bluuebunny/crossref_metadata_2025_split huggingface dataset:
Induction of Mannanase, Xylanase, and Endoglucanase Activities inSclerotium rolfsii
Authors: Sachslehner Alois , Nidetzky Bernd , Kulbe Klaus D. , Haltrich Dietmar 
Published: December 2019

ABSTRACTInduction of mannanase, xylanase, and cellulase (endoglucanase) synthesis in the plant-pathogenic basidiomyceteSclerotium rolfsiiwas studied by incubating noninduced, resting mycelia with a number of mono-, oligo-, and polysaccharides. The simultaneous formation of these three endoglycanases could be provoked by several polysaccharides structurally resembling the carbohydrate constituents of lignocellulose (e.g., mannan and cellulose), by various disaccharide catabolites of these lignocellulose constituents (e.g., cellobiose, mannobiose, and xylobiose), or by structurally related disaccharides (e.g., lactose, sophorose, and galactosyl-β-1,4-mannose), as well as byl-sorbose. Synthesis of mannanase, xylanase, and endoglucanase always occurred concomitantly and could not be separated by selecting an appropriate inducer. Various structurally different inducing carbohydrates promoted the excretion of the same multiple isoforms of endoglycanases, as judged from the similar banding patterns obtained in zymogram analyses of enzyme preparations obtained in response to these different inducers and resolved by analytical isoelectric focusing. Whereas enhanced xylanase and endoglucanase formation is strictly dependent on the presence of suitable inducers, increased levels of mannanase are excreted byS. rolfsiieven under noninducing, derepressed conditions, as shown in growth experiments with glucose as the substrate. Significant mannanase formation commenced only when glucose was exhausted from the medium. Under these conditions, only very low, presumably constitutive levels of xylanase and endoglucanase were formed. Although the induction of the three endoglycanases is very closely related inS. rolfsii, it was concluded that there is no common, coordinated regulatory mechanism that controls the synthesis of mannanase, xylanase, and endoglucanase.
Metabolism of Dichloromethane by the Strict Anaerobe
Dehalobacterium formicoaceticum
Authors: Mägli Andreas , Messmer Michael , Leisinger Thomas 
Published: December 2019

ABSTRACT

The metabolism of dichloromethane by
Dehalobacterium formicoaceticum
in cell suspensions and crude cell extracts was investigated. The organism is a strictly anaerobic gram-positive bacterium that utilizes exclusively dichloromethane as a growth substrate and ferments this compound to formate and acetate in a molar ratio of 2:1. When [
13
C]dichloromethane was degraded by cell suspensions, formate, the methyl group of acetate, and minor amounts of methanol were labeled, but there was no nuclear magnetic resonance signal corresponding to the carboxyl group of acetate. This finding and previously established carbon and electron balances suggested that dichloromethane was converted to methylene tetrahydrofolate, of which two-thirds was oxidized to formate while one-third gave rise to acetate by incorporation of CO
2
from the medium in the acetyl coenzyme A synthase reaction. When crude desalted extracts were incubated in the presence of dichloromethane, tetrahydrofolate, ATP, methyl viologen, and molecular hydrogen, dichloromethane and tetrahydrofolate were consumed, with the concomitant formation of stoichiometric amounts of methylene tetrahydrofolate. The in vitro transfer of the methylene group of dichloromethane onto tetrahydrofolate required substoichiometric amounts of ATP. The reaction was inhibited in a light-reversible fashion by 20 μM propyl iodide, thus suggesting involvement of a Co(I) corrinoid in the anoxic dehalogenation of dichloromethane.
D. formicoaceticum
exhibited normal growth with 0.8 mM sodium in the medium, and crude extracts contained ATPase activity that was partially inhibited by
N
,
N
′-dicyclohexylcarbodiimide and azide. During growth with dichloromethane, the organism thus may conserve energy not only by substrate-level phosphorylation but also by a chemiosmotic mechanism involving a sodium-independent F
0
F
1
-type ATP synthase.
Extended Survival and Persistence of
Campylobacter
spp. in Water and Aquatic Biofilms and Their Detection by Immunofluorescent-Antibody and -rRNA Staining
Authors: Buswell Clive M. , Herlihy Yvonne M. , Lawrence Lorna M. , McGuiggan James T. M. , Marsh Philip D. , Keevil C. William , Leach Steve A. 
Published: December 2019

ABSTRACT

In water microcosm experiments, the survival times of
Campylobacter
isolates differed by up to twofold, as determined by culturing; this difference increased to fourfold when particular combinations of temperature and oxygenation were used. The mean survival times were much longer at 4 and 10°C (202 and 176 h, respectively) than at 22 and 37°C (43 and 22 h, respectively). The influence of anaerobiosis on survival time was less dramatic and differed considerably between isolates. In a two-stage water distribution model preparation containing a biofilm consisting of standardized autochthonous water microflora,
Campylobacter
isolates continued to differ in survival time. However, the survival times of cultures were considerably longer in the presence of the autochthonous water microflora (strains CH1 and 9752 survived 700 and 360 h, respectively, at 4°C) than in the sterile microcosms (strains CH1 and 9752 survived 230 and 157 h, respectively). Although increased temperature and oxygenation were generally detrimental to culturability, the interaction of these two factors influenced the two strains examined differently. When the organisms were grown aerobically at 30°C, the survival of the two strains was reversed; aerobiosis decreased the survival time of strain CH1 by 30%, but unexpectedly improved the persistence time of strain 9752 by more than threefold. Persistence times within biofilms were much longer when they were determined by detection methods not involving culturing. Immunofluorescent-antibody staining demonstrated that the pathogen persisted up to the termination of the experiments after 28 and 42 days of incubation at 30 and 4°C, respectively. The specificity of detection within intact biofilms was reduced because of high background fluorescence. However, preliminary studies with a
Campylobacter
-specific rRNA probe revealed the same extended persistence of the pathogen within the biofilms.
Engineering of Quasi-Natural
Pseudomonas putida
Strains for Toluene Metabolism through an
ortho
-Cleavage Degradation Pathway
Authors: Panke Sven , Sánchez-Romero Juan M. , de Lorenzo Víctor 
Published: December 2019

ABSTRACT

To construct a bacterial catalyst for bioconversion of toluene and several alkyl and chloro- and nitro-substituted derivatives into the corresponding benzoates, the upper TOL operon of plasmid pWW0 of
Pseudomonas putida
was fully reassembled as a single gene cassette along with its cognate regulatory gene,
xylR
. The corresponding DNA segment was then targeted to the chromosome of a
P. putida
strain by using a genetic technique that allows deletion of all recombinant tags inherited from previous cloning steps and leaves the otherwise natural strain bearing exclusively the DNA segment encoding the phenotype of interest. The resulting strains grew on toluene as the only carbon source through a two-step process: conversion of toluene into benzoate, mediated by the upper TOL enzymes, and further metabolism of benzoate through the housekeeping
ortho
-ring cleavage pathway of the catechol intermediate.
Environmental Occurrence of the Whipple’s Disease Bacterium (
Tropheryma whippelii
)
Authors: Maiwald Matthias , Schuhmacher Frank , Ditton Hans-Jürgen , von Herbay Axel 
Published: December 2019

ABSTRACT

Whipple’s disease is a systemic disorder in which a gram-positive rod-shaped bacterium is constantly present in infected tissues. After numerous unsuccessful attempts to culture this bacterium, it was eventually characterized by 16S rRNA gene analysis to be a member of the actinomycetes. The name
Tropheryma whippelii
was proposed. Until now, the bacterium has only been found in infected human tissues, but there is no evidence for human-to-human transmission. Here we report the detection of DNA specific for the Whipple’s disease bacterium in 25 of 38 wastewater samples from five different sewage treatment plants in the area of Heidelberg, Germany. These findings provide the first evidence that
T. whippelii
occurs in the environment, within a polymicrobial community. This is in accordance with the phylogenetic relationship of this bacterium as well as with known epidemiological aspects of Whipple’s disease. Our data argue for an environmental source for infection with the Whipple’s disease bacterium.
An Anaerobic, Intrachamber Incubator for Growth of
Methanosarcina
spp. on Methanol-Containing Solid Media
Authors: Metcalf William W. , Zhang Jun Kai , Wolfe Ralph S. 
Published: December 2019

ABSTRACT

To simplify the incubation of
Methanosarcina
spp. on solid agar medium, a two-port, manual, rectangular air lock was modified to serve as an anaerobic incubator. In one operation, it is possible to incubate 153 petri plates, the equivalent of 11 standard anaerobic jars, with plating efficiencies identical to those of traditional protocols.
Inactivation of
Cryptosporidium parvum
Oocysts by Ammonia
Authors: Jenkins Michael B. , Bowman Dwight D. , Ghiorse William C. 
Published: December 2019

ABSTRACT

The survival of
Cryptosporidium parvum
oocysts in soil and water microhabitats may be affected by the environmental production and release of free ammonia. The objective of this study was to determine the effects of increasing free ammonia concentrations and times of exposure on oocyst viability. Wild-type oocysts were obtained from naturally infected calf feces by chemical (continuous-flow) centrifugation and sucrose gradients. Ammonia (NH
3
) from a commercial solution was applied in concentrations ranging from 0.007 to 0.148 M. Exposure times ranged from 10 min to 24 h at a constant temperature of 24 ± 1°C. Viability of oocysts was determined with a dye permeability assay and an in vitro excystation assay (M. B. Jenkins, L. J. Anguish, D. D. Bowman, M. J. Walker, and W. C. Ghiorse, Appl. Environ. Microbiol. 63:3844–3850, 1997). Even the lowest concentration of ammonia decreased significantly the viability of oocysts after 24 h of exposure. Increasing concentrations of ammonia increased inactivation rates, which ranged from 0.014 to 0.066 h
−1
. At the highest concentration of ammonia, a small fraction of viable oocysts still remained. Exposure to pH levels corresponding to those associated with the ammonia concentrations showed minimal effects of alkaline pH alone on oocyst viability. This study shows that environmentally relevant concentrations of free ammonia may significantly increase the inactivation of oocysts in ammonia-containing environments.
Design and Evaluation of Useful Bacterium-Specific PCR Primers That Amplify Genes Coding for Bacterial 16S rRNA
Authors: Marchesi Julian R. , Sato Takuichi , Weightman Andrew J. , Martin Tracey A. , Fry John C. , Hiom Sarah J. , Wade William G. 
Published: December 2019

ABSTRACT
We report the design and evaluation of PCR primers 63f and 1387r for amplification of 16S rRNA genes from bacteria. Their specificity and efficacy were tested systematically with a variety of bacterial species and environmental samples. They were found to be more useful for 16S rRNA gene amplification in ecological and systematic studies than PCR amplimers that are currently more generally used.
Purification, Characterization, and Mechanism of a Flavin Mononucleotide-Dependent 2-Nitropropane Dioxygenase from
Neurospora crassa
Authors: Gorlatova Natalia , Tchorzewski Marek , Kurihara Tatsuo , Soda Kenji , Esaki Nobuyoshi 
Published: December 2019

ABSTRACT

A nitroalkane-oxidizing enzyme was purified to homogeneity from
Neurospora crassa
. The enzyme is composed of two subunits; the molecular weight of each subunit is approximately 40,000. The enzyme catalyzes the oxidation of nitroalkanes to produce the corresponding carbonyl compounds. It acts on 2-nitropropane better than on nitroethane and 1-nitropropane, and anionic forms of nitroalkanes are much better substrates than are neutral forms. The enzyme does not act on aromatic compounds. When the enzyme reaction was conducted in an
18
O
2
atmosphere with the anionic form of 2-nitropropane as the substrate, acetone (with a molecular mass of 60 Da) was produced. This indicates that the oxygen atom of acetone was derived from molecular oxygen, not from water; hence, the enzyme is an oxygenase. The reaction stoichiometry was 2CH
3
CH(NO
2
)-CH
3
+ O
2
→2CH
3
COCH
3
+ 2HNO
2
, which is identical to that of the reaction of 2-nitropropane dioxygenase from
Hansenula mrakii
. The reaction of the
Neurospora
enzyme was inhibited by superoxide anion scavengers in the same manner as that of the
Hansenula
enzyme. Both of these enzymes are flavoenzymes; however, the
Neurospora
enzyme contains flavin mononucleotide as a prosthetic group, whereas the
Hansenula
enzyme contains flavin adenine dinucleotide.
Microbial Reductive Dechlorination of Aroclor 1260 in Anaerobic Slurries of Estuarine Sediments
Authors: Wu Qingzhong , Sowers Kevin R. , May Harold D. 
Published: December 2019

ABSTRACT

Reductive dechlorination of Aroclor 1260 was investigated in anaerobic slurries of estuarine sediments from Baltimore Harbor (Baltimore, Md.). The sediment slurries were amended with 800 ppm Aroclor 1260 with and without the addition of 350 μM 2,3,4,5-tetrachlorobiphenyl (2,3,4,5-CB) or 2,3,5,6-tetrachlorobiphenyl (2,3,5,6-CB) and incubated in triplicate at 30°C under methanogenic conditions in an artificial estuarine medium. After 6 months, extensive
meta
dechlorination and moderate
ortho
dechlorination of Aroclor 1260 occurred in all incubated cultures except for sterilized controls. Overall, total chlorines per biphenyl decreased by up to 34%.
meta
chlorines per biphenyl decreased by 65, 55, and 45% and
ortho
chlorines declined by 18, 12, and 9%, respectively, when 2,3,4,5-CB, 2,3,5,6-CB, or no additional congener was supplied. This is the first confirmed report of microbial
ortho
dechlorination of a commercial polychlorinated biphenyl mixture. In addition, compared with incubated cultures supplied with Aroclor 1260 alone, the dechlorination of Aroclor 1260 plus 2,3,4,5-CB or 2,3,5,6-CB occurred with shorter lag times (31 to 60 days versus 90 days) and was more extensive, indicating that the addition of a single congener stimulated the dechlorination of Aroclor 1260.
Expression of
Clostridium acetobutylicum
ATCC 824 Genes in
Escherichia coli
for Acetone Production and Acetate Detoxification
Authors: Bermejo Lourdes L. , Welker Neil E. , Papoutsakis Eleftherios T. 
Published: December 2019

ABSTRACT

A synthetic acetone operon (
ace4
) composed of four
Clostridium acetobutylicum
ATCC 824 genes (
adc
,
ctfAB
, and
thl
, coding for the acetoacetate decarboxylase, coenzyme A transferase, and thiolase, respectively) under the control of the
thl
promoter was constructed and was introduced into
Escherichia coli
on vector pACT. Acetone production demonstrated that
ace4
is expressed in
E. coli
and resulted in the reduction of acetic acid levels in the fermentation broth. Since different
E. coli
strains vary significantly in their growth characteristics and acetate metabolism,
ace4
was expressed in three
E. coli
strains: ER2275, ATCC 11303, and MC1060. Shake flask cultures of MC1060(pACT) produced ca. 2 mM acetone, while both strains ER2275(pACT) and ATCC 11303(pACT) produced ca. 40 mM acetone. Glucose-fed cultures of strain ATCC 11303(pACT) resulted in a 150% increase in acetone titers compared to those of batch shake flask cultures. External addition of sodium acetate to glucose-fed cultures of ATCC 11303(pACT) resulted in further increased acetone titers. In bioreactor studies, acidic conditions (pH 5.5 versus 6.5) improved acetone production. Despite the substantial acetone evaporation due to aeration and agitation in the bioreactor, 125 to 154 mM acetone accumulated in ATCC 11303(pACT) fermentations. These acetone titers are equal to or higher than those produced by wild-type
C. acetobutylicum
. This is the first study to demonstrate the ability to use clostridial genes in nonclostridial hosts for solvent production. In addition, acetone-producing
E. coli
strains may be useful hosts for recombinant protein production in that detrimental acetate accumulation can be avoided.
Characterization of EngF from
Clostridium cellulovorans
and Identification of a Novel Cellulose Binding Domain
Authors: Ichi-ishi Akihiko , Sheweita Salah , Doi Roy H. 
Published: December 2019

ABSTRACT

The physical and enzymatic properties of noncellulosomal endoglucanase F (EngF) from
Clostridium cellulovorans
were studied. Binding studies revealed that the

K
d

and the maximum amount of protein bound for acid-swollen cellulose were 1.8 μM and 7.1 μmol/g of cellulose, respectively. The presence of cellobiose but not glucose or maltose could dissociate EngF from cellulose. N- and C-terminally truncated enzymes showed that binding activity was located at some site between amino acid residues 356 and 557 and that enzyme activity was still present when 20 amino acids but not 45 amino acids were removed from the N terminus and when 32 amino acids were removed from the C terminus; when 57 amino acids were removed from the C terminus, all activity was lost. EngF showed low endoglucanase activity and could hydrolyze cellotetraose and cellopentaose but not cellotriose. Activity studies suggested that EngF plays a role as an endoglucanase during cellulose degradation. Comparative sequence analyses indicated strongly that the cellulose binding domain (CBD) is different from previously reported CBDs.
Surface Charge Properties of and Cu(II) Adsorption by Spores of the Marine
Bacillus
sp. Strain SG-1
Authors: He Lee M. , Tebo Bradley M. 
Published: December 2019

ABSTRACT

Spores of marine
Bacillus
sp. strain SG-1 are capable of oxidizing Mn(II) and Co(II), which results in the precipitation of Mn(III, IV) and Co(III) oxides and hydroxides on the spore surface. The spores also bind other heavy metals; however, little is known about the mechanism and capacity of this metal binding. In this study the characteristics of the spore surface and Cu(II) adsorption to this surface were investigated. The specific surface area of wet SG-1 spores was 74.7 m
2
per g of dry weight as measured by the methylene blue adsorption method. This surface area is 11-fold greater than the surface area of dried spores, as determined with an N
2
adsorption surface area analyzer or as calculated from the spore dimensions, suggesting that the spore surface is porous. The surface exchange capacity as measured by the proton exchange method was found to be 30.6 μmol m
−2
, which is equal to a surface site density of 18.3 sites nm
−2
. The SG-1 spore surface charge characteristics were obtained from acid-base titration data. The surface charge density varied with pH, and the zero point of charge was pH 4.5. The titration curves suggest that the spore surface is dominated by negatively charged sites that are largely carboxylate groups but also phosphate groups. Copper adsorption by SG-1 spores was rapid and complete within minutes. The spores exhibited a high affinity for Cu(II). The amounts of copper adsorbed increased from negligible at pH 3 to maximum levels at pH >6. Their great surface area, site density, and affinity give SG-1 spores a high capability for binding metals on their surfaces, as demonstrated by our experiments with Cu(II).
Common Elements Regulating Gene Expression in Temperate and Lytic Bacteriophages of
Lactococcus
Species
Authors: Walker Shirley A. , Dombroski Carol S. , Klaenhammer Todd R. 
Published: December 2019

ABSTRACT

A phage-inducible middle promoter (P
15A10
) from the lytic, lactococcal bacteriophage φ31, a member of the P335 species, is located in an 888-base pair fragment near the right cohesive end. Sequence analysis revealed extensive homology (>95%) to the right cohesive ends of two temperate phages of the P335 species, φr1t and φLC3. Sequencing upstream and downstream of P
15A10
showed that the high degree of homology between φ31 and φr1t continued beyond the phage promoter. With the exception of one extra open reading frame in φ31, the sequences were highly homologous (95 to 98%) between nucleotides 13448 and 16320 of the published φr1t sequence. By use of a β-galactosidase (β-Gal) gene under the control of a smaller, more tightly regulated region within the P
15A10
promoter, P
566–888
, it was established that mitomycin C induction of a lactococcal strain harboring the prophage φr1t induced the P
566–888
promoter, as determined from an increase in β-Gal activity. Hybridization of nine other lactococcal strains with
32
P-labeled P
566–888
showed that the
Lactococcus lactis
strains C10, ML8, and NCK203 harbored sequences homologous to that of the phage-inducible promoter. Mitomycin C induced the resident prophages in all these strains and concurrently induced the P
566–888
promoter, as determined from an increase in β-Gal activity. DNA restriction analysis revealed that the prophages in C10, ML8, and NCK203 had identical restriction patterns which were different from that of φr1t. In addition, DNA sequencing showed that the promoter elements in the three phages were identical to each other and to P
566–888
from the lytic phage φ31. These results point to a conserved mechanism in the regulation of gene expression between the lytic phage φ31 and at least two temperate bacteriophages and provide further evidence for a link in the evolution of certain temperate phages and lytic phages.
Diversity and Structure of the Methanogenic Community in Anoxic Rice Paddy Soil Microcosms as Examined by Cultivation and Direct 16S rRNA Gene Sequence Retrieval
Authors: Großkopf Regine , Janssen Peter H. , Liesack Werner 
Published: December 2019

ABSTRACT

A dual approach consisting of cultivation and molecular retrieval of partial archaeal 16S rRNA genes was carried out to characterize the diversity and structure of the methanogenic community inhabiting the anoxic bulk soil of flooded rice microcosms. The molecular approach identified four groups of known methanogens. Three environmental sequences clustered with
Methanobacterium bryantii
and
Methanobacterium formicicum
, six were closely related but not identical to those of strains of
Methanosaeta concilii
, two grouped with members of the genus
Methanosarcina
, and two were related to the methanogenic endosymbiont of
Plagiopyla nasuta
. The cultivation approach via most-probable-number counts with a subsample of the same soil as an inoculum yielded cell numbers of up to 10
7
per g of dry soil for the H
2
-CO
2
-utilizing methanogens and of up to 10
6
for the acetate-utilizing methanogens. Strain VeH52, isolated from the terminal positive dilution on H
2
-CO
2
, grouped within the phylogenetic radiation characterized by
M. bryantii
and
M. formicicum
and the environmental sequences of the
Methanobacterium
-like group. A consortium of two distinct methanogens grew in the terminal positive culture on acetate. These two organisms showed absolute 16S rRNA gene identities with environmental sequences of the novel
Methanosaeta
-like group and the
Methanobacterium
-like group.
Methanosarcina
spp. were identified only in the less-dilute levels of the same dilution series on acetate. These data correlate well with acetate concentrations of about 11 μM in the pore water of this rice paddy soil. These concentrations are too low for the growth of known
Methanosarcina
spp. but are at the acetate utilization threshold of
Methanosaeta
spp. Thus, our data indicated
Methanosaeta
spp. and
Methanobacterium
spp. to be the dominant methanogenic groups in the anoxic rice soil, whereas
Methanosarcina
spp. appeared to be less abundant.