bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of an Intelligent Control System To Evaluate Multiparametric Effects on Iron Oxidation by Thermophilic Bacteria
Authors: Stoner Daphne L. , Miller Karen S. , Fife Dee Jay , Larsen Eric D. , Tolle Charles R. , Johnson John A. 
Published: December 2019

ABSTRACT
A learning-based intelligent control system, the BioExpert, was developed and applied to the evaluation of multiparametric effects on iron oxidation by enrichment cultures of moderately thermophilic, acidophilic mining bacteria. The control system acquired and analyzed the data and then selected and maintained the sets of conditions that were evaluated. Through multiple iterations, the BioExpert selected sets of conditions that resulted in improved iron oxidation rates. The results obtained with the BioExpert suggested that temperature and pH were coupled, or interactive, parameters. Elevated temperatures (51.5°C) in combination with a moderately high pH (pH 1.84) impaired the growth of and iron oxidation by the enrichment culture. Moderate-to-high oxidation rates were achieved with a relatively high pH in combination with a relatively low temperature or, conversely, with a relatively low pH in combination with a relatively high temperature. The interactive effect of pH and temperature was not apparent from the results obtained in an experiment in which temperature was the only parameter that was varied. When the BioExpert was applied to a mixed culture containing mesophilic and thermophilic bacteria, the computer “learned” that pH 1.8, 45°C, and an inlet iron concentration from 30 to 35 mM were most favorable for iron oxidation. In conclusion, this study demonstrated that the learning-based intelligent control system BioExpert was an effective experimental tool that can be used to examine multiparametric effects on the growth and metabolic activity of mining bacteria.
Evidence for the Interplay between Trehalose Metabolism and Hsp104 in Yeast
Authors: Iwahashi Hitoshi , Nwaka Solomon , Obuchi Kaoru , Komatsu Yasuhiko 
Published: December 2019

ABSTRACT

Disruption of the
HSP104
gene in a mutant which cannot accumulate trehalose during heat shock treatment caused trehalose accumulation (H. Iwahashi, K. Obuchi, S. Fujii, and Y. Komatsu, Lett. Appl. Microbiol 25:43–47, 1997). This implies that Hsp104 affects trehalose metabolism. Thus, we measured the activities of enzymes involved in trehalose metabolism. The activities of trehalose-synthesizing and -hydrolyzing enzymes are low in the
HSP104
disruption mutant during heat shock. This data is correlated with intracellular trehalose and glucose levels observed in the
HSP104
disruption mutant. These results suggest that during heat shock, Hsp104 contributes to the simultaneous increase in both accumulation and degradation of trehalose.
Heterogeneity among Isolates of
Vibrio vulnificus
Recovered from Eels (
Anguilla anguilla
) in Denmark
Authors: Høi Lise , Dalsgaard Inger , DePaola Angelo , Siebeling Ronald J. , Dalsgaard Anders 
Published: December 2019

ABSTRACT

The findings of this study demonstrate that
Vibrio vulnificus
isolates recovered from diseased eels in Denmark are heterogeneous as shown by O serovars, capsule types, ribotyping, phage typing, and plasmid profiling. The study includes 85
V. vulnificus
isolates isolated from the gills, intestinal contents, mucus, spleen, and kidneys of eels during five disease outbreaks on two Danish eel farms from 1995 to 1997, along with a collection of 12
V. vulnificus
reference strains. The results showed that more than one serovar may be capable of causing disease in eels and that these isolates are genetically heterogenous as shown by ribotyping. Ribotyping also showed that the same isolates may persist in an eel farm and cause recurrent outbreaks. Phage typing did not correlate with ribotyping or serotyping. However, we observed that 26 of 28 isolates, which were not susceptible to any of the phages, showed the same ribotype, O serovar, and capsule type. This suggests that these isolates may possess features that make them resistant to lysis by the phages used in this study. Ninety-three of 97 isolates harbored between one and three high-molecular-weight plasmids which previously had been suggested to be associated with eel virulence. The subdivision of
V. vulnificus
into two biotypes based on the indole reaction can no longer be supported, since 82 of 97 isolates in this study were indole positive, and a subdivision into serovars appears to be more correct.
Effect of Canavanine from Alfalfa Seeds on the Population Biology of
Bacillus cereus
Authors: Emmert Elizabeth A. B. , Milner Jocelyn L. , Lee Julie C. , Pulvermacher Kristie L. , Olivares Heidi A. , Clardy Jon , Handelsman Jo 
Published: December 2019

ABSTRACT

Bacillus cereus
UW85 suppresses diseases of alfalfa seedlings, although alfalfa seed exudate inhibits the growth of UW85 in culture (J. L. Milner, S. J. Raffel, B. J. Lethbridge, and J. Handelsman, Appl. Microbiol. Biotechnol. 43:685–691, 1995). In this study, we determined the chemical basis for and biological role of the inhibitory activity. All of the alfalfa germ plasm tested included seeds that released inhibitory material. We purified the inhibitory material from one alfalfa cultivar and identified it as canavanine, which was present in the cultivar Iroquois seed exudate at a concentration of 2 mg/g of seeds. Multiple lines of evidence suggested that canavanine activity accounted for all of the inhibitory activity. Both canavanine and seed exudate inhibited the growth of UW85 on minimal medium; growth inhibition by either canavanine or seed exudate was prevented by arginine, histidine, or lysine; and canavanine and crude seed exudate had the same spectrum of activity against
B. cereus
,
Bacillus thuringiensis
, and
Vibrio cholerae
. The
B. cereus
UW85 populations surrounding canavanine-exuding seeds were up to 100-fold smaller than the populations surrounding non-canavanine-exuding seeds, but canavanine did not affect the growth of UW85 on seed surfaces. The spermosphere populations of canavanine-resistant mutants of UW85 were larger than the spermosphere populations of UW85, but the mutants and UW85 were similar in spermoplane colonization. These results indicate that canavanine exuded from alfalfa seeds affects the population biology of
B. cereus.
Cloning and Characterization of NADP-Mannitol Dehydrogenase cDNA from the Button Mushroom,
Agaricus bisporus
, and Its Expression in Response to NaCl Stress
Authors: Stoop Johan M. H. , Mooibroek Hans 
Published: December 2019

ABSTRACT

Mannitol, a six-carbon sugar alcohol, is the main storage carbon in the button mushroom,
Agaricus bisporus
. Given the physiological importance of mannitol metabolism in growth, fruit body development, and salt tolerance of
A. bisporus
, the enzyme responsible for mannitol biosynthesis, NADP-dependent mannitol dehydrogenase (MtDH) (EC
1.1.1.138
), was purified to homogeneity, and
MtDH
cDNA was cloned, sequenced, and characterized. To our knowledge, this represents the first report on the isolation of a cDNA encoding an NADP-dependent mannitol dehydrogenase. The
MtDH
cDNA contains an open reading frame of 789 bp encoding a protein of approximately 28 kDa. The N-terminal and internal amino acid sequences of the deduced protein exactly matched the ones determined from the purified MtDH subunit, whereas the amino acid composition of the deduced protein was nearly identical to that of the purified MtDH. The
MtDH
cDNA showed high homology with a plant-induced short-chain dehydrogenase from
Uromyces fabae
. Phylogenetic analysis based on amino acid sequences from mannitol(-1-phosphate) dehydrogenases indicated a close relationship between the substrate specificity of the enzymes and phylogenetic differentiation. Salt-stressed fruit bodies showed an overall increase in mannitol biosynthesis, as was evident from the increase in MtDH activity, MtDH abundance, and
MtDH
RNA accumulation. Furthermore, the
MtDH
transcript level seems to be under developmental control, as
MtDH
RNA accumulated during maturation of the fruit body.
Insertion-Duplication Mutagenesis in
Streptococcus pneumoniae
: Targeting Fragment Length Is a Critical Parameter in Use as a Random Insertion Tool
Authors: Lee Myeong S. , Seok Chaok , Morrison Donald A. 
Published: December 2019

ABSTRACT

To examine whether insertion-duplication mutagenesis with chimeric DNA as a transformation donor could be valuable as a gene knockout tool for genomic analysis in
Streptococcus pneumoniae
, we studied the transformation efficiency and targeting specificity of the process by using a nonreplicative vector with homologous targeting inserts of various sizes. Insertional recombination was very specific in targeting homologous sites. While the recombination rate did not depend on which site or region was targeted, it did depend strongly on the size of the targeting insert in the donor plasmid, in proportion to the fifth power of its length for inserts of 100 to 500 bp. The dependence of insertion-duplication events on the length of the targeting homology was quite different from that for linear allele replacement and places certain limits on the design of mutagenesis experiments. The number of independent pneumococcal targeting fragments of uniform size required to knock out any desired fraction of the genes in a model genome with a defined probability was calculated from these data by using a combinatorial theory with simplifying assumptions. The results show that efficient and thorough mutagenesis of a large part of the pneumococcal genome should be practical when using insertion-duplication mutagenesis.
Use of a Genetically Enhanced, Pediocin-Producing Starter Culture,
Lactococcus lactis
subsp.
lactis
MM217, To Control
Listeria monocytogenes
in Cheddar Cheese
Authors: Buyong Nurliza , Kok Jan , Luchansky John B. 
Published: December 2019

ABSTRACT

Cheddar cheese was prepared with
Lactococcus lactis
subsp.
lactis
MM217, a starter culture which contains pMC117 coding for pediocin PA-1. About 75 liters of pasteurized milk (containing ca. 3.6% fat) was inoculated with strain MM217 (ca. 10
6
CFU per ml) and a mixture of three
Listeria monocytogenes
strains (ca. 10
3
CFU per ml). The viability of the pathogen and the activity of pediocin in the cheese were monitored at appropriate intervals throughout the manufacturing process and during ripening at 8°C for 6 months. In control cheese made with the isogenic, non-pediocin-producing starter culture
L. lactis
subsp.
lactis
MM210, the counts of the pathogen increased to about 10
7
CFU per g after 2 weeks of ripening and then gradually decreased to about 10
3
CFU per g after 6 months. In the experimental cheese made with strain MM217, the counts of
L. monocytogenes
decreased to 10
2
CFU per g within 1 week of ripening and then decreased to about 10 CFU per g within 3 months. The average titer of pediocin in the experimental cheese decreased from approximately 64,000 arbitrary units (AU) per g after 1 day to 2,000 AU per g after 6 months. No pediocin activity (<200 AU per g) was detected in the control cheese. Also, the presence of pMC117 in strain MM217 did not alter the cheese-making quality of the starter culture, as the rates of acid production, the pH values, and the levels of moisture, NaCl, and fat of the control cheese and the experimental cheese were similar. Our data revealed that pediocin-producing starter cultures have significant potential for protecting natural cheese against
L. monocytogenes
.
Enumeration and Detection of Anaerobic Ferrous Iron-Oxidizing, Nitrate-Reducing Bacteria from Diverse European Sediments
Authors: Straub Kristina L. , Buchholz-Cleven Berit E. E. 
Published: December 2019

ABSTRACT

Anaerobic, nitrate-dependent microbial oxidation of ferrous iron was recently recognized as a new type of metabolism. In order to study the occurrence of three novel groups of ferrous iron-oxidizing, nitrate-reducing bacteria (represented by strains BrG1, BrG2, and BrG3), 16S rRNA-targeted oligonucleotide probes were developed. In pure-culture experiments, these probes were shown to be suitable for fluorescent in situ hybridization, as well as for hybridization analysis of denaturing gradient gel electrophoresis (DGGE) patterns. However, neither enumeration by in situ hybridization nor detection by the DGGE-hybridization approach was feasible with sediment samples. Therefore, the DGGE-hybridization approach was combined with microbiological methods. Freshwater sediment samples from different European locations were used for enrichment cultures and most-probable-number (MPN) determinations. Bacteria with the ability to oxidize ferrous iron under nitrate-reducing conditions were detected in all of the sediment samples investigated. At least one of the previously described types of bacteria was detected in each enrichment culture. MPN studies showed that sediments contained from 1 × 10
5
to 5 × 10
8
ferrous iron-oxidizing, nitrate-reducing bacteria per g (dry weight) of sediment, which accounted for at most 0.8% of the nitrate-reducing bacteria growing with acetate. Type BrG1, BrG2, and BrG3 bacteria accounted for an even smaller fraction (0.2% or less) of the ferrous iron-oxidizing, nitrate-reducing community. The DGGE patterns of MPN cultures suggested that more organisms than those isolated thus far are able to oxidize ferrous iron with nitrate. A comparison showed that among the anoxygenic phototrophic bacteria, organisms that have the ability to oxidize ferrous iron also account for only a minor fraction of the population.
Assimilation of Cellooligosaccharides by a Cell Surface-Engineered Yeast Expressing β-Glucosidase and Carboxymethylcellulase from
Aspergillus aculeatus
Authors: Murai Toshiyuki , Ueda Mitsuyoshi , Kawaguchi Takashi , Arai Motoo , Tanaka Atsuo 
Published: December 2019

ABSTRACT

Since
Saccharomyces cerevisiae
lacks the cellulase complexes that hydrolyze cellulosic materials, which are abundant in the world, two types of hydrolytic enzymes involved in the degradation of cellulosic materials to glucose were genetically co-immobilized on its cell surface for direct utilization of cellulosic materials, one of the final goals of our studies. The genes encoding FI-carboxymethylcellulase (CMCase) and β-glucosidase from the fungus
Aspergillus aculeatus
were individually fused with the gene encoding the C-terminal half (320 amino acid residues from the C terminus) of yeast α-agglutinin and introduced into
S. cerevisiae
. The delivery of CMCase and β-glucosidase to the cell surface was carried out by the secretion signal sequence of the native signal sequence of CMCase and by the secretion signal sequence of glucoamylase from
Rhizopus oryzae
for β-glucosidase, respectively. The genes were expressed by the glyceraldehyde-3-phosphate dehydrogenase promoter from
S. cerevisiae
. The CMCase and β-glucosidase activities were detected in the cell pellet fraction, not in the culture supernatant. The display of CMCase and β-glucosidase proteins on the cell surface was confirmed by immunofluorescence microscopy. The cells displaying these cellulases could grow on cellobiose or water-soluble cellooligosaccharides as the sole carbon source. The degradation and assimilation of cellooligosaccharides were confirmed by thin-layer chromatography. This result showed that the cell surface-engineered yeast with these enzymes can be endowed with the ability to assimilate cellooligosaccharides. This is the first step in the assimilation of cellulosic materials by
S. cerevisiae
expressing heterologous cellulase genes.
Expression of Active Human Tissue-Type Plasminogen Activator inEscherichia coli
Authors: Qiu Ji , Swartz James R. , Georgiou George 
Published: December 2019

ABSTRACTThe formation of native disulfide bonds in complex eukaryotic proteins expressed inEscherichia coliis extremely inefficient. Tissue plasminogen activator (tPA) is a very important thrombolytic agent with 17 disulfides, and despite numerous attempts, its expression in an active form in bacteria has not been reported. To achieve the production of active tPA inE. coli, we have investigated the effect of cooverexpressing native (DsbA and DsbC) or heterologous (rat and yeast protein disulfide isomerases) cysteine oxidoreductases in the bacterial periplasm. Coexpression of DsbC, an enzyme which catalyzes disulfide bond isomerization in the periplasm, was found to dramatically increase the formation of active tPA both in shake flasks and in fermentors. The active protein was purified with an overall yield of 25% by using three affinity steps with, in sequence, lysine-Sepharose, immobilizedErythrina caffrainhibitor, and Zn-Sepharose resins. After purification, approximately 180 μg of tPA with a specific activity nearly identical to that of the authentic protein can be obtained per liter of culture in a high-cell-density fermentation. Thus, heterologous proteins as complex as tPA may be produced in an active form in bacteria in amounts suitable for structure-function studies. In addition, these results suggest the feasibility of commercial production of extremely complex proteins inE. coliwithout the need for in vitro refolding.
Ralstonia solanacearum
Pectin Methylesterase Is Required for Growth on Methylated Pectin but Not for Bacterial Wilt Virulence
Authors: Tans-Kersten Julie , Guan Yanfen , Allen Caitilyn 
Published: December 2019

ABSTRACT

Ralstonia
(
Pseudomonas
)
solanacearum
causes bacterial wilt, a serious disease of many crop plants. The pathogen produces several extracellular plant cell wall-degrading enzymes, including polygalacturonases (PGs) and pectin methylesterase (Pme). Pme removes methyl groups from pectin, thereby facilitating subsequent breakdown of this cell wall component by PGs, which are known bacterial wilt virulence factors.
R. solanacearum
PGs could not degrade 93% methylated pectin unless the substrate was first demethylated by Pme, but as the degree of methylation of the pectin substrate decreased, PG activity increased. Primers derived from a published
pme
sequence generated an 800-bp DNA probe fragment, which identified Pme-encoding plasmids from a
R. solanacearum
genomic library. A
pme
chromosomal mutant had no detectable Pme activity in vitro and no longer grew on 93% methylated pectin as a carbon source. Curiously, the
pme
mutant, which had no detectable PG activity on highly methylated pectin, was just as virulent as the wild-type strain on tomato, eggplant (aubergine), and tobacco. Since PG activity is required for full virulence, this result suggests that the pectin in these particular hosts may not be highly methylated, or that the breakdown of highly methylated pectin is not a significant factor in the disease process in general. A positive response regulator of PG production called PehR was not required for wild-type Pme production. However, a mutant strain lacking PhcA, which is a global regulator of several virulence genes, produced no detectable Pme activity. Thus,
pme
expression is directly or indirectly regulated by PhcA but not by PehR.
Utility of Green Fluorescent Nucleic Acid Dyes and Aluminum Oxide Membrane Filters for Rapid Epifluorescence Enumeration of Soil and Sediment Bacteria
Authors: Weinbauer Markus G. , Beckmann Christiane , Höfle Manfred G. 
Published: December 2019

ABSTRACT
High background fluorescence and unspecific staining hampered the epifluorescence enumeration of bacteria in 45% of the tested soil and sediment samples with 4′,6-diamidino-2-phenylindole (DAPI) and polycarbonate membrane filters. These problems of the determination of total cell counts can be circumvented by using green fluorescent high-affinity nucleic acid dyes and aluminum oxide membrane filters. Due to the bright staining of cells, we recommend SYBR Green II as dye.
Recombinant
Klebsiella oxytoca
Strains with Improved Efficiency in Removal of High Nitrate Loads
Authors: Piñar Guadalupe , Ramos Juan L. 
Published: December 2019

ABSTRACT

Klebsiella oxytoca
CECT 4460 removes high nitrate loads from industrial wastewaters without accumulation of nitrite under optimal culture conditions; however, under nonoptimal conditions nitrite accumulates. This situation reflects an in vivo-limited functioning of nitrite reductase in this strain. As a way to overcome this limitation, an increase in the nitrite reductase gene dose in
K. oxytoca
CECT 4460 was considered. To achieve this, we cloned and transferred into this strain the
Klebsiella pneumoniae nasB
gene, which encodes assimilatory nitrite reductase (Lin et al., J. Bacteriol. 176:2551–2559, 1994). The delivery vector was either the wide-host-range plasmid pUPE2, in which the
nasB
gene is expressed from the
Escherichia coli
P
lac
promoter, or a mini-Tn
5
-Km vector, which upon random insertion in the host chromosome allowed expression of the
nasB
gene from an unidentified chromosomal host promoter. The effect of the increase in the dose of the
nasB
gene in
K. oxytoca
CECT 4460 on the accumulation of nitrite in the culture medium was tested in two recombinant strains. The results obtained showed that
K. oxytoca
CECT 4460 bearing pUPE2 accumulated 88% less nitrite than the wild-type strain, while the recombinant strain bearing the
K. pneumoniae nasB
gene in the host chromosome showed a 25% lower level of nitrite accumulation in the culture medium than that of the wild type.
Occurrence of Male-Specific Bacteriophage in Feral and Domestic Animal Wastes, Human Feces, and Human-Associated Wastewaters
Authors: Calci Kevin R. , Burkhardt William , Watkins William D. , Rippey Scott R. 
Published: December 2019

ABSTRACT
Male-specific bacteriophage (MSB) densities were determined in animal and human fecal wastes to assess their potential impact on aquatic environments. Fecal samples (1,031) from cattle, chickens, dairy cows, dogs, ducks, geese, goats, hogs, horses, seagulls, sheep, and humans as well as 64 sewerage samples were examined for MSB. All animal species were found to harbor MSB, although the great majority excreted these viruses at very low levels. The results from this study demonstrate that in areas affected by both human and animal wastes, wastewater treatment plants are the principal contributors of MSB to fresh, estuarine, and marine waters.
Delineating the Specific Influence of Virus Isoelectric Point and Size on Virus Adsorption and Transport through Sandy Soils
Authors: Dowd Scot E. , Pillai Suresh D. , Wang Sookyun , Corapcioglu M. Yavuz 
Published: December 2019

ABSTRACT
Many of the factors controlling viral transport and survival within the subsurface are still poorly understood. In order to identify the precise influence of viral isoelectric point on viral adsorption onto aquifer sediment material, we employed five different spherical bacteriophages (MS2, PRD1, Qβ, φX174, and PM2) having differing isoelectric points (pI 3.9, 4.2, 5.3, 6.6, and 7.3 respectively) in laboratory viral transport studies. We employed conventional batch flowthrough columns, as well as a novel continuously recirculating column, in these studies. In a 0.78-m batch flowthrough column, the smaller phages (MS2, φX174, and Qβ), which had similar diameters, exhibited maximum effluent concentration/initial concentration values that correlated exactly with their isoelectric points. In the continuously recirculating column, viral adsorption was negatively correlated with the isoelectric points of the viruses. A model of virus migration in the soil columns was created by using a one-dimensional transport model in which kinetic sorption was used. The data suggest that the isoelectric point of a virus is the predetermining factor controlling viral adsorption within aquifers. The data also suggest that when virus particles are more than 60 nm in diameter, viral dimensions become the overriding factor.