bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viral Pollution in the Environment and in Shellfish: Human Adenovirus Detection by PCR as an Index of Human Viruses
Authors: Pina Sonia , Puig Montserrat , Lucena Francisco , Jofre Joan , Girones Rosina 
Published: December 2019

ABSTRACT

A study of the presence of human viruses (adenoviruses, enteroviruses, and hepatitis A viruses [HAVs]) in environmental and shellfish samples was carried out by applying DNA and cDNA amplification techniques by PCR. The detection of human adenoviruses by PCR was also examined as a potential molecular test to monitor viral pollution. The samples studied were urban and slaughterhouse sewage, river water, seawater, and shellfish. Enteroviruses were quantified by PFU in Buffalo green monkey kidney cells and fecal coliforms and phages of
Bacteroides fragilis
HSP40 were also evaluated in some of the samples. The amplification of viral DNA and cDNA has shown a high prevalence of human viruses that would not be detected by the use of classical techniques, such as the quantification of PFU in cell lines. The results of the analysis of slaughterhouse sewage samples together with the test of farm animal feces indicate that the adenoviruses and the HAVs detected in the environment are mostly of human origin. A significative correlation between the detection of human viruses by PCR and the values of bacteriophages of
B. fragilis
HSP40 in urban raw sewage was observed. Human adenoviruses were the viruses most frequently detected throughout the year, and all the samples that were positive for enteroviruses or HAVs were also positive for human adenoviruses. The results suggest that the detection of adenoviruses by PCR could be used as an index of the presence of human viruses in the environment where a molecular index is acceptable.
Mercury Resistance Is Encoded by Transferable Giant Linear Plasmids in Two Chesapeake Bay
Streptomyces
Strains
Authors: Ravel Jacques , Schrempf Hildgund , Hill Russell T. 
Published: December 2019

ABSTRACT

The
Streptomyces
strains CHR3 and CHR28, isolated from the Baltimore Inner Harbor, contained two and one, respectively, giant linear plasmids which carry terminally bound proteins. The plasmids pRJ3L (322 kb), from CHR3, and pRJ28 (330 kb), from CHR28, carry genes homologous to the previously characterized chromosomal
Streptomyces lividans
66 operon encoding resistance against mercuric compounds. Both plasmids are transmissible (without any detectable rearrangement) to the chloramphenicol-resistant
S. lividans
TK24 strain lacking plasmids and carrying a chromosomal deletion of the
mer
operon.
S. lividans
TK24 conjugants harboring pRJ3L or pRJ28 exhibited profiles of mercury resistance to mercuric compounds similar to those of
Streptomyces
strains CHR3 and CHR28.
Antibiotic Resistance in
Acinetobacter
spp. Isolated from Sewers Receiving Waste Effluent from a Hospital and a Pharmaceutical Plant
Authors: Guardabassi Luca , Petersen Andreas , Olsen John E. , Dalsgaard Anders 
Published: December 2019

ABSTRACT

The possible increase of antibiotic-resistant bacteria in sewage associated with the discharge of wastewater from a hospital and a pharmaceutical plant was investigated by using
Acinetobacter
species as environmental bacterial indicators. The level of susceptibility to six antimicrobial agents was determined in 385
Acinetobacter
strains isolated from samples collected upstream and downstream from the discharge points of the hospital and the pharmaceutical plant. Results indicated that while the hospital waste effluent affected only the prevalence of oxytetracycline resistance, the discharge of wastewater from the pharmaceutical plant was associated with an increase in the prevalence of both single- and multiple-antibiotic resistance among
Acinetobacter
species in the sewers.
Influence of Growth Mode and Sucrose on Susceptibility of
Streptococcus sanguis
to Amine Fluorides and Amine Fluoride-Inorganic Fluoride Combinations
Authors: Embleton J. V. , Newman H. N. , Wilson M. 
Published: December 2019

ABSTRACT

This study evaluated the susceptibility to amine fluorides (AmFs) of planktonic and biofilm cultures of
Streptococcus sanguis
grown with and without sucrose. Cultures were incubated with AmFs (250 mg of fluoride liter
−1
) for 1 min. The susceptibility of biofilms was less than that of the planktonic form and was further decreased by growth in the presence of sucrose.
Influence of Lipid Composition on Pediocin PA-1 Binding to Phospholipid Vesicles
Authors: Chen Yuhuan , Ludescher Richard D. , Montville Thomas J. 
Published: December 2019

ABSTRACT
Pediocin PA-1 bound to anionic lipid vesicles with saturated or unsaturated fatty acid chains in a lipid concentration-dependent fashion. Little change in binding parameters was observed for zwitterionic lipid vesicles. Decreasing the anionic lipid content of the vesicles gave a higher relative dissociation constant for the peptide-lipid interactions and further supports the electrostatic interaction model of binding.
Thermal Gradient Gel Electrophoresis Analysis of Bioprotection from Pollutant Shocks in the Activated Sludge Microbial Community
Authors: Eichner Christine A. , Erb Rainer W. , Timmis Kenneth N. , Wagner-Döbler Irene 
Published: December 2019

ABSTRACT

We used a culture-independent approach, namely, thermal gradient gel electrophoresis (TGGE) analysis of ribosomal sequences amplified directly from community DNA, to determine changes in the structure of the microbial community following phenol shocks in the highly complex activated sludge ecosystem. Parallel experimental model sewage plants were given shock loads of chlorinated and methylated phenols and simultaneously were inoculated (i) with a genetically engineered microorganism (GEM) able to degrade the added substituted phenols or (ii) with the nonengineered parental strain. The sludge community DNA was extracted, and 16S rDNA was amplified and analyzed by TGGE. To allow quantitative analysis of TGGE banding patterns, they were normalized to an external standard. The samples were then compared with each other for similarity by using the coefficient of Dice. The Shannon index of diversity,
H
, was calculated for each sludge sample, which made it possible to determine changes in community diversity. We observed a breakdown in community structure following shock loads of phenols by a decrease in the Shannon index of diversity from 1.13 to 0.22 in the noninoculated system. Inoculation with the GEM (
Pseudomonas
sp. strain B13 SN45RE) effectively protected the microbial community, as indicated by the maintenance of a high diversity throughout the shock load experiment (
H
decreased from 1.03 to only 0.82). Inoculation with the nonengineered parental strain,
Pseudomonas
sp. strain B13, did not protect the microbial community from being severely disturbed;
H
decreased from 1.22 to 0.46 for a 3-chlorophenol–4-methylphenol shock and from 1.03 to 0.70 for a 4-chlorophenol–4-methylphenol shock. The catabolic trait present in the GEM allowed for bioprotection of the activated sludge community from breakdown caused by toxic shock loading. In-depth TGGE analysis with similarity and diversity algorithms proved to be a very sensitive tool to monitor changes in the structure of the activated sludge microbial community, ranging from subtle shifts during adaptation to laboratory conditions to complete collapse following pollutant shocks.
Plasmid-Encoded Anthranilate Synthase (TrpEG) inBuchnera aphidicolafrom Aphids of the Family Pemphigidae
Authors: Van Ham Roeland C. H. J. , Martínez-Torres David , Moya Andrés , Latorre Amparo 
Published: December 2019

ABSTRACTBuchnera aphidicolais an obligate intracellular symbiont of aphids. One of its proposed functions is the synthesis of essential amino acids, nutrients required by aphids but deficient in their diet of plant phloem sap. The genetic organization of the tryptophan pathway inBuchnerafrom proliferous aphids of the family Aphididae has previously been shown to reflect a capacity to overproduce this essential amino acid (C.-Y. Lai, L. Baumann, and P. Baumann, Proc. Natl. Acad. Sci. USA 91:3819–3823, 1994). This involved amplification of the genes for the first enzyme in the pathway, anthranilate synthase (TrpEG), on a low-copy-number plasmid. Here we report on the finding and molecular characterization of TrpEG-encoding plasmids inBuchnerafrom aphids of the distantly related family Pemphigidae.BuchnerafromTetraneura caerulescenscontained a 3.0-kb plasmid (pBTc2) that carried a single copy oftrpEGand resembledtrpEGplasmids ofBuchnerafrom the Aphididae. The second plasmid (pBPs2), isolated fromBuchneraofPemphigus spyrothecae, contained a different replicon. It consisted of a putative origin of replication containing iterons and an open reading frame, designatedrepAC, which showed a high similarity to the gene encoding the replication initiation protein RepA of the RepA/C replicon from the broad-host-range IncA/C group of plasmids. The plasmid population was heterogeneous with respect to the number of tandem repeats of a 1.8-kb unit carryingrepAC1,trpG, and remnants oftrpE. The two principal forms consisted of either five or six copies of this repeat and a single-copy region carryingrepAC2, the putative origin of replication, andtrpE. The unexpected finding of elements of the RepA/C replicon in previously characterizedtrpEGplasmids fromBuchneraof the Aphididae suggests that a replacement of replicons has occurred during the evolution of these plasmids, which may point to a common ancestry for allBuchnera trpEGamplifications.
A Hemorrhagic Factor (Apicidin) Produced by Toxic
Fusarium
Isolates from Soybean Seeds
Authors: Park Jun-Suk , Lee Kyung-Rim , Kim Jin-Cheol , Lim Sun-Hee , Seo Jeong-Ah , Lee Yin-Won 
Published: December 2019

ABSTRACT

Fifty-two isolates of
Fusarium
species were obtained from soybean seeds from various parts of Korea and identified as
Fusarium oxysporum
,
F. moniliforme
,
F. semitectum
,
F. solani
,
F. graminearum
, or
F. lateritium
. These isolates were grown on autoclaved wheat grains and examined for toxicity in a rat-feeding test. Nine cultures were toxic to rats. One of these, a culture of
Fusarium
sp. strain KCTC 16677, produced apicidin, an antiprotozoal agent that caused toxic effects in rats (including body weight loss; hemorrhage in the stomach, intestines, and bladder; and finally death) when rats were fed diets supplemented with 0.05 and 0.1% apicidin. The toxin was toxic to brine shrimp (the 50% lethal concentration was 40 μg/ml) and was weakly cytotoxic to human and mouse tumor cell lines.
Glycerol Overproduction by EngineeredSaccharomyces cerevisiaeWine Yeast Strains Leads to Substantial Changes in By-Product Formation and to a Stimulation of Fermentation Rate in Stationary Phase
Authors: Remize F. , Roustan J. L. , Sablayrolles J. M. , Barre P. , Dequin S. 
Published: December 2019

ABSTRACTSix commercial wine yeast strains and three nonindustrial strains (two laboratory strains and one haploid strain derived from a wine yeast strain) were engineered to produce large amounts of glycerol with a lower ethanol yield. Overexpression of theGPD1gene, encoding a glycerol-3-phosphate dehydrogenase, resulted in a 1.5- to 2.5-fold increase in glycerol production and a slight decrease in ethanol formation under conditions simulating wine fermentation. All the strains overexpressingGPD1produced a larger amount of succinate and acetate, with marked differences in the level of these compounds between industrial and nonindustrial engineered strains. Acetoin and 2,3-butanediol formation was enhanced with significant variation between strains and in relation to the level of glycerol produced. Wine strains overproducing glycerol at moderate levels (12 to 18 g/liter) reduced acetoin almost completely to 2,3-butanediol. A lower biomass concentration was attained byGPD1-overexpressing strains, probably due to high acetaldehyde production during the growth phase. Despite the reduction in cell numbers, complete sugar exhaustion was achieved during fermentation in a sugar-rich medium. Surprisingly, the engineered wine yeast strains exhibited a significant increase in the fermentation rate in the stationary phase, which reduced the time of fermentation.
Changes in Quinone Profiles of Hot Spring Microbial Mats with a Thermal Gradient
Authors: Hiraishi Akira , Umezawa Taichi , Yamamoto Hiroyuki , Kato Kenji , Maki Yonosuke 
Published: December 2019

ABSTRACT

The respiratory and photosynthetic quinones of microbial mats which occurred in Japanese sulfide-containing neutral-pH hot springs at different temperatures were analyzed by spectrochromatography and mass spectrometry. All of the microbial mats that developed at high temperatures (temperatures above 68°C) were so-called sulfur-turf bacterial mats and produced methionaquinones (MTKs) as the major quinones. A 78°C hot spring sediment had a similar quinone profile.
Chloroflexus
-mixed mats occurred at temperatures of 61 to 65°C and contained menaquinone 10 (MK-10) as the major component together with significant amounts of either MTKs or plastoquinone 9 (PQ-9). The sunlight-exposed biomats growing at temperatures of 45 to 56°C were all cyanobacterial mats, in which the photosynthetic quinones (PQ-9 and phylloquinone) predominated and MK-10 was the next most abundant component in most cases. Ubiquinones (UQs) were not found or were detected in only small amounts in the biomats growing at temperatures of 50°C and above, whereas the majority of the quinones of a purple photosynthetic mat growing at 34°C were UQs. A numerical analysis of the quinone profiles was performed by using the following three parameters: dissimilarity index (
D
), microbial divergence index (

MD
q

), and bioenergetic divergence index (

BD
q

). A
D
matrix tree analysis showed that the hot spring mats consisting of the sulfur-turf bacteria,
Chloroflexus
spp., cyanobacteria, and purple phototrophic bacteria formed distinct clusters. Analyses of

MD
q

and

BD
q

values indicated that the microbial diversity of hot spring mats decreased as the temperature of the environment increased. The changes in quinone profiles and physiological types of microbial mats in hot springs with thermal gradients are discussed from evolutionary viewpoints.
In Situ Detection of Novel Bacterial Endosymbionts of
Acanthamoeba
spp. Phylogenetically Related to Members of the Order
Rickettsiales
Authors: Fritsche Thomas R. , Horn Matthias , Seyedirashti Seyedreza , Gautom Romesh K. , Schleifer Karl-Heinz , Wagner Michael 
Published: December 2019

ABSTRACT

Acanthamoebae are ubiquitous soil and water bactivores which may serve as amplification vehicles for a variety of pathogenic facultative bacteria and as hosts to other, presently uncultured bacterial endosymbionts. The spectrum of uncultured endosymbionts includes gram-negative rods and gram-variable cocci, the latter recently shown to be members of the
Chlamydiales
. We report here the isolation from corneal scrapings of two
Acanthamoeba
strains that harbor gram-negative rod endosymbionts that could not be cultured by standard techniques. These bacteria were phylogenetically characterized following amplification and sequencing of the near-full-length 16S rRNA gene. We used two fluorescently labelled oligonucleotide probes targeting signature regions within the retrieved sequences to detect these organisms in situ. Phylogenetic analyses demonstrated that they displayed 99.6% sequence similarity and formed an independent and well-separated lineage within the
Rickettsiales
branch of the alpha subdivision of the
Proteobacteria
. Nearest relatives included members of the genus
Rickettsia
, with sequence similarities of approximately 85 to 86%, suggesting that these symbionts are representatives of a new genus and, perhaps, family. Distance matrix, parsimony, and maximum-likelihood tree-generating methods all consistently supported deep branching of the 16S rDNA sequences within the
Rickettsiales
. The oligonucleotide probes displayed at least three mismatches to all other available 16S rDNA sequences, and they both readily permitted the unambiguous detection of rod-shaped bacteria within intact acanthamoebae by confocal laser-scanning microscopy. Considering the long-standing relationship of most
Rickettsiales
with arthropods, the finding of a related lineage of endosymbionts in protozoan hosts was unexpected and may have implications for the preadaptation and/or recruitment of rickettsia-like bacteria to metazoan hosts.
Production of Wax Esters during Aerobic Growth of Marine Bacteria on Isoprenoid Compounds
Authors: Rontani Jean-Francois , Bonin Patricia C. , Volkman John K. 
Published: December 2019

ABSTRACT

This paper describes the production of isoprenoid wax esters during the aerobic degradation of 6,10,14-trimethylpentadecan-2-one and phytol by four bacteria (
Acinetobacter
sp. strain PHY9,
Pseudomonas nautica
[IP85/617],
Marinobacter
sp. strain CAB [DSMZ 11874], and
Marinobacter hydrocarbonoclasticus
[ATCC 49840]) isolated from the marine environment. Different pathways are proposed to explain the formation of these compounds. In the case of 6,10,14-trimethylpentadecan-2-one, these esters result from the condensation of some acidic and alcoholic metabolites produced during the biodegradation, while phytol constitutes the alcohol moiety of most of the esters produced during growth on this isoprenoid alcohol. The amount of these esters formed increased considerably in N-limited cultures, in which the ammonium concentration corresponds to conditions often found in marine sediments. This suggests that the bacterial formation of isoprenoid wax esters might be favored in such environments. Although conflicting evidence exists regarding the stability of these esters in sediments, it seems likely that, under some conditions, bacterial esterification can enhance the preservation potential of labile compounds such as phytol.
Molecular Epidemiology of
Campylobacter jejuni
in Broiler Flocks Using Randomly Amplified Polymorphic DNA-PCR and 23S rRNA-PCR and Role of Litter in Its Transmission
Authors: Payne Randy E. , Lee Margie D. , Dreesen David W. , Barnhart Harold M. 
Published: December 2019

ABSTRACT

Poultry has long been cited as a reservoir for
Campylobacter
spp., and litter has been implicated as a vehicle in their transmission. Chicks were raised on litter removed from a broiler house positive for
Campylobacter jejuni
. Litter was removed from the house on days 0, 3, and 9 after birds were removed for slaughter. Chicks were raised on these three litters under controlled conditions in flocks of 25. None of these birds yielded
C. jejuni
in their cecal droppings through 7 weeks. Two successive flocks from the same
Campylobacter
-positive broiler house were monitored for
Campylobacter
colonization.
Campylobacter jejuni
prevalence rates were determined for each flock. Randomly amplified polymorphic DNA (RAPD)-PCR and 23S rRNA-PCR typing methods were used to group isolates. A high prevalence (60%) of
C. jejuni
in flock 1 coincided with the presence of an RAPD profile not appearing in flock 2, which had a lower rate of prevalence (28%). A 23S rRNA-PCR typing method was used to determine if strains with different RAPD profiles and different prevalence rates contained different 23S sequences. RAPD profiles detected with higher prevalence rates contained a spacer in the 23S rRNA region 100% of the time, while RAPD profiles found with lower prevalence rates contained an intervening sequence less than 2% of the time. Data suggest varying colonizing potentials of different RAPD profiles and a source other than previously used litter as a means of transmission of
C. jejuni
. These molecular typing methods demonstrate their usefulness, when used together, in this epidemiologic investigation.
New Mobilizable Vectors Suitable for Gene Replacement in Gram-Negative Bacteria and Their Use in Mapping of the 3′ End of the
Xanthomonas campestris
pv. campestris
gum
Operon
Authors: Katzen Federico , Becker Anke , Ielmini M. Verónica , Oddo Cristian G. , Ielpi Luis 
Published: December 2019

ABSTRACT

We describe useful vectors to select double-crossover events directly in site-directed marker exchange mutagenesis in gram-negative bacteria. These vectors contain the
gusA
marker gene, providing colorimetric screens to identify bacteria harboring those sequences. The applicability of these vectors was shown by mapping the 3′ end of the
Xanthomonas campestris gum
operon, involved in biosynthesis of xanthan.
Rapid Detection of
Ophiostoma piceae
and
O. quercus
in Stained Wood by PCR
Authors: Kim Seong Hwan , Uzunovic Adnan , Breuil Colette 
Published: December 2019

ABSTRACT

A rapid, sensitive, and simple method was developed to detect the sapstain fungi
Ophiostoma piceae
and
O. quercus
in stained wood. By using microwave heating for DNA extraction and PCR with internal transcribed spacer-derived-specific primers, detection was feasible within 4 h, even with DNA obtained from a single synnema. This method can easily be extended for the detection of other wood-inhabiting fungi.
Organic Solvent Tolerance of
Escherichia coli
Is Independent of OmpF Levels in the Membrane
Authors: Asako Hiroyuki , Kobayashi Kei , Aono Rikizo 
Published: December 2019

ABSTRACT

The organic solvent tolerance of
Escherichia coli
was measured under conditions in which OmpF levels were controlled by various means as follows: alteration of NaCl concentration in the medium, transformation with a stress-responsive gene (
marA
,
robA
, or
soxS
), or disruption of the
ompF
gene. It was shown that solvent tolerance of
E. coli
did not depend upon OmpF levels in the membrane.
The α Subunit of Toluene Dioxygenase from
Pseudomonas putida
F1 Can Accept Electrons from Reduced Ferredoxin
TOL
but Is Catalytically Inactive in the Absence of the β Subunit
Authors: Jiang Haiyan , Parales Rebecca E. , Gibson David T. 
Published: December 2019

ABSTRACT

The oxygenase component of toluene dioxygenase from
Pseudomonas putida
F1 is an iron-sulfur protein (ISP
TOL
) consisting of α (TodC1) and β (TodC2) subunits. Purified TodC1 gave absorbance and electron paramagnetic resonance spectra identical to those given by purified ISP
TOL
. TodC1 was reduced by NADH and catalytic amounts of Reductase
TOL
and Ferredoxin
TOL
. Reduced TodC1 did not oxidize toluene, and catalysis was strictly dependent on the presence of purified TodC2.
Bacterial Leaching of Metal Sulfides Proceeds by Two Indirect Mechanisms via Thiosulfate or via Polysulfides and Sulfur
Authors: Schippers Axel , Sand Wolfgang 
Published: December 2019

ABSTRACT

The acid-insoluble metal sulfides FeS
2
, MoS
2
, and WS
2
are chemically attacked by iron(III) hexahydrate ions, generating thiosulfate, which is oxidized to sulfuric acid. Other metal sulfides are attacked by iron(III) ions and by protons, resulting in the formation of elemental sulfur via intermediary polysulfides. Sulfur is biooxidized to sulfuric acid. This explains leaching of metal sulfides by
Thiobacillus thiooxidans
.
Sources of
Vibrio mimicus
Contamination of Turtle Eggs
Authors: Acuña María T. , Díaz Gerardo , Bolaños Hilda , Barquero Candy , Sánchez Olga , Sánchez Luz M. , Mora Grettel , Chaves Anny , Campos Elena 
Published: December 2019

ABSTRACT

Vibrio mimicus
contamination of sand increased significantly during the arrival of the olive ridley sea turtles (
Lepidochelys olivacea
) at Ostional anidation beach, Costa Rica. Statistical analysis supports that eggs are contaminated with
V. mimicus
by contact with the sand nest.
V. mimicus
was isolated from eggs of all nests tested, and
ctxA
+
strains were found in 31% of the nests, all of which were near the estuary.