bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biochemical and Structural Characterization of the Glucan and Fructan Exopolysaccharides Synthesized by the
Lactobacillus reuteri
Wild-Type Strain and by Mutant Strains
Authors: Van Geel-Schutten G. H. , Faber E. J. , Smit E. , Bonting K. , Smith M. R. , Ten Brink B. , Kamerling J. P. , Vliegenthart J. F. G. , Dijkhuizen L. 
Published: December 2019

ABSTRACT

Lactobacillus reuteri
LB 121 cells growing on sucrose synthesize large amounts of a glucan (
d
-glucose) and a fructan (
d
-fructose) with molecular masses of 3,500 and 150 kDa, respectively. Methylation studies and
13
C or
1
H nuclear magnetic resonance analysis showed that the glucan has a unique structure consisting of terminal, 4-substituted, 6-substituted, and 4,6-disubstituted α-glucose in a molar ratio of 1.1:2.7:1.5:1.0. The fructan was identified as a (2→6)-β-
d
-fructofuranan or levan, the first example of levan synthesis by a
Lactobacillus
species. Strain LB 121 possesses glucansucrase and levansucrase enzymes that occur in a cell-associated and a cell-free state after growth on sucrose, raffinose, or maltose but remain cell associated during growth on glucose. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of sucrose culture supernatants, followed by staining of gels for polysaccharide synthesizing activity with sucrose as a substrate, revealed the presence of a single glucansucrase protein of 146 kDa. Growth of strain LB 121 in chemostat cultures resulted in rapid accumulation of spontaneous exopolysaccharide-negative mutants that had lost both glucansucrase and levansucrase (e.g., strain K-24). Mutants lacking all levansucrase activity specifically emerged following a pH shiftdown (e.g., strain 35-5). Strain 35-5 still possessed glucansucrase and synthesized wild-type glucan.
Production of Cry11A and Cry11Ba Toxins in
Bacillus sphaericus
Confers Toxicity towards
Aedes aegypti
and Resistant
Culex
Populations
Authors: Servant Pascale , Rosso Marie-Laure , Hamon Sylviane , Poncet Sandrine , Delécluse Armelle , Rapoport Georges 
Published: December 2019

ABSTRACT

Cry11A from
Bacillus thuringiensis
subsp.
israelensis
and Cry11Ba from
Bacillus thuringiensis
subsp.
jegathesan
were introduced, separately and in combination, into the chromosome of
Bacillus sphaericus
2297 by in vivo recombination. Two loci on the
B. sphaericus
chromosome were chosen as target sites for recombination: the binary toxin locus and the gene encoding the 36-kDa protease that may be responsible for the cleavage of the Mtx protein. Disruption of the protease gene did not increase the larvicidal activity of the recombinant strain against
Aedes aegypti
and
Culex pipiens
. Synthesis of the Cry11A and Cry11Ba toxins made the recombinant strains toxic to
A. aegypti
larvae to which the parental strain was not toxic. The strain containing Cry11Ba was more toxic than strains containing the added Cry11A or both Cry11A and Cry11Ba. The production of the two toxins together with the binary toxin did not significantly increase the toxicity of the recombinant strain to susceptible
C. pipiens
larvae. However, the production of Cry11A and/or Cry11Ba partially overcame the resistance of
C. pipiens
SPHAE and
Culex quinquefasciatus
GeoR to
B. sphaericus
strain 2297.
Formation of Hyodeoxycholic Acid from Muricholic Acid and Hyocholic Acid by an Unidentified Gram-Positive Rod Termed HDCA-1 Isolated from Rat Intestinal Microflora
Authors: Eyssen H. J. , De Pauw G. , Van Eldere J. 
Published: December 2019

ABSTRACT

From the rat intestinal microflora we isolated a gram-positive rod, termed HDCA-1, that is a member of a not previously described genomic species and that is able to transform the 3α,6β,7β-trihydroxy bile acid β-muricholic acid into hyodeoxycholic acid (3α,6α-dihydroxy acid) by dehydroxylation of the 7β-hydroxy group and epimerization of the 6β-hydroxy group into a 6α-hydroxy group. Other bile acids that were also transformed into hyodeoxycholic acid were hyocholic acid (3α,6α,7α-trihydroxy acid), α-muricholic acid (3α,6β,7α-trihydroxy acid), and ω-muricholic acid (3α,6α,7β-trihydroxy acid). The strain HDCA-1 could not be grown unless a nonconjugated 7-hydroxylated bile acid and an unidentified growth factor produced by a
Ruminococcus productus
strain that was also isolated from the intestinal microflora were added to the culture medium. Germfree rats selectively associated with the strain HDCA-1 plus a bile acid-deconjugating strain and the growth factor-producing
R. productus
strain converted β-muricholic acid almost completely into hyodeoxycholic acid.
Seasonal Dynamics of Bacterioplankton Community Structure in a Eutrophic Lake as Determined by 5S rRNA Analysis
Authors: Höfle Manfred G. , Haas Heike , Dominik Katja 
Published: December 2019

ABSTRACTCommunity structure of bacterioplankton was studied during the major growth season for phytoplankton (April to October) in the epilimnion of a temperate eutrophic lake (Lake Plußsee, northern Germany) by using comparative 5S rRNA analysis. Estimates of the relative abundances of single taxonomic groups were made on the basis of the amounts of single 5S rRNA bands obtained after high-resolution electrophoresis of RNA directly from the bacterioplankton. Full-sequence analysis of single environmental 5S rRNAs enabled the identification of single taxonomic groups of bacteria. Comparison of partial 5S rRNA sequences allowed the detection of changes of single taxa over time. Overall, the whole bacterioplankton community showed two to eight abundant (>4% of the total 5S rRNA) taxa. A distinctive seasonal succession was observed in the taxonomic structure of this pelagic community. A rather-stable community structure, with seven to eight different taxonomic units, was observed beginning in April during the spring phytoplankton bloom. A strong reduction in this diversity occurred at the beginning of the clear-water phase (early May), when only two to four abundant taxa were observed, with one taxon dominating (up to 72% of the total 5S rRNA). The community structure during summer stagnation (June and July) was characterized by frequent changes of different dominating taxa. During late summer, a dinoflagellate bloom (Ceratium hirudinella) occurred, withComamonas acidovorans(β-subclass of the classProteobacteria) becoming the dominant bacterial species (average abundance of 43% of the total 5S rRNA). Finally, the seasonal dynamics of the community structure of bacterioplankton were compared with the abundances of other major groups of the aquatic food web, such as phyto- and zooplankton, revealing that strong grazing pressure by zooplankton can reduce microbial diversity substantially in pelagic environments.
Phosphate Stress in Cultures and Field Populations of the Dinoflagellate
Prorocentrum minimum
Detected by a Single-Cell Alkaline Phosphatase Assay
Authors: Dyhrman Sonya T. , Palenik Brian 
Published: December 2019

ABSTRACT

Alkaline phosphatase activity is a common marker of phosphate stress in many phytoplankton, but it has been difficult to attribute alkaline phosphatase activity to specific organisms or groups of phytoplankton in the field with traditional biochemical procedures. A new alkaline phosphatase substrate, ELF-97 (enzyme-labeled fluorescence), shows promise in this regard. When a phosphate group is cleaved from the ELF-97 reagent, the remaining molecule precipitates near the site of enzyme activity, thus fluorescently tagging cells with alkaline phosphatase activity. We characterized ELF-97 labeling in axenic cultures of a common dinoflagellate,
Prorocentrum minimum
, in order to understand ELF-97 labeling dynamics when phosphate nutrition varies. Enzyme activity, as detected by ELF-97 labeling, appears to be induced in late-log- or early-stationary-phase cultures if cells are grown in low-phosphate media and is lost when phosphate-stressed cells are refed with phosphate. ELF-97 appears to label an inducible intracellular alkaline phosphatase in
P. minimum
based on confocal microscopy studies. This may limit the use of this reagent to organisms that lack high levels of constitutive intracellular phosphatases. After laboratory cultures were characterized, ELF-97 was used to assay field populations of
P. minimum
in Narragansett Bay during two 1-week periods, and 12 to 100% of the
P. minimum
cells were labeled. The level of cell labeling was reduced by 3 days of incubation with added inorganic phosphate. Our results indicate that ELF-97 is an excellent new tool for monitoring phytoplankton phosphate stress in the environment when the data are supported by appropriate laboratory studies.
Electrophoretic Mobilities of
Escherichia coli
O157:H7 and Wild-Type
Escherichia coli
Strains
Authors: Lytle Darren A. , Rice Eugene W. , Johnson Clifford H. , Fox Kim R. 
Published: December 2019

ABSTRACT

The electrophoretic mobilities (EPMs) of a number of
Escherichia coli
O157:H7 and wild-type
E. coli
strains were measured. The effects of pH and ionic strength on the EPMs were investigated. The EPMs of
E. coli
O157:H7 strains differed from those of wild-type strains. As the suspension pH decreased, the EPMs of both types of strains increased.
Key Physiology of Anaerobic Ammonium Oxidation
Authors: Strous Marc , Kuenen J. Gijs , Jetten Mike S. M. 
Published: December 2019

ABSTRACT
The physiology of anaerobic ammonium oxidizing (anammox) aggregates grown in a sequencing batch reactor was investigated quantitatively. The physiological pH and temperature ranges were 6.7 to 8.3 and 20 to 43°C, respectively. The affinity constants for the substrates ammonium and nitrite were each less than 0.1 mg of nitrogen per liter. The anammox process was completely inhibited by nitrite concentrations higher than 0.1 g of nitrogen per liter. Addition of trace amounts of either of the anammox intermediates (1.4 mg of nitrogen per liter of hydrazine or 0.7 mg of nitrogen per liter of hydroxylamine) restored activity completely.
Identification of Mimotope Peptides Which Bind to the Mycotoxin Deoxynivalenol-Specific Monoclonal Antibody
Authors: Yuan Qiaoping , Pestka James J. , Hespenheide Brandon M. , Kuhn Leslie A. , Linz John E. , Hart L. Patrick 
Published: December 2019

ABSTRACTMonoclonal antibody 6F5 (mAb 6F5), which recognizes the mycotoxin deoxynivalenol (DON) (vomitoxin), was used to select for peptides that mimic the mycotoxin by employing a library of filamentous phages that have random 7-mer peptides on their surfaces. Two phage clones selected from the random peptide phage-displayed library coded for the amino acid sequences SWGPFPF and SWGPLPF. These clones were designated DONPEP.2 and DONPEP.12, respectively. The results of a competitive enzyme-linked immunosorbent assay (ELISA) suggested that the two phage displayed peptides bound to mAb 6F5 specifically at the DON binding site. The amino acid sequence of DONPEP.2 plus a structurally flexible linker at the C terminus (SWGPFPFGGGSC) was synthesized and tested to determine its ability to bind to mAb 6F5. This synthetic peptide (designated peptide C430) and DON competed with each other for mAb 6F5 binding. When translationally fused with bacterial alkaline phosphatase, DONPEP.2 bound specifically to mAb 6F5, while the fusion protein retained alkaline phosphatase activity. The potential of using DONPEP.2 as an immunochemical reagent in a DON immunoassay was evaluated with a DON-spiked wheat extract. When peptide C430 was conjugated to bovine serum albumin, it elicited antibody specific to peptide C430 but not to DON in both mice and rabbits. In an in vitro translation system containing rabbit reticulocyte lysate, synthetic peptide C430 did not inhibit protein synthesis but did show antagonism toward DON-induced protein synthesis inhibition. These data suggest that the peptides selected in this study bind to mAb 6F5 and that peptide C430 binds to ribosomes at the same sites as DON.
Abundance and Diversity of
Archaea
in Heavy-Metal-Contaminated Soils
Authors: Sandaa Ruth-Anne , Enger Øivind , Torsvik Vigdis 
Published: December 2019

ABSTRACT

The impact of heavy-metal contamination on archaean communities was studied in soils amended with sewage sludge contaminated with heavy metals to varying extents. Fluorescent in situ hybridization showed a decrease in the percentage of
Archaea
from 1.3% ± 0.3% of 4′,6-diamidino-2-phenylindole-stained cells in untreated soil to below the detection limit in soils amended with heavy metals. A comparison of the archaean communities of the different plots by denaturing gradient gel electrophoresis revealed differences in the structure of the archaean communities in soils with increasing heavy-metal contamination. Analysis of cloned 16S ribosomal DNA showed close similarities to a unique and globally distributed lineage of the kingdom
Crenarchaeota
that is phylogenetically distinct from currently characterized crenarchaeotal species.
Anaerobic Mineralization of Quaternary Carbon Atoms: Isolation of Denitrifying Bacteria on Dimethylmalonate
Authors: Kniemeyer Olaf , Probian Christina , Rosselló-Mora Ramon , Harder Jens 
Published: December 2019

ABSTRACT

The microbial capacity to degrade simple organic compounds with quaternary carbon atoms was demonstrated by enrichment and isolation of five denitrifying strains on dimethylmalonate as the sole electron donor and carbon source. Quantitative growth experiments showed a complete mineralization of dimethylmalonate. According to phylogenetic analysis of the complete 16S rRNA genes, two strains isolated from activated sewage sludge were related to the genus
Paracoccus
within the α-
Proteobacteria
(98.0 and 98.2% 16S rRNA gene similarity to
Paracoccus denitrificans
T
), and three strains isolated from freshwater ditches were affiliated with the β-
Proteobacteria
(97.4 and 98.3% 16S rRNA gene similarity to
Herbaspirillum seropedicae
T
and
Acidovorax facilis
T
, respectively). Most-probable-number determinations for denitrifying populations in sewage sludge yielded 4.6 × 10
4
dimethylmalonate-utilizing cells ml
−1
, representing up to 0.4% of the total culturable nitrate-reducing population.
Genetic Diversity of
Fusarium oxysporum
Strains from Common Bean Fields in Spain
Authors: Alves-Santos Fernando M. , Benito Ernesto P. , Eslava Arturo P. , Díaz-Mínguez JoséMaría 
Published: December 2019

ABSTRACT

Fusarium wilt is an endemic disease in El Barco de Avila (Castilla y León, west-central Spain), where high-quality common bean cultivars have been cultured for the last century. We used intergenic spacer (IGS) region polymorphism of ribosomal DNA, electrophoretic karyotype patterns, and vegetative compatibility and pathogenicity analyses to assess the genetic diversity within
Fusarium oxysporum
isolates recovered from common bean plants growing in fields around El Barco de Avila. Ninety-six vegetative compatibility groups (VCGs) were found among 128 isolates analyzed; most of these VCGs contained only a single isolate. The strains belonging to pathogenic VCGs and the most abundant nonpathogenic VCGs were further examined for polymorphisms in the IGS region and electrophoretic karyotype patterns. Isolates belonging to the same VCG exhibited the same IGS haplotype and very similar electrophoretic karyotype patterns. These findings are consistent with the hypothesis that VCGs represent clonal lineages that rarely, if ever, reproduce sexually. The
F. oxysporum
f. sp.
phaseoli
strains recovered had the same IGS haplotype and similar electrophoretic karyotype patterns, different from those found for
F. oxysporum
f. sp.
phaseoli
from the Americas, and were assigned to three new VCGs (VCGs 0166, 0167, and 0168). Based on our results, we do not consider the strains belonging to
F. oxysporum
f. sp.
phaseoli
to be a monophyletic group within
F. oxysporum
, as there is no correlation between pathogenicity and VCG, IGS restriction fragment length polymorphism, or electrophoretic karyotype.
Genetic Diversity within
Cryptosporidium parvum
and Related
Cryptosporidium
Species
Authors: Xiao Lihua , Morgan Una M. , Limor Josef , Escalante Ananias , Arrowood Michael , Shulaw William , Thompson R. C. A. , Fayer Ronald , Lal Altaf A. 
Published: December 2019

ABSTRACT

To assess the genetic diversity in
Cryptosporidium parvum
, we have sequenced the small subunit (SSU) rRNA gene of seven
Cryptosporidium
spp., various isolates of
C. parvum
from eight hosts, and a
Cryptosporidium
isolate from a desert monitor. Phylogenetic analysis of the SSU rRNA sequences confirmed the multispecies nature of the genus
Cryptosporidium
, with at least four distinct species (
C. parvum
,
C. baileyi
,
C. muris
, and
C. serpentis
). Other species previously defined by biologic characteristics, including
C. wrairi
,
C. meleagridis
, and
C. felis
, and the desert monitor isolate, clustered together or within
C. parvum
. Extensive genetic diversities were present among
C. parvum
isolates from humans, calves, pigs, dogs, mice, ferrets, marsupials, and a monkey. In general, specific genotypes were associated with specific host species. A PCR-restriction fragment length polymorphism technique previously developed by us could differentiate most
Cryptosporidium
spp. and
C. parvum
genotypes, but sequence analysis of the PCR product was needed to differentiate
C. wrairi
and
C. meleagridis
from some of the
C. parvum
genotypes. These results indicate a need for revision in the taxonomy and assessment of the zoonotic potential of some animal
C. parvum
isolates.
Culture-Independent Identification of Microorganisms That Respond to Specified Stimuli
Authors: Borneman James 
Published: December 2019

ABSTRACT
A new approach that permits culture-independent identification of microorganisms that respond to specified stimuli was developed. This approach was illustrated by examination of microorganisms that grew in response to various nutrient supplements added to soil. A thymidine nucleotide analog, bromodeoxyuridine (BrdU), and supplements were added to soil and incubated for 3 days. DNA was extracted from the soil, and the newly synthesized DNA was isolated by immunocapture of the BrdU-labeled DNA. The unique perspective this approach offers was demonstrated by comparing the microbial community structures obtained from total soil DNA and the BrdU-labeled fraction in an rRNA gene (rDNA) analysis. The traditional total DNA analysis revealed no notable differences between the treatments, whereas the BrdU-labeled DNA showed significantly different banding patterns between the nutrient supplement treatments and compared with total DNA banding patterns. PCR primers were developed to specifically amplify the intergenic region of an rDNA sequence unique to the BrdU analysis of a phosphate supplement treatment. Amplification of DNA from all treatments using these primers showed that it was unique to the phosphate treatment and that it was present in both the total DNA and BrdU-labeled DNA fractions. This result demonstrates the promise of this new strategy, because it was able to permit identification of a sequence from a phosphate-responsive organism that was not discernable in the traditional total DNA community structure analysis.
Differentiation of
Fusarium subglutinans
f. sp.
pini
by Histone Gene Sequence Data
Authors: Steenkamp E. T. , Wingfield B. D. , Coutinho T. A. , Wingfield M. J. , Marasas W. F. O. 
Published: December 2019

ABSTRACT

Fusarium subglutinans
f. sp.
pini
(=
F. circinatum
) is a pathogen of pine and is one of eight mating populations (i.e., biological species) in the
Gibberella fujikuroi
species complex. This species complex includes
F. thapsinum
,
F. moniliforme
(=
F. verticillioides
),
F. nygamai
, and
F. proliferatum
, as well as
F. subglutinans
associated with sugarcane, maize, mango, and pineapple. Differentiating these forms of
F. subglutinans
usually requires pathogenicity tests, which are often time-consuming and inconclusive. Our objective was to develop a technique to differentiate isolates of
F. subglutinans
f. sp.
pini
from other isolates identified as
F. subglutinans
. We sequenced the histone H3 gene from a representative set of
Fusarium
isolates. The H3 gene sequence was conserved and contained two introns in all the isolates studied. From both the intron and the exon sequence data, we developed a PCR-restriction fragment length polymorphism technique that reliably distinguishes
F. subglutinans
f. sp.
pini
from the other biological species in the
G. fujikuroi
species complex.
Purification and Properties of an Esterase from the Yeast
Saccharomyces cerevisiae
and Identification of the Encoding Gene
Authors: Degrassi Giuliano , Uotila Lasse , Klima Raffaella , Venturi Vittorio 
Published: December 2019

ABSTRACT

We purified an intracellular esterase that can function as an
S
-formylglutathione hydrolase from the yeast
Saccharomyces cerevisiae
. Its molecular mass was 40 kDa, as determined by gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The isoelectric point was 5.0 by isoelectric focusing. The enzyme activity was optimal at 50°C and pH 7.0. The corresponding gene,
YJLO68C
, was identified by its N-terminal amino acid sequence and is not essential for cell viability. Null mutants have reduced esterase activities and grow slowly in the presence of formaldehyde. This enzyme may be involved in the detoxification of formaldehyde, which can be metabolized to
S
-formylglutathione by
S. cerevisiae
.
Optimization of Terminal-Restriction Fragment Length Polymorphism Analysis for Complex Marine Bacterioplankton Communities and Comparison with Denaturing Gradient Gel Electrophoresis
Authors: Moeseneder Markus M. , Arrieta Jesús M. , Muyzer Gerard , Winter Christian , Herndl Gerhard J. 
Published: December 2019

ABSTRACT
The potential of terminal-restriction fragment length polymorphism (T-RFLP) and the detection of operational taxonomic units (OTUs) by capillary electrophoresis (CE) to characterize marine bacterioplankton communities was compared with that of denaturing gradient gel electrophoresis (DGGE). A protocol has been developed to optimize the separation and detection of OTUs between 20 and 1,632 bp by using CE and laser-induced fluorescence detection. Additionally, we compared T-RFLP fingerprinting to DGGE optimized for detection of less abundant OTUs. Similar results were obtained with both fingerprinting techniques, although the T-RFLP approach and CE detection of OTUs was more sensitive, as indicated by the higher number of OTUs detected. We tested the T-RFLP fingerprinting technique on complex marine bacterial communities by using the 16S rRNA gene and 16S rRNA as templates for PCR. Samples from the Northern and Middle Adriatic Sea and from the South and North Aegean Sea were compared. Distinct clusters were identifiable for different sampling sites. Thus, this technique is useful for rapid evaluation of the biogeographical distribution and relationships of bacterioplankton communities.
Characterization of Muscle Sarcoplasmic and Myofibrillar Protein Hydrolysis Caused by
Lactobacillus plantarum
Authors: Fadda Silvina , Sanz Yolanda , Vignolo Graciela , Aristoy M.-Concepción , Oliver Guillermo , Toldrá Fidel 
Published: December 2019

ABSTRACT

Strains of
Lactobacillus plantarum
originally isolated from sausages were screened for proteinase and aminopeptidase activities toward synthetic substrates; on the basis of that screening,
L. plantarum
CRL 681 was selected for further assays on muscle proteins. The activities of whole cells, cell extracts (CE), and a combination of both on sarcoplasmic and myofibrillar protein extracts were determined by protein, peptide, and free-amino-acid analyses. Proteinase from whole cells initiated the hydrolysis of sarcoplasmic proteins. The addition of CE intensified the proteolysis. Whole cells generated hydrophilic peptides from both sarcoplasmic and myofibrillar proteins. Other peptides of a hydrophobic nature resulted from the combination of whole cells and CE. The action of both enzymatic sources on myofibrillar proteins caused maximal increases in lysine, arginine, and leucine, while the action of those on sarcoplasmic proteins mainly released alanine. In general, pronounced hydrolysis of muscle proteins required enzyme activities from whole cells in addition to those supplied by CE.