bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dephosphorylation of Phytate by Using the
Aspergillus niger
Phytase with a High Affinity for Phytate
Authors: Nagashima Tadashi , Tange Tatsuya , Anazawa Hideharu 
Published: December 2019

ABSTRACT

A phytase (EC
3.1.3.8
) with a high affinity for phytic acid was found in
Aspergillus niger
SK-57 and purified to homogeneity in four steps by using ion-exchange chromatography (two types), gel filtration, and chromatofocusing. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the purified enzyme gave a single stained band at a molecular mass of approximately 60 kDa. The Michaelis constant of the enzyme for phytic acid (18.7 ± 4.6 μM) was statistically analyzed. In regard to the orthophosphate released from phytic acid, a significant difference between a low

K
m

phytase from
A. niger
SK-57 and a high

K
m

phytase from
Aspergillus ficuum
was recognized.
Antiproliferative Effects of Homogenates Derived from Five Strains of Candidate Probiotic Bacteria
Authors: Pessi Tanja , Sütas Yelda , Saxelin Maija , Kallioinen Harri , Isolauri Erika 
Published: December 2019

ABSTRACT

Unheated and heat-treated homogenates were separately prepared from candidate probiotic bacteria, including
Lactobacillus rhamnosus
GG,
Bifidobacterium lactis
,
Lactobacillus acidophilus
,
Lactobacillus delbrueckii
subsp.
bulgaricus
, and
Streptococcus thermophilus
. We compared the phytohemagglutinin-induced proliferation of mononuclear cells in the presence of homogenates and in the presence of a control containing no homogenate by assessing thymidine incorporation in cell cultures. All homogenates suppressed proliferation, whether the enzymatic activity was inactivated or not inactivated by heating. When the proliferation assays were repeated with cytoplasmic and cell wall extracts derived from the homogenate of
L. rhamnosus
GG, the cytoplasmic extract but not the cell wall extract was suppressive. These findings indicate that candidate probiotic bacteria possess a heat-stable antiproliferative component(s). These bacteria may be used to generate microbiologically nonviable yet immunologically active probiotic food products that are easier to store and have a longer shelf life.
Direct Analysis of Genes Encoding 16S rRNA from Complex Communities Reveals Many Novel Molecular Species within the Human Gut
Authors: Suau Antonia , Bonnet Régis , Sutren Malène , Godon Jean-Jacques , Gibson Glenn R. , Collins Matthew D. , Doré Joel 
Published: December 2019

ABSTRACT

The human intestinal tract harbors a complex microbial ecosystem which plays a key role in nutrition and health. Although this microbiota has been studied in great detail by culture techniques, microscopic counts on human feces suggest that 60 to 80% of the observable bacteria cannot be cultivated. Using comparative analysis of cloned 16S rRNA gene (rDNA) sequences, we have investigated the bacterial diversity (both cultivated and noncultivated bacteria) within an adult-male fecal sample. The 284 clones obtained from 10-cycle PCR were classified into 82 molecular species (at least 98% similarity). Three phylogenetic groups contained 95% of the clones: the
Bacteroides
group, the
Clostridium coccoides
group, and the
Clostridium leptum
subgroup. The remaining clones were distributed among a variety of phylogenetic clusters. Only 24% of the molecular species recovered corresponded to described organisms (those whose sequences were available in public databases), and all of these were established members of the dominant human fecal flora (e.g.,
Bacteroides thetaiotaomicron
,
Fusobacterium prausnitzii
, and
Eubacterium rectale
). However, the majority of generated rDNA sequences (76%) did not correspond to known organisms and clearly derived from hitherto unknown species within this human gut microflora.
In Vitro Utilization of Amylopectin and High-Amylose Maize (Amylomaize) Starch Granules by Human Colonic Bacteria
Authors: Wang Xin , Conway Patricia Lynne , Brown Ian Lewis , Evans Anthony John 
Published: December 2019

ABSTRACT

It has been well established that a certain amount of ingested starch can escape digestion in the human small intestine and consequently enters the large intestine, where it may serve as a carbon source for bacterial fermentation. Thirty-eight types of human colonic bacteria were screened for their capacity to utilize soluble starch, gelatinized amylopectin maize starch, and high-amylose maize starch granules by measuring the clear zones on starch agar plates. The six cultures which produced clear zones on amylopectin maize starch- containing plates were selected for further studies for utilization of amylopectin maize starch and high-amylose maize starch granules A (amylose; Sigma) and B (Culture Pro 958N). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was used to detect bacterial starch-degrading enzymes. It was demonstrated that
Bifidobacterium
spp.,
Bacteroides
spp.,
Fusobacterium
spp., and strains of
Eubacterium
,
Clostridium
,
Streptococcus
, and
Propionibacterium
could hydrolyze the gelatinized amylopectin maize starch, while only
Bifidobacterium
spp. and
Clostridium butyricum
could efficiently utilize high-amylose maize starch granules. In fact,
C. butyricum
and
Bifidobacterium
spp. had higher specific growth rates in the autoclaved medium containing high-amylose maize starch granules and hydrolyzed 80 and 40% of the amylose, respectively. Starch-degrading enzymes were cell bound on
Bifidobacterium
and
Bacteroides
cells and were extracellular for
C. butyricum
. Active staining for starch-degrading enzymes on SDS-PAGE gels showed that the
Bifidobacterium
cells produced several starch-degrading enzymes with high relative molecular (
M
r
) weights (>160,000), medium-sized relative molecular weights (>66,000), and low relative molecular weights (<66,000). It was concluded that
Bifidobacterium
spp. and
C. butyricum
degraded and utilized granules of amylomaize starch.
Survival, Physiology, and Lysis of
Lactococcus lactis
in the Digestive Tract
Authors: Drouault Sophie , Corthier Gérard , Ehrlich S. Dusko , Renault Pierre 
Published: December 2019

ABSTRACT

The survival and the physiology of lactococcal cells in the different compartments of the digestive tracts of rats were studied in order to know better the fate of ingested lactic acid bacteria after oral administration. For this purpose, we used strains marked with reporter genes, the
luxA-luxB
gene of
Vibrio harveyi
and the
gfp
gene of
Aequora victoria
, that allowed us to differentiate the inoculated bacteria from food and the other intestinal bacteria. Luciferase was chosen to measure the metabolic activity of
Lactococcus lactis
in the digestive tract because it requires NADH, which is available only in metabolically active cells. The green fluorescent protein was used to assess the bacterial lysis independently of death. We report not only that specific factors affect the cell viability and integrity in some digestive tract compartments but also that the way bacteria are administrated has a dramatic impact. Lactococci which transit with the diet are quite resistant to gastric acidity (90 to 98% survival). In contrast, only 10 to 30% of bacteria survive in the duodenum. Viable cells are metabolically active in each compartment of the digestive tract, whereas most dead cells appear to be subject to rapid lysis. This property suggests that lactococci could be used as a vector to deliver specifically into the duodenum the proteins produced in the cytoplasm. This type of delivery vector would be particularly appropriate for targeting digestive enzymes such as lipase to treat pancreatic deficiencies.
Characterization, Molecular Cloning, and Differential Expression Analysis of Laccase Genes from the Edible Mushroom
Lentinula edodes
Authors: Zhao J. , Kwan H. S. 
Published: December 2019

ABSTRACT

The effect of different substrates and various developmental stages (mycelium growth, primordium appearance, and fruiting-body formation) on laccase production in the edible mushroom
Lentinula edodes
was studied. The cap of the mature mushroom showed the highest laccase activity, and laccase activity was not stimulated by some well-known laccase inducers or sawdust. For our molecular studies, two genomic DNA sequences, representing allelic variants of the
L. edodes lac1
gene, were isolated, and DNA sequence analysis demonstrated that
lac1
encodes a putative polypeptide of 526 amino acids which is interrupted by 13 introns. The two allelic genes differ at 95 nucleotides, which results in seven amino acid differences in the encoded protein. The copper-binding domains found in other laccase enzymes are conserved in the
L. edodes
Lac1 proteins. A fragment of a second laccase gene (
lac2
) was also isolated, and competitive PCR showed that expression of
lac1
and
lac2
genes was different under various conditions. Our results suggest that laccases may play a role in the morphogenesis of the mushroom. To our knowledge, this is the first report on the cloning of genes involved in lignocellulose degradation in this economically important edible fungus.
Stress Responses as a Tool To Detect and Characterize the Mode of Action of Antibacterial Agents
Authors: Bianchi Allison A. , Baneyx François 
Published: December 2019

ABSTRACT

Single-copy gene fusions between the
lacZ
reporter gene and
Escherichia coli
strains containing promoters induced by cold shock (
cspA
), cytoplasmic stress (
ibp
), or protein misfolding in the cell envelope (P3
rpoH
) were constructed and tested to determine their ability to detect antibacterial agents while simultaneously providing information on their cellular targets. Antibiotics that affect prokaryotic ribosomes selectively induced the
cspA
::
lacZ
or
ibp
::
lacZ
gene fusion, depending on their mode of action. The membrane-damaging peptide polymyxin B induced both the P3
rpoH
::
lacZ
and
ibp
::
lacZ
fusions, while the β-lactam antibacterial agent carbenicillin activated only the P3
rpoH
promoter. Nalidixic acid, a compound that causes DNA damage, downregulated β-galactosidase synthesis from P3
rpoH
but had little effect on expression of the reporter enzyme from either the
cspA
or
ibp
promoter. All model antibiotics could be identified over a wide range of sublethal concentrations with signal-to-noise ratios between 2 and 11. A blue halo assay was developed to rapidly characterize the modes of action of antibacterial agents by visual inspection, and this assay was used to detect chloramphenicol secreted into the growth medium of
Streptomyces venezuelae
cultures. This simple system holds promise for screening natural or combinatorial libraries of antimicrobial compounds.
Characterization and Identification of Numerically Abundant Culturable Bacteria from the Anoxic Bulk Soil of Rice Paddy Microcosms
Authors: Chin Kuk-Jeong , Hahn Dittmar , Hengstmann Ulf , Liesack Werner , Janssen Peter H. 
Published: December 2019

ABSTRACT

Most-probable-number (liquid serial dilution culture) counts were obtained for polysaccharolytic and saccharolytic fermenting bacteria in the anoxic bulk soil of flooded microcosms containing rice plants. The highest viable counts (up to 2.5 × 10
8
cells per g [dry weight] of soil) were obtained by using xylan, pectin, or a mixture of seven mono- and disaccharides as the growth substrate. The total cell count for the soil, as determined by using 4′,6-diamidino-2-phenylindole staining, was 4.8 × 10
8
cells per g (dry weight) of soil. The nine strains isolated from the terminal positive tubes in counting experiments which yielded culturable populations that were equivalent to about 5% or more of the total microscopic count population belonged to the division
Verrucomicrobia
, the
Cytophaga-Flavobacterium-Bacteroides
division, clostridial cluster XIVa, clostridial cluster IX,
Bacillus
spp., and the class
Actinobacteria
. Isolates originating from the terminal positive tubes of liquid dilution series can be expected to be representatives of species whose populations in the soil are large. None of the isolates had 16S rRNA gene sequences identical to 16S rRNA gene sequences of previously described species for which data are available. Eight of the nine strains isolated fermented sugars to acetate and propionate (and some also fermented sugars to succinate). The closest relatives of these strains (except for the two strains of actinobacteria) were as-yet-uncultivated bacteria detected in the same soil sample by cloning PCR-amplified 16S rRNA genes (U. Hengstmann, K.-J. Chin, P. H. Janssen, and W. Liesack, Appl. Environ. Microbiol. 65:5050–5058, 1999). Twelve other isolates, which originated from most-probable-number counting series indicating that the culturable populations were smaller, were less closely related to cloned 16S rRNA genes.
Gene Transfer in the Gastrointestinal Tract
Authors: Netherwood Trudy , Bowden R. , Harrison P. , O’Donnell A. G. , Parker D. S. , Gilbert H. J. 
Published: December 2019

ABSTRACT
The maximum in vivo transfer rate of plasmid pAMβ1 in the gut was 0.03 transconjugant per recipient cell, and this rate could be simulated in vitro only by forced filter mating. Transfer was not detected in liquid culture matings. Our findings demonstrate that in vitro methods, such as forced filter mating and liquid mating, underestimate the in vivo rates of gene transfer.
Isolation from the
Sorghum bicolor
Mycorrhizosphere of a Bacterium Compatible with Arbuscular Mycorrhiza Development and Antagonistic towards Soilborne Fungal Pathogens
Authors: Budi S. W. , van Tuinen D. , Martinotti G. , Gianinazzi S. 
Published: December 2019

ABSTRACT

A gram-positive bacterium with antagonistic activity towards soilborne fungal pathogens has been isolated from the mycorrhizosphere of
Sorghum bicolor
inoculated with
Glomus mosseae
. It has been identified as
Paenibacillus
sp. strain B2 based on its analytical profile index and on 16S ribosomal DNA analysis. Besides having antagonistic activity, this bacterium stimulates mycorrhization.
Cloning, Overexpression, and Mutagenesis of the
Sporobolomyces salmonicolor
AKU4429 Gene Encoding a New Aldehyde Reductase, Which Catalyzes the Stereoselective Reduction of Ethyl 4-Chloro-3-Oxobutanoate to Ethyl (
S
)-4-Chloro-3-Hydroxybutanoate
Authors: Kita Keiko , Fukura Takanobu , Nakase Koh-Ichi , Okamoto Kenji , Yanase Hideshi , Kataoka Michihiko , Shimizu Sakayu 
Published: December 2019

ABSTRACT

We cloned and sequenced the gene encoding an NADPH-dependent aldehyde reductase (ARII) in
Sporobolomyces salmonicolor
AKU4429, which reduces ethyl 4-chloro-3-oxobutanoate (4-COBE) to ethyl (
S
)-4-chloro-3-hydroxybutanoate. The
ARII
gene is 1,032 bp long, is interrupted by four introns, and encodes a 37,315-Da polypeptide. The deduced amino acid sequence exhibited significant levels of similarity to the amino acid sequences of members of the mammalian 3β-hydroxysteroid dehydrogenase–plant dihydroflavonol 4-reductase superfamily but not to the amino acid sequences of members of the aldo-keto reductase superfamily or to the amino acid sequence of an aldehyde reductase previously isolated from the same organism (K. Kita, K. Matsuzaki, T. Hashimoto, H. Yanase, N. Kato, M. C.-M. Chung, M. Kataoka, and S. Shimizu, Appl. Environ. Microbiol. 62:2303–2310, 1996). The ARII protein was overproduced in
Escherichia coli
about 2,000-fold compared to the production in the original yeast cells. The enzyme expressed in
E. coli
was purified to homogeneity and had the same catalytic properties as ARII purified from
S. salmonicolor
. To examine the contribution of the dinucleotide-binding motif G
19
-X-X-G
22
-X-X-A
25
, which is located in the N-terminal region, during ARII catalysis, we replaced three amino acid residues in the motif and purified the resulting mutant enzymes. Substrate inhibition of the G
19
→A and G
22
→A mutant enzymes by 4-COBE did not occur. The A
25
→G mutant enzyme could reduce 4-COBE when NADPH was replaced by an equimolar concentration of NADH.
Cloning and Characterization of an
Aspergillus nidulans
Gene Involved in the Regulation of Penicillin Biosynthesis
Authors: Van den Brulle Jan , Steidl Stefan , Brakhage Axel A. 
Published: December 2019

ABSTRACT

To identify regulators of penicillin biosynthesis, a previously isolated mutant of
Aspergillus nidulans
(Prg-1) which carried the
trans
-acting
prgA1
mutation was used. This mutant also contained fusions of the penicillin biosynthesis genes
acvA
and
ipnA
with reporter genes (
acvA
-
uidA
and
ipnA
-
lacZ
) integrated in a double-copy arrangement at the chromosomal
argB
gene. The
prgA1
mutant strain exhibited only 20 to 50% of the
ipnA
-
lacZ
and
acvA
-
uidA
expression exhibited by the wild-type strain and had only 20 to 30% of the penicillin produced by the wild-type strain. Here, using complementation with a genomic cosmid library, we isolated a gene (
suAprgA1
) which complemented the
prgA1
phenotype to the wild-type phenotype; i.e., the levels of expression of both gene fusions and penicillin production were nearly wild-type levels. Analysis of the
suAprgA1
gene in the
prgA1
mutant did not reveal any mutation in the
suAprgA1
gene or unusual transcription of the gene. This suggested that the
suAprgA1
gene is a suppressor of the
prgA1
mutation. The
suAprgA1
gene is 1,245 bp long. Its five exons encode a deduced protein that is 303 amino acids long. The putative SUAPRGA1 protein was similar to both the human p32 protein and Mam33p of
Saccharomyces cerevisiae
. Analysis of the ordered gene library of
A. nidulans
indicated that
suAprgA1
is located on chromosome VI. Deletion of the
suAprgA1
gene resulted in an approximately 50% reduction in
ipnA
-
lacZ
expression and in a slight reduction in
acvA
-
uidA
expression. The Δ
suAprgA1
strain produced about 60% of the amount of penicillin produced by the wild-type strain.
Biosynthesis of Novel Exopolymers by
Aureobasidium pullulans
Authors: Lee Jin W. , Yeomans Walter G. , Allen Alfred L. , Deng Fang , Gross Richard A. , Kaplan David L. 
Published: December 2019

ABSTRACT

Aureobasidium pullulans
ATCC 42023 was cultured under aerobic conditions with glucose, mannose, and glucose analogs as energy sources. The exopolymer extracts produced under these conditions were composed of glucose and mannose. The molar ratio of glucose to mannose in the exopolymer extract and the molecular weight of the exopolymer varied depending on the energy source and culture time. The glucose content of exopolymer extracts formed with glucose and mannose as the carbon sources was between 91 and 87%. The molecular weight decreased from 3.5 × 10
6
to 2.12 × 10
6
to 0.85 × 10
6
to 0.77 × 10
6
with culture time. As the culture time increased, the glucose content of the exopolymer extract formed with glucosamine decreased from 55 ± 3 to 29 ± 2 mol%, and the molecular weight increased from 2.73 × 10
6
to 4.86 × 10
6
. There was no evidence that glucosamine was directly incorporated into exopolymers. The molar ratios of glucose to mannose in exopolymer extracts ranged from 87 ± 3:13 ± 3 to 28 ± 2:72 ± 2 and were affected by the energy source added. On the basis of the results of an enzyme hydrolysis analysis of the exopolymer extracts and the compositional changes observed, mannose (a repeating unit) was substituted for glucose, which gave rise to a new family of exopolymer analogs.
Transformation of
Escherichia coli
with DNA from
Saccharomyces cerevisiae
Cell Lysates
Authors: Adam Ana Cristina , González-Blasco Gracia , Rubio-Texeira Marta , Polaina Julio 
Published: December 2019

ABSTRACT

We developed a system to monitor the transfer of heterologous DNA from a genetically manipulated strain of
Saccharomyces cerevisiae
to
Escherichia coli
. This system is based on a yeast strain that carries multiple integrated copies of a pUC-derived plasmid. The bacterial sequences are maintained in the yeast genome by selectable markers for lactose utilization. Lysates of the yeast strain were used to transform
E. coli
. Transfer of DNA was measured by determining the number of ampicillin-resistant
E. coli
clones. Our results show that transmission of the Amp
r
gene to
E. coli
by genetic transformation, caused by DNA released from the yeast, occurs at a very low frequency (about 50 transformants per μg of DNA) under optimal conditions (a highly competent host strain and a highly efficient transformation procedure). These results suggest that under natural conditions, spontaneous transmission of chromosomal genes from genetically modified organisms is likely to be rare.
Secretion of Cryparin, a Fungal Hydrophobin
Authors: McCabe Patricia M. , Van Alfen Neal K. 
Published: December 2019

ABSTRACT

Cryparin is a cell-surface-associated hydrophobin of the filamentous ascomycete
Cryphonectria parasitica
. This protein contains a signal peptide that directs it to the vesicle-mediated secretory pathway. We detected a glycosylated form of cryparin in a secretory vesicle fraction, but secreted forms of this protein are not glycosylated. This glycosylation occurred in the proprotein region, which is cleaved during maturation by a Kex2-like serine protease, leaving a mature form of cryparin that could be isolated from both the cell wall and culture medium. Pulse-chase labeling experiments showed that cryparin was secreted through the cell wall, without being bound, into the culture medium. The secreted protein then binds to the cell walls of
C. parasitica
, where it remains. Binding of cryparin to the cell wall occurred in submerged culture, presumably because of the lectin-like properties unique to this hydrophobin. Thus, the binding of this hydrophobin to the cell wall is different from that of other hydrophobins which are reported to require a hydrophobic-hydrophilic interface for assembly.
The Hemolytic Enterotoxin HBL Is Broadly Distributed among Species of the
Bacillus cereus
Group
Authors: Prüß Birgit M. , Dietrich Richard , Nibler Birgit , Märtlbauer Erwin , Scherer Siegfried 
Published: December 2019

ABSTRACT

The prevalence of the hemolytic enterotoxin complex HBL was determined in all species of the
Bacillus cereus
group with the exception of
Bacillus anthracis. hblA
, encoding the binding subunit B, was detected by PCR and Southern analysis and was confirmed by partial sequencing of 18 strains. The sequences formed two clusters, one including
B. cereus
and
Bacillus thuringiensis
strains and the other one consisting of
Bacillus mycoides
,
Bacillus pseudomycoides
, and
Bacillus weihenstephanensis
strains. From eight
B. thuringiensis
strains, the enterotoxin gene
hblA
could be amplified. Seven of them also expressed the complete HBL complex as determined with specific antibodies against the L
1
, L
2
, and B components. Eleven of 16
B. mycoides
strains, all 3
B. pseudomyoides
strains, 9 of 15
B. weihenstephanensis
strains, and 10 of 23
B. cereus
strains carried
hblA
. While HBL was not expressed in the
B. pseudomycoides
strains, the molecular assays were in accordance with the immunological assays for the majority of the remaining strains. In summary, the hemolytic enterotoxin HBL seems to be broadly distributed among strains of the
B. cereus
group and relates neither to a certain species nor to a specific environment. The consequences of this finding for food safety considerations need to be evaluated.