bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anaerobic Degradation of Phthalate Isomers by Methanogenic Consortia
Authors: Kleerebezem Robbert , Pol Look W. Hulshoff , Lettinga Gatze 
Published: December 2019

ABSTRACT

Three methanogenic enrichment cultures, grown on
ortho
-phthalate,
iso
-phthalate, or terephthalate were obtained from digested sewage sludge or methanogenic granular sludge. Cultures grown on one of the phthalate isomers were not capable of degrading the other phthalate isomers. All three cultures had the ability to degrade benzoate. Maximum specific growth rates (μ
S
max
) and biomass yields (Y

X
tot

S
) of the mixed cultures were determined by using both the phthalate isomers and benzoate as substrates. Comparable values for these parameters were found for all three cultures. Values for μ
S
max
and Y

X
tot

S
were higher for growth on benzoate compared to the phthalate isomers. Based on measured and estimated values for the microbial yield of the methanogens in the mixed culture, specific yields for the phthalate and benzoate fermenting organisms were calculated. A kinetic model, involving three microbial species, was developed to predict intermediate acetate and hydrogen accumulation and the final production of methane. Values for the ratio of the concentrations of methanogenic organisms, versus the phthalate isomer and benzoate fermenting organisms, and apparent half-saturation constants (K
S
) for the methanogens were calculated. By using this combination of measured and estimated parameter values, a reasonable description of intermediate accumulation and methane formation was obtained, with the initial concentration of phthalate fermenting organisms being the only variable. The energetic efficiency for growth of the fermenting organisms on the phthalate isomers was calculated to be significantly smaller than for growth on benzoate.
Stimulation of Strontium Accumulation in Linoleate-Enriched
Saccharomyces cerevisiae
Is a Result of Reduced Sr
2+
Efflux
Authors: Avery Simon V. , Smith Shareeka L. , Ghazi A. Mohamad , Hoptroff Michael J. 
Published: December 2019

ABSTRACT

The influence of modified plasma membrane fatty acid composition on cellular strontium accumulation in
Saccharomyces cerevisiae
was investigated. Growth of
S. cerevisiae
in the presence of 1 mM linoleate (18:2) (which results in 18:2 incorporation to ∼70% of total cellular and plasma membrane fatty acids, with no effect on growth rate) yielded cells that accumulated Sr
2+
intracellularly at approximately twice the rate of
S. cerevisiae
grown without a fatty acid supplement. This effect was evident over a wide range of external Sr
2+
concentrations (25 μM to 5 mM) and increased with the extent of cellular 18:2 incorporation. Stimulation of Sr
2+
accumulation was not evident following enrichment of
S. cerevisiae
with either palmitoleate (16:1), linolenate (18:3) (
n
-3 and
n
-6 isomers), or eicosadienoate (20:2) (
n
-6 and
n
-9 isomers). Competition experiments revealed that Ca
2+
- and Mg
2+
-induced inhibition of Sr
2+
accumulation did not differ between unsupplemented and 18:2-supplemented cells. Treatment with trifluoperazine (TFP) (which can act as a calmodulin antagonist and Ca
2+
-ATPase inhibitor), at a low concentration that precluded nonspecific K
+
efflux, increased intracellular Sr
2+
accumulation by approximately 3.6- and 1.4-fold in unsupplemented and 18:2-supplemented cells, respectively. Thus, TFP abolished the enhanced Sr
2+
accumulation ability of 18:2-supplemented cells. Moreover, the rate of Sr
2+
release from Sr
2+
-loaded fatty acid-unsupplemented cells was found to be at least twice as great as that from Sr
2+
-loaded 18:2-enriched cells. The influence of enrichment with other fatty acids on Sr
2+
efflux was variable. The results reveal an enhanced Sr
2+
accumulation ability of
S. cerevisiae
following 18:2-enrichment, which is attributed to diminished Sr
2+
efflux activity in these cells.
Cloning and Characterization of a cDNA Encoding a Novel Extracellular Peroxidase from
Trametes versicolor
Authors: Collins Patrick J. , O’Brien Margaret M. , Dobson Alan D. W. 
Published: December 2019

ABSTRACT

The white rot basidiomycete
Trametes versicolor
secretes a large number of peroxidases which are believed to be involved in the degradation of polymeric lignin. These peroxidases have been classified previously as lignin peroxidases or manganese peroxidases (MnP). We have isolated a novel extracellular peroxidase-encoding cDNA sequence from
T. versicolor
CU1, the transcript levels of which are repressed by low concentrations of Mn
2+
and induced by nitrogen and carbon but not induced in response to a range of stresses which have been reported to induce MnP expression.
Role of the
Trichoderma harzianum
Endochitinase Gene,
ech42
, in Mycoparasitism
Authors: Carsolio Carolina , Benhamou Nicole , Haran Shoshan , Cortés Carlos , Gutiérrez Ana , Chet Ilan , Herrera-Estrella Alfredo 
Published: December 2019

ABSTRACT

The role of the
Trichoderma harzianum
endochitinase (Ech42) in mycoparasitism was studied by genetically manipulating the gene that encodes Ech42,
ech42
. We constructed several transgenic
T. harzianum
strains carrying multiple copies of
ech42
and the corresponding gene disruptants. The level of extracellular endochitinase activity when
T. harzianum
was grown under inducing conditions increased up to 42-fold in multicopy strains as compared with the wild type, whereas gene disruptants exhibited practically no activity. The densities of chitin labeling of
Rhizoctonia solani
cell walls, after interactions with gene disruptants were not statistically significantly different than the density of chitin labeling after interactions with the wild type. Finally, no major differences in the efficacies of the strains generated as biocontrol agents against
R. solani
or
Sclerotium rolfsii
were observed in greenhouse experiments.
Antisense RNA Strategies for Metabolic Engineering of
Clostridium acetobutylicum
Authors: Desai Ruchir P. , Papoutsakis Eleftherios T. 
Published: December 2019

ABSTRACT

We examined the effectiveness of antisense RNA (as RNA) strategies for metabolic engineering of
Clostridium acetobutylicum
. Strain ATCC 824(pRD4) was developed to produce a 102-nucleotide asRNA with 87% complementarity to the butyrate kinase (BK) gene. Strain ATCC 824(pRD4) exhibited 85 to 90% lower BK and acetate kinase specific activities than the control strain. Strain ATCC 824(pRD4) also exhibited 45 to 50% lower phosphotransbutyrylase (PTB) and phosphotransacetylase specific activities than the control strain. This strain exhibited earlier induction of solventogenesis, which resulted in 50 and 35% higher final concentrations of acetone and butanol, respectively, than the concentrations in the control. Strain ATCC 824(pRD1) was developed to putatively produce a 698-nucleotide asRNA with 96% complementarity to the PTB gene. Strain ATCC 824(pRD1) exhibited 70 and 80% lower PTB and BK activities, respectively, than the control exhibited. It also exhibited 300% higher levels of a lactate dehydrogenase activity than the control exhibited. The growth yields of ATCC 824(pRD1) were 28% less than the growth yields of the control. While the levels of acids were not affected in ATCC 824(pRD1) fermentations, the acetone and butanol concentrations were 96 and 75% lower, respectively, than the concentrations in the control fermentations. The lower level of solvent production by ATCC 824(pRD1) was compensated for by ∼100-fold higher levels of lactate production. The lack of any significant impact on butyrate formation fluxes by the lower PTB and BK levels suggests that butyrate formation fluxes are not controlled by the levels of the butyrate formation enzymes.
Initial Reactions in the Biodegradation of 1-Chloro-4-Nitrobenzene by a Newly Isolated Bacterium, Strain LW1
Authors: Katsivela Eleftheria , Wray Victor , Pieper Dietmar H. , Wittich Rolf-Michael 
Published: December 2019

ABSTRACT

Bacterial strain LW1, which belongs to the family
Comamonadaceae
, utilizes 1-chloro-4-nitrobenzene (1C4NB) as a sole source of carbon, nitrogen, and energy. Suspensions of 1C4NB-grown cells removed 1C4NB from culture fluids, and there was a concomitant release of ammonia and chloride. Under anaerobic conditions LW1 transformed 1C4NB into a product which was identified as 2-amino-5-chlorophenol by
1
H and
13
C nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry. This transformation indicated that there was partial reduction of the nitro group to the hydroxylamino substituent, followed by Bamberger rearrangement. In the presence of oxygen but in the absence of NAD, fast transformation of 2-amino-5-chlorophenol into a transiently stable yellow product was observed with resting cells and cell extracts. This compound exhibited an absorption maximum at 395 nm and was further converted to a dead-end product with maxima at 226 and 272 nm. The compound formed was subsequently identified by
1
H and
13
C NMR spectroscopy and mass spectrometry as 5-chloropicolinic acid. In contrast, when NAD was added in the presence of oxygen, only minor amounts of 5-chloropicolinic acid were formed, and a new product, which exhibited an absorption maximum at 306 nm, accumulated.
Suppression of the Biocontrol Agent
Trichoderma harzianum
by Mycelium of the Arbuscular Mycorrhizal Fungus
Glomus intraradices
in Root-Free Soil
Authors: Green Helge , Larsen John , Olsson Pål Axel , Jensen Dan Funck , Jakobsen Iver 
Published: December 2019

ABSTRACT

Trichoderma harzianum
is an effective biocontrol agent against several fungal soilborne plant pathogens. However, possible adverse effects of this fungus on arbuscular mycorrhizal fungi might be a drawback in its use in plant protection. The objective of the present work was to examine the interaction between
Glomus intraradices
and
T. harzianum
in soil. The use of a compartmented growth system with root-free soil compartments enabled us to study fungal interactions without the interfering effects of roots. Growth of the fungi was monitored by measuring hyphal length and population densities, while specific fatty acid signatures were used as indicators of living fungal biomass. Hyphal
33
P transport and β-glucuronidase (GUS) activity were used to monitor activity of
G. intraradices
and a GUS-transformed strain of
T. harzianum
, respectively. As growth and metabolism of
T. harzianum
are requirements for antagonism, the impact of wheat bran, added as an organic nutrient source for
T. harzianum
, was investigated. The presence of
T. harzianum
in root-free soil reduced root colonization by
G. intraradices
. The external hyphal length density of
G. intraradices
was reduced by the presence of
T. harzianum
in combination with wheat bran, but the living hyphal biomass, measured as the content of a membrane fatty acid, was not reduced. Hyphal
33
P transport by
G. intraradices
also was not affected by
T. harzianum
. This suggests that
T. harzianum
exploited the dead mycelium but not the living biomass of
G. intraradices
. The presence of external mycelium of
G. intraradices
suppressed
T. harzianum
population development and GUS activity. Stimulation of the hyphal biomass of
G. intraradices
by organic amendment suggests that nutrient competition is a likely means of interaction. In conclusion, it seemed that growth of and phosphorus uptake by the external mycelium of
G. intraradices
were not affected by the antagonistic fungus
T. harzianum
; in contrast,
T. harzianum
was adversely affected by
G. intraradices
.
Regional Differences in Production of Aflatoxin B
1
and Cyclopiazonic Acid by Soil Isolates of
Aspergillus flavus
along a Transect within the United States
Authors: Horn B. W. , Dorner J. W. 
Published: December 2019

ABSTRACT

Soil isolates of
Aspergillus flavus
from a transect extending from eastern New Mexico through Georgia to eastern Virginia were examined for production of aflatoxin B
1
and cyclopiazonic acid in a liquid medium. Peanut fields from major peanut-growing regions (western Texas; central Texas; Georgia and Alabama; and Virginia and North Carolina) were sampled, and fields with other crops were sampled in regions where peanuts are not commonly grown. The
A. flavus
isolates were identified as members of either the L strain (
n
= 774), which produces sclerotia that are >400 μm in diameter, or the S strain (
n
= 309), which produces numerous small sclerotia that are <400 μm in diameter. The S-strain isolates generally produced high levels of aflatoxin B
1
, whereas the L-strain isolates were more variable in aflatoxin production; variation in cyclopiazonic acid production also was greater in the L strain than in the S strain. There was a positive correlation between aflatoxin B
1
production and cyclopiazonic acid production in both strains, although 12% of the L-strain isolates produced only cyclopiazonic acid. Significant differences in production of aflatoxin B
1
and cyclopiazonic acid by the L-strain isolates were detected among regions. In the western half of Texas and the peanut-growing region of Georgia and Alabama, 62 to 94% of the isolates produced >10 μg of aflatoxin B
1
per ml. The percentages of isolates producing >10 μg of aflatoxin B
1
per ml ranged from 0 to 52% in the remaining regions of the transect; other isolates were often nonaflatoxigenic. A total of 53 of the 126 L-strain isolates that did not produce aflatoxin B
1
or cyclopiazonic acid were placed in 17 vegetative compatibility groups. Several of these groups contained isolates from widely separated regions of the transect.
Expression of the
Corynebacterium glutamicum panD
Gene Encoding
l
-Aspartate-α-Decarboxylase Leads to Pantothenate Overproduction in
Escherichia coli
Authors: Dusch Nicole , Pühler Alfred , Kalinowski Jörn 
Published: December 2019

ABSTRACT

The
Corynebacterium glutamicum panD
gene was identified by functional complementation of an
Escherichia coli panD
mutant strain. Sequence analysis revealed that the coding region of
panD
comprises 411 bp and specifies a protein of 136 amino acid residues with a deduced molecular mass of 14.1 kDa. A defined
C. glutamicum panD
mutant completely lacked
l
-aspartate-α-decarboxylase activity and exhibited β-alanine auxotrophy. The
C. glutamicum panD
(

panD
C.g.

) as well as the
E. coli panD
(

panD
E.c.

) genes were cloned into a bifunctional expression plasmid to allow gene analysis in
C. glutamicum
as well as in
E. coli
. The enhanced expression of

panD
C.g.

in
C. glutamicum
resulted in the formation of two distinct proteins in sodium dodecyl sulfate-polyacrylamide gel electrophoresis, leading to the assumption that the

panD
C.g.

gene product is proteolytically processed into two subunits. By increased expression of

panD
C.g.

in
C. glutamicum
, the activity of
l
-aspartate-α-decarboxylase was 288-fold increased, whereas the

panD
E.c.

gene resulted only in a 4-fold enhancement. The similar experiment performed in
E. coli
revealed that

panD
C.g.

achieved a 41-fold increase and that

panD
E.c.

achieved a 3-fold increase of enzyme activity. The effect of the

panD
C.g.

and

panD
E.c.

gene expression in
E. coli
was studied with a view to pantothenate accumulation. Only by expression of the

panD
C.g.

gene was sufficient β-alanine produced to abolish its limiting effect on pantothenate production. In cultures expressing the

panD
E.c.

gene, the maximal pantothenate production was still dependent on external β-alanine supplementation. The enhanced expression of

panD
C.g.

in
E. coli
yielded the highest amount of pantothenate in the culture medium, with a specific productivity of 140 ng of pantothenate mg (dry weight)
−1
h
−1
.
Use of Green Fluorescent Protein To Detect Expression of an Endopolygalacturonase Gene of
Colletotrichum lindemuthianum
during Bean Infection
Authors: Dumas Bernard , Centis Sylvie , Sarrazin Nathalie , Esquerré-Tugayé Marie-Thérèse 
Published: December 2019

ABSTRACT

The 5′ noncoding region of
clpg2
, an endopolygalacturonase gene of the bean pathogen
Colletotrichum lindemuthianum
, was fused to the coding sequence of a gene encoding a green fluorescent protein (GFP), and the construct was introduced into the fungal genome. Detection of GFP accumulation by fluorescence microscopy examination revealed that
clpg2
was expressed at the early stages of germination of the conidia and during appressorium formation both in vitro and on the host plant.
Diversity ofBacteroides fragilisStrains in Their Capacity To Recover Phages from Human and Animal Wastes and from Fecally Polluted Wastewater
Authors: Puig Anna , Queralt Nuria , Jofre Juan , Araujo Rosa 
Published: December 2019

ABSTRACTGreat differences in capability to detect bacteriophages from urban sewage of the area of Barcelona existed among 115 strains ofBacteroides fragilis. The capability of six of the strains to detect phages in a variety of feces and wastewater was studied. Strains HSP40 and RYC4023 detected similar numbers of phages in urban sewage and did not detect phages in animal feces. The other four strains detected phages in the feces of different animal species and in wastewater of both human and animal origin. Strain RYC2056 recovered consistently higher counts than the other strains and also detected counts ranging from 101to approximately 103phages per ml in urban sewage from different geographical areas. This strain detected bacteriophages in animal feces even though their relative concentration with respect to the other fecal indicators was significantly lower in wastewater polluted with animal feces than in urban sewage.
Genetic Analysis of Biodegradation of Tetralin by a
Sphingomonas
Strain
Authors: Hernáez María José , Reineke Walter , Santero Eduardo 
Published: December 2019

ABSTRACT

A strain designated TFA which very efficiently utilizes tetralin has been isolated from the Rhine river. The strain has been identified as
Sphingomonas macrogoltabidus
, based on 16S rDNA sequence similarity. Genetic analysis of tetralin biodegradation has been performed by insertion mutagenesis and by physical analysis and analysis of complementation between the mutants. The genes involved in tetralin utilization are clustered in a region of 9 kb, comprising at least five genes grouped in two divergently transcribed operons.
Biological and Molecular Detection of Toxic Lipodepsipeptide-Producing
Pseudomonas syringae
Strains and PCR Identification in Plants
Authors: Bultreys Alain , Gheysen Isabelle 
Published: December 2019

ABSTRACT

Toxin-based identification procedures are useful for differentiating
Pseudomonas syringae
pathovars. A biological test on peptone-glucose-NaCl agar in which the yeast
Rhodotorula pilimanae
was used proved to be more reliable for detecting lipodepsipeptide-producing strains of
P. syringae
than the more usual test on potato dextrose agar in which
Geotrichum candidum
is used. A PCR test performed with primers designed to amplify a 1,040-bp fragment in the coding sequence of the
syrD
gene, which was assumed to be involved in syringomycin and syringopeptin secretion, efficiently detected the gene in pathovars that produce the lipodepsipeptides. Comparable results were obtained in both tests performed with strains of the syringomycin-producing organisms
P. syringae
pv. syringae,
P. syringae
pv. atrofaciens, and
P. syringae
pv. aptata, but the PCR test failed with a syringotoxin-producing
Pseudomonas fuscovaginae
strain. The specificity of the test was verified by obtaining negative PCR test results for related pathovars or species that do not produce the toxic lipodepsipeptides.
P. syringae
pv. syringae was detected repeatedly in liquid medium inoculated with diseased vegetative tissue and assayed by the PCR test. Our procedure was also adapted to detect
P. syringae
pv. morsprunorum with a
cfl
gene-based PCR test.
Sensitive Detection of
Escherichia coli
O157:H7 in Food and Water by Immunomagnetic Separation and Solid-Phase Laser Cytometry
Authors: Pyle Barry H. , Broadaway Susan C. , McFeters Gordon A. 
Published: December 2019

ABSTRACT

Rapid, direct methods are needed to assess active bacterial populations in water and foods. Our objective was to determine the efficiency of bacterial detection by immunomagnetic separation (IMS) and the compatibility of IMS with cyanoditolyl tetrazolium chloride (CTC) incubation to determine respiratory activity, using the pathogen
Escherichia coli
O157:H7. Counterstaining with a specific fluorescein-conjugated anti-O157 antibody (FAb) following CTC incubation was used to allow confirmation and visualization of bacteria by epifluorescence microscopy. Broth-grown
E. coli
O157:H7 was used to inoculate fresh ground beef (<17% fat), sterile 0.1% peptone, or water. Inoculated meat was diluted and homogenized in a stomacher and then incubated with paramagnetic beads coated with anti-O157 specific antibody. After IMS, cells with magnetic beads attached were stained with CTC and then an anti-O157 antibody-fluorescein isothiocyanate conjugate and filtered for microscopic enumeration or solid-phase laser cytometry. Enumeration by laser scanning permitted detection of ca. 10 CFU/g of ground beef or <10 CFU/ml of liquid sample. With inoculated meat, the regression results for log-transformed respiring FAb-positive counts of cells recovered on beads versus sorbitol-negative plate counts in the inoculum were as follows: intercept = 1.06, slope = 0.89, and
r
2
= 0.95 (
n
= 13). The corresponding results for inoculated peptone were as follows: intercept = 0.67, slope = 0.88, and
r
2
= 0.98 (
n
= 24). Recovery of target bacteria on beads by the IMS-CTC-FAb method, compared with recovery by sorbitol MacConkey agar plating, yielded greater numbers (beef, 6.0 times; peptone, 3.0 times; water, 2.4 times). Thus, within 5 to 7 h, the IMS-CTC-FAb method detected greater numbers of
E. coli
O157 cells than were detected by plating. The results show that the IMS-CTC-FAb technique with enumeration by either fluorescence microscopy or solid-phase laser scanning cytometry gave results that compared favorably with plating following IMS.
Identification and Disruption of BetL, a Secondary Glycine Betaine Transport System Linked to the Salt Tolerance of
Listeria monocytogenes
LO28
Authors: Sleator Roy D. , Gahan Cormac G. M. , Abee Tjakko , Hill Colin 
Published: December 2019

ABSTRACT

The trimethylammonium compound glycine betaine (
N
,
N
,
N
-trimethylglycine) can be accumulated to high intracellular concentrations, conferring enhanced osmo- and cryotolerance upon
Listeria monocytogenes
. We report the identification of
betL
, a gene encoding a glycine betaine uptake system in
L. monocytogenes
, isolated by functional complementation of the betaine uptake mutant
Escherichia coli
MKH13. The
betL
gene is preceded by a consensus ς
B
-dependent promoter and is predicted to encode a 55-kDa protein (507 amino acid residues) with 12 transmembrane regions. BetL exhibits significant sequence homologies to other glycine betaine transporters, including OpuD from
Bacillus subtilis
(57% identity) and BetP from
Corynebacterium glutamicum
(41% identity). These high-affinity secondary transporters form a subset of the trimethylammonium transporter family specific for glycine betaine, whose substrates possess a fully methylated quaternary ammonium group. The observed

K
m

value of 7.9 μM for glycine betaine uptake after heterologous expression of
betL
in
E. coli
MKH13 is consistent with values obtained for
L. monocytogenes
in other studies. In addition, a
betL
knockout mutant which is significantly affected in its ability to accumulate glycine betaine in the presence or absence of NaCl has been constructed in
L. monocytogenes
. This mutant is also unable to withstand concentrations of salt as high as can the BetL
+
parent, signifying the role of the transporter in
Listeria
osmotolerance.