bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does Virus-Induced Lysis Contribute Significantly to Bacterial Mortality in the Oxygenated Sediment Layer of Shallow Oxbow Lakes?
Authors: Fischer Ulrike R. , Wieltschnig Claudia , Kirschner Alexander K. T. , Velimirov Branko 
Published: September 2003

ABSTRACT

Despite the recognition that viruses are ubiquitous components of aquatic ecosystems, the number of studies on viral abundance and the ecological role of viruses in sediments is scarce. In this investigation, the interactions between viruses and bacteria were studied in the oxygenated silty sediment layer of a mesotrophic oxbow lake. A long-term study (13 months) and a diel study revealed that viruses are a numerically important and dynamic component of the microbial community. The abundance and decay rates ranged from 4.3 × 10
9
to 7.2 × 10
9
particles ml of wet sediment
−1
and from undetectable to 22.2 × 10
7
particles ml
−1
h
−1
, respectively, and on average the values were 2 orders of magnitude higher than the values for the overlying water. In contrast to our expectations, viruses did not contribute significantly to the bacterial mortality in the sediment, since on average only 6% (range, 0 to 25%) of the bacterial secondary production was controlled by viruses. The low impact of viruses on the bacterial community may be associated with the quantitatively low viral burden that benthic bacteria have to cope with compared to the viral burden with which bacterial assemblages in the water column are confronted. The virus-to-bacterium ratio of the sediment varied between 0.9 and 3.2, compared to a range of 5.0 to 12.4 obtained for the water column. We speculate that despite high numbers of potential hosts, the possibility of encountering a host cell is limited by the physical conditions in the sediment, which is therefore not a favorable environment for viral proliferation. Our data suggest that viruses do not play an important role in the processing and transfer of bacterial carbon in the oxygenated sediment layer of the environment investigated.
Effect of Acidic pH on Expression of Surface-Associated Proteins of
Streptococcus oralis
Authors: Wilkins Joanna C. , Beighton David , Homer Karen A. 
Published: September 2003

ABSTRACT

Streptococcus oralis
, a member of the mitis group of oral streptococci, is implicated in the pathogenesis of infective endocarditis and is the predominant aciduric non-mutans-group streptococcus in dental plaque. We undertook to identify the most abundant surface-associated proteins of
S. oralis
and to investigate changes in protein expression when the organism was grown under acidic culture conditions. Surface-associated proteins were extracted from cells grown in batch culture, separated by two-dimensional gel electrophoresis, excised, digested with trypsin, and analyzed by matrix-assisted laser desorption ionization-time of flight mass spectrometry and liquid chromatography-tandem mass spectrometry. Putative functions were assigned by homology to a translated genomic database of
Streptococcus pneumoniae
. A total of 27 proteins were identified; these included a lipoprotein, a ribosome recycling factor, and the glycolytic enzymes phosphoglycerate kinase, fructose bisphosphate aldolase, glyceraldehyde-3-phosphate dehydrogenase, and enolase. The most abundant protein, phosphocarrier protein HPr, was present as three isoforms. Neither lactate dehydrogenase nor pyruvate oxidase, dominant intracellular proteins, were present among the proteins on the gels, demonstrating that proteins in the surface-associated pool did not arise as a result of cell lysis. Eleven of the proteins identified were differentially expressed when cells were grown at pH 5.2 versus pH 7.0, and these included superoxide dismutase, a homologue of dipeptidase V from
Lactococcus lactis
, and the protein translation elongation factors G, Tu, and Ts. This study has extended the range of streptococcal proteins known to be expressed at the cell surface. Further investigations are required to ascertain their functions at this extracellular location and determine how their expression is influenced by other environmental conditions.
Angiotensin I-Converting-Enzyme-Inhibitory and Antibacterial Peptides from
Lactobacillus helveticus
PR4 Proteinase-Hydrolyzed Caseins of Milk from Six Species
Authors: Minervini F. , Algaron F. , Rizzello C. G. , Fox P. F. , Monnet V. , Gobbetti M. 
Published: September 2003

ABSTRACT

Sodium caseinates prepared from bovine, sheep, goat, pig, buffalo or human milk were hydrolyzed by a partially purified proteinase of
Lactobacillus helveticus
PR4. Peptides in each hydrolysate were fractionated by reversed-phase fast-protein liquid chromatography. The fractions which showed the highest angiotensin I-converting-enzyme (ACE)-inhibitory or antibacterial activity were sequenced by mass spectrum and Edman degradation analyses. Various ACE-inhibitory peptides were found in the hydrolysates: the bovine α
S1
-casein (α
S1
-CN) 24-47 fragment (f24-47), f169-193, and β-CN f58-76; ovine α
S1
-CN f1-6 and α
S2
-CN f182-185 and f186-188; caprine β-CN f58-65 and α
S2
-CN f182-187; buffalo β-CN f58-66; and a mixture of three tripeptides originating from human β-CN. A mixture of peptides with a C-terminal sequence, Pro-Gly-Pro, was found in the most active fraction of the pig sodium caseinate hydrolysate. The highest ACE-inhibitory activity of some peptides corresponded to the concentration of the ACE inhibitor (
S
)-
N
-(1-[ethoxycarbonyl]-3-phenylpropyl)-ala-pro maleate (enalapril) of 49.253 μg/ml (100 μmol/liter). Several of the above sequences had features in common with other ACE-inhibitory peptides reported in the literature. The 50% inhibitory concentration (IC
50
) of some of the crude peptide fractions was very low (16 to 100 μg/ml). Some identified peptides were chemically synthesized, and the ACE-inhibitory activity and IC
50
s were confirmed. An antibacterial peptide corresponding to β-CN f184-210 was identified in human sodium caseinate hydrolysate. It showed a very large spectrum of inhibition against gram-positive and -negative bacteria, including species of potential clinical interest, such as
Enterococcus faecium
,
Bacillus megaterium
,
Escherichia coli
,
Listeria innocua
,
Salmonella
spp.,
Yersinia enterocolitica
, and
Staphylococcus aureus
. The MIC for
E. coli
F19 was ca. 50 μg/ml. Once generated, the bioactive peptides were resistant to further degradation by proteinase of
L. helveticus
PR4 or by trypsin and chymotrypsin.
Population Genetics of the Nomenspecies
Enterobacter cloacae
Authors: Hoffmann Harald , Roggenkamp Andreas 
Published: September 2003

ABSTRACT

The genetic heterogeneity of the nomenspecies
Enterobacter cloacae
is well known.
Enterobacter asburiae
,
Enterobacter cancerogenus
,
Enterobacter dissolvens
,
Enterobacter hormaechei
,
Enterobacter kobei
, and
Enterobacter nimipressuralis
are closely related to it and are subsumed in the so-called
E. cloacae
complex. DNA-DNA hybridization studies performed previously identified at least five DNA-relatedness groups of this complex. In order to analyze the genetic structure and the phylogenetic relationships between the clusters of the nomenspecies
E. cloacae
, 206 strains collected from 22 hospitals, a veterinarian, and an agricultural center in 11 countries plus all 13 type strains of the genus and reference strain CDC 1347-71
R
were examined with a combination of sequence and PCR-restriction fragment length polymorphism (PCR-RFLP) analyses of the three housekeeping genes
hsp60
,
rpoB
, and
hemB
as well as
ampC
, the gene of a class C β-lactamase. Based on the neighbor-joining tree of the
hsp60
sequences, 12 genetic clusters (I to XII) and an unstable sequence crowd (xiii) were identified. The robustness of the genetic clusters was confirmed by analyses of
rpoB
and
hemB
sequences and
ampC
PCR-RFLPs. Sequence crowd xiii split into two groups after
rpoB
analysis. Only three strains formed a cluster with the type strain of
E. cloacae
, indicating that the minority of isolates identified as
E. cloacae
truly belong to the species; 13% of strains grouped with other type strains of the genus, suggesting that the phenotypes of these species seem to be more heterogeneous than so far believed. Three clusters represented 70% of strains, but none of them included a type or reference strain. The genetic clustering presented in this study might serve as a framework for future studies dealing with taxonomic, evolutionary, epidemiological, or pathogenetic characteristics of bacteria belonging to the
E. cloacae
complex.
Novel Derivatives of 9,10-Anthraquinone Are Selective Algicides against the Musty-Odor CyanobacteriumOscillatoria perornata
Authors: Schrader Kevin K. , Nanayakkara N. P. Dhammika , Tucker Craig S. , Rimando Agnes M. , Ganzera Markus , Schaneberg Brian T. 
Published: September 2003

ABSTRACTMusty “off-flavor” in pond-cultured channel catfish (Ictalurus punctatus) costs the catfish production industry in the United States at least $30 million annually. The cyanobacteriumOscillatoria perornata(Skuja) is credited with being the major cause of musty off-flavor in farm-raised catfish in Mississippi. The herbicides diuron and copper sulfate, currently used by catfish producers as algicides to help mitigate musty off-flavor problems, have several drawbacks, including broad-spectrum toxicity towards the entire phytoplankton community that can lead to water quality deterioration and subsequent fish death. By use of microtiter plate bioassays, a novel group of compounds derived from the natural compound 9,10-anthraquinone have been found to be much more selectively toxic towardsO. perornatathan diuron and copper sulfate. In efficacy studies using limnocorrals placed in catfish production ponds, application rates of 0.3 μM (125 μg/liter) of the most promising anthraquinone derivative, 2-[methylamino-N-(1′-methylethyl)]-9,10-anthraquinone monophosphate (anthraquinone-59), dramatically reduced the abundance ofO. perornataand levels of 2-methylisoborneol, the musty compound produced byO. perornata. The abundance of green algae and diatoms increased dramatically 2 days after application of a 0.3 μM concentration of anthraquinone-59 to pond water within the limnocorrals. The half-life of anthraquinone-59 in pond water was determined to be 19 h, making it much less persistent than diuron. Anthraquinone-59 appears to be promising for use as a selective algicide in catfish aquaculture.
Fluorescence-Activated Cell Sorting of Specific Affibody-Displaying Staphylococci
Authors: Wernérus Henrik , Samuelson Patrik , Ståhl Stefan 
Published: September 2003

ABSTRACT

Efficient enrichment of staphylococcal cells displaying specific heterologous affinity ligands on their cell surfaces was demonstrated by using fluorescence-activated cell sorting. Using bacterial surface display of peptide or protein libraries for the purpose of combinatorial protein engineering has previously been investigated by using gram-negative bacteria. Here, the potential for using a gram-positive bacterium was evaluated by employing the well-established surface expression system for
Staphylococcus carnosus
.
Staphylococcus aureus
protein A domains with binding specificity to immunoglobulin G or engineered specificity for the G protein of human respiratory syncytial virus were expressed as surface display on
S. carnosus
cells. The surface accessibility and retained binding specificity of expressed proteins were demonstrated in whole-cell enzyme and flow cytometry assays. Also, affibody-expressing target cells could be sorted essentially quantitatively from a moderate excess of background cells in a single step by using a high-stringency sorting mode. Furthermore, in a simulated library selection experiment, a more-than-25,000-fold enrichment of target cells could be achieved through only two rounds of cell sorting and regrowth. The results obtained indicate that staphylococcal surface display of affibody libraries combined with fluoresence-activated cell sorting might indeed constitute an attractive alternative to existing technology platforms for affinity-based selections.
Similarity of Tetracycline Resistance Genes Isolated from Fish Farm Bacteria to Those from Clinical Isolates
Authors: Furushita Manabu , Shiba Tsuneo , Maeda Toshimichi , Yahata Megumi , Kaneoka Azusa , Takahashi Yukinori , Torii Keizo , Hasegawa Tadao , Ohta Michio 
Published: September 2003

ABSTRACT

Tetracycline-resistant (Tet
r
) bacteria were isolated from fishes collected at three different fish farms in the southern part of Japan in August and September 2000. Of the 66 Tet
r
gram-negative strains, 29 were identified as carrying
tetB
only. Four carried
tetY
, and another four carried
tetD
. Three strains carried
tetC
, two strains carried
tetB
and
tetY
, and one strain carried
tetC
and
tetG
. Sequence analyses indicated the identity in Tet
r
genes between the fish farm bacteria and clinical bacteria: 99.3 to 99.9% for
tetB
, 98.2 to 100% for
tetC
, 99.7 to 100% for
tetD
, 92.0 to 96.2% for
tetG
, and 97.1 to 100% for
tetY
. Eleven of the Tet
r
strains transferred Tet
r
genes by conjugation to
Escherichia coli
HB-101. All transconjugants were resistant to tetracycline, oxycycline, doxycycline, and minocycline. The donors included strains of
Photobacterium
,
Vibrio
,
Pseudomonas
,
Alteromonas
,
Citrobacter
, and
Salmonella
spp., and they transferred
tetB
,
tetY
, or
tetD
to the recipients. Because NaCl enhanced their growth, these Tet
r
strains, except for the
Pseudomonas
,
Citrobacter
, and
Salmonella
strains, were recognized as marine bacteria. Our results suggest that
tet
genes from fish farm bacteria have the same origins as those from clinical strains.
Introduction of
Culex
Toxicity into
Bacillus thuringiensis
Cry4Ba by Protein Engineering
Authors: Abdullah Mohd Amir F. , Alzate Oscar , Mohammad Marwan , McNall Rebecca J. , Adang Michael J. , Dean Donald H. 
Published: September 2003

ABSTRACT

Bacillus thuringiensis
mosquitocidal toxin Cry4Ba has no significant natural activity against
Culex quinquefasciatus
or
Culex pipiens
(50% lethal concentrations [LC
50
], >80,000 and >20,000 ng/ml, respectively). We introduced amino acid substitutions in three putative loops of domain II of Cry4Ba. The mutant proteins were tested on four different species of mosquitoes,
Aedes aegypti
,
Anopheles quadrimaculatus
,
C
.
quinquefasciatus
, and
C
.
pipiens
. Putative loop 1 and 2 exchanges eliminated activity towards
A
.
aegypti
and
A
.
quadrimaculatus
. Mutations in a putative loop 3 resulted in a final increase in toxicity of >700-fold and >285-fold against
C
.
quinquefasciatus
(LC
50
≅ 114 ng/ml) and
C
.
pipiens
(LC
50
⩬ 37 ng/ml), respectively. The enhanced protein (mutein) has very little negative effect on the activity against
Anopheles
or
Aedes
. These results suggest that the introduction of short variable sequences of the loop regions from one toxin into another might provide a general rational design approach to enhancing
B
.
thuringiensis
Cry toxins.
Characterization of Microbial Communities in Gas Industry Pipelines
Authors: Zhu Xiang Y. , Lubeck John , Kilbane John J. 
Published: September 2003

ABSTRACT

Culture-independent techniques, denaturing gradient gel electrophoresis (DGGE) analysis, and random cloning of 16S rRNA gene sequences amplified from community DNA were used to determine the diversity of microbial communities in gas industry pipelines. Samples obtained from natural gas pipelines were used directly for DNA extraction, inoculated into sulfate-reducing bacterium medium, or used to inoculate a reactor that simulated a natural gas pipeline environment. The variable V2-V3 (average size, 384 bp) and V3-V6 (average size, 648 bp) regions of bacterial and archaeal 16S rRNA genes, respectively, were amplified from genomic DNA isolated from nine natural gas pipeline samples and analyzed. A total of 106 bacterial 16S rDNA sequences were derived from DGGE bands, and these formed three major clusters: beta and gamma subdivisions of
Proteobacteria
and gram-positive bacteria. The most frequently encountered bacterial species was
Comamonas denitrificans
, which was not previously reported to be associated with microbial communities found in gas pipelines or with microbially influenced corrosion. The 31 archaeal 16S rDNA sequences obtained in this study were all related to those of methanogens and phylogenetically fall into three clusters: order I,
Methanobacteriales
; order III,
Methanomicrobiales
; and order IV,
Methanosarcinales
. Further microbial ecology studies are needed to better understand the relationship among bacterial and archaeal groups and the involvement of these groups in the process of microbially influenced corrosion in order to develop improved ways of monitoring and controlling microbially influenced corrosion.
Morphological, Host Range, and Genetic Characterization of Two Coliphages
Authors: Goodridge Lawrence , Gallaccio Alicia , Griffiths Mansel W. 
Published: September 2003

ABSTRACTTwo coliphages, AR1 and LG1, were characterized based on their morphological, host range, and genetic properties. Transmission electron microscopy showed that both phages belonged to theMyoviridae; phage particles of LG1 were smaller than those of AR1 and had an isometric head 68 nm in diameter and a complex contractile tail 111 nm in length. Transmission electron micrographs of AR1 showed phage particles consisting of an elongated isometric head of 103 by 74 nm and a complex contractile tail 116 nm in length. Both phages were extensively tested on many strains ofEscherichia coliand other enterobacteria. The results showed that both phages could infect many serotypes ofE.coli. Among the enterobacteria,Proteus mirabilis,Shigella dysenteriae, and twoSalmonellastrains were lysed by the phages. The genetic material of AR1 and LG1 was characterized. Phage LG1 had a genome size of 49.5 kb compared to 150 kb for AR1. Restriction endonuclease analysis showed that several restriction enzymes could degrade DNA from both phages. The morphological, genome size, and restriction endonuclease similarities between AR1 and phage T4 were striking. Southern hybridizations showed that AR1 and T4 are genetically related. The wide host ranges of phages AR1 and LG1 suggest that they may be useful as biocontrol, therapeutic, or diagnostic agents to control and detect the prevalence ofE.coliin animals and food.
Effect of
Campylobacter
-Specific Maternal Antibodies on
Campylobacter jejuni
Colonization in Young Chickens
Authors: Sahin Orhan , Luo Naidan , Huang Shouxiong , Zhang Qijing 
Published: September 2003

ABSTRACT

Using laboratory challenge experiments, we examined whether
Campylobacter-
specific maternal antibody (MAB) plays a protective role in young chickens, which are usually free of
Campylobacter
under natural production conditions. Kinetics of
C. jejuni
colonization were compared by infecting 3-day-old broiler chicks, which were naturally positive for
Campylobacter
-specific MAB, and 21-day-old broilers, which were negative for
Campylobacter
-specific MAB. The onset of colonization occurred much sooner in birds challenged at the age of 21 days than it did in the birds inoculated at 3 days of age, which suggested a possible involvement of specific MAB in the delay of colonization. To further examine this possibility, specific-pathogen-free layer chickens were raised under laboratory conditions with or without
Campylobacter
infection, and their 3-day-old progenies with (MAB
+
) or without (MAB
−
)
Campylobacter
-specific MAB were orally challenged with
C. jejuni
. Significant decreases in the percentage of colonized chickens were observed in the MAB
+
group during the first week compared with the MAB
−
group. These results indicate that
Campylobacter-
specific MAB plays a partial role in protecting young chickens against colonization by
C. jejuni
. Presence of MAB in young chickens did not seem to affect the development of systemic immune response following infection with
C. jejuni
. However, active immune responses to
Campylobacter
occurred earlier and more strongly in birds infected at 21 days of age than those infected at 3 days of age. Clearance of
Campylobacter
infection was also observed in chickens infected at 21 days of age. Taken together, these findings (i) indicate that anti-
Campylobacter
MAB contributes to the lack of
Campylobacter
infection in young broiler chickens in natural environments and (ii) provide further evidence supporting the feasibility of development of immunization-based approaches for control of
Campylobacter
infection in poultry.
Assessment of Methods for Detection of Infectious
Cryptosporidium
Oocysts and
Giardia
Cysts in Reclaimed Effluents
Authors: Quintero-Betancourt W. , Gennaccaro A. L. , Scott T. M. , Rose J. B. 
Published: September 2003

ABSTRACT

This study evaluates the occurrence of
Cryptosporidium
oocysts and
Giardia
cysts in reclaimed effluents if method 1623 with the Envirochek capsule filters (standard and high-volume [HV] filters) and a modified version of the Information Collection Rule method (ICR) with the polypropylene yarn-wound cartridge filter are used. The recovery efficiency of the analytical methods was evaluated with samples of reagent, tap, and reclaimed water by using flow cytometer-sorted spike suspensions. (Oo)cyst recovery efficiency determined filter performance and method reproducibility in the water matrix tested. Method 1623 with the Envirochek HV capsule filter generated significantly higher recovery rates than did the standard Envirochek filter and the modified ICR method. Notwithstanding, large variations in recovery rates (>80%) occurred with samples of reclaimed water, and none of the water quality parameters analyzed in the reclaimed effluents could explain such variability. The highest concentrations of indigenous oocysts were detected by method 1623 with the HV filter, which provided a sufficient number of oocysts for further confirmation of infectious potential. Confirmation of species and potential infectivity for all positive protozoan samples was made by using a nested PCR restriction fragment polymorphism assay and the focus detection method most-probable-number assay, respectively. The methodology and results described in the present investigation provide useful information for the establishment of pathogen numeric standards for reclaimed effluents used for unrestricted irrigation.
18S rRNA Gene Variation among Common Airborne Fungi, and Development of Specific Oligonucleotide Probes for the Detection of Fungal Isolates
Authors: Wu Zhihong , Tsumura Yoshihiko , Blomquist Göran , Wang Xiao-Ru 
Published: September 2003

ABSTRACT

In this study, we sequenced 18S rRNA genes (rDNA) from 49 fungal strains representing 31 species from 15 genera. Most of these species are common airborne fungi and pathogens that may cause various public health concerns. Sequence analysis revealed distinct divergence between
Zygomycota
and
Ascomycota
. Within
Ascomycota
, several strongly supported clades were identified that facilitate the taxonomic placement of several little-studied fungi.
Wallemia
appeared as the group most diverged from all the other
Ascomycota
species. Based on the 18S rDNA sequence variation, 108 oligonucleotide probes were designed for each genus and species included in this study. After homology searches and DNA hybridization evaluations, 33 probes were verified as genus or species specific. The optimal hybridization temperatures to achieve the best specificity for these 33 probes were determined. These new probes can contribute to the molecular diagnostic research for environmental monitoring.