bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computation of the Electrical Double Layer Properties of Semipermeable Membranes in Multicomponent Electrolytes
Authors: Wasserman Evgeny , Felmy Andrew R. 
Published: December 2019

ABSTRACT

A methodology is presented for calculating of the surface potential, Donnan potential, and ion concentration profiles for semipermeable microbial membranes that is valid for an arbitrary electrolyte composition. This model for surface potential, Donnan potential, and charge density was applied to recently reported experimental data for gram-positive bacteria, including
Bacillus brevis
,
Rhodococcus opacus
,
Rhodococcus erythropolis
, and
Corynebacterium
species. These calculations show that previously unconsidered trace amounts of divalent and trivalent cations at very low concentrations (10
−6
M) can have significant effects on the calculated surface and Donnan potentials, at ionic strengths of I ≤ 0.01 M, and that these effects need to be considered in accurate modeling of microbial surface. In addition, the calculated ion concentration profiles show that owing to the relatively high surface charges that can develop in microbial membranes, electrostatic effects can act to significantly concentrate divalent (factors of 5 × 10
3
) and trivalent (factors of 2 × 10
4
) cations within the bacterial cell wall. Comparison of the calculated concentration factors with those derived from experiments shows that a significant fraction of the uptake of metal by bacteria can be explained by the proposed electrostatic model.
Root Colonization by
Agrobacterium tumefaciens
Is Reduced in
cel
,
attB
,
attD
, and
attR
Mutants
Authors: Matthysse Ann G. , McMahan Susan 
Published: December 2019

ABSTRACT

Root colonization by
Agrobacterium tumefaciens
was measured by using tomato and
Arabidopsis thaliana
roots dipped in a bacterial suspension and planted in soil. Wild-type bacteria showed extensive growth on tomato roots; the number of bacteria increased from 10
3
bacteria/cm of root length at the time of inoculation to more than 10
7
bacteria/cm after 10 days. The numbers of cellulose-minus and nonattaching
attB
,
attD
, and
attR
mutant bacteria were less than 1/10,000th the number of wild-type bacteria recovered from tomato roots. On roots of
A. thaliana
ecotype Landsberg
erecta
, the numbers of wild-type bacteria increased from about 30 to 8,000 bacteria/cm of root length after 8 days. The numbers of cellulose-minus and nonattaching mutant bacteria were 1/100th to 1/10th the number of wild-type bacteria recovered after 8 days. The attachment of
A. tumefaciens
to cut
A. thaliana
roots incubated in 0.4% sucrose and observed with a light microscope was also reduced with
cel
and
att
mutants. These results suggest that cellulose synthesis and attachment genes play a role in the ability of the bacteria to colonize roots, as well as in bacterial pathogenesis.
Molecular Cloning, Sequencing, and Expression of a Chemoreceptor Gene from
Leptospirillum ferrooxidans
Authors: Delgado Mónica , Toledo Héctor , Jerez Carlos A. 
Published: December 2019

ABSTRACT

We have cloned and sequenced a 2,262-bp chromosomal DNA fragment from the chemolithoautotrophic acidophilic bacterium
Leptospirillum ferrooxidans
. This DNA contained an open reading frame for a 577-amino-acid protein showing several characteristics of the bacterial chemoreceptors and, therefore, we named this gene
lcrI
for
Leptospirillum
chemotaxis receptor I. This is the first sequence reported for a gene from
L. ferrooxidans
encoding a protein. The
lcrI
gene showed both ς
28
-like and ς
70
-like putative promoters. The LcrI deduced protein contained two hydrophobic regions most likely corresponding to the two transmembrane regions present in all of the methyl-accepting chemotaxis proteins (MCPs) which make them fold with both periplasmic and cytoplasmic domains. We have proposed a cytoplasmic domain for LcrI, which also contains the highly conserved domain (HCD region), present in all of the chemotactic receptors, and two probable methylation sites. The in vitro expression of a DNA plasmid containing the 2,262-bp fragment showed the synthesis of a 58-kDa protein which was immunoprecipitated by antibodies against the Tar protein (an MCP from
Escherichia coli
), confirming some degree of antigenic conservation. In addition, this 58-kDa protein was expressed in
E. coli
, being associated with its cytoplasmic membrane fraction. It was not possible to determine a chemotactic receptor function for LcrI expressed in
E. coli
. This was most likely due to the fact that the periplasmic pH of
E. coli
, which differs by 3 to 4 pH units from that of acidophilic chemolithotrophs, does not allow the right conformation for the LcrI periplasmic domain.
Cloning and Characterization of the Lactococcal Plasmid-Encoded Type II Restriction/Modification System,
Lla
DII
Authors: Madsen Annette , Josephsen Jytte 
Published: December 2019

ABSTRACT

The
Lla
DII restriction/modification (R/M) system was found on the naturally occurring 8.9-kb plasmid pHW393 in
Lactococcus lactis
subsp.
cremoris
W39. A 2.4-kb
Pst
I-
Eco
RI fragment inserted into the
Escherichia coli-L. lactis
shuttle vector pCI3340 conferred to
L. lactis
LM2301 and
L. lactis
SMQ86 resistance against representatives of the three most common lactococcal phage species: 936, P335, and c2. The
Lla
DII endonuclease was partially purified and found to recognize and cleave the sequence 5′-GC↓NGC-3′, where the arrow indicates the cleavage site. It is thus an isoschizomer of the commercially available restriction endonuclease
Fnu
4HI. Sequencing of the 2.4-kb
Pst
I-
Eco
RI fragment revealed two open reading frames arranged tandemly and separated by a 105-bp intergenic region. The endonuclease gene of 543 bp preceded the methylase gene of 954 bp. The deduced amino acid sequence of the
Lla
DII R/M system showed high homology to that of its only sequenced isoschizomer,
Bsp
6I from
Bacillus
sp. strain RFL6, with 41% identity between the endonucleases and 60% identity between the methylases. The genetic organizations of the
Lla
DII and
Bsp
6I R/M systems are identical. Both methylases have two recognition sites (5′-GCGGC-3′ and 5′-GCCGC-3′) forming a putative stem-loop structure spanning part of the presumed −35 sequence and part of the intervening region between the −35 and −10 sequences. Alignment of the
Lla
DII and
Bsp
6I methylases with other m
5
C methylases showed that the protein primary structures possessed the same organization.
Modeling of Growth of
Lactobacillus sanfranciscensis
and
Candida milleri
in Response to Process Parameters of Sourdough Fermentation
Authors: Gänzle Michael G. , Ehmann Michaela , Hammes Walter P. 
Published: December 2019

ABSTRACT

We investigated the effect of the ecological factors pH, temperature, ionic strength, and lactate, acetate, and ethanol levels on
Candida milleri
and two strains of
Lactobacillus sanfranciscensis
, organisms representative of the microflora of sourdough. A mathematical model describing the single and combined effects of these factors on the growth of these organisms was established in accordance with the following criteria: quality of fit, biological significance of the parameters, and applicability of the in vitro data to in situ processes. The growth rates of
L. sanfranciscensis
LTH1729 and LTH2581 were virtually identical under all conditions tested. These organisms tolerated >160 mmol of undissociated acetic acid per liter. Growth occurred in the pH range of 3.9 to 6.7 and was completely inhibited by 4% NaCl.
C. milleri
had a lower optimum temperature for growth (27°C) than the lactobacilli. The growth of the yeast was not affected by pH in the range of 3.5 to 7, and up to 8% NaCl was tolerated. Complete inhibition of growth occurred at 150 mmol of undissociated acetic acid per liter, but acetate at concentrations of up to 250 mmol/liter exerted virtually no effect. The model provides insight into factors contributing to the stability of the sourdough microflora and can facilitate the design of novel sourdough processes.
Quantification of Toxic Cyanobacteria in Water by Use of Competitive PCR Followed by Sequence-Specific Labeling of Oligonucleotide Probes
Authors: Rudi Knut , Skulberg Olav M. , Larsen Frank , Jakobsen Kjetill S. 
Published: December 2019

ABSTRACT

A complete nucleic-acid-based assay which consists of sample preparation, DNA amplification, and chromogenic detection was developed for quantifying potential toxin-producing cyanobacteria of interest to the public. The sample preparation strategy involves the same solid phase for cell concentration and DNA purification. For the detection step, we used a combination of competitive PCR amplification, sequence-specific labeling of oligonucleotide probes, hybridization of the labeled oligonucleotides to immobilized complements and, finally, chromogenic detection. The complete assay was tested with water containing toxin-producing cyanobacteria belonging to the genus
Microcystis
. A detection limit of 100 cells/ml and a quantitative range of more than 3 orders of magnitude were obtained. This approach can easily be adapted to a wide range of bacterial species and has the potential for simultaneous detection and quantitation of several different target organisms by a single assay.
Enhanced Broth Media for Selective Growth of
Vibrio vulnificus
Authors: Hsu Wei-Yea , Wei Cheng-i , Tamplin Mark L. 
Published: December 2019

ABSTRACT

Rapid detection of
Vibrio vulnificus
can be enhanced by optimizing the components of enrichment broth. PNC (5% peptone, 1% NaCl, and 0.08% cellobiose [pH 8.0]) enhanced the growth of
V. vulnificus
compared to alkaline peptone broth. PNCC (PNC with 1.0 to 4.1 U of colistin methanesulfonate per ml) increased the growth of low levels of
V. vulnificus
while suppressing non-target bacteria.
Design and Application of Two Rapid Screening Techniques for Isolation of Mn(IV) Reduction-Deficient Mutants of
Shewanella putrefaciens
Authors: Burnes Brian S. , Mulberry Michael J. , DiChristina Thomas J. 
Published: December 2019

ABSTRACT

Chemical mutagenesis procedures and two newly developed rapid plate assays were used to identify two Mn(IV) reduction-deficient (Mnr) mutants of
Shewanella putrefaciens
. All eleven members of a set of previously isolated Fe(III) reduction-deficient (Fer) mutants displayed Mnr-positive phenotypes on the plate assays and were also capable of anaerobic growth on Mn(IV) as the sole terminal electron acceptor.
Microbial Characterization of Biological Filters Used for Drinking Water Treatment
Authors: Moll Deborah M. , Summers R. Scott , Breen Alec 
Published: December 2019

ABSTRACT
The impact of preozonation and filter contact time (depth) on microbial communities was examined in drinking water biofilters treating Ohio River water which had undergone conventional treatment (coagulation, flocculation, sedimentation) or solutions of natural organic matter isolated from groundwater (both ozonated and nonozonated). With respect to filter depth, compared to filters treating nonozonated waters, preozonation of treated water led to greater differences in community phospholipid fatty acid (PLFA) profiles, utilization of sole carbon sources (Biolog), and arbitrarily primed PCR fingerprints. PLFA profiles indicated that there was a shift toward anaerobic bacteria in the communities found in the filter treating ozonated water compared to the communities found in the filter treating nonozonated settled water, which had a greater abundance of eukaryotic markers.
De Novo Synthesis of Amino Acids by the Ruminal Bacteria
Prevotella bryantii
B
1
4,
Selenomonas ruminantium
HD4, and
Streptococcus bovis
ES1
Authors: Atasoglu Cengiz , Valdés Carmen , Walker Nicola D. , Newbold C. James , Wallace R. John 
Published: December 2019

ABSTRACT

The influence of peptides and amino acids on ammonia assimilation and de novo synthesis of amino acids by three predominant noncellulolytic species of ruminal bacteria,
Prevotella bryantii
B
1
4,
Selenomonas ruminantium
HD4, and
Streptococcus bovis
ES1, was determined by growing these bacteria in media containing
15
NH
4
Cl and various additions of pancreatic hydrolysates of casein (peptides) or amino acids. The proportion of cell N and amino acids formed de novo decreased as the concentration of peptides increased. At high concentrations of peptides (10 and 30 g/liter), the incorporation of ammonia accounted for less than 0.16 of bacterial amino acid N and less than 0.30 of total N. At 1 g/liter, which is more similar to peptide concentrations found in the rumen, 0.68, 0.87, and 0.46 of bacterial amino acid N and 0.83, 0.89, and 0.64 of total N were derived from ammonia by
P. bryantii
,
S. ruminantium
, and
S. bovis
, respectively. Concentration-dependent responses were also obtained with amino acids. No individual amino acid was exhausted in any incubation medium. For cultures of
P. bryantii
, peptides were incorporated and stimulated growth more effectively than amino acids, while cultures of the other species showed no preference for peptides or amino acids. Apparent growth yields increased by between 8 and 57%, depending on the species, when 1 g of peptides or amino acids per liter was added to the medium. Proline synthesis was greatly decreased when peptides or amino acids were added to the medium, while glutamate and aspartate were enriched to a greater extent than other amino acids under all conditions. Thus, the proportion of bacterial protein formed de novo in noncellulolytic ruminal bacteria varies according to species and the form and identity of the amino acid and in a concentration-dependent manner.
Aerobic Degradation of 2,4,6-Trinitrotoluene by
Enterobacter cloacae
PB2 and by Pentaerythritol Tetranitrate Reductase
Authors: French Christopher E. , Nicklin Stephen , Bruce Neil C. 
Published: December 2019

ABSTRACT

Enterobacter cloacae
PB2 was originally isolated on the basis of its ability to utilize nitrate esters, such as pentaerythritol tetranitrate (PETN) and glycerol trinitrate, as the sole nitrogen source for growth. The enzyme responsible is an NADPH-dependent reductase designated PETN reductase.
E. cloacae
PB2 was found to be capable of slow aerobic growth with 2,4,6-trinitrotoluene (TNT) as the sole nitrogen source. Dinitrotoluenes were not produced and could not be used as nitrogen sources. Purified PETN reductase was found to reduce TNT to its hydride-Meisenheimer complex, which was further reduced to the dihydride-Meisenheimer complex. Purified PETN reductase and recombinant
Escherichia coli
expressing PETN reductase were able to liberate nitrogen as nitrite from TNT. The ability to remove nitrogen from TNT suggests that PB2 or recombinant organisms expressing PETN reductase may be useful for bioremediation of TNT-contaminated soil and water.
Deletion of the
rbo
Gene Increases the Oxygen Sensitivity of the Sulfate-Reducing Bacterium
Desulfovibrio vulgaris
Hildenborough
Authors: Voordouw Johanna K. , Voordouw Gerrit 
Published: December 2019

ABSTRACT

The
rbo
gene of
Desulfovibrio vulgaris
Hildenborough encodes rubredoxin oxidoreductase (Rbo), a 14-kDa iron sulfur protein; forms an operon with the gene for rubredoxin; and is preceded by the gene for the oxygen-sensing protein DcrA. We have deleted the
rbo
gene from
D. vulgaris
with the
sacB
mutagenesis procedure developed previously (R. Fu and G. Voordouw, Microbiology 143:1815–1826, 1997). The absence of the
rbo
-gene in the resulting mutant,
D. vulgaris
L2, was confirmed by PCR and protein blotting with Rbo-specific polyclonal antibodies.
D. vulgaris
L2 grows like the wild type under anaerobic conditions. Exposure to air for 24 h caused a 100-fold drop in CFU of L2 relative to the wild type. The lag times of liquid cultures of inocula exposed to air were on average also greater for L2 than for the wild type. These results demonstrate that Rbo, which is not homologous with superoxide dismutase or catalase, acts as an oxygen defense protein in the anaerobic, sulfate-reducing bacterium
D. vulgaris
Hildenborough and likely also in other sulfate-reducing bacteria and anaerobic archaea in which it has been found.
Enzyme-Linked Immunofiltration Assay To Estimate Attachment of Thiobacilli to Pyrite
Authors: Dziurla Marie-Antoinette , Achouak Wafa , Lam Bach-Tuyet , Heulin Thierry , Berthelin Jacques 
Published: December 2019

ABSTRACT

An enzyme-linked immunofiltration assay (ELIFA) has been developed in order to estimate directly and specifically
Thiobacillus ferrooxidans
attachment on sulfide minerals. This method derives from the enzyme-linked immunosorbent assay but is performed on filtration membranes which allow the retention of mineral particles for a subsequent immunoenzymatic reaction in microtiter plates. The polyclonal antiserum used in this study was raised against
T. ferrooxidans
DSM 583 and recognized cell surface antigens present on bacteria belonging to the genus
Thiobacillus
. This antiserum and the ELIFA allowed the direct quantification of attached bacteria with high sensitivity (10
4
bacteria were detected per well of the microtiter plate). The mean value of bacterial attachment has been estimated to be about 10
5
bacteria mg
−1
of pyrite at a particle size of 56 to 65 μm. The geometric coverage ratio of pyrite by
T. ferrooxidans
ranged from 0.25 to 2.25%. This suggests an attachment of
T. ferrooxidans
on the pyrite surface to well-defined limited sites with specific electrochemical or surface properties. ELIFA was shown to be compatible with the measurement of variable levels of adhesion. Therefore, this method may be used to establish adhesion isotherms of
T. ferrooxidans
on various sulfide minerals exhibiting different physicochemical properties in order to understand the mechanisms of bacterial interaction with mineral surfaces.
Characteristics and Efficiency of Glutamine Production by Coupling of a Bacterial Glutamine Synthetase Reaction with the Alcoholic Fermentation System of Baker’s Yeast
Authors: Wakisaka Shinji , Ohshima Yoshifumi , Ogawa Masahiro , Tochikura Tatsurokuro , Tachiki Takashi 
Published: December 2019

ABSTRACT
Glutamine production with bacterial glutamine synthetase (GS) and the sugar-fermenting system of baker’s yeast for ATP regeneration was investigated by determining the product yield obtained with the energy source for ATP regeneration (i.e., glucose) for yeast fermentation. Fructose 1,6-bisphosphate was accumulated temporarily prior to the formation of glutamine in mixtures which consisted of dried yeast cells, GS, their substrate (glucose and glutamate and ammonia), inorganic phosphate, and cofactors. By an increase in the amounts of GS and inorganic phosphate, the amounts of glutamine formed increased to 19 to 54 g/liter, with a yield increase of 69 to 72% based on the energy source (glucose) for ATP regeneration. The analyses of sugar fermentation of the yeast in the glutamine-producing mixtures suggested that the apparent hydrolysis of ATP by a futile cycle(s) at the early stage of glycolysis in the yeast cells reduces the efficiency of ATP utilization. Inorganic phosphate inhibits phosphatase(s) and thus improves glutamine yield. However, the analyses of GS activity in the glutamine-producing mixtures suggested that the higher concentration of inorganic phosphate as well as the limited amount of ATP-ADP caused the low reactivity of GS in the glutamine-producing mixtures. A result suggestive of improved glutamine yield under the conditions with lower concentrations of inorganic phosphate was obtained by using a yeast mutant strain that had low assimilating ability for glycerol and ethanol. In the mutant, the activity of the enzymes involved in gluconeogenesis, especially fructose 1,6-bisphosphatase, was lower than that in the wild-type strain.
Genetic Variation in the Free-Living AmoebaNaegleria fowleri
Authors: Pélandakis Michel , De Jonckheere Johan F. , Pernin Pierre 
Published: December 2019

ABSTRACTIn this study, 30 strains of the pathogenic free-living amoebaNaegleria fowleriwere investigated by using the randomly amplified polymorphic DNA (RAPD) method. The present study confirmed our previous finding that RAPD variation is not correlated with geographical origin. In particular, Mexican strains belong to the variant previously detected in Asia, Europe, and the United States. In France, surprisingly, strains from Cattenom gave RAPD patterns identical to those of the Japanese strains. In addition, all of these strains, together with an additional French strain from Chooz, exhibited similarities to South Pacific strains. The results also confirmed the presence of numerous variants in Europe, whereas only two variants were detected in the United States. The two variants found in the United States were different from the South Pacific variants. These findings do not support the previous hypothesis concerning the origin and modes of dispersal ofN. fowleri.
Conversion of Phenylalanine to Benzaldehyde Initiated by an Aminotransferase in
Lactobacillus plantarum
Authors: Nierop Groot Masja N. , de Bont Jan A. M. 
Published: December 2019

ABSTRACT

The production of benzaldehyde from phenylalanine has been studied in various microorganisms, and several metabolic pathways have been proposed in the literature for the formation of this aromatic flavor compound. In this study, we describe benzaldehyde formation from phenylalanine by using a cell extract of
Lactobacillus plantarum
. Phenylalanine was initially converted to phenylpyruvic acid by an aminotransferase in the cell extract, and the keto acid was further transformed to benzaldehyde. However, control experiments with boiled cell extract revealed that the subsequent conversion of phenylpyruvic acid was a chemical oxidation step. It was observed that several cations could replace the extract in the conversion of phenylpyruvic acid to benzaldehyde. Addition of Cu(II) ions to phenylpyruvic acid resulted not only in the formation of benzaldehyde, but also in the generation of phenylacetic acid, mandelic acid, and phenylglyoxylic acid. These compounds have been considered intermediates in the biological conversion of phenylalanine. The chemical conversion step of phenylpyruvic acid was dependent on temperature, pH, the availability of cations, and the presence of oxygen.