bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptive Changes in Membrane Lipids of Barophilic Bacteria in Response to Changes in Growth Pressure
Authors: Yano Yutaka , Nakayama Akihiko , Ishihara Kenji , Saito Hiroaki 
Published: December 2019

ABSTRACT
The lipid compositions of barophilic bacterial strains which contained docosahexaenoic acid (DHA [22:6n-3]) were examined, and the adaptive changes of these compositions were analyzed in response to growth pressure. In the facultatively barophilic strain 16C1, phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) were major components which had the same fatty acid chains. However, in PE, monounsaturated fatty acids such as hexadecenoic acid were major components, and DHA accounted for only 3.7% of the total fatty acids, while in PG, DHA accounted for 29.6% of the total fatty acids. In response to an increase in growth pressure in strain 16C1, the amounts of saturated fatty acids in PE were reduced, and these decreases were mainly balanced by an increase in unsaturated fatty acids, including DHA. In PG, the decrease in saturated fatty acids was mainly balanced by an increase in DHA. Similar adaptive changes in fatty acid composition were observed in response to growth pressure in obligately barophilic strain 2D2. Furthermore, these adaptive changes in response were also observed in response to low temperature in strain 16C1. These results confirm that the general shift from saturated to unsaturated fatty acids including DHA is one of the adaptive changes in response to increases in pressure and suggest that DHA may play a role in maintaining the proper fluidity of membrane lipids under high pressure.
Physiological Characterization of a Bacterial Consortium Reductively Dechlorinating 1,2,3- and 1,2,4-Trichlorobenzene
Authors: Adrian Lorenz , Manz Werner , Szewzyk Ulrich , Görisch Helmut 
Published: December 2019

ABSTRACT

A bacterial mixed culture reductively dechlorinating trichlorobenzenes was established in a defined, synthetic mineral medium without any complex additions and with pyruvate as the carbon and energy source. The culture was maintained over 39 consecutive transfers of small inocula into fresh media, enriching the dechlorinating activity. In situ probing with fluorescence-labeled rRNA-targeted oligonucleotide probes revealed that two major subpopulations within the microbial consortium were phylogenetically affiliated with a sublineage within the
Desulfovibrionaceae
and the gamma subclass of
Proteobacteria
. The bacterial consortium grew by fermentation of pyruvate, forming acetate, propionate, CO
2
, formate, and hydrogen. Acetate and propionate supported neither the reduction of trichlorobenzenes nor the reduction of sulfate when sulfate was present. Hydrogen and formate were used for sulfate reduction to sulfide. Sulfate strongly inhibited the reductive dechlorination of trichlorobenzenes. However, when sulfate was depleted in the medium due to sulfate reduction, dechlorination of trichlorobenzenes started. Similar results were obtained when sulfite was present in the cultures. Molybdate at a concentration of 1 mM strongly inhibited the dechlorination of trichlorobenzenes. Cultures supplied with molybdate plus sulfate did not reduce sulfate, but dechlorination of trichlorobenzenes occurred. Supplementation of electron-depleted cultures with various electron sources demonstrated that formate was used as a direct electron donor for reductive dechlorination, whereas hydrogen was not.
Determination of Complement-Mediated Killing of Bacteria by Viability Staining and Bioluminescence
Authors: Virta Marko , Lineri Sanna , Kankaanpää Pasi , Karp Matti , Peltonen Karita , Nuutila Jari , Lilius Esa-Matti 
Published: December 2019

ABSTRACT

Complement-mediated killing of bacteria was monitored by flow cytometric, luminometric, and conventional plate counting methods. A flow cytometric determination of bacterial viability was carried out by using dual staining with a LIVE/DEAD BacLight bacterial viability kit. In addition to the viable cell population, several other populations emerged in the fluorescence histogram, and there was a dramatic decrease in the total cell count in the light-scattering histogram in the course of the complement reaction. To permit luminometric measurements,
Bacillus subtilis
and
Escherichia coli
were made bioluminescent by expressing an insect luciferase gene. Addition of substrate after the complement reaction resulted in bioluminescence, the level of which was a measure of the viable cell population. All three methods gave essentially the same killing rate, suggesting that the bacteriolytic activity of serum complement can be measured rapidly and conveniently by using viability stains or bioluminescence. In principle, any bacterial strain can be used for viability staining and flow cytometric analysis. For the bioluminescence measurements genetically engineered bacteria are needed, but the advantage is that it is possible to screen automatically a large number of samples.
Measurement of the Effects of Acetic Acid and Extracellular pH on Intracellular pH of Nonfermenting, Individual
Saccharomyces cerevisiae
Cells by Fluorescence Microscopy
Authors: Guldfeldt Lars Uhre , Arneborg Nils 
Published: December 2019

ABSTRACT

The effects of acetic acid and extracellular pH (pH
ex
) on the intracellular pH (pH
i
) of nonfermenting, individual
Saccharomyces cerevisiae
cells were studied by using a new experimental setup comprising a fluorescence microscope and a perfusion system.
S. cerevisiae
cells grown in brewer’s wort to the stationary phase were stained with fluorescein diacetate and transferred to a perfusion chamber. The extracellular concentration of undissociated acetic acid at various pH
ex
values was controlled by perfusion with 2 g of total acetic acid per liter at pH
ex
3.5, 4.5, 5.6, and 6.5 through the chamber by using a high-precision pump. The pH
i
of individual
S. cerevisiae
cells during perfusion was measured by fluorescence microscopy and ratio imaging. Potential artifacts, such as fading and efflux of fluorescein, could be neglected within the experimental time used. At pH
ex
6.5, the pH
i
of individual
S. cerevisiae
cells decreased as the extracellular concentration of undissociated acetic acid increased from 0 to 0.035 g/liter, whereas at pH
ex
3.5, 4.5, and 5.6, the pH
i
of individual
S. cerevisiae
cells decreased as the extracellular concentration of undissociated acetic acid increased from 0 to 0.10 g/liter. At concentrations of undissociated acetic acid of more than 0.10 g/liter, the pH
i
remained constant. The decreases in pH
i
were dependent on the pH
ex
; i.e., the decreases in pH
i
at pH
ex
5.6 and 6.5 were significantly smaller than the decreases in pH
i
at pH
ex
3.5 and 4.5.
Intracellular Signal Triggered by Cholera Toxin in
Saccharomyces boulardii
and
Saccharomyces cerevisiae
Authors: Brandão Rogelio L. , Castro Ieso M. , Bambirra Eduardo A. , Amaral Sheila C. , Fietto Luciano G. , Tropia Maria José M. , Neves Maria José , Dos Santos Raquel G. , Gomes Newton C. M. , Nicoli Jacques R. 
Published: December 2019

ABSTRACT

As is the case for
Saccharomyces boulardii, Saccharomyces cerevisiae
W303 protects Fisher rats against cholera toxin (CT). The addition of glucose or dinitrophenol to cells of
S. boulardii
grown on a nonfermentable carbon source activated trehalase in a manner similar to that observed for
S. cerevisiae
. The addition of CT to the same cells also resulted in trehalase activation. Experiments performed separately on the A and B subunits of CT showed that both are necessary for activation. Similarly, the addition of CT but not of its separate subunits led to a cyclic AMP (cAMP) signal in both
S. boulardii
and
S. cerevisiae
. These data suggest that trehalase stimulation by CT probably occurred through the cAMP-mediated protein phosphorylation cascade. The requirement of CT subunit B for both the cAMP signal and trehalase activation indicates the presence of a specific receptor on the yeasts able to bind to the toxin, a situation similar to that observed for mammalian cells. This hypothesis was reinforced by experiments with
125
I-labeled CT showing specific binding of the toxin to yeast cells. The adhesion of CT to a receptor on the yeast surface through the B subunit and internalization of the A subunit (necessary for the cAMP signal and trehalase activation) could be one more mechanism explaining protection against the toxin observed for rats treated with yeasts.
Fot
1 Insertions in the
Fusarium oxysporum
f. sp.
albedinis
Genome Provide Diagnostic PCR Targets for Detection of the Date Palm Pathogen
Authors: Fernandez Diana , Ouinten Mohamed , Tantaoui Abdelaziz , Geiger Jean-Paul , Daboussi Marie-Josée , Langin Thierry 
Published: December 2019

ABSTRACT

Populations of
Fusarium oxysporum
f. sp.
albedinis
, the causal agent of Bayoud disease of date palm, are derivatives of a single clonal lineage and exhibit very similar
Fot
1 hybridization patterns. In order to develop a sensitive diagnostic tool for
F. oxysporum
f. sp.
albedinis
detection, we isolated several DNA clones containing a copy of the transposable element
Fot
1 from a genomic library of the date palm pathogen. Regions flanking the insertion sites were sequenced, and these sequences were used to design PCR primers that amplify the DNA regions at several
Fot
1 insertion sites. When tested on a large sample of
Fusarium
isolates, including 286
F. oxysporum
f. sp.
albedinis
isolates, 17 other special forms, nonpathogenic
F. oxysporum
isolates from palm grove soils, and 8 other
Fusarium
species, the primer pair TL3-FOA28 allowed amplification of a 400-bp fragment found only in
F. oxysporum
f. sp.
albedinis
. Sequence analysis showed that one of the
Fot
1 copies was truncated, lacking 182 bp at its 3′ terminus. The primer pair BI03-FOA1 amplified a 204-bp fragment which overlapped the
Fot
1 truncated copy and its 3′ site of insertion in the
F. oxysporum
f. sp.
albedinis
genome and identified 95% of the isolates. The primer pairs BIO3-FOA1 and TL3-FOA28 used in PCR assays thus provide a useful diagnostic tool for
F. oxysporum
f. sp.
albedinis
isolates.
Genomic Analysis of
Clostridium botulinum
Group II by Pulsed-Field Gel Electrophoresis
Authors: Hielm Sebastian , Björkroth Johanna , Hyytiä Eija , Korkeala Hannu 
Published: December 2019

ABSTRACT

Pulsed-field gel electrophoresis (PFGE) was optimized for genomic analyses of
Clostridium botulinum
(nonproteolytic) group II. DNA degradation problems caused by extracellular DNases were overcome by fixation of cells with formaldehyde prior to isolation. A rapid (4-h) in situ DNA isolation method was also assessed and gave indistinguishable results. Genomic DNA from 21 strains of various geographical and temporal origins was digested with 15 rare-cutting restriction enzymes. Of these,
Apa
I,
Mlu
I,
Nru
I,
Sma
I, and
Xho
I gave the most revealing PFGE patterns, enabling strain differentiation. Twenty strains yielded PFGE patterns containing 13 pulsotypes. From summation of
Mlu
I,
Sma
I, and
Xho
I restriction fragments, the genome size of
C. botulinum
group II was estimated to be 3.6 to 4.1 Mb (mean ± standard deviation = 3,890 ± 170 kb). The results substantiate that after problems due to DNases are overcome, PFGE analysis will be a reproducible and highly discriminating epidemiological method for studying
C. botulinum
group II at the molecular level.
Differential Gene Expression in the Laccase Gene Family from Basidiomycete I-62 (CECT 20197)
Authors: Mansur Mariana , Suárez Teresa , González Aldo E. 
Published: December 2019

ABSTRACT

A family of genes encoding laccases has recently been described for the basidiomycete I-62 (CECT 20197). Transcript levels of genes
lcc1
,
lcc2
, and
lcc3
were analyzed under four different culture conditions to study their expression patterns. Two of the laccase genes were clearly inducible by veratryl alcohol: the
lcc1
gene is inducible in early stages of growth, and the
lcc2
gene is also inducible but only when the organism reaches the stationary phase. Transcript levels for the third gene,
lcc3
, were uninduced by veratryl alcohol and repressed by glucose.
Anaerobic Benzene Degradation in Petroleum-Contaminated Aquifer Sediments after Inoculation with a Benzene-Oxidizing Enrichment
Authors: Weiner Jonathan M. , Lovley Derek R. 
Published: December 2019

ABSTRACT
Sediments from the sulfate-reduction zone of a petroleum-contaminated aquifer, in which benzene persisted, were inoculated with a benzene-oxidizing, sulfate-reducing enrichment from aquatic sediments. Benzene was degraded, with apparent growth of the benzene-degrading population over time. These results suggest that the lack of benzene degradation in the sulfate-reduction zones of some aquifers may result from the failure of the appropriate benzene-degrading sulfate reducers to colonize the aquifers rather than from environmental conditions that are adverse for anaerobic benzene degradation.
Construction of a Sorbitol-Based Vector for Expression of Heterologous Proteins in
Saccharomyces cerevisiae
Authors: McGonigal T. , Bodelle P. , Schopp C. , Sarthy A. V. 
Published: December 2019

ABSTRACT

A new inducible yeast expression vector, pXS7, was constructed by using the promoter and terminator sequences from the
Saccharomyces cerevisiae SOR1
gene, which codes for the sorbitol dehydrogenase protein. We cloned the coding sequence of the
Saccharomyces YEF3
gene in this vector and demonstrated an increase in YEF3 protein levels when cells were grown in the presence of the sugar sorbitol.
Purification and Characterization of Anti-
Listeria
Compounds Produced by
Geotrichum candidum
Authors: Dieuleveux V. , Van Der Pyl D. , Chataud J. , Gueguen M. 
Published: December 2019

ABSTRACT

Geotrichum candidum
can produce and excrete compounds that inhibit
Listeria monocytogenes
. These were purified by ultrafiltration, centrifugal partition chromatography, thin-layer chromatography, gel filtration, and high-pressure liquid chromatography, and analyzed by liquid chromatography-mass spectrometry, infrared spectrometry, nuclear magnetic resonance spectrometry, and optical rotation. Two inhibitors were identified:
d
-3-phenyllactic acid and
d
-3-indollactic acid.
Enzyme Characteristics of β-
d
-Galactosidase- and β-
d
-Glucuronidase-Positive Bacteria and Their Interference in Rapid Methods for Detection of Waterborne Coliforms and
Escherichia coli
Authors: Tryland I. , Fiksdal L. 
Published: December 2019

ABSTRACT

Bacteria which were β-
d
-galactosidase and β-
d
-glucuronidase positive or expressed only one of these enzymes were isolated from environmental water samples. The enzymatic activity of these bacteria was measured in 25-min assays by using the fluorogenic substrates 4-methylumbelliferyl-β-
d
-galactoside and 4-methylumbelliferyl-β-
d
-glucuronide. The enzyme activity, enzyme induction, and enzyme temperature characteristics of target and nontarget bacteria in assays aimed at detecting coliform bacteria and
Escherichia coli
were investigated. The potential interference of false-positive bacteria was evaluated. Several of the β-
d
-galactosidase-positive nontarget bacteria but none of the β-
d
-glucuronidase-positive nontarget bacteria contained unstable enzyme at 44.5°C. The activity of target bacteria was highly inducible. Nontarget bacteria were induced much less or were not induced by the inducers used. The results revealed large variations in the enzyme levels of different β-
d
-galactosidase- and β-
d
-glucuronidase-positive bacteria. The induced and noninduced β-
d
-glucuronidase activities of
Bacillus
spp. and
Aerococcus viridans
were approximately the same as the activities of induced
E. coli
. Except for some isolates identified as
Aeromonas
spp., all of the induced and noninduced β-
d
-galactosidase-positive, noncoliform isolates exhibited at least 2 log units less mean β-
d
-galactosidase activity than induced
E. coli
. The noncoliform bacteria must be present in correspondingly higher concentrations than those of target bacteria to interfere in the rapid assay for detection of coliform bacteria.
Detection of
Escherichia coli
O157:H7 in the Beef Marketed in Malaysia
Authors: Radu Son , Mutalib Shahilah Abdul , Rusul Gulam , Ahmad Zainori , Morigaki Tadaaki , Asai Norio , Kim Yung Bu , Okuda Jun , Nishibuchi Mitsuaki 
Published: December 2019

ABSTRACT

Twelve strains of
Escherichia coli
O157:H7 were isolated from 9 of 25 beef samples purchased from retail stores in Malaysia. These strains produced Shiga toxin 2 with or without Shiga toxin 1 and had the
eae
gene and a 60-MDa plasmid. The antibiograms and the profiles of the arbitrarily primed PCR of the strains were diverse, suggesting that the strains may have originated from diverse sources.
Direct Detection of Viable Bacteria, Molds, and Yeasts by Reverse Transcriptase PCR in Contaminated Milk Samples after Heat Treatment
Authors: Vaitilingom Marc , Gendre Francois , Brignon Pierre 
Published: December 2019

ABSTRACT

A fast, sensitive, and target contaminant-modulable method was developed to detect viable bacteria, molds, and yeasts after heat treatment. By reverse transcriptase PCR with elongation factor gene (EF-Tu or EF-1α)-specific primers, the detection level was 10 cells ml of milk
−1
. The simplicity and rapidity (4 h) of the procedure suggests that this method may be easily transposable to other foods and other contaminants.
2-Chloro-1,4-Dimethoxybenzene as a Novel Catalytic Cofactor for Oxidation of Anisyl Alcohol by Lignin Peroxidase
Authors: Teunissen Pauline J. M. , Field Jim A. 
Published: December 2019

ABSTRACT

2-Chloro-1,4-dimethoxybenzene (2Cl-14DMB) is a natural compound produced de novo by several white rot fungi. This chloroaromatic metabolite was identified as a cofactor superior to veratryl alcohol (VA) in the oxidation of anisyl alcohol (AA) by lignin peroxidase (LiP). Our results reveal that good LiP substrates, such as VA and tryptophan, are comparatively poor cofactors in the oxidation of AA. Furthermore, we show that a good cofactor does not necessarily serve a role in protecting LiP against H
2
O
2
inactivation. 2Cl-14DMB was not a direct mediator of AA oxidation, since increasing AA concentrations did not inhibit the oxidation of 2Cl-14DMB at all. However, the high molar ratio of anisaldehyde formed to 2Cl-14DMB consumed, up to 13:1, indicates that a mechanism which recycles the cofactor is present.
Isolation, Characterization, and Transfer of Cryptic Gene-Mobilizing Plasmids in the Wheat Rhizosphere
Authors: van Elsas Jan Dirk , McSpadden Gardener Brian B. , Wolters Anneke C. , Smit Eric 
Published: December 2019

ABSTRACT

A set of self-transmissible plasmids with IncQ plasmid-mobilizing capacity was isolated by triparental exogenous isolation from the wheat rhizosphere with an
Escherichia coli
IncQ plasmid host and a
Ralstonia eutropha
recipient. Three plasmids of 38 to 45 kb, denoted pIPO1, pIPO2, and pIPO3, were selected for further study. No selectable traits (antibiotic or heavy-metal resistance) were identified in these plasmids. The plasmids were characterized by replicon typing via PCR and hybridization with replicon-specific probes and other hybridizations. pIPO1 and pIPO3 were similar to each other, whereas pIPO2 was different. None of these plasmids belonged to any known incompatibility group. pIPO2 was selected for further work, and a mini-Tn
5-tet
transposon was inserted to confer selectability. Plasmid pIPO2 had a broad IncQ plasmid mobilization and self-transfer range among the alpha, beta, and gamma subclasses of the
Proteobacteria
but did not show productive transfer to gram-positive bacteria. Plasmid pIPO2 mobilized IncQ plasmid pIE723 from
Pseudomonas fluorescens
to diverse indigenous proteobacteria in the rhizosphere of field-grown wheat. Transfer of pIE723 to indigenous bacteria was not observed in the absence of added pIPO2. A specific PCR primer system and a probe were developed for the detection of pIPO2-type plasmids in soil and rhizosphere. Analysis of soil DNA provided evidence for the presence of pIPO2 in inoculated wheat rhizosphere soil in the field study, as well as in the rhizosphere of uninoculated wheat plants growing in soil microcosms. The system failed to identify major reservoirs of pIPO2 in a variety of other soils.
Detection of
Clostridium proteoclasticum
and Closely Related Strains in the Rumen by Competitive PCR
Authors: Reilly K. , Attwood G. T. 
Published: December 2019

ABSTRACT

A competitive PCR technique was used to enumerate the proteolytic bacterium
Clostridium proteoclasticum
from the rumen. A PCR primer, which circumscribes this organism and several closely related strains, was designed for a variable region within their 16S rRNA genes and was used in conjunction with a universal forward primer. This primer pair was tested for specificity against 85 ruminal bacterial strains. An internal control DNA was constructed for use in competitive PCRs and was shown to amplify under the same reaction conditions and with the same amplification efficiency as the target DNA. DNA from a known number of
C. proteoclasticum
cells was coamplified with the internal control to construct a standard curve. Rumen samples were collected from eight dairy cows fed four diets in rotation: high nitrogen, high nitrogen supplemented with carbohydrate, low nitrogen, and low nitrogen supplemented with carbohydrate. DNA extracted from these and spiked with internal control DNA was amplified with the
C. proteoclasticum
primer pair. The relative intensities of the PCR products were used to quantitate the numbers of
C. proteoclasticum
cell equivalents from the rumen samples. The numbers ranged from 2.01 × 10
6
ml
−1
to 3.12 × 10
7
ml
−1
. There was no significant effect on the numbers of
C. proteoclasticum
detected in rumen samples among cows fed the four diets. The utility of the competitive PCR approach for quantifying ruminal bacterial populations in vivo and the occurrence of
C. proteoclasticum
in forage-fed dairy cows are discussed.
Comparative Recoveries of
Naegleria fowleri
Amoebae from Seeded River Water by Filtration and Centrifugation
Authors: Pernin P. , Pélandakis M. , Rouby Y. , Faure A. , Siclet F. 
Published: December 2019

ABSTRACT

Detection of pathogenic
Naegleria fowleri
in environmental water samples, which is necessary for the prevention of primary amoebic meningoencephalitis, generally requires concentrating the samples. Two concentration techniques, filtration and centrifugation, were used to study the recovery of
N. fowleri
, in vegetative or cystic form, that had been mixed with the two other thermotolerant
Naegleria
species,
N. lovaniensis
and
N. australiensis
. Counting of amoebae was performed by the most probable number method on 10 water replicates of 100 ml and 10 ml each. With both concentration methods, recovery was better for cysts than for trophozoites (53% ± 21% versus 5% ± 5% by filtration and 57% ± 25% versus 22% ± 5% by centrifugation). The recovery of
Naegleria
trophozoites by filtration was very low, and centrifugation was significantly better than filtration in recovery of
Naegleria
trophozoites (22% ± 5% versus 5% ± 5%;
P
< 0.001). For cysts, however, filtration appeared as efficient as centrifugation, with equivalent values for recovery (53% ± 21% versus 57% ± 25%;
P
> 0.7). Although the recovery of cysts of
N. fowleri
obtained by filtration (51% ± 24%) appeared higher than that by centrifugation (36% ± 23%), the difference was not significant (
P
> 0.1). Both concentration methods have highly variable recovery rates, making accurate quantification of low concentrations (<100/liter) of
N. fowleri
in the environment difficult.