates of
Prevotella
, indicating that 74% of the isolates were identified with the four pairs of primers. The remaining 79 isolates were identified by 16S ribosomal DNA sequence analysis and consisted of 40 isolates of
Collinsella
, 24 isolates of the
Clostridium leptum
subgroup, and 15 isolates of disparate clusters. In addition, qualitative detection of these bacterial groups was accomplished without cultivation by using DNA extracted from the fecal samples. The goal for this specific PCR technique is to develop a procedure for quantitative detection of these bacterial groups, and a real-time quantitative PCR for detection of
Bifidobacterium
is now being investigated (T. Requena, J. Burton, T. Matsuki, K. Munro, M. A. Simon, R. Tanaka, K. Watanabe, and G. W. Tannock, Appl. Environ. Microbiol.
68:
2420-2427, 2002). Therefore, the approaches used to detect and identify predominant bacteria with the group-specific primers described here should contribute to future studies of the composition and dynamics of the intestinal microflora.
Characterization of SixLeuconostoc fallaxBacteriophages Isolated from an Industrial Sauerkraut Fermentation
Authors: Barrangou Rodolphe , Yoon Sung-Sik , Breidt, Frederick , Fleming Henry P. , Klaenhammer Todd R. 
Published: April 2009

ABSTRACTSix bacteriophages active againstLeuconostoc fallaxstrains were isolated from industrial sauerkraut fermentation brines. These phages were characterized as to host range, morphology, structural proteins, and genome fingerprint. They were exclusively lytic against the speciesL. fallaxand had different host ranges among the strains of this species tested. Morphologically, three of the phages were assigned to the familySiphoviridae, and the three others were assigned to the familyMyoviridae. Major capsid proteins detected by electrophoresis were distinct for each of the two morphotypes. Restriction fragment length polymorphism analysis and randomly amplified polymorphic DNA fingerprinting showed that all six phages were genetically distinct. These results revealed for the first time the existence of bacteriophages that are active againstL. fallaxand confirmed the presence and diversity of bacteriophages in a sauerkraut fermentation. Since a variety ofL. fallaxstrains have been shown to be present in sauerkraut fermentation, bacteriophages active againstL. fallaxare likely to contribute to the microbial ecology of sauerkraut fermentation and could be responsible for some of the variability observed in this type of fermentation.
Molecular Characterization of Cadmium Resistance inStreptococcus thermophilusStrain 4134: an Example of Lateral Gene Transfer
Authors: Schirawski Jan , Hagens Werner , Fitzgerald Gerald F. , van Sinderen Douwe 
Published: April 2009

ABSTRACTTwo genes (cadCStandcadASt[subscriptStrepresentsStreptococcus thermophilus]), located on the chromosome ofS. thermophilus4134, were shown to constitute a cadmium/zinc resistance cassette. The genes seem to be organized in an operon, and their transcription is cadmium dependent in vivo. The proposed product of thecadAopen reading frame (CadASt) is highly similar to P-type cadmium efflux ATPases, whereas the predicted protein encoded bycadCSt(CadCSt) shows high similarity to ArsR-type regulatory proteins. The observed homologies and G+C content of this cassette and surrounding regions suggest that this DNA was derived fromLactococcus lactisand may have been introduced relatively recently into theS. thermophilus4134 genome by a lateral gene transfer event. The complete cassette confers cadmium and zinc resistance to bothS. thermophilusandL. lactis, but expression ofcadAStalone is sufficient to give resistance. By using electrophoretic mobility shift assays it was shown that the CadCStprotein is a DNA binding protein that binds specifically to its own promoter region, possibly to two copies of an inverted repeat, and that this CadCSt-DNA interaction is lost in the presence of cadmium. UsinglacZfusion constructs it was shown that the cadmium-dependent expression of CadAStis mediated by the negative regulator CadCSt. A model for the regulation of the expression of cadmium resistance inS. thermophilusis discussed.
Isolation and Molecular Analysis of the Gene Cluster for the Arginine Deiminase System from
Streptococcus gordonii
DL1
Authors: Dong Yiqian , Chen Yi-Ywan M. , Snyder Jennifer A. , Burne R. A. 
Published: April 2009

ABSTRACT

The arginine deiminase (AD) system (ADS) is one of two major ammonia-generating pathways in the oral cavity that play important roles in oral biofilm pH homeostasis and oral biofilm ecology. To initiate a study of the
Streptococcus gordonii
ADS, the ADS gene cluster was isolated from subgenomic DNA libraries of
S. gordonii
DL1 by using an
arcB
-specific probe. Nucleotide sequence analysis revealed six open reading frames (ORFs) that were arranged contiguously; the first five ORFs were transcribed in the same direction, as an apparent operon, and the sixth was transcribed in the opposite direction. The ORFs were found to share significant homologies and to correspond closely in molecular mass to previously characterized
arc
genes; thus, they were designated
arcA
(AD)
, arcB
(ornithine carbamyltransferase)
, arcC
(carbamate kinase)
, arcD
(arginine-ornithine antiporter)
, arcT
(dipeptidase), and
arcR
(regulator). A putative σ
70
promoter (
ParcA
[TTGTGT-N
19
-TAGAAT]) was mapped 5′ to
arcA
by primer extension, and the expression of
ParcA
was shown to be inducible by arginine and repressible by glucose, in agreement with AD specific activities measured in the wild-type strain. To investigate the function of ArcR in the differential expression of the
arc
operon,
arcR
was insertionally inactivated by a KM resistance marker flanked by T4 transcription/translation termination signals, and the expression of
ParcA
was monitored by primer extension in the wild-type and ArcR-deficient strains. Lower levels of
arcA
expression, as well as lower levels of AD activity, were consistently observed in the ArcR-deficient strain compared to wild-type cells, regardless of the growth conditions. Thus, ArcR is a transcriptional activator that is required for induction and optimal expression of the
S. gordonii
ADS gene cluster.
Effect of Soil Ammonium Concentration on N
2
O Release and on the Community Structure of Ammonia Oxidizers and Denitrifiers
Authors: Avrahami Sharon , Conrad Ralf , Braker Gesche 
Published: April 2009

ABSTRACT

The effect of ammonium addition (6.5, 58, and 395 μg of NH
4
+
-N g [dry weight] of soil
−1
) on soil microbial communities was explored. For medium and high ammonium concentrations, increased N
2
O release rates and a shift toward a higher contribution of nitrification to N
2
O release occurred after incubation for 5 days at 4°C. Communities of ammonia oxidizers were assayed after 4 weeks of incubation by denaturant gradient gel electrophoresis (DGGE) of the
amoA
gene coding for the small subunit of ammonia monooxygenase. The DGGE fingerprints were invariably the same whether the soil was untreated or incubated with low, medium, or high ammonium concentrations. Phylogenetic analysis of cloned PCR products from excised DGGE bands detected
amoA
sequences which probably belonged to
Nitrosospira
16S rRNA clusters 3 and 4. Additional clones clustered with
Nitrosospira
sp. strains Ka3 and Ka4 and within an
amoA
cluster from unknown species. A
Nitrosomonas-
like
amoA
gene was detected in only one clone. In agreement with the
amoA
results, community profiles of total bacteria analyzed by terminal restriction fragment length polymorphism (T-RFLP) showed only minor differences. However, a community shift occurred for denitrifier populations based on T-RFLP analysis of
nirK
genes encoding copper-containing nitrite reductase with incubation at medium and high ammonia concentrations. Major terminal restriction fragments observed in environmental samples were further described by correspondence to cloned
nirK
genes from the same soil. Phylogenetic analysis grouped these clones into clusters of soil
nirK
genes. However, some clones were also closely related to genes from known denitrifiers. The shift in the denitrifier community was probably the consequence of the increased supply of oxidized nitrogen through nitrification. Nitrification activity increased upon addition of ammonium, but the community structure of ammonium oxidizers did not change.
Differential Enantioselective Transformation of Atropisomeric Polychlorinated Biphenyls by Multiple Bacterial Strains with Different Inducing Compounds
Authors: Singer Andrew C. , Wong Charles S. , Crowley David E. 
Published: April 2009

ABSTRACT
Five polychlorinated biphenyl (PCB)-degrading bacteria were tested for the ability to differentiate between the enantiomers of four atropisomeric PCB congeners (2,2′,3,6-tetra-CB; 2,2′,3,3′,6-penta-CB; 2,2′,3,4′,6-penta-CB; and 2,2′,3,5′,6-penta-CB) after growth in the presence of tryptone-soytone, biphenyl, carvone, or cymene. Enantioselectivity was shown to vary with respect to strain, congener, and cosubstrate.
Diversity of Diazotrophic Unicellular Cyanobacteria in the Tropical North Atlantic Ocean
Authors: Falcón Luisa I. , Cipriano Frank , Chistoserdov Andrei Y. , Carpenter Edward J. 
Published: April 2009

ABSTRACT

We present data on the genetic diversity and phylogenetic affinities of N
2
-fixing unicellular cyanobacteria in the plankton of the tropical North Atlantic Ocean. Our dinitrogenase gene (
nifH
) sequences grouped together with a group of cyanobacteria from the subtropical North Pacific; another subtropical North Pacific group was only distantly related. Most of the 16S ribosomal DNA sequences from our tropical North Atlantic samples were closely allied with sequences from a symbiont of the diatom
Climacodium frauenfeldianum
. These findings suggest a complex pattern of evolutionary and ecological divergence among unicellular cyanobacteria within and between ocean basins.
Anti-Alpha-Hemolysin Monoclonal Antibodies Mediate Protection againstStaphylococcus aureusPneumonia
Authors: Ragle Brook E. , Bubeck Wardenburg Juliane 
Published: April 2009

ABSTRACTStaphylococcus aureuspneumonia is one of the most common invasive diseases caused by this human pathogen.S. aureusalpha-hemolysin, a pore-forming cytotoxin, is an essential virulence factor in the pathogenesis of pneumonia. Vaccine-based targeting of this toxin provides protection against lethal staphylococcal pneumonia in a murine model system, suggesting that a monoclonal antibody-based therapy may likewise prove to be efficacious for prevention and treatment of this disease. We report the generation of two distinct anti-alpha-hemolysin monoclonal antibodies that antagonize toxin activity, preventing human lung cell injury in vitro and protecting experimental animals against lethalS. aureuspneumonia. Each of these two monoclonal antibodies recognized an epitope within the first 50 amino acid residues of the mature toxin and blocked the formation of a stable alpha-hemolysin oligomer on the target cell surface. Active immunization with the first 50 amino acids of the toxin also conferred protection againstS. aureuspneumonia. Together, these data reveal passive and active immunization strategies for prevention or therapy of staphylococcal pneumonia and highlight the potential role that a critical epitope may play in defining human susceptibility to this deadly disease.
MEMMU
Authors: Bai Lan S. , Yang Lei , Dick Robert P. 
Published: April 2009

Random access memory (RAM) is tightly constrained in the least expensive, lowest-power embedded systems such as sensor network nodes and portable consumer electronics. The most widely used sensor network nodes have only 4 to 10KB of RAM and do not contain memory management units (MMUs). It is difficult to implement complex applications under such tight memory constraints. Nonetheless, price and power-consumption constraints make it unlikely that increases in RAM in these systems will keep pace with the increasing memory requirements of applications.
We propose the use of automated compile-time and runtime techniques to increase the amount of usable memory in MMU-less embedded systems. The proposed techniques do not increase hardware cost, and require few or no changes to existing applications. We have developed runtime library routines and compiler transformations to control and optimize the automatic migration of application data between compressed and uncompressed memory regions, as well as a fast compression algorithm well suited to this application. These techniques were experimentally evaluated on Crossbow TelosB sensor network nodes running a number of data-collection and signal-processing applications. Our results indicate that available memory can be increased by up to 50% with less than 10% performance degradation for most benchmarks.
A novel software framework for embedded multiprocessor smart cameras
Authors: Doblander Andreas , Zoufal Andreas , Rinner Bernhard 
Published: April 2009

Distributed smart cameras (DSC) are an emerging technology for a broad range of important applications including smart rooms, surveillance, entertainment, tracking, and motion analysis. By having access to many views and through cooperation among the individual cameras, these DSCs have the potential to realize many more complex and challenging applications than single-camera systems.
This article focuses on the system-level software required for efficient streaming applications on single smart cameras as well as on networks of DSCs. Embedded platforms with limited resources do not provide middleware services well known on general-purpose platforms. Our software framework supports transparent intra- and interprocessor communication while keeping the memory and computation overhead very low. The software framework is based on a publisher--subscriber architecture and provides mechanisms for dynamically loading and unloading software components as well as for graceful degradation in case of software- and hardware-related faults. The software framework has been completely implemented and tested on our embedded smart cameras consisting of an ARM-based network processor and several digital signal processors. Two case studies demonstrate the feasibility of our approach.
JMT
Authors: Bertoli Marco , Casale Giuliano , Serazzi Giuseppe 
Published: April 2009

We present the Java Modelling Tools (JMT) suite, an integrated framework of Java tools for performance evaluation of computer systems using queueing models. The suite offers a rich user interface that simplifies the definition of performance models by means of wizard dialogs and of a graphical design workspace.
The performance evaluation features of JMT span a wide range of state-of-the-art methodologies including discrete-event simulation, mean value analysis of product-form networks, analytical identification of bottleneck resources in multiclass environments, and workload characterization with fuzzy clustering. The discrete-event simulator supports several advanced modeling features such as finite capacity regions, load-dependent service times, bursty processes, fork-and-join nodes, and implements spectral estimation for analysis of simulative results. The suite is open-source, released under the GNU general public license (GPL), and it is available for free download at: http://jmt.sourceforge.net.