bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strain-Specific Identification of Probiotic
Lactobacillus rhamnosus
with Randomly Amplified Polymorphic DNA-Derived PCR Primers
Authors: Tilsala-Timisjärvi Anu , Alatossava Tapani 
Published: December 2019

ABSTRACT

In the present work, strain-specific PCR primers for
Lactobacillus rhamnosus
Lc 1/3 are described. The randomly amplified polymorphic DNA (RAPD) technique was used to produce potential strain-specific markers. They were screened for specificity by hybridization with DNA from 11
L. rhamnosus
strains. A 613-bp RAPD marker found to be strain-specific was sequenced, and a primer pair specific to
L. rhamnosus
Lc 1/3 was constructed based on the sequence. The primer pair was tested with 11
Lactobacillus
species and 11
L. rhamnosus
strains and was found to be strain specific. The nucleotide sequence of the specific RAPD marker was found to contain part of a protein encoding region which showed significant similarity to several transposases for insertion sequence elements of various bacteria, including other lactic acid bacterium species.
Metabolism of Benzene, Toluene, and Xylene Hydrocarbons in Soil
Authors: Tsao C.-W. , Song H.-G. , Bartha R. 
Published: December 2019

ABSTRACTEnrichment cultures obtained from soil exposed to benzene, toluene, and xylene (BTX) mineralized benzene and toluene but cometabolized only xylene isomers, forming polymeric residues. This observation prompted us to investigate the metabolism of14C-labeled BTX hydrocarbons in soil, either individually or as mixtures. BTX-supplemented soil was incubated aerobically for up to 4 weeks in a sealed system that automatically replenished any O2consumed. The decrease in solvent vapors and the production of14CO2were monitored. At the conclusion of each experiment,14C distribution in solvent-extractable polymers, biomass, and humic material was determined, obtaining14C mass balances of 85 to 98%. BTX compounds were extensively mineralized in soil, regardless of whether they were presented singly or in combinations. No evidence was obtained for the formation of solvent-extractable polymers from xylenes in soil, but14C distribution in biomass (5 to 10%) and humus (12 to 32%) was unusual for all BTX compounds and especially for toluene and the xylenes. The results suggest that catechol intermediates of BTX degradation are preferentially polymerized into the soil humus and that the methyl substituents of the catechols derived from toluene and especially from xylenes enhance this incorporation. In contrast to inhibitory residues formed from xylene cometabolism in culture, the humus-incorporated xylene residues showed no significant toxicity in the Microtox assay.
Carbon Monoxide Oxidation by Bacteria Associated with the Roots of Freshwater Macrophytes
Authors: Rich Jeremy J. , King G. M. 
Published: December 2019

ABSTRACT

The potential rates and control of aerobic root-associated carbon monoxide (CO) consumption were assessed by using excised plant roots from five common freshwater macrophytes. Kinetic analyses indicated that the maximum potential uptake velocities for CO consumption ranged from 0.4 to 2.7 μmol of CO g (dry weight)
−1
h
−1
for the five species. The observed rates were comparable to previously reported rates of root-associated methane uptake. The apparent half-saturation constants for CO consumption ranged from 50 to 370 nM CO; these values are considerably lower than the values obtained for methane uptake. The CO consumption rates reached maximum values at temperatures between 27 and 32°C, and there was a transition to CO production at ≥44°C, most likely as a result of thermochemical organic matter decomposition. Incubation of roots with organic substrates (e.g., 5 mM syringic acid, glucose, alanine, and acetate) dramatically reduced the rate of CO consumption, perhaps reflecting a shift in metabolism by facultative CO oxidizers. Based on responses to a suite of antibiotics, most of the CO consumption (about 90%) was due to eubacteria rather than fungi or other eucaryotes. Based on the results of acetylene inhibition experiments, methanotrophs and ammonia oxidizers were not active CO consumers.
Ink and Vinegar, a Simple Staining Technique for Arbuscular-Mycorrhizal Fungi
Authors: Vierheilig Horst , Coughlan Andrew P. , Wyss Urs , Piché Yves 
Published: December 2019

ABSTRACT
We developed a reliable, inexpensive, and simple method for staining arbuscular-mycorrhizal fungal colonizations in root tissues. Apart from applications in research, this nontoxic, high-quality staining method also could be of great utility in teaching exercises. After adequate clearing with KOH, an ink-vinegar solution successfully stained all fungal structures, rendering them clearly visible.
Construction of a Bioluminescent Reporter Strain To Detect Polychlorinated Biphenyls
Authors: Layton A. C. , Muccini M. , Ghosh M. M. , Sayler G. S. 
Published: December 2019

ABSTRACT

A bioluminescent reporter strain,
Ralstonia eutropha
ENV307(pUTK60), was constructed for the detection of polychlorinated biphenyls by inserting the biphenyl promoter upstream of the bioluminescence genes. In the presence of a nonionic surfactant, which enhances the solubility of chlorinated biphenyls, bioluminescence was induced three- to fourfold over background by biphenyl, monochlorinated biphenyls, and Aroclor 1242. The minimum detection limits for these compounds ranged from 0.15 mg/liter for 4-chlorobiphenyl to 1.5 mg/liter for Aroclor 1242.
Production of Monoclonal Antibodies Specific for the i and
1,2
Flagellar Antigens of
Salmonella typhimurium
and Characterization of Their Respective Epitopes
Authors: de Vries N. , Zwaagstra K. A. , Huis in’t Veld J. H. J. , van Knapen F. , van Zijderveld F. G. , Kusters J. G. 
Published: December 2019

ABSTRACT

Salmonella typhimurium
expresses two antigenically distinct flagellins, each containing a different H antigen (
i
and
1,2
), the combination of which is highly specific for this serotype. In this study, overlapping recombinant flagellin fragments were constructed from the
fliC
(H:
i
) and
fljB
(H:
1,2
) flagellin genes, and the expression products were tested for binding to H antigen-specific monoclonal and polyclonal antibodies. A minimal area, 86 amino acids for H:
i
and 102 amino acids for H:
1,2
, located in the central variable domain of each flagellin was required for the binding of serotype-specific antibodies, providing further evidence for the presence of a discontinuous H epitope. Two peptides comprising these areas were shown to be highly suitable for application as antigens in an enzyme-linked immunosorbent assay detecting
S. typhimurium
-specific antibody.
A Simple and Reliable Method for Hybridization of Homothallic Wine Strains ofSaccharomyces cerevisiae
Authors: Ramírez Manuel , Peréz Francisco , Regodón José A. 
Published: December 2019

ABSTRACTA procedure was developed for the hybridization and improvement of homothallic industrial wine yeasts. Killer cycloheximide-sensitive strains were crossed with killer-sensitive cycloheximide-resistant strains to get killer cycloheximide-resistant hybrids, thereby enabling hybrid selection and identification. This procedure also allows backcrossing of spore colonies from the hybrids with parental strains.
The Bactericidal Activity of Pediocin PA-1 Is Specifically Inhibited by a 15-mer Fragment That Spans the Bacteriocin from the Center toward the C Terminus
Authors: Fimland Gunnar , Jack Ralph , Jung Günther , Nes Ingolf F. , Nissen-Meyer Jon 
Published: December 2019

ABSTRACT
A 15-mer peptide fragment derived from pediocin PA-1 (from residue 20 to residue 34) specifically inhibited the bactericidal activity of pediocin PA-1. The fragment did not inhibit the pediocin-like bacteriocins sakacin P, leucocin A, and curvacin A to nearly the same extent as it inhibited pediocin PA-1. Enterocin A, however, was also significantly inhibited by this fragment, although not as greatly as pediocin PA-1. This is consistent with the fact that enterocin A contains the longest continuous sequence identical to that of pediocin PA-1 in the region spanned by the fragment. The fragment inhibited pediocin PA-1 to a much greater extent than did the other 29 possible 15-mer fragments that span pediocin PA-1. The results suggest that the fragment—by interacting with the target cells and/or pediocin PA-1—interferes specifically with pediocin-target cell interaction.
Quantitative Measure of Small-Subunit rRNA Gene Sequences of the Kingdom
Korarchaeota
Authors: Brunk Clifford F. , Eis Nicole 
Published: December 2019

ABSTRACT
Comparative PCR amplification of small-subunit (SSU) rRNA gene (rDNA) sequences indicates substantial preferential PCR amplification of pJP27 sequences with korarchaeote-specific PCR primers. The coamplification of a modified SSU rDNA sequence can be used as an internal standard to determine the amount of a specific SSU rDNA sequence.
A New 4-Nitrotoluene Degradation Pathway in a
Mycobacterium
Strain
Authors: Spiess Tilmann , Desiere Frank , Fischer Peter , Spain Jim C. , Knackmuss Hans-Joachim , Lenke Hiltrud 
Published: December 2019

ABSTRACT

Mycobacterium
sp. strain HL 4-NT-1, isolated from a mixed soil sample from the Stuttgart area, utilized 4-nitrotoluene as the sole source of nitrogen, carbon, and energy. Under aerobic conditions, resting cells of the
Mycobacterium
strain metabolized 4-nitrotoluene with concomitant release of small amounts of ammonia; under anaerobic conditions, 4-nitrotoluene was completely converted to 6-amino-
m
-cresol. 4-Hydroxylaminotoluene was converted to 6-amino-
m
-cresol by cell extracts and thus could be confirmed as the initial metabolite in the degradative pathway. This enzymatic equivalent to the acid-catalyzed Bamberger rearrangement requires neither cofactors nor oxygen. In the same crucial enzymatic step, the homologous substrate hydroxylaminobenzene was rearranged to 2-aminophenol. Abiotic oxidative dimerization of 6-amino-
m
-cresol, observed during growth of the
Mycobacterium
strain, yielded a yellow dihydrophenoxazinone. Another yellow metabolite (λ
max
, 385 nm) was tentatively identified as 2-amino-5-methylmuconic semialdehyde, formed from 6-amino-
m
-cresol by
meta
ring cleavage.
High-Level Production of Recombinant Human Parathyroid Hormone 1-34
Authors: Suzuki Yuji , Yabuta Masayuki , Ohsuye Kazuhiro 
Published: December 2019

ABSTRACT

Expression of the synthetic human parathyroid hormone 1-34 [hPTH(1-34)] gene by a gene fusion strategy was demonstrated. hPTH(1-34) was produced at the C terminus of the partner peptides involving amino acids 1 to 97, 1 to 117, or 1 to 139 of a modified
Escherichia coli
β-galactosidase by linker peptides containing oligohistidine of different lengths. The fusion proteins in the inclusion bodies were rendered soluble with urea and subjected to site-specific cleavage with the secretory type yeast Kex2 protease. Optimal expression and enzymatic processing were achieved in the fusion protein βG-117S4HPT, constructed from amino acids 1 to 117 of β-galactosidase and the linker of HHHHPGGSVKKR. The fusion protein accumulated more than 20% of the
E. coli
total protein. The hPTH(1-34) was purified up to 99.5% with a good yield of 0.5 g/liter of culture. The purified product was identified as intact hPTH(1-34) by amino acid analysis and N-terminal sequencing.
Molecular Characterization and Heterologous Expression of the Gene Encoding a Low-Molecular-Mass Endoglucanase from
Trichoderma reesei
QM9414
Authors: Okada Hirofumi , Tada Kohji , Sekiya Tadashi , Yokoyama Kengo , Takahashi Akinori , Tohda Hideki , Kumagai Hiromichi , Morikawa Yasushi 
Published: December 2019

ABSTRACT

We have isolated the genomic and cDNA clones encoding EG III (a low-molecular-mass endo-β-1,4-glucanase) gene from
Trichoderma reesei
QM9414. The nucleotide sequence of the cDNA fragment was verified to contain a 702-bp open reading frame that encodes a 234-amino-acid propeptide. The deduced protein sequence has significant homologies with family H endo-β-1,4-glucanases. The 16-amino-acid N-terminal sequence was shown to function as a leader peptide for possible secretion. Northern blot analysis showed that the EG III gene transcript, with a length of about 700 bp, was expressed markedly by cellulose but not by glucose. The protein has been expressed as a mature form in
Escherichia coli
and as secreted forms in
Saccharomyces cerevisiae
and
Schizosaccharomyces pombe
under the control of
tac
, alcohol dehydrogenase (
ADH1
), and human cytomegalovirus promoters, respectively. The
S. cerevisiae
and
Schizosaccharomyces pombe
recombinant strains showed strong cellulolytic activities on agar plates containing carboxymethyl cellulose. The
E. coli
strain expressed small amounts of EG III in an active form and large amounts of EG III in an inactive form. The molecular masses of the recombinant EG IIIs were estimated to be 25, 28, and 29 kDa for
E. coli
,
S. cerevisiae
, and
Schizosaccharomyces pombe
, respectively, by immunoblot analysis following sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Parts of the yeast recombinant EG IIIs decreased their molecular masses to 25 kDa after treatment with endoglycosidase H and α-mannosidase, suggesting that they are N glycosylated at least partly.
Enterococcus faecalis
Gene Transfer under Natural Conditions in Municipal Sewage Water Treatment Plants
Authors: Marcinek Herbert , Wirth Reinhard , Muscholl-Silberhorn Albrecht , Gauer Matthias 
Published: December 2019

ABSTRACT

The ability of
Enterococcus faecalis
to transfer various genetic elements under natural conditions was tested in two municipal sewage water treatment plants. Experiments in activated sludge basins of the plants were performed in a microcosm which allowed us to work under sterile conditions; experiments in anoxic sludge digestors were performed in dialysis bags. We used the following naturally occurring genetic elements: pAD1 and pIP1017 (two so-called sex pheromone plasmids with restricted host ranges, which are transferred at high rates under laboratory conditions); pIP501 (a resistance plasmid possessing a broad host range for gram-positive bacteria, which is transferred at low rates under laboratory conditions); and Tn
916
(a conjugative transposon which is transferred under laboratory conditions at low rates to gram-positive bacteria and at very low rates to gram-negative bacteria). The transfer rate between different strains of
E. faecalis
under natural conditions was, compared to that under laboratory conditions, at least 10
5
-fold lower for the sex pheromone plasmids, at least 100-fold lower for pIP501, and at least 10-fold lower for Tn
916
. In no case was transfer from
E. faecalis
to another bacterial species detected. By determining the dependence of transfer rates for pIP1017 on bacterial concentration and extrapolating to actual concentrations in the sewage water treatment plant, we calculated that the maximum number of transfer events for the sex pheromone plasmids between different strains of
E. faecalis
in the municipal sewage water treatment plant of the city of Regensburg ranged from 10
5
to 10
8
events per 4 h, indicating that gene transfer should take place under natural conditions.
A Rapid, Specific Membrane Filtration Procedure for Enumeration of Enterococci in Recreational Water
Authors: Messer James W. , Dufour Alfred P. 
Published: December 2019

ABSTRACT

A two-step membrane filter (MF) method with mE medium, upon which the membrane must be incubated for 48 h and then transferred to a substrate medium to differentiate enterococci, is recommended by the U.S. Environmental Protection Agency to measure enterococci in fresh and marine recreational waters. The original mE medium was modified by reducing the triphenyltetrazolium chloride from 0.15 to 0.02 g/liter and adding 0.75 g of indoxyl β-
d
-glucoside per liter. The new MF medium, mEI medium, detected levels of enterococci in 24 h comparable to those detected by the original mE medium in 48 h, with the same level of statistical confidence. In addition, the use of mEI medium eliminated the need to transfer the membrane to a substrate medium to differentiate enterococci from other genera of the fecal streptococcal group. Colonies from mEI medium were examined to determine the rates of false-positive and false-negative occurrences. mEI medium had a false-positive rate of 6.0% and a false-negative rate of 6.5%. Interlaboratory testing of the MF method with mEI medium demonstrated that the relative reproducibility standard deviations among laboratories ranged from 2.2% for marine water to 18.9% for freshwater. The comparative recovery studies, specificity determinations, and multilaboratory evaluation indicated that mEI medium has analytical performance characteristics equivalent to those of mE medium. The simplicity of use and decreased incubation time with mEI medium will facilitate the detection and quantification of enterococci in fresh and marine recreational waters.
Protein Method for Investigating Mercuric Reductase Gene Expression in Aquatic Environments
Authors: Ogunseitan O. A. 
Published: December 2019

ABSTRACT

A colorimetric assay for NADPH-dependent, mercuric ion-specific oxidoreductase activity was developed to facilitate the investigation of mercuric reductase gene expression in polluted aquatic ecosystems. Protein molecules extracted directly from unseeded freshwater and samples seeded with
Pseudomonas aeruginosa
PU21(Rip64) were quantitatively assayed for mercuric reductase activity in microtiter plates by stoichiometric coupling of mercuric ion reduction to a colorimetric redox chain through NADPH oxidation. Residual NADPH was determined by titration with phenazine methosulfate-catalyzed reduction of methyl thiazolyl tetrazolium to produce visible formazan. Spectrophotometric determination of formazan concentration showed a positive correlation with the amount of NADPH remaining in the reaction mixture (
r
2
= 0.99). Mercuric reductase activity in the protein extracts was inversely related to the amount of NADPH remaining and to the amount of formazan produced. A qualitative nitrocellulose membrane-based version of the method was also developed, where regions of mercuric reductase activity remained colorless against a stained-membrane background. The assay detected induced mercuric reductase activity from 10
2
CFU, and up to threefold signal intensity was detected in seeded freshwater samples amended with mercury compared to that in mercury-free samples. The efficiency of extraction of bacterial proteins from the freshwater samples was (97 ± 2)% over the range of population densities investigated (10
2
to 10
8
CFU/ml). The method was validated by detection of enzyme activity in protein extracts of water samples from a polluted site harboring naturally occurring mercury-resistant bacteria. The new method is proposed as a supplement to the repertoire of molecular techniques available for assessing specific gene expression in heterogeneous microbial communities impacted by mercury pollution.
Microbial Conversion Products of Leptomycin B
Authors: Kuhnt Michaela , Bitsch Francis , Ponelle Monique , Sanglier Jean-Jacques , Wang Ying , Wolff Barbara 
Published: December 2019

ABSTRACT

Leptomycin B (LMB), a secondary metabolite produced by
Streptomyces
sp. strain ATS 1287, with known antifungal and antitumor effects, inhibits the nucleo-cytoplasmic translocation of the human immunodeficiency virus type 1 regulatory protein Rev and exhibits significant antiproliferative activity. Since LMB itself turned out to be distinctly cytotoxic, a bioconversion screening with a selected set of 29 bacterial and 72 fungal strains was performed in order to obtain metabolites of LMB with reduced antiproliferative effects. Several derivatives of LMB, more polar than the parent compound and produced in yields of >5%, were detected. Liquid chromatography-mass spectroscopy analysis indicated the type of bioconversion. Fermentations (1-liter scale) of those strains with high rates of transformation were suitable for isolation and characterization of the most prominent metabolites. Thus, bioconversion of LMB with
Aspergillus flavus
ATCC 9170 and
Emericella unguis
ATCC 13431 served for isolation of the novel derivatives 26-hydroxy-LMB (30% was the concentration of the metabolite [with respect to LMB] used for bioconversion) and LMB-24-glutaminamide (90%), respectively.
Streptomyces rimosus
ATCC 28893 converted LMB into 4,11-dihydroxy-LMB (13%) and 2,3-dihydro-LMB (55%). Although the antiproliferative effects of the LMB metabolites could be reduced through microbial conversion, none of these metabolites inhibited the nuclear export of Rev better than LMB itself.
Purification and Characterization of an Acetyl Xylan Esterase fromBacillus pumilus
Authors: Degrassi Giuliano , Okeke Benedict C. , Bruschi Carlo V. , Venturi Vittorio 
Published: December 2019

ABSTRACTBacillus pumilusPS213 was found to be able to release acetate from acetylated xylan. The enzyme catalyzing this reaction has been purified to homogeneity and characterized. The enzyme was secreted, and its production was induced by corncob powder and xylan. Its molecular mass, as determined by gel filtration, is 190 kDa, while sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed a single band of 40 kDa. The isoelectric point was found to be 4.8, and the enzyme activity was optimal at 55°C and pH 8.0. The activity was inhibited by most of the metal ions, while no enhancement was observed. The Michaelis constant (Km) andVmaxfor α-naphthyl acetate were 1.54 mM and 360 μmol min−1mg of protein−1, respectively.
Mercury Methylation and Demethylation in Anoxic Lake Sediments and by Strictly Anaerobic Bacteria
Authors: Pak K.-R. , Bartha R. 
Published: December 2019

ABSTRACT

After spiking anoxic sediment slurries of three acidic oligotrophic lakes with either HgCl
2
at 1.0 μg/ml or CH
3
HgI at 0.1 μg/ml, both mercury methylation and demethylation rates were measured. High mercury methylation potentials were accompanied by high demethylation potentials in the same sediment. These high potentials correlated positively with the concentrations of organic matter and dissolved sulfate in the sediment and with mercury levels in fish. Adjustment of the acidic sediment pH to neutrality failed to influence either the methylation or the demethylation rate of mercury. The opposing methylation and demethylation processes converged to establish similar Hg
2+
-CH
3
Hg
+
equilibria in all three sediments. Because of their metabolic dominance in anoxic sediments, mercury methylation and demethylation in pure cultures of sulfidogenic, methanogenic, and acetogenic bacteria were also measured. Sulfidogens both methylated and demethylated mercury, but the methanogen tested only catalyzed demethylation and the acetogen neither methylated nor demethylated mercury.
A Fermentor System for Regulating Oxygen at Low Concentrations in Cultures of
Saccharomyces cerevisiae
Authors: Burke Patricia V. , Kwast Kurt E. , Everts Frank , Poyton Robert O. 
Published: December 2019

ABSTRACT
The growth of yeast cells to high densities at low, but constant, oxygen concentrations is difficult because the cells themselves respire oxygen; hence, as cell mass increases, so does oxygen consumption. To circumvent this problem, we have designed a system consisting of a computer-controlled gas flow train that adjusts oxygen concentration in the gas flow to match cellular demand. It does this by using a proportional-integral-differential algorithm in conjunction with a three-way valve to mix two gases, adjusting their proportions to maintain the desired oxygen concentration. By modeling yeast cell yields at intermediate to low oxygen concentrations, we have found that cellular respiration declines with oxygen concentration, most likely because of a decrease in the expression of genes for respiratory proteins. These lowered rates of oxygen consumption, together with the gas flow system described here, allow the growth of yeast cells to high densities at low oxygen concentrations. This system can also be used to grow cells at any desired oxygen concentration and for regulated shifts between oxygen concentrations.