bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Strategy for Detection of Viruses in Groundwater by PCR
Authors: Abbaszadegan Morteza , Stewart Peter , LeChevallier Mark 
Published: December 2019

ABSTRACT
We evaluated the use of the PCR for detection of enteric viruses in groundwater. To do this, we used an improved sample-processing technique and a large-volume amplification protocol. The objective of this study was to use advanced molecular techniques to develop a rapid and simple method which can be used by the water industry for detection of viral contamination in a variety of water samples. The strategy described here fulfills the water industry’s need for a rapid, reliable, easily performed method for analyzing groundwater for virus contamination. Viruses were detected after concentration from at least 400 gallons (1,512 liters) of water by a filter adsorption and elution method, which resulted in a concentrate containing viruses. A total of 150 samples were analyzed by performing cell culture assays for enteroviruses and by performing reverse transcription PCR (RT-PCR) analyses for enteroviruses, hepatitis A virus, and rotavirus. Thirteen samples (8.7%) produced cellular cytopathic effects when the Buffalo green monkey cell line was used. When primers specific for enteroviruses were used in RT-PCR, 40 of 133 samples (30.1%) tested positive for the presence of enterovirus RNA. When hepatitis A virus-specific primers were used, 12 of 139 samples (8.6%) were considered positive for the presence of hepatitis A viral RNA. The RT-PCR analysis performed with rotavirus-specific primers identified 18 of 130 samples (13.8%) that were positive for rotavirus RNA sequences. Our sample-processing technique and large-volume PCR protocol (reaction volume, 300 μl) resulted in sufficient removal or dilution of inhibitors so that more than 95% of the samples could be assayed by PCR. Because of its sensitivity for detecting viral nucleic acid sequences, PCR analysis should produce more positive results than cell culture analysis. Since either cell culture analysis or PCR can reveal only a “snapshot” of the quality of the groundwater being sampled, PCR seems to be a desirable rapid initial screening tool.
Multiple α-Glucoside Transporter Genes in Brewer’s Yeast
Authors: Jespersen Lene , Cesar Lene B. , Meaden Philip G. , Jakobsen Mogens 
Published: December 2019

ABSTRACT

Maltose and maltotriose are the two most abundant fermentable sugars in brewer’s wort, and the rate of uptake of these sugars by brewer’s yeast can have a major impact on fermentation performance. In spite of this, no information is currently available on the genetics of maltose and maltotriose uptake in brewing strains of yeast. In this work, we studied 30 brewing strains of yeast (5 ale strains and 25 lager strains) with the aim of examining the alleles of maltose and maltotriose transporter genes contained by them. To do this, we hybridized gene probes to chromosome blots. Studies performed with laboratory strains have shown that maltose utilization is conferred by any one of five unlinked but highly homologous
MAL
loci (
MAL1
to
MAL4
and
MAL6
). Gene 1 at each locus encodes a maltose transporter. All of the strains of brewer’s yeast examined except two were found to contain
MAL11
and
MAL31
sequences, and only one of these strains lacked
MAL41. MAL21
was not present in the five ale strains and 12 of the lager strains.
MAL61
was not found in any of the yeast strains. In three of the lager strains, there was evidence that
MAL
transporter gene sequences occurred on chromosomes other than those known to carry
MAL
loci. Sequences corresponding to the
AGT1
gene, which encodes a transporter of several α-glucosides, including maltose and maltotriose, were detected in all but one of the yeast strains. Homologues of
AGT1
were identified in three of the lager strains, and two of these homologues were mapped, one to chromosome II and the other to chromosome XI.
AGT1
appears to be a member of a family of closely related genes, which may have arisen in brewer’s yeast in response to selective pressure.
Screening, Nucleotide Sequence, and Biochemical Characterization of an Esterase from
Pseudomonas fluorescens
with High Activity towards Lactones
Authors: Khalameyzer V. , Fischer I. , Bornscheuer U. T. , Altenbuchner J. 
Published: December 2019

ABSTRACT

A genomic library of
Pseudomonas fluorescens
DSM 50106 in a λRESIII phage vector was screened in
Escherichia coli
K-12 for esterase activity by using α-naphthyl acetate and Fast Blue RR. A 3.2-kb DNA fragment was subcloned from an esterase-positive clone and completely sequenced. Esterase EstF1 was encoded by a 999-bp open reading frame (ORF) and exhibited significant amino acid sequence identity with members of the serine hydrolase family. The deduced amino acid sequences of two other C-terminal truncated ORFs exhibited homology to a cyclohexanone monooxygenase and an alkane hydroxylase. However, esterase activity was not induced by growing of
P. fluorescens
DSM 50106 in the presence of several cyclic ketones. The esterase gene was fused to a His tag and expressed in
E. coli
. The gene product was purified by zinc ion affinity chromatography and characterized. Detergents had to be added for purification, indicating that the enzyme was membrane bound or membrane associated. The optimum pH of the purified enzyme was 7.5, and the optimum temperature was 43°C. The showed highest purified enzyme activities towards lactones. The activity increased from γ-butyrolactone (18.1 U/mg) to ɛ-caprolactone (21.8 U/mg) to δ-valerolactone (36.5 U/mg). The activities towards the aliphatic esters were significantly lower; the only exception was the activity toward ethyl caprylate, which was the preferred substrate.
Manganese Deficiency Can Replace High Oxygen Levels Needed for Lignin Peroxidase Formation by
Phanerochaete chrysosporium
Authors: Rothschild Nathan , Levkowitz Ayala , Hadar Yitzhak , Dosoretz Carlos G. 
Published: December 2019

ABSTRACT

The combined effects of Mn and oxygen on lignin peroxidase (LIP) activity and isozyme composition in
Phanerochaete chrysosporium
were studied by using shallow stationary cultures grown in the presence of limited or excess N. When no Mn was added, LIP was formed in both N-limited and N-excess cultures exposed to air, but no LIP activity was observed at Mn concentrations greater than 13 mg/liter. In oxygen-flushed, N-excess cultures, LIP was formed at all Mn concentrations, and the peak LIP activity values in the extracellular fluid were nearly identical in the presence of Mn concentrations ranging from 3 to 1,500 mg/liter. When the availability of oxygen to cultures exposed to air was increased by growing the fungus under nonimmersed liquid conditions, higher levels of Mn were needed to suppress LIP formation compared with the levels needed in shallow stationary cultures. The composition of LIP isozymes was affected by the levels of N and Mn. Addition of veratryl alcohol to cultures exposed to air did not eliminate the suppressive effect of Mn on LIP formation. A deficiency of Mn in N-excess cultures resulted in lower biomass and a lower rate of glucose consumption than in the presence of Mn. In addition, almost no activity of the antioxidant enzyme Mn superoxide dismutase was observed in Mn-deficient, N-excess cultures, but the activity of this enzyme increased as the Mn concentration increased from 3 to 13 mg/liter. No Zn/Cu superoxide dismutase activity was observed in N-excess cultures regardless of the Mn concentration.
Effect of Acetate on Molecular and Physiological Aspects of
Clostridium beijerinckii
NCIMB 8052 Solvent Production and Strain Degeneration
Authors: Chen Chih-Kuang , Blaschek Hans P. 
Published: December 2019

ABSTRACT

The addition of sodium acetate to chemically defined MP2 medium was found to increase and stabilize solvent production and also increase glucose utilization by
Clostridium beijerinckii
NCIMB 8052. RNA and enzyme analyses indicated that coenzyme A (CoA) transferase was highly expressed and has higher activity in
C. beijerinckii
NCIMB 8052 grown in MP2 medium containing added sodium acetate than in the microorganism grown without sodium acetate. RNA analysis suggested the existence of a
sol
operon and confirmed the presence of a
ptb-buk
operon in
C. beijerinckii
NCIMB 8052. In addition to CoA transferase,
C. beijerinckii
NCIMB 8052 grown in MP2 medium containing added acetate demonstrated higher acetate kinase- and butyrate kinase-specific activity than when the culture was grown in MP2 medium containing no added acetate. Southern blot analysis with chromosomal DNA isolated from solventogenic and degenerated
C. beijerinckii
NCIMB 8052 indicated that
C. beijerinckii
NCIMB 8052 strain degeneration does not involve loss of the CoA transferase genes. The addition of acetate to MP2 medium may induce the expression of the
sol
operon, which ensures solvent production and prevents strain degeneration in
C. beijerinckii
NCIMB 8052.
Diversity of Free-Living and Attached Bacteria in Offshore Western Mediterranean Waters as Depicted by Analysis of Genes Encoding 16S rRNA
Authors: Acinas Silvia G. , Antón Josefa , Rodríguez-Valera Francisco 
Published: December 2019

ABSTRACT

In a previous study (S. G. Acinas, F. Rodrı́guez-Valera, and C. Pedrós-Alió, FEMS Microbiol. Ecol. 24:27–40, 1997), community fingerprinting by 16S rDNA restriction analysis applied to Mediterranean offshore waters showed that the free-living pelagic bacterial community was very different from the bacterial cells aggregated or attached to particles of more than about 8 μm. Here we have studied both assemblages at three depths (5, 50, and 400 m) by cloning and sequencing the 16S rDNA obtained from the same samples, and we have also studied the samples by scanning electron microscopy to detect morphology patterns. As expected, the sequences retrieved from the assemblages were very different. The subsample of attached bacteria contained very little diversity, with close relatives of a well-known species of marine bacteria,
Alteromonas macleodii
, representing the vast majority of the clones at every depth. On the other hand, the free-living assemblage was highly diverse and varied with depth. At 400 m, close relatives of cultivated γ
Proteobacteria
predominated, but as shown by other authors, near the surface most clones were related to phylotypes described only by sequence, in which the α
Proteobacteria
of the SAR11 cluster predominated. The new technique of rDNA internal spacer analysis has been utilized, confirming these results. Clones representative of the
A. macleodii
cluster have been completely sequenced, producing a picture that fits well with the idea that they could represent a genus with at least two species and with a characteristic depth distribution.
Molecular Analysis of Expression of the Lantibiotic Pep5 Immunity Phenotype
Authors: Pag Ulrike , Heidrich Christoph , Bierbaum Gabriele , Sahl Hans-Georg 
Published: December 2019

ABSTRACT

The lantibiotic Pep5 is produced by
Staphylococcus epidermidis
5. Within its biosynthetic gene cluster, the immunity gene
pepI
, providing producer self-protection, is localized upstream of the structural gene
pepA
. Pep5 production and the immunity phenotype have been found to be tightly coupled (M. Reis, M. Eschbach-Bludau, M. I. Iglesias-Wind, T. Kupke, and H.-G. Sahl, Appl. Environ. Microbiol. 60:2876–2883, 1994). To study this phenomenon, we analyzed
pepA
and
pepI
transcription and translation and constructed a number of strains containing various fragments of the gene cluster and expressing different levels of immunity. Complementation of a
pepA
-expressing strain with
pepI
in
trans
did not result in phenotypic immunity or production of PepI. On the other hand, neither
pepA
nor its product was found to be involved in immunity, since suppression of the translation of the
pepA
mRNA by mutation of the ATG start codon did not reduce the level of immunity. Moreover, homologous and heterologous expression of
pepI
from a xylose-inducible promoter resulted in significant Pep5 insensitivity. Most important for expression of the immunity phenotype was the stability of
pepI
transcripts, which in the wild-type strain, is achieved by an inverted repeat with a free energy of −56.9 kJ/mol, localized downstream of
pepA
. We performed site-directed mutagenesis to study the functional role of PepI and constructed F13D PepI, I17R PepI, and PepI 1-65; all mutants showed reduced levels of immunity. Western blot analysis indicated that F13D PepI and PepI 1-65 were not produced correctly or were partially degraded, while I17R PepI apparently was less efficient in providing self-protection than the wild-type PepI.
Identification of Lactic Acid Bacteria from Chili Bo, a Malaysian Food Ingredient
Authors: Leisner Jørgen J. , Pot Bruno , Christensen Henrik , Rusul Gulam , Olsen John E. , Wee Bee Wah , Muhamad Kharidah , Ghazali Hasanah M. 
Published: December 2019

ABSTRACT

Ninety-two strains of lactic acid bacteria (LAB) were isolated from a Malaysian food ingredient, chili bo, stored for up to 25 days at 28°C with no benzoic acid (product A) or with 7,000 mg of benzoic acid kg
−1
(product B). The strains were divided into eight groups by traditional phenotypic tests. A total of 43 strains were selected for comparison of their sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) whole-cell protein patterns with a SDS-PAGE database of LAB. Isolates from product A were identified as
Lactobacillus plantarum
,
Lactobacillus fermentum
,
Lactobacillus farciminis
,
Pediococcus acidilactici
,
Enterococcus faecalis
, and
Weissella confusa
. Five strains belonging to clusters which could not be allocated to existing species by SDS-PAGE were further identified by 16S rRNA sequence comparison. One strain was distantly related to the
Lactobacillus casei/Pediococcus
group. Two strains were related to
Weissella
at the genus or species level. Two other strains did not belong to any previously described 16S rRNA group of LAB and occupied an intermediate position between the
L. casei/Pediococcus
group and the
Weissella
group and species of
Carnobacterium
. The latter two strains belong to the cluster of LAB that predominated in product B. The incidence of new species and subspecies of LAB in chili bo indicate the high probability of isolation of new LAB from certain Southeast Asian foods. None of the isolates exhibited bacteriocin activity against
L. plantarum
ATCC 14917 and LMG 17682.
Genetic and Morphological Characterization of
Cladobotryum
Species Causing Cobweb Disease of Mushrooms
Authors: McKay Gareth J. , Egan Damian , Morris Elizabeth , Scott Carol , Brown Averil E. 
Published: December 2019

ABSTRACT

Cladobotryum dendroides
(=
Dactylium dendroides
) has hitherto been regarded as the major causal agent of cobweb disease of the cultivated mushroom,
Agaricus bisporus
. Nucleotide sequence data for the internal transcribed spacer (ITS) regions of four
Cladobotryum/Hypomyces
species reported to be associated with cobweb disease, however, indicate that the most common pathogen is now
C. mycophilum
. This cobweb pathogen varies somewhat in conidial septation from published descriptions of
C. mycophilum
and lacks the distinctive colony odor. ITS sequencing revealed minor nucleotide variation which split isolates of the pathogen into three subgroups, two comprising isolates that were sensitive to methylbenzimidazole carbamate (MBC) fungicides and one comprising MBC-resistant isolates. The MBC-resistant isolates, which were only obtained from Ireland and Great Britain, clustered together strongly in randomly amplified polymorphic DNA (RAPD) PCR analysis, suggesting that they may be clonal. The MBC-sensitive isolates were more diverse. A RAPD fragment of 800 to 900 bp, containing a microsatellite and found in the MBC-resistant isolates, also indicated their clonal nature; the microsatellites of these isolates contained the same number of GA repeats. Smaller, polymorphic microsatellites, similarly comprising GA repeats, in the MBC-sensitive isolates in general correlated with their geographic origin.
Cold-Active Serine Alkaline Protease from the Psychrotrophic Bacterium
Shewanella
Strain Ac10: Gene Cloning and Enzyme Purification and Characterization
Authors: Kulakova Ljudmila , Galkin Andrey , Kurihara Tatsuo , Yoshimura Tohru , Esaki Nobuyoshi 
Published: December 2019

ABSTRACT

The gene encoding serine alkaline protease (SapSh) of the psychrotrophic bacterium
Shewanella
strain Ac10 was cloned in
Escherichia coli
. The amino acid sequence deduced from the 2,442-bp nucleotide sequence revealed that the protein was 814 amino acids long and had an estimated molecular weight of 85,113. SapSh exhibited sequence similarities with members of the subtilisin family of proteases, and there was a high level of conservation in the regions around a putative catalytic triad consisting of Asp-30, His-65, and Ser-369. The amino acid sequence contained the following regions which were assigned on the basis of homology to previously described sequences: a signal peptide (26 residues), a propeptide (117 residues), and an extension up to the C terminus (about 250 residues). Another feature of SapSh is the fact that the space between His-65 and Ser-369 is approximately 150 residues longer than the corresponding spaces in other proteases belonging to the subtilisin family. SapSh was purified to homogeneity from the culture supernatant of
E. coli
recombinant cells by affinity chromatography with a bacitracin-Sepharose column. The recombinant SapSh (rSapSh) was found to have a molecular weight of about 44,000 and to be highly active in the alkaline region (optimum pH, around 9.0) when azocasein and synthetic peptides were used as substrates. rSapSh was characterized by its high levels of activity at low temperatures; it was five times more active than subtilisin Carlsberg at temperatures ranging from 5 to 15°C. The activation energy for hydrolysis of azocasein by rSapSh was much lower than the activation energy for hydrolysis of azocasein by the subtilisin. However, rSapSh was far less stable than the subtilisin.
Effect of Compressed Carbon Dioxide on Microbial Cell Viability
Authors: Debs-Louka E. , Louka N. , Abraham G. , Chabot V. , Allaf K. 
Published: December 2019

ABSTRACT

In order to study the influence of compressed carbon dioxide, over a range of pressures (1.5 to 5.5 MPa) and exposure times (up to 7 h), on the survival of
Escherichia coli
,
Saccharomyces cerevisiae
, and
Enterococcus faecalis
, a new pressurizable reactor system was conceived. Microbial cells were inoculated onto a solid hydrophilic medium and treated at room temperature; their sensitivities to inactivation varied greatly. The CO
2
treatment had an enhanced efficiency in cell destruction when the pressure and the duration of exposure were increased. The effects of these parameters on the loss of viability was also studied by response-surface methodology. This study showed that a linear correlation exists between microbial inactivation and CO
2
pressure and exposure time, and in it models were proposed which were adequate to predict the experimental values. The end point acidity was measured for all the samples in order to understand the mechanism of microbial inactivation. The pHs of the treated samples did not vary, regardless of the experimental conditions. Other parameters, such as water content and pressure release time, were also investigated.
De Novo Synthesis of 4,5-Dimethoxycatechol and 2,5-Dimethoxyhydroquinone by the Brown Rot Fungus
Gloeophyllum trabeum
Authors: Paszczynski Andrzej , Crawford Ronald , Funk David , Goodell Barry 
Published: December 2019

ABSTRACT

The new dimethoxycatechol 4,5-dimethoxy-1,2-benzenediol (DMC) and the new dimethoxyhydroquinone 2,5-dimethoxy-1,4-benzenediol (DMH) were isolated from stationary cultures of the brown rot fungus
Gloeophyllum trabeum
growing on a glucose mineral medium protected from light. The structure was elucidated by gas chromatography-mass spectrometry through comparison to a synthetic standard. Further confirmation was obtained by forming a dimethoxyoxazole derivative by condensation of DMC with methylene chloride and through examination of methylated derivatives. DMC and DMH may serve as ferric chelators, oxygen-reducing agents, and redox-cycling molecules, which would include functioning as electron transport carriers to Fenton’s reactions. Thus, they appear to be important components of the brown rot decay system of the fungus.
Changes in Bacterial and Eukaryotic Community Structure after Mass Lysis of Filamentous Cyanobacteria Associated with Viruses
Authors: van Hannen Erik J. , Zwart Gabriel , van Agterveld Miranda P. , Gons Herman J. , Ebert Jeannine , Laanbroek Hendrikus J. 
Published: December 2019

ABSTRACT

During an experiment in two laboratory-scale enclosures filled with lake water (130 liters each) we noticed the almost-complete lysis of the cyanobacterial population. Based on electron microscopic observations of viral particles inside cyanobacterial filaments and counts of virus-like particles, we concluded that a viral lysis of the filamentous cyanobacteria had taken place. Denaturing gradient gel electrophoresis (DGGE) of 16S ribosomal DNA fragments qualitatively monitored the removal of the cyanobacterial species from the community and the appearance of newly emerging bacterial species. The majority of these bacteria were related to the
Cytophagales
and actinomycetes, bacterial divisions known to contain species capable of degrading complex organic molecules. A few days after the cyanobacteria started to lyse, a rotifer species became dominant in the DGGE profile of the eukaryotic community. Since rotifers play an important role in the carbon transfer between the microbial loop and higher trophic levels, these observations confirm the role of viruses in channeling carbon through food webs. Multidimensional scaling analysis of the DGGE profiles showed large changes in the structures of both the bacterial and eukaryotic communities at the time of lysis. These changes were remarkably similar in the two enclosures, indicating that such community structure changes are not random but occur according to a fixed pattern. Our findings strongly support the idea that viruses can structure microbial communities.
Comparative Study of Biological Properties and Electrophoretic Characteristics of Lipopolysaccharide from Eel-Virulent and Eel-A virulent
Vibrio vulnificus
Strains
Authors: Biosca Elena G. , Collado Rosa M. , Oliver James D. , Amaro Carmen 
Published: December 2019

ABSTRACT

In
Vibrio vulnificus
, virulence for eels is associated with serovar E strains. In this study, we investigated some biological properties of purified lipopolysaccharides (LPSs) from serovar E and non-serovar E strains. Purified LPSs retained their O-polysaccharidic side chains and did not show any differences that could be related to host specificity, except for serological differences.
Decolorization and Detoxification of Extraction-Stage Effluent from Chlorine Bleaching of Kraft Pulp by
Rhizopus oryzae
Authors: Nagarathnamma R. , Bajpai Pratima 
Published: December 2019

ABSTRACT

Rhizopus oryzae
, a zygomycete, was found to decolorize, dechlorinate, and detoxify bleach plant effluent at lower cosubstrate concentrations than the basidiomycetes previously investigated. With glucose at 1 g/liter, this fungus removed 92 to 95% of the color, 50% of the chemical oxygen demand, 72% of the adsorbable organic halide, and 37% of the extractable organic halide in 24 h at temperatures of 25 to 45°C and a pH of 3 to 5. Even without added cosubstrate the fungus removed up to 78% of the color. Monomeric chlorinated aromatic compounds were removed almost completely, and toxicity to zebra fish was eliminated. The fungal mycelium could be immobilized in polyurethane foam and used repeatedly to treat batches of effluent. The residue after treatment was not further improved by exposure to fresh
R. oryzae
mycelium.