bluuebunny/crossref_metadata_2025_split huggingface dataset:
Survival of Genetically Modified and Self-Cloned Strains of Commercial Baker's Yeast in Simulated Natural Environments: Environmental Risk Assessment
Authors: Ando Akira , Suzuki Chise , Shima Jun 
Published: November 2005

ABSTRACT

Although genetic engineering techniques for baker's yeast might improve the yeast's fermentation characteristics, the lack of scientific data on the survival of such strains in natural environments as well as the effects on human health prevent their commercial use. Disruption of acid trehalase gene (
ATH1
) improves freeze tolerance, which is a crucial characteristic in frozen-dough baking. In this study,
ATH1
disruptants constructed by genetic modification (GM) and self-cloning (SC) techniques were used as models to study such effects because these strains have higher freeze tolerance and are expected to be used commercially. Behavior of the strains in simulated natural environments, namely, in soil and water, was studied by measuring the change in the number of viable cells and in the concentration of DNA that contains
ATH1
loci. Measurements were made using a real-time PCR method during 40 days of cultivation. Results showed that the number of viable cells of GM and SC strains decreased in a time-dependent manner and that the decrease rate was nearly equal to or higher than that for wild-type (WT) yeast. For all three strains (SC, GM, and WT) in the two simulated natural environments (water and soil), the DNA remained longer than did viable cells but the decrease patterns of either the DNA or the viable cells of SC and GM strains had tendencies similar to those of the WT strain. In conclusion, disruption of
ATH1
by genetic engineering apparently does not promote the survival of viable cells and DNA in natural environments.
Real-Time Nucleic Acid Sequence-Based Amplification Assay for Detection of Hepatitis A Virus
Authors: Abd El Galil Khaled H. , El Sokkary M. A. , Kheira S. M. , Salazar Andre M. , Yates Marylynn V. , Chen Wilfred , Mulchandani Ashok 
Published: November 2005

ABSTRACT
A nucleic acid sequence-based amplification (NASBA) assay in combination with a molecular beacon was developed for the real-time detection and quantification of hepatitis A virus (HAV). A 202-bp, highly conserved 5′ noncoding region of HAV was targeted. The sensitivity of the real-time NASBA assay was tested with 10-fold dilutions of viral RNA, and a detection limit of 1 PFU was obtained. The specificity of the assay was demonstrated by testing with other environmental pathogens and indicator microorganisms, with only HAV positively identified. When combined with immunomagnetic separation, the NASBA assay successfully detected as few as 10 PFU from seeded lake water samples. Due to its isothermal nature, its speed, and its similar sensitivity compared to the real-time RT-PCR assay, this newly reported real-time NASBA method will have broad applications for the rapid detection of HAV in contaminated food or water.
Prevalence of Pathogenic
Yersinia enterocolitica
Strains in Pigs in the United States
Authors: Bhaduri Saumya , Wesley Irene V. , Bush Eric J. 
Published: November 2005

ABSTRACT

Yersinia enterocolitica
is considered an important food-borne pathogen
impacting the pork production and processing industry in the United
States. Since this bacterium is a commensal of swine, the primary goal
of this study was to determine the prevalence of pathogenic
Y
.
enterocolitica
in pigs in the United Sates using feces as the
sample source. A total of 2,793 fecal samples were tested for its
presence in swine. Fecal samples were collected from late finisher pigs
from 77 production sites in the 15 eastern and midwestern
pork-producing states over a period of 27 weeks (6 September 2000 to 20
March 2001). The prevalence of
ail
-positive
Y
.
enterocolitica
was determined in samples using both a
fluorogenic 5′ nuclease PCR assay and a culture method. The
mean prevalence was 13.10% (366 of 2,793 fecal samples tested) when
both PCR- and culture-positive results were combined. Forty-one of 77
premises (53.25%) contained at least one fecal sample positive for the
ail
sequence. The PCR assay indicated a contamination rate of
12.35% (345/2,793) compared to 4.08% (114/2,793) by the culture method.
Of the 345 PCR-positive samples, 252 were culture negative, while of
the 114 culture-positive samples, 21 were PCR negative. Among 77
premises, the PCR assay revealed a significantly (
P
<
0.05) higher percentage (46.75%,
n
= 36 sites) of
samples positive for the pathogen (
ail
sequence) than the
culture method (22.08%,
n
= 17 sites). Thus, higher
sensitivity, with respect to number of samples and sites identified as
positive for the PCR method compared with the culture method for
detecting pathogenic
Y. enterocolitica
, was
demonstrated in this study. The results support the hypothesis that
swine are a reservoir for
Y. enterocolitica
strains
potentially pathogenic for
humans.
Engineering of
Bacillus subtilis
for Enhanced Total Synthesis of Folic Acid
Authors: Zhu T. , Pan Z. , Domagalski N. , Koepsel R. , Ataai M. M. , Domach M. M. 
Published: November 2005

ABSTRACT

We investigated whether the yield of the B vitamin folic acid could be elevated in
Bacillus subtilis
. Strategies for increasing the folic acid yield were investigated by employing computer-aided flux analysis and mutation. Controlling the activity of the enzyme pyruvate kinase by placing it under inducible control was one strategy devised to elevate yield while insuring that a rapid growth rate results. Other single mutation strategies included amplifying the expression of the genes in the folate operon and overexpressing the
Escherichia coli aroH
gene, which encodes 2-dehydro-3-deoxyphosphoheptonate aldolase. The latter could conceivably elevate the abundance of the folic acid precursor,
para
-aminobenzoic acid. Strains that combined two or more mutations were also constructed. Overall, a strain possessing inducible pyruvate kinase, overexpressed
aroH
, and increased transcription and translation of genes from the folic operon exhibited the best yield. The yield was eightfold higher than that displayed by the parent
B. subtilis
168 strain.
Novel DNA Sequences from Natural Strains of the Nitrogen-Fixing Symbiotic Bacterium
Sinorhizobium meliloti
Authors: Guo Hong , Sun Sheng , Finan Turlough M. , Xu Jianping 
Published: November 2005

ABSTRACT

Variation in genome size and content is common among bacterial strains. Identifying these naturally occurring differences can accelerate our understanding of bacterial attributes, such as ecological specialization and genome evolution. In this study, we used representational difference analysis to identify potentially novel sequences not present in the sequenced laboratory strain Rm1021 of the nitrogen-fixing bacterium
Sinorhizobium meliloti
. Using strain Rm1021 as the driver and the type strain of
S. meliloti
ATCC 9930, which has a genome size ∼370 kilobases bigger than that of strain Rm1021, as the tester, we identified several groups of sequences in the ATCC 9930 genome not present in strain Rm1021. Among the 85 novel DNA fragments examined, 55 showed no obvious homologs anywhere in the public databases. Of the remaining 30 sequences, 24 contained homologs to the Rm1021 genome as well as unique segments not found in Rm1021, 3 contained sequences homologous to those published for another
S. meliloti
strain but absent in Rm1021, 2 contained sequences homologous to other symbiotic nitrogen-fixing bacteria (
Rhizobium etli
and
Bradyrhizobium japonicum
), and 1 contained a sequence homologous to a gene in a non-nitrogen-fixing species,
Pseudomonas
sp. NK87. Using PCR, we assayed the distribution of 12 of the above 85 novel sequences in a collection of 59 natural
S. meliloti
strains. The distribution varied widely among the 12 novel DNA fragments, from 1.7% to 72.9%. No apparent correlation was found between the distribution of these novel DNA sequences and their genotypes obtained using multilocus enzyme electrophoresis. Our results suggest potentially high rates of gene gain and loss in
S. meliloti
genomes.
Proteomic Signature of
Lactococcus lactis
NCDO763 Cultivated in Milk
Authors: Gitton Christophe , Meyrand Mickael , Wang Juhui , Caron Christophe , Trubuil Alain , Guillot Alain , Mistou Michel-Yves 
Published: November 2005

ABSTRACT

We have compared the proteomic profiles of
L. lactis
subsp.
cremoris
NCDO763 growing in the synthetic medium M17Lac, skim milk microfiltrate (SMM), and skim milk. SMM was used as a simple model medium to reproduce the initial phase of growth of
L. lactis
in milk. To widen the analysis of the cytoplasmic proteome, we used two different gel systems (pH ranges of 4 to 7 and 4.5 to 5.5), and the proteins associated with the cell envelopes were also studied by two-dimensional electrophoresis. In the course of the study, we analyzed about 800 spots and identified 330 proteins by mass spectrometry. We observed that the levels of more than 50 and 30 proteins were significantly increased upon growth in SMM and milk, respectively. The large redeployment of protein synthesis was essentially associated with an activation of pathways involved in the metabolism of nitrogenous compounds: peptidolytic and peptide transport systems, amino acid biosynthesis and interconversion, and de novo biosynthesis of purines. We also showed that enzymes involved in reactions feeding the purine biosynthetic pathway in one-carbon units and amino acids have an increased level in SMM and milk. The analysis of the proteomic data suggested that the glutamine synthetase (GS) would play a pivotal role in the adaptation to SMM and milk. The analysis of
glnA
expression during growth in milk and the construction of a
glnA
-defective mutant confirmed that GS is an essential enzyme for the development of
L. lactis
in dairy media. This analysis thus provides a proteomic signature of
L. lactis
, a model lactic acid bacterium, growing in its technological environment.
Alteration of Leucine Aminopeptidase from
Streptomyces septatus
TH-2 to Phenylalanine Aminopeptidase by Site-Directed Mutagenesis
Authors: Arima Jiro , Uesugi Yoshiko , Iwabuchi Masaki , Hatanaka Tadashi 
Published: November 2005

ABSTRACT

To tailor leucine aminopeptidase from
Streptomyces septatus
TH-2 (SSAP) to become a convenient biocatalyst, we are interested in Phe221 of SSAP, which is thought to interact with the side chain of the N-terminal residue of the substrate. By using saturation mutagenesis, the feasibility of altering the performance of SSAP was evaluated. The hydrolytic activities of 19 mutants were investigated using aminoacyl
p
-nitroanilide (
p
NA) derivatives as substrates. Replacement of Phe221 resulted in changes in the activities of all the mutants. Three of these mutants, F221G, F221A, and F221S, specifically hydrolyzed
l
-Phe-
p
NA, and F221I SSAP exhibited hydrolytic activity with
l
-Leu-
p
NA exceeding that of the wild type. Although the hydrolytic activities with peptide substrates decreased, the hydrolytic activities with amide and methyl ester substrates were proportional to the changes in the hydrolytic activities with
p
NA derivatives. Furthermore, based on a comparative kinetic study, the mechanism underlying the alteration in the preference of SSAP from leucine to phenylalanine is discussed.
First Genome Data from Uncultured Upland Soil Cluster Alpha Methanotrophs Provide Further Evidence for a Close Phylogenetic Relationship toMethylocapsa acidiphilaB2 and for High-Affinity Methanotrophy Involving Particulate Methane Monooxygenase
Authors: Ricke Peter , Kube Michael , Nakagawa Satoshi , Erkel Christoph , Reinhardt Richard , Liesack Werner 
Published: November 2005

ABSTRACTMembers of upland soil cluster alpha (USCα) are assumed to be methanotrophic bacteria (MB) adapted to the trace level of atmospheric methane. So far, these MB have eluded all cultivation attempts. While the 16S rRNA phylogeny of USCα members is still not known, phylogenies constructed for the active-site polypeptide (encoded bypmoA) of particulate methane monooxygenase (pMMO) placed USCα next to the alphaproteobacterialMethylocapsa acidiphilaB2. To assess whether thepmoAtree reflects the evolutionary identity of USCα, a 42-kb genomic contig of a USCα representative was obtained from acidic forest soil by screening a metagenomic fosmid library of 250,000 clones usingpmoA-targeted PCR. For comparison, a 101-kb genomic contig fromM. acidiphilawas analyzed, including thepmooperon. The following three lines of evidence confirmed a close phylogenetic relationship between USCα andM. acidiphila: (i) tetranucleotide frequency patterns of 5-kb genomic subfragments, (ii) annotation and comparative analysis of the genomic fragments against all completely sequenced genomes available in public domain databases, and (iii) three single gene phylogenies constructed using the deduced amino acid sequences of a putative prephenate dehydratase, a staphylococcal-like nuclease, and a putative zinc metalloprotease. A comparative analysis of thepmooperons of USCα andM. acidiphilacorroborated previous reports that both thepmooperon structure and the predicted secondary structure of deduced pMMO are highly conserved among all MB.
Isolation, Sequence Analysis, and Comparison of Two Plasmids (28 and 29 Kilobases) from the Biomining Bacterium
Leptospirillum ferrooxidans
ATCC 49879
Authors: Coram Nicolette J. , van Zyl Leonardo J. , Rawlings Douglas E. 
Published: November 2005

ABSTRACT

Two plasmids, of 28,878 bp and 28,012 bp, were isolated from
Leptospirillum ferrooxidans
ATCC 49879. Altogether, a total of 67 open reading frames (ORFs) were identified on both plasmids, of which 32 had predicted products with high homology to proteins of known function, while 11 ORFs had predicted products with homology to previously identified proteins of unknown function. Twenty-four ORFs had products with no homologues in the GenBank/NCBI database. An analysis of the ORFs and other features of the two plasmids, the first to be isolated from a bacterium of the genus
Leptospirillum
, is presented.
Symbiotic Hydrogenase Activity in
Bradyrhizobium
sp. (
Vigna
) Increases Nitrogen Content in
Vigna unguiculata
Plants
Authors: Baginsky Cecilia , Brito Belén , Imperial Juan , Ruiz-Argüeso Tomás , Palacios Jose M. 
Published: November 2005

ABSTRACT

Bradyrhizobium
sp. (
Lupinus
) and
Bradyrhizobium
sp. (
Vigna
) mutants in which hydrogenase (
hup
) activity was affected were constructed and analyzed.
Vigna unguiculata
plants inoculated with the
Bradyrhizobium
sp. (
Vigna
)
hup
mutant showed reduced nitrogenase activity and also a significant decrease in nitrogen content, suggesting a relevant contribution of hydrogenase activity to plant yield.
Comparison of the Levels of Heat Resistance of Wild-Type,
cpe
Knockout, and
cpe
Plasmid-Cured
Clostridium perfringens
Type A Strains
Authors: Raju Deepa , Sarker Mahfuzur R. 
Published: November 2005

ABSTRACT

An enterotoxin (
cpe
) plasmid was cured from a
Clostridium perfringens
non-food-borne gastrointestinal disease (NFBGID) isolate, and the heat resistance levels of wild-type,
cpe
knockout, and
cpe
plasmid-cured strains were compared. Our results demonstrated that (i) wild-type
cpe
has no influence in mediating high-level heat resistance in
C. perfringens
and (ii) the
cpe
plasmid does not confer heat sensitivity on NFBGID isolates.
Keep people informed or leave them alone? A suggested tool for identifying research participants who rightly want only limited information
Authors: Eriksson S , Helgesson G 
Published: November 2005

People taking part in research vary in the extent to which they understand information concerning their participation. Since they may choose to limit the time and effort spent on such information, lack of understanding is not necessarily an ethical problem. Researchers who notice a lack of understanding are in the quandary of not knowing whether this is due to flaws in the information process or to participants’ deliberate choices. We argue that the two explanations call for different responses.A tool for identifying those research participants who want limited information is presented. This consists of a restricted number of questions about trust in and appraisal of research, priority of time and privacy, and perception of a duty to participate. It is argued that an important group of participants who purposely lack understanding of the study can be identified with this tool. Some limitations to this approach are also discussed.
Early Event-related Potential Effects of Syllabic Processing during Visual Word Recognition
Authors: Carreiras Manuel , Vergara Marta , Barber Horacio 
Published: October 2005

Abstract
A number of behavioral studies have suggested that syllables might play an important role in visual word recognition in some languages. We report two event-related potential (ERP) experiments using a new paradigm showing that syllabic units modulate early ERP components. In Experiment 1, words and pseudowords were presented visually and colored so that there was a match or a mismatch between the syllable boundaries and the color boundaries. The results showed color-syllable congruency effects in the time window of the P200. Lexicality modulated the N400 amplitude, but no effects of this variable were obtained at the P200 window. In Experiment 2, high-and low-frequency words and pseudowords were presented in the congruent and incongruent conditions. The results again showed congruency effects at the P200 for low-frequency words and pseudowords, but not for high-frequency words. Lexicality and lexical frequency effects showed up at the N400 component. The results suggest a dissociation between syllabic and lexical effects with important consequences for models of visual word recognition.
Analysis of Single-Unit Responses to Emotional Scenes in Human Ventromedial Prefrontal Cortex
Authors: Kawasaki Hiroto , Adolphs Ralph , Oya Hiroyuki , Kovach Christopher , Damasio Hanna , Kaufman Olaf , Howard Matthew 
Published: October 2005

AbstractLesion and functional imaging studies in humans have shown that the ventral and medial prefrontal cortex is critically involved in the processing of emotional stimuli, but both of these methods have limited spatiotemporal resolution. Conversely, neurophysiological studies of emotion in nonhuman primates typically rely on stimuli that do not require elaborate cognitive processing. To begin bridging this gap, we recorded from a total of 267 neurons in the left and right orbital and anterior cingulate cortices of four patients who had chronically implanted depth electrodes for monitoring epilepsy. Peristimulus activity was recorded to standardized, complex visual scenes depicting neutral, pleasant, or aversive content. Recording locations were verified with postoperative magnetic resonance imaging. Using a conservative, multistep statistical evaluation, we found significant responses in 56 neurons; 16 of these were selective for only one emotion class, most often aversive. The findings suggest sparse and widely distributed processing of emotional value in the prefrontal cortex, with a predominance of responses to aversive stimuli.
fMRI Reveals a Common Neural Substrate of Illusory and Real Contours in V1 after Perceptual Learning
Authors: Maertens Marianne , Pollmann Stefan 
Published: October 2005

AbstractPerceptual learning involves the specific and relatively permanent modification of perception following a sensory experience. In psychophysical experiments, the specificity of the learning effects to the trained stimulus attributes (e.g., visual field position or stimulus orientation) is often attributed to assumed neural modifications at an early cortical site within the visual processing hierarchy. We directly investigated a neural correlate of perceptual learning in the primary visual cortex using fMRI. Twenty volunteers practiced a curvature discrimination on Kanizsa-type illusory contours in the MR scanner. Practice-induced changes in the BOLD response to illusory contours were compared between the pretraining and the posttraining block in those areas of the primary visual cortex (V1) that, in the same session, had been identified to represent real contours at corresponding visual field locations. A retinotopically specific BOLD signal increase to illusory contours was observed as a consequence of the training, possibly signaling the formation of a contour representation, which is necessary for performing the curvature discrimination. The effects of perceptual training were maintained over a period of about 10 months, and they were specific to the trained visual field position. The behavioral specificity of the learning effects supports an involvement of V1 in perceptual learning, and not in unspecific attentional effects.
Animal-Assisted Prolonged Exposure: A Treatment for Survivors of Sexual Assault Suffering Posttraumatic Stress Disorder
Authors: Bleiberg James , Prout Maurice , Debiak Dennis , Lefkowitz Carin , Paharia Indira 
Published: November 2005

AbstractThis paper proposes the development of a new model of treatment for survivors of sexual abuse suffering from Posttraumatic Stress Disorder (PTSD). Foa, Rothbaum, Riggs, and Murdock (1991) and Foa, Rothbaum, and Furr (2003) support Prolonged Exposure (PE) as a highly effective treatment for PTSD. However, PE can be intimidating to survivors, contributing to hesitancy to participate in the treatment. This paper posits that animal-assisted therapy (AAT) will decrease anxiety, lower physiological arousal, enhance the therapeutic alliance, and promote social lubrication. The paper also posits that AAT will enhance the value of PE by making it more accessible to survivors, increasing social interaction, and perhaps decreasing the number of sessions required for habituation to the traumatic memories.
The Song of Moses: a basis for Isaiah's prophecy
Authors: Keiser Thomas A. 
Published: November 2005

AbstractSimilarities between II Isaiah and Deuteronomy xxxii are commonly noted, however, little work has been done regarding the nature of that relationship. This article argues that there is a direct and conscious literary, theological and thematic dependence between these texts. Theologically, both passages proclaim the incomparability of Yahweh in the context of judgment-deliverance intervention with respect to Israel with the basis for the switch from judgment to deliverance the same in both texts. Thematic similarities are evident in a common presentation of the Lord, and with similar motifs such as remembrance, creation, witness, etc. Direct literary dependence is evident in the utilization of uncommon words and expressions, some of which occur in similar contexts.
Xerxes und (k)eine Marduk-Statue Überlegungen zu einem Randthema alttestamentlicher Prophetenexegese
Authors: Höffken Peter 
Published: November 2005

AbstractUntil now the story about Xerxes, carrying off a statue of Marduk from Babylon, is used in OT scholarship (U. Berges; M. Kessler e.a.). Herodot, however, is silent about that theme. He speaks about a statue, which is not Marduk. Also the archaeological findings are not clear in speaking about such an catastrophe of Esangila. We should therefore not use the Xerxes-story in OT scholarship in the future.
The call for revenge in Jeremiah's complaints (Jer xi-xx)
Authors: Avioz Michael 
Published: November 2005

AbstractThis article deals with the troublesome issue of Jeremiah's calls for revenge in the so-called 'Jeremiah's laments' (Jer xi-xx). Such calls are strange due to the fact Israelite prophets are usually conceived as intercessors. After surveying the different views and criticizing them, the author offers three solutions to the problem. Instead of focusing on our moral judgment of Jeremiah's calls for revenge, the author tries to show how they were interpreted by the author of the book of Jeremiah. Jeremiah's calls are designed according to the principle of measure for measure; the prophet is described as God's messenger who is worthy of being protected; and finally Jeremiah is conceived as trying to let justice be shown.