bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biogeographical patterns of genetic differentiation in dung beetles of the genusTrypocopris(Coleoptera, Geotrupidae) inferred from mtDNA and AFLP analyses
Authors: Carisio Loredana , Cervella Piero , Palestrini Claudia , DelPero Massimiliano , Rolando Antonio 
Published: June 2004

AbstractAim To examine the phylogeography and population structure of three dung beetle species of the genusTrypocopris(Coleoptera, Geotrupidae). We wanted to test whether genetic differences and genealogies among populations were in accordance with morphologically described subspecies and we aimed to establish times of divergence among subspecies to depict the appropriate temporal framework of their phylogeographical differentiation. We also wished to investigate the historical demographic events and the relative influences of gene flow and drift on the distribution of genetic variability of the different populations.Location Europe (mostly Italy).Methods We collected adult males from dung pats from 15 Italian localities over the period 2000–2002. For sequence analysis, some dried specimens from Albania, Croatia, Slovakia and Spain were also used. We applied cytochrome oxidase I mitochondrial DNA sequencing and the amplified fragment length polymorphism (AFLP) technique to determine whether phylogeographical patterns within the three species support the proposed hypotheses of subspecies designations, and to detect further structure among populations that might mediate diversification.Results and main conclusions The results show a high concordance between the distribution of mtDNA variation and the main morphological groups recognized as subspecies, which thus may represent independent evolutionary units. The degree of mitochondrial divergence suggests that speciation events occurred during the Pliocene, while diversification of the main subspecific lineages took place in the Pleistocene, fromc.0.3 to 1.5 Ma. Mitochondrial and nuclear data also reveal that there is phylogeographical structuring among populations within each of the main groups and that both contemporary and historical processes determined this pattern of genetic structure. Geographical populations form monophyletic clades in both phylogenetic and network reconstructions. Despite the high levels of intrapopulational diversity,FSTvalues indicate moderate but significant genetic differentiation among populations, and a Bayesian clustering analysis of the AFLP data clearly separates the geographical populations. Nucleotide and gene diversity estimates reveal interspecific differences in the degree of diversification among populations that may be related to the different ecological requirements of the three species.
Distraction produces an increase in pain‐evoked anterior cingulate activity
Authors: Dowman Robert 
Published: June 2004

AbstractThis study examined the effects of distraction on pain‐evoked activity in the anterior cingulate cortex (ACC). Twenty‐eight healthy adults were given painful electrical stimulation of the sural nerve during an attend condition, where they rated the subjective magnitude of each electrical stimulus, and during a distraction condition, where they performed an arithmetic distraction task. The magnitude of the pain‐evoked ACC activity was estimated from the dipole source localization analysis of the somatosensory evoked potential. Subjective pain ratings were smaller and pain‐evoked ACC activity was larger during the distraction condition than during the attend condition. Recent regional cerebral blood flow studies have also reported a distraction‐related increase in pain‐evoked ACC activity. Our results confirm these reports, and verify that the distraction effect specifically involves pain‐evoked ACC activity. The cognitive demands of the distraction task present the possibility that the pain‐evoked ACC activity might be involved, at least in part, in response competition and/or orienting attention toward painful stimuli.
Characterization and Heterologous Gene Expression of a Novel Esterase fromLactobacillus caseiCL96
Authors: Choi Young J. , Miguez Carlos B. , Lee Byong H. 
Published: June 2004

ABSTRACTA novel esterase gene (estI) ofLactobacillus caseiCL96 was localized on a 3.3-kb BamHI DNA fragment containing an open reading frame (ORF) of 1,800 bp. The ORF ofestIwas isolated by PCR and expressed inEscherichia coli, the methylotrophic bacteriumMethylobacterium extorquens, and the methylotrophic yeastPichia pastorisunder the control of T7, methanol dehydrogenase (PmxaF), and alcohol oxidase (AOX1) promoters, respectively. The amino acid sequence of EstI indicated that the esterase is a novel member of the GHSMG family of lipolytic enzymes and that the enzyme contains a lipase-like catalytic triad, consisting of Ser325, Asp516, and His558.E. coliBL21(DE3)/pLysS containingestIexpressed a novel 67.5-kDa protein corresponding to EstI in an N-terminal fusion with the S · tag peptide. The recombinantL. caseiCL96 EstI protein was purified to electrophoretic homogeneity in a one-step affinity chromatography procedure on S-protein agarose. The optimum pH and temperature of the purified enzyme were 7.0 and 37°C, respectively. Among the pNP (p-nitrophenyl) esters tested, the most selective substrate was pNP-caprylate (C8), withKmandkcatvalues of 14 ± 1.08 μM and 1,245 ± 42.3 S−1, respectively.
Biofilm Development and Cell Death in the Marine Bacterium
Pseudoalteromonas tunicata
Authors: Mai-Prochnow Anne , Evans Flavia , Dalisay-Saludes Doralyn , Stelzer Sacha , Egan Suhelen , James Sally , Webb Jeremy S. , Kjelleberg Staffan 
Published: June 2004

ABSTRACT

The newly described green-pigmented bacterium
Pseudoalteromonas tunicata
(D2) produces target-specific inhibitory compounds against bacteria, algae, fungi, and invertebrate larvae and is frequently found in association with living surfaces in the marine environment. As part of our studies on the ecology of
P. tunicata
and its interaction with marine surfaces, we examined the ability of
P. tunicata
to form biofilms under continuous culture conditions within the laboratory.
P. tunicata
biofilms exhibited a characteristic architecture consisting of differentiated microcolonies surrounded by water channels. Remarkably, we observed a repeatable pattern of cell death during biofilm development of
P. tunicata
, similar to that recently reported for biofilms of
Pseudomonas aeruginosa
(J. S. Webb et al., J. Bacteriol.
185:
4585-4595, 2003). Killing and lysis occurred inside microcolonies, apparently resulting in the formation of voids within these structures. A subpopulation of viable cells was always observed within the regions of killing in the biofilm. Moreover, extensive killing in mature biofilms appeared to result in detachment of the biofilm from the substratum. A novel 190-kDa autotoxic protein produced by
P. tunicata
, designated AlpP, was found to be involved in this biofilm killing and detachment. A Δ
alpP
mutant derivative of
P. tunicata
was generated, and this mutant did not show cell death during biofilm development. We propose that AlpP-mediated cell death plays an important role in the multicellular biofilm development of
P. tunicata
and subsequent dispersal of surviving cells within the marine environment.
Engineering the
nifH
Promoter Region and Abolishing Poly-β-Hydroxybutyrate Accumulation in
Rhizobium etli
Enhance Nitrogen Fixation in Symbiosis with
Phaseolus vulgaris
Authors: Peralta Humberto , Mora Yolanda , Salazar Emmanuel , Encarnación Sergio , Palacios Rafael , Mora Jaime 
Published: June 2004

ABSTRACT

Rhizobium etli
, as well as some other rhizobia, presents nitrogenase reductase (
nifH
) gene reiterations. Several
R. etli
strains studied in this laboratory showed a unique organization and contained two complete
nifHDK
operons (copies a and b) and a truncated
nifHD
operon (copy c). Expression analysis of
lacZ
fusion demonstrated that copies a and b in strain CFN42 are transcribed at lower levels than copy c, although this copy has no discernible role during nitrogen fixation. To increase nitrogenase production, we constructed a chimeric
nifHDK
operon regulated by the strong
nifHc
promoter sequence and expressed it in symbiosis with the common bean plant (
Phaseolus vulgaris
), either cloned on a stably inherited plasmid or incorporated into the symbiotic plasmid (pSym). Compared with the wild-type strain, strains with the nitrogenase overexpression construction assayed in greenhouse experiments had, increased nitrogenase activity (58% on average), increased plant weight (32% on average), increased nitrogen content in plants (15% at 32 days postinoculation), and most importantly, higher seed yield (36% on average), higher nitrogen content (25%), and higher nitrogen yield (72% on average) in seeds. Additionally, expression of the chimeric
nifHDK
operon in a poly-β-hydroxybutyrate-negative
R. etli
strain produced an additive effect in enhancing symbiosis. To our knowledge, this is the first report of increased seed yield and nutritional content in the common bean obtained by using only the genetic material already present in
Rhizobium
.
Novel Expression System for Large-Scale Production and Purification of Recombinant Class IIa Bacteriocins and Its Application to Piscicolin 126
Authors: Gibbs Gerard M. , Davidson Barrie E. , Hillier Alan J. 
Published: June 2004

ABSTRACT

Piscicolin 126 is a class IIa bacteriocin isolated from
Carnobacterium piscicola
JG126 that exhibits strong activity against
Listeria monocytogenes
. The gene encoding mature piscicolin 126 (m-
pisA
) was cloned into an
Escherichia coli
expression system and expressed as a thioredoxin-piscicolin 126 fusion protein that was purified by affinity chromatography. Purified recombinant piscicolin 126 was obtained after CNBr cleavage of the fusion protein followed by reversed-phase chromatography. Recombinant piscicolin 126 contained a single disulfide bond and had a mass identical to that of native piscicolin 126. This novel bacteriocin expression system generated approximately 26 mg of purified bacteriocin from 1 liter of
E. coli
culture. The purified recombinant piscicolin 126 acted by disruption of the bacterial cell membrane.
Morphological, Chemical, and Genetic Diversity of Tropical Marine Cyanobacteria
Lyngbya
spp. and
Symploca
spp. (
Oscillatoriales
)
Authors: Thacker Robert W. , Paul Valerie J. 
Published: June 2004

ABSTRACT

Although diverse natural products have been isolated from the benthic, filamentous cyanobacterium
Lyngbya majuscula
, it is unclear whether this chemical variation can be used to establish taxonomic relationships among disparate collections. We compared morphological characteristics, secondary-metabolite compositions, and partial 16S ribosomal DNA (rDNA) sequences among several collections of
L. majuscula
Gomont,
Lyngbya
spp., and
Symploca
spp. from Guam and the Republic of Palau. The morphological characteristics examined were cell length, cell width, and the presence or absence of a calyptra. Secondary metabolites were analyzed by two-dimensional thin-layer chromatography. Each collection possessed a distinct cellular morphology that readily distinguished
Lyngbya
spp. from
Symploca
spp. Each collection yielded a unique chemotype, but common chemical characteristics were shared among four collections of
L. majuscula
. A phylogeny based on secondary-metabolite composition supported the reciprocal monophyly of
Lyngbya
and
Symploca
but yielded a basal polytomy for
Lyngbya
. Pairwise sequence divergence among species ranged from 10 to 14% across 605 bp of 16S rDNA, while collections of
L. majuscula
showed 0 to 1.3% divergence. Although the phylogeny of 16S rDNA sequences strongly supported the reciprocal monophyly of
Lyngbya
and
Symploca
as well as the monophyly of
Lyngbya bouillonii
and
L. majuscula
, genetic divergence was not correlated with chemical and morphological differences. These data suggest that 16S rDNA sequence analyses do not predict chemical variability among
Lyngbya
species. Other mechanisms, including higher rates of evolution for biosynthetic genes, horizontal gene transfer, and interactions between different genotypes and environmental conditions, may play important roles in generating qualitative and quantitative chemical variation within and among
Lyngbya
species.
Evidence for the Presence of
Simkania negevensis
in Drinking Water and in Reclaimed Wastewater in Israel
Authors: Kahane Simona , Platzner Nizhia , Dvoskin Bella , Itzhaki Amir , Friedman Maureen G. 
Published: June 2004

ABSTRACT

Simkania negevensis
is a recently discovered chlamydia-like intracellular microorganism which has been associated with bronchiolitis in infants and with community-acquired pneumonia in adults; a high seroprevalence of antibodies to the microorganism has been found in various population groups.
S. negevensis
can be grown in various cell lines as well as in free-living amoebae such as
Acanthamoeba polyphaga
. In this study, evidence for the existence of
Simkania
or
Simkania
-like microorganisms in drinking water and in reclaimed wastewater is presented for the first time. Detection of the microorganism was made possible by the development of a specific and sensitive filter membrane immunoassay and was confirmed by PCR detection of microbial DNA in the water samples. The common presence of
S. negevensis
in water sources together with the high seroprevalence of antibodies to it and early age of acquisition of infection may implicate water as a source of infection. The possible significance of this finding for public health and for municipal water testing and treatment needs to be further examined.
Evaluation of a Cocktail of Three Bacteriophages for Biocontrol of
Escherichia coli
O157:H7
Authors: O'Flynn G. , Ross R. P. , Fitzgerald G. F. , Coffey A. 
Published: June 2004

ABSTRACT

Escherichia coli
O157:H7 is an endemic pathogen causing a variety of human diseases including mild diarrhea, hemorrhagic colitis, hemolytic-uremic syndrome, and thrombotic thrombocytopenic purpura. This study concerns the exploitation of bacteriophages as biocontrol agents to eliminate the pathogen
E. coli
O157:H7. Two distinct lytic phages (e11/2 and e4/1c) isolated against a human strain of
E. coli
O157:H7, a previously isolated lytic phage (pp01), and a cocktail of all three phages were evaluated for their ability to lyse the bacterium in vivo and in vitro. Phage e11/2, pp01, and the cocktail of all three virulent phages resulted in a 5-log-unit reduction of pathogen numbers in 1 h at 37°C. However, bacteriophage-insensitive mutants (BIMs) emerged following the challenge. All tested BIMs had a growth rate which approximated that of the parental O157 strain, although many of these BIMs had a smaller, more coccoid cellular morphology. The frequency of BIM formation (10
−6
CFU) was similar for e11/2, pp01, and the phage cocktail, while BIMs insensitive to e4/1c occurred at the higher frequency (10
−4
CFU). In addition, BIMs commonly reverted to phage sensitivity within 50 generations. In an initial meat trial experiment, the phage cocktail completely eliminated
E. coli
O157:H7 from the beef meat surface in seven of nine cases. Given that the frequency of BIM formation is low (10
−6
CFU) for two of the phages, allied to the propensity of these mutants to revert to phage sensitivity, we expect that BIM formation should not hinder the use of these phages as biocontrol agents, particularly since low levels of the pathogen are typically encountered in the environment.
Virus-Binding Proteins Recovered from Bacterial Culture Derived from Activated Sludge by Affinity Chromatography Assay Using a Viral Capsid Peptide
Authors: Sano Daisuke , Matsuo Takahiro , Omura Tatsuo 
Published: June 2004

ABSTRACT

The contamination of water environments by pathogenic viruses has raised concerns about outbreaks of viral infectious diseases in our society. Because conventional water and wastewater treatment systems are not effective enough to inactivate or remove pathogenic viruses, a new technology for virus removal needs to be developed. In this study, the virus-binding proteins (VBPs) in a bacterial culture derived from activated sludge were successfully recovered. The recovery of VBPs was achieved by applying extracted crude proteins from a bacterial culture to an affinity column in which a custom-made peptide of capsid protein from the poliovirus type 1 (PV1) Mahoney strain (H
2
N-DNPASTTNKDKL-COOH) was immobilized as a ligand. VBPs exhibited the ability to adsorb infectious particles of PV1 Sabin 1 as determined by enzyme-linked immunosorbent assay. The evaluation of surface charges of VBPs with ion-exchange chromatography found that a majority of VBP molecules had a net negative charge under the conditions of affinity chromatography. On the other hand, a calculated isoelectric point implied that the viral peptide in the affinity column was also charged negatively. As a result, the adsorption of the VBPs to the viral peptide in the affinity column occurred with a strong attractive force that was able to overcome the electrostatic repulsive force. Two-dimensional electrophoresis revealed that the isolated VBPs include a number of proteins, and their molecular masses were widely distributed but smaller than 100 kDa. Amino acid sequences of N termini of five VBPs were determined. Homology searches for the N termini against all protein sequences in the National Center for Biotechnology Information (NCBI) database showed that the isolated VBPs in this study were newly discovered proteins. These VBPs that originated with bacteria in activated sludge might be stable, because they are existing in the environment of wastewater treatments. Therefore, a virus removal technology utilizing VBPs as viral adsorbents can be developed, since it is possible to replicate VBPs by protein cloning techniques.
Distribution of RuBisCO Genotypes along a Redox Gradient in Mono Lake, California
Authors: Giri Bruno J. , Bano Nasreen , Hollibaugh James T. 
Published: June 2004

ABSTRACT

Partial sequences of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) (EC 4.1.1.39) genes were retrieved from samples taken along a redox gradient in alkaline, hypersaline Mono Lake, Calif. The form I gene (
cbbL
) was found in all samples, whereas form II (
cbbM
) was not retrieved from any of the samples. None of the RuBisCO sequences we obtained were closely related (nucleotide similarity, <90%) to sequences in the database. Some could be attributed to organisms isolated from the lake (
Cyanobium
) or appearing in enrichment cultures. Most (52%) of the sequences fell into in one clade, containing sequences that were identical to sequences retrieved from an enrichment culture grown with nitrate and sulfide, and another clade contained sequences identical to those retrieved from an arsenate-reducing, sulfide-oxidizing enrichment.
Effects of Quaternary-Ammonium-Based Formulations on Bacterial Community Dynamics and Antimicrobial Susceptibility
Authors: McBain Andrew J. , Ledder Ruth G. , Moore Louise E. , Catrenich Carl E. , Gilbert Peter 
Published: June 2004

ABSTRACTQuaternary ammonium compounds (QACs) are widely used as adjuncts to hygiene in domestic cleaning products. Current concern that the increased use of such biocides in consumer products might contribute to the emergence of antibiotic resistance has led us to examine the effects of a QAC-containing domestic cleaning fluid on the population dynamics and antimicrobial susceptibility of domestic sink drain biofilm communities. QAC susceptibilities of numerically dominant, culturable drain bacteria (15 genera, 17 species) were determined in vitro before and after repeated QAC exposure (14 passages). A fully characterized drain microcosm was then exposed to short-term (12 days) and long-term (3 months) dosing with a QAC-containing domestic detergent (QD). QAC exposure of isolated cultures caused both increases (three species) and circa twofold decreases (six species) in QAC susceptibility. The susceptibility ofRalstoniasp. was considerably decreased following 14 consecutive QAC passages. Control drain microcosm biofilms maintained dynamic stability, as evidenced by culture and denaturing gradient gel electrophoresis (DGGE) analysis. Bacterial population densities were largely unaffected during short-term exposure to use levels of QD, although 50% QD caused circa 10-fold viability reductions. DGGE analysis supported these observations; identified the major microcosm genera asPseudomonas,Pseudoalteromonas,Erwinia, andEnterobacter, and showed that aeromonads increased in abundance under 10 to 50% QD. Long-term exposure of the microcosms to QD did not significantly alter the pattern of antimicrobial susceptibility. These data demonstrate the recalcitrance of domestic drain biofilms toward QAC and that although repeated QAC exposure of drain isolates in pure culture results in susceptibility change in some test bacteria, such changes do not necessarily occur within complex communities.
Adaptation of
Escherichia coli
O157:H7 to pH Alters Membrane Lipid Composition, Verotoxin Secretion, and Resistance to Simulated Gastric Fluid Acid
Authors: Yuk Hyun-Gyun , Marshall Douglas L. 
Published: June 2004

ABSTRACT

The influence of adaptation to pH (from pH 5.0 to 9.0) on membrane lipid composition, verotoxin concentration, and resistance to acidic conditions in simulated gastric fluid (SGF) (pH 1.5, 37°C) was determined for
Escherichia coli
O157:H7 (HEC, ATCC 43895), an
rpoS
-deficient mutant of ATCC 43895 (HEC-RM, FRIK 816-3), and nonpathogenic
E. coli
(NPEC, ATCC 25922). Regardless of the strain, D values (in SGF) of acid-adapted cells were higher than those of non-acid-adapted cells, with HEC adapted at pH 5.0 having the greatest D value, i.e., 25.6 min. Acid adaptation increased the amounts of palmitic acid (C16:0) and decreased
cis
-vaccenic acid (C18:1ω7c) in the membrane lipids of all strains. The ratio of
cis
-vaccenic acid to palmitic acid increased at acidic pH, causing a decrease in membrane fluidity. HEC adapted to pH 8.3 and HEC-RM adapted to pH 7.3 exhibited the greatest verotoxin concentrations (2,470 and 1,460 ng/ml, respectively) at approximately 10
8
CFU/ml. In addition, the ratio of extracellular to intracellular verotoxin concentration decreased at acidic pH, possibly due to the decrease of membrane fluidity. These results suggest that while the
rpoS
gene does not influence acid resistance in acid-adapted cells it does confer decreased membrane fluidity, which may increase acid resistance and decrease verotoxin secretion.