bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genotypic Characterization of
Bradyrhizobium
Strains Nodulating Endemic Woody Legumes of the Canary Islands by PCR-Restriction Fragment Length Polymorphism Analysis of Genes Encoding 16S rRNA (16S rDNA) and 16S-23S rDNA Intergenic Spacers, Repetitive Extragenic Palindromic PCR Genomic Fingerprinting, and Partial 16S rDNA Sequencing
Authors: Vinuesa Pablo , Rademaker Jan L. W. , de Bruijn Frans J. , Werner Dietrich 
Published: December 2019

ABSTRACT

We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated from nodules of tagasaste (
Chamaecytisus proliferus
) and other endemic woody legumes of the Canary Islands, Spain. These and several reference strains were characterized genotypically at different levels of taxonomic resolution by computer-assisted analysis of 16S ribosomal DNA (rDNA) PCR-restriction fragment length polymorphisms (PCR-RFLPs), 16S-23S rDNA intergenic spacer (IGS) RFLPs, and repetitive extragenic palindromic PCR (rep-PCR) genomic fingerprints with BOX, ERIC, and REP primers. Cluster analysis of 16S rDNA restriction patterns with four tetrameric endonucleases grouped the Canarian isolates with the two reference strains,
Bradyrhizobium japonicum
USDA 110
spc
4 and
Bradyrhizobium
sp. strain (
Centrosema
) CIAT 3101, resolving three genotypes within these bradyrhizobia. In the analysis of IGS RFLPs with three enzymes, six groups were found, whereas rep-PCR fingerprinting revealed an even greater genotypic diversity, with only two of the Canarian strains having similar fingerprints. Furthermore, we show that IGS RFLPs and even very dissimilar rep-PCR fingerprints can be clustered into phylogenetically sound groupings by combining them with 16S rDNA RFLPs in computer-assisted cluster analysis of electrophoretic patterns. The DNA sequence analysis of a highly variable 264-bp segment of the 16S rRNA genes of these strains was found to be consistent with the fingerprint-based classification. Three different DNA sequences were obtained, one of which was not previously described, and all belonged to the
B. japonicum/Rhodopseudomonas
rDNA cluster. Nodulation assays revealed that none of the Canarian isolates nodulated
Glycine max
or
Leucaena leucocephala
, but all nodulated
Acacia pendula
,
C. proliferus
,
Macroptilium atropurpureum
, and
Vigna unguiculata
.
Role of
Streptococcus thermophilus
MR-1C Capsular Exopolysaccharide in Cheese Moisture Retention
Authors: Low Deborah , Ahlgren Jeffrey A. , Horne Diane , McMahon Donald J. , Oberg Craig J. , Broadbent Jeffery R. 
Published: December 2019

ABSTRACT

Recent work by our group has shown that an exopolysaccharide (EPS)-producing starter pair,
Streptococcus thermophilus
MR-1C and
Lactobacillus delbrueckii
subsp.
bulgaricus
MR-1R, can significantly increase moisture retention in low-fat mozzarella (D. B. Perry, D. J. McMahon, and C. J. Oberg, J. Dairy Sci. 80:799–805, 1997). The objectives of this study were to determine whether MR-1C, MR-1R, or both of these strains are required for enhanced moisture retention and to establish the role of EPS in this phenomenon. Analysis of low-fat mozzarella made with different combinations of MR-1C, MR-1R, and the non-EPS-producing starter culture strains
S. thermophilus
TA061 and
Lactobacillus helveticus
LH100 showed that
S. thermophilus
MR-1C was responsible for the increased cheese moisture level. To investigate the role of the
S. thermophilus
MR-1C EPS in cheese moisture retention, the
epsE
gene in this bacterium was inactivated by gene replacement. Low-fat mozzarella made with
L. helveticus
LH100 plus the non-EPS-producing mutant
S. thermophilus
DM10 had a significantly lower moisture content than did cheese made with strains LH100 and MR-1C, which confirmed that the MR-1C capsular EPS was responsible for the water-binding properties of this bacterium in cheese. Chemical analysis of the
S. thermophilus
MR-1C EPS indicated that the polymer has a novel basic repeating unit composed of
d
-galactose,
l
-rhamnose, and
l
-fucose in a ratio of 5:2:1.
Culture Conditions Control Expression of the Genes for Aflatoxin and Sterigmatocystin Biosynthesis in
Aspergillus parasiticus
and
A. nidulans
Authors: Feng Guo Hong , Leonard Thomas J. 
Published: December 2019

ABSTRACT

High temperature and nitrate supported gene expression for sterigmatocystin biosynthesis in
Aspergillus nidulans
; ammonium did not. Homologous genes for aflatoxin biosynthesis in
A. parasiticus
showed the opposite transcript expression pattern, suggesting that the two mycotoxins are regulated differently. The
aflR
gene is postulated to require additional genetic elements to effect its own activation by the different culture conditions. A patulin polyketide synthase (PKS) gene was found to be regulated differently than the aflatoxin PKS. Thus, the biosyntheses of structurally similar compounds in these two fungi appear to be regulated very differently.
Detection of
Toxoplasma gondii
Oocysts in Drinking Water
Authors: Isaac-Renton Judith , Bowie William R. , King Arlene , Irwin G. Stewart , Ong Corinne S. , Fung C. P. , Shokeir M. Omar , Dubey J. P. 
Published: December 2019

ABSTRACT

The world’s largest outbreak of waterborne toxoplasmosis occurred in a municipality in the western Canadian province of British Columbia. When drinking water emerged as a possible source of infection during the outbreak investigation, a laboratory method was needed to attempt detection of the parasite,
Toxoplasma gondii
. The method developed was based on the current U.S. Environmental Protection Agency method for detection of
Cryptosporidium
oocysts. Collection of large-volume drinking water samples and cartridge filter processing were unchanged, although identification of
Toxoplasma
oocysts in the filter retentate was carried out by using a previously described rodent model. Validation of the method developed was tested by using oocysts from a well-characterized
Toxoplasma
strain.
Evaluation of Lacticin 3147 and a Teat Seal Containing This Bacteriocin for Inhibition of Mastitis Pathogens
Authors: Ryan Máire P. , Meaney William J. , Ross R. Paul , Hill Colin 
Published: December 2019

ABSTRACTLacticin 3147 is a broad-spectrum bacteriocin produced byLactococcus lactissubsp.lactisDPC3147 which is bactericidal against a range of mastitis-causing streptococci and staphylococci. In this study, both lacticin 3147 and the lantibiotic nisin were separately incorporated into an intramammary teat seal product. The seal containing lacticin 3147 exhibited excellent antimicrobial activity and might form the basis of an improved treatment for the prevention of mastitis in dry cows.
Epidemiological Typing of
Campylobacter
Isolates from Meat Processing Plants by Pulsed-Field Gel Electrophoresis, Fatty Acid Profile Typing, Serotyping, and Biotyping
Authors: Steele M. , McNab B. , Fruhner L. , DeGrandis S. , Woodward D. , Odumeru J. A. 
Published: December 2019

ABSTRACT

Campylobacter
spp. are a leading cause of bacterial gastroenteritis. Foods of animal origin, particularly undercooked poultry, are common sources of
Campylobacter
species associated with disease in humans. A collection of 110
Campylobacter jejuni
and 31
C. coli
human and environmental isolates from different Ontario, Canada, abattoirs were analyzed by pulsed-field gel electrophoresis, fatty acid profile typing, and biotyping. Previously collected serotyping data for the same isolates were also analyzed in this study. Pulsed-field gel electrophoresis was found to be the most discriminatory of the typing methods, followed by serotyping, fatty acid profile typing, and biotyping. A wide variety of typing profiles were observed within the isolates, suggesting that several different
Campylobacter
sp. strains were present within the abattoirs.
Kinetic Parameters of Denitrification in a River Continuum
Authors: García-Ruiz Roberto , Pattinson Sarah N. , Whitton Brian A. 
Published: December 2019

ABSTRACTKinetic parameters for nitrate reduction in intact sediment cores were investigated by using the acetylene blockage method at five sites along the Swale-Ouse river system in northeastern England, including a highly polluted tributary, R. Wiske. The denitrification rate in sediment containing added nitrate exhibited a Michaelis-Menten-type curve. The concentration of nitrate for half-maximal activity (Kmap) by denitrifying bacteria increased on passing downstream from 13.1 to 90.4 μM in the main river, but it was highest (640 μM) in the Wiske. The apparent maximal rate (Vmaxap) ranged between 35.8 and 324 μmol of N m−2h−1in the Swale-Ouse (increasing upstream to downstream), but it was highest in the Wiske (1,194 μmol N m−2h−1). A study of nitrous oxide (N2O) production at the same time showed that rates ranged from below the detection limit (0.05 μmol of N2O-N m−2h−1) at the headwater site to 27 μmol of N2O-N m−2h−1at the downstream site. In the Wiske the rate was up to 570 μmol of N2O-N m−2h−1, accounting for up to 80% of total N gas production.
Seasonal and Spatial Variability of Bacterial and Archaeal Assemblages in the Coastal Waters near Anvers Island, Antarctica
Authors: Murray A. E. , Preston C. M. , Massana R. , Taylor L. T. , Blakis A. , Wu K. , DeLong E. F. 
Published: December 2019

ABSTRACT

A previous report of high levels of members of the domain
Archaea
in Antarctic coastal waters prompted us to investigate the ecology of Antarctic planktonic prokaryotes. rRNA hybridization techniques and denaturing gradient gel electrophoresis (DGGE) analysis of the bacterial V3 region were used to study variation in Antarctic picoplankton assemblages. In Anvers Island nearshore waters during late winter to early spring, the amounts of archaeal rRNA ranged from 17.1 to 3.6% of the total picoplankton rRNA in 1996 and from 16.0 to 1.0% of the total rRNA in 1995. Offshore in the Palmer Basin, the levels of archaeal rRNA throughout the water column were higher (average, 24% of the total rRNA) during the same period in 1996. The archaeal rRNA levels in nearshore waters followed a highly seasonal pattern and markedly decreased during the austral summer at two stations. There was a significant negative correlation between archaeal rRNA levels and phytoplankton levels (as inferred from chlorophyll
a
concentrations) in nearshore surface waters during the early spring of 1995 and during an 8-month period in 1996 and 1997. In situ hybridization experiments revealed that 5 to 14% of DAPI (4′,6-diamidino-2-phenylindole)-stained cells were archaeal, corresponding to 0.9 × 10
4
to 2.7 × 10
4
archaeal cells per ml, in late winter 1996 samples. Analysis of bacterial ribosomal DNA fragments by DGGE revealed that the assemblage composition may reflect changes in water column stability, depth, or season. The data indicate that changes in Antarctic seasons are accompanied by significant shifts in the species composition of bacterioplankton assemblages and by large decreases in the relative proportion of archaeal rRNA in the nearshore water column.
Trifolitoxin Production Increases Nodulation Competitiveness of
Rhizobium etli
CE3 under Agricultural Conditions
Authors: Robleto Eduardo A. , Kmiecik Kenneth , Oplinger Edward S. , Nienhuis James , Triplett Eric W. 
Published: December 2019

ABSTRACT

A major barrier to the use of nitrogen-fixing inoculum strains for the enhancement of legume productivity is the inability of commercially available strains to compete with indigenous rhizobia for nodule formation. Despite extensive research on nodulation competitiveness, there are no examples of field efficacy studies of strains that have been genetically improved for nodulation competitiveness. We have shown previously that production of the peptide antibiotic trifolitoxin (TFX) by
Rhizobium etli
results in significantly increased nodule occupancy values in nonsterile soil in growth chamber experiments (E. A. Robleto, A. J. Scupham, and E. W. Triplett, Mol. Plant-Microbe Interact. 10:228–233, 1997). To determine whether TFX production by
Rhizobium etli
increases nodulation competitiveness in field-grown plants, seeds of
Phaseolus vulgaris
were inoculated with mixtures of
Rhizobium etli
strains at different ratios. The three nearly isogenic inoculum strains used included TFX-producing and non-TFX-producing strains, as well as a TFX-sensitive reference strain. Data was obtained over 2 years for nodule occupancy and over 3 years for assessment of the effect of the TFX production phenotype on grain yield. In comparable mixtures in which the test strain accounted for between 5 and 50% of the inoculum, the TFX-producing strain exhibited at least 20% greater nodule occupancy than the non-TFX-producing strain in both years. The TFX production phenotype had no effect on grain yield over 3 years; the average yields reached 2,400 kg/ha. These results show that addition of the TFX production phenotype significantly increases nodule occupancy under field conditions without adverse effects on grain yield. As we used common inoculation methods in this work, there are no practical barriers to the commercial adoption of the TFX system for agriculture.
Increased Carotenoid Production by the Food Yeast
Candida utilis
through Metabolic Engineering of the Isoprenoid Pathway
Authors: Shimada Hiroshi , Kondo Keiji , Fraser Paul D. , Miura Yutaka , Saito Toshiko , Misawa Norihiko 
Published: December 2019

ABSTRACT

The yeast
Candida utilis
does not possess an endogenous biochemical pathway for the synthesis of carotenoids. The central isoprenoid pathway concerned with the synthesis of prenyl lipids is present in
C. utilis
and active in the biosynthesis of ergosterol. In our previous study, we showed that the introduction of exogenous carotenoid genes,
crtE
,
crtB
, and
crtI
, responsible for the formation of lycopene from the precursor farnesyl pyrophosphate, results in the
C. utilis
strain that yields lycopene at 1.1 mg per g (dry weight) of cells (Y. Miura, K. Kondo, T. Saito, H. Shimada, P. D. Fraser, and N. Misawa, Appl. Environ. Microbiol. 64:1226–1229, 1998). Through metabolic engineering of the isoprenoid pathway, a sevenfold increase in the yield of lycopene has been achieved. The influential steps in the pathway that were manipulated were 3-hydroxy methylglutaryl coenzyme A (HMG-CoA) reductase, encoded by the
HMG
gene, and squalene synthase, encoded by the
ERG9
gene. Strains overexpressing the
C. utilis
HMG-CoA reductase yielded lycopene at 2.1 mg/g (dry weight) of cells. Expression of the HMG-CoA catalytic domain alone gave 4.3 mg/g (dry weight) of cells; disruption of the
ERG9
gene had no significant effect, but a combination of
ERG9
gene disruption and the overexpression of the HMG catalytic domain yielded lycopene at 7.8 mg/g (dry weight) of cells. The findings of this study illustrate how modifications in related biochemical pathways can be utilized to enhance the production of commercially desirable compounds such as carotenoids.
Specific Detection of
Legionella pneumophila
: Construction of a New 16S rRNA-Targeted Oligonucleotide Probe
Authors: Grimm Dorothee , Merkert Hilde , Ludwig Wolfgang , Schleifer Karl-Heinz , Hacker Jörg , Brand Bettina C. 
Published: December 2019

ABSTRACT

Based on comparative sequence analysis, we have designed an oligonucleotide probe complementary to a region of 16S rRNA of
Legionella pneumophila
which allows the differentiation of
L. pneumophila
from other
Legionella
species without cultivation. The specificity of the new probe, LEGPNE1, was tested by in situ hybridization to a total of four serogroups of six strains of
L. pneumophila
, five different
Legionella
spp. and three nonlegionella species as reference strains. Furthermore,
L. pneumophila
cells could be easily distinguished from
Legionella micdadei
and
Pseudomonas aeruginosa
cells by using in situ hybridization with probes LEGPNE1, LEG705, and EUB338 after infection of the protozoan
Acanthamoeba castellanii
.
Giardia
sp. Cysts and Infectious
Cryptosporidium parvum
Oocysts in the Feces of Migratory Canada Geese (
Branta canadensis
)
Authors: Graczyk Thaddeus K. , Fayer Ronald , Trout James M. , Lewis Earl J. , Farley C. Austin , Sulaiman Irshad , Lal Altaf A. 
Published: December 2019

ABSTRACT

Fecal droppings of migratory Canada geese,
Branta canadensis
, collected from nine sites near the Chesapeake Bay (Maryland), were examined for the presence of
Cryptosporidium parvum
and
Giardia
spp.
Cryptosporidium
sp. oocysts were found in feces at seven of nine sites, and
Giardia
cysts were found at all nine sites. The oocysts from three sites were infectious for mice and molecularly identified as the zoonotic genotype of
Cryptosporidium parvum
. Waterfowl can disseminate infectious
C. parvum
oocysts in the environment.
Use of the Lactococcal
nisA
Promoter To Regulate Gene Expression in Gram-Positive Bacteria: Comparison of Induction Level and Promoter Strength
Authors: Eichenbaum Zehava , Federle Michael J. , Marra Diana , de Vos Willem M. , Kuipers Oscar P. , Kleerebezem Michiel , Scott June R. 
Published: December 2019

ABSTRACT

We characterized the regulated activity of the lactococcal
nisA
promoter in strains of the gram-positive species
Streptococcus pyogenes
,
Streptococcus agalactiae
,
Streptococcus pneumoniae
,
Enterococcus faecalis
, and
Bacillus subtilis. nisA
promoter activity was dependent on the proteins NisR and NisK, which constitute a two-component signal transduction system that responds to the extracellular inducer nisin. The nisin sensitivity and inducer concentration required for maximal induction varied among the strains. Significant induction of the
nisA
promoter (10- to 60-fold induction) was obtained in all of the species studied at a nisin concentration just below the concentration at which growth is inhibited. The efficiency of the
nisA
promoter was compared to the efficiencies of the
Spac
,
xylA
, and
lacA
promoters in
B. subtilis
and in
S. pyogenes
. Because
nisA
promoter-driven expression is regulated in many gram-positive bacteria, we expect it to be useful for genetic studies, especially studies with pathogenic streptococci in which no other regulated promoters have been described.
Transformation of Industrial Dyes by Manganese Peroxidases from
Bjerkandera adusta
and
Pleurotus eryngii
in a Manganese-Independent Reaction
Authors: Heinfling A. , Martínez M. J. , Martínez A. T. , Bergbauer M. , Szewzyk U. 
Published: December 2019

ABSTRACT

We investigated the transformation of six industrial azo and phthalocyanine dyes by ligninolytic peroxidases from
Bjerkandera adusta
and other white rot fungi. The dyes were not oxidized or were oxidized very little by
Phanerochaete chrysosporium
manganese peroxidase (MnP) or by a chemically generated Mn
3+
-lactate complex. Lignin peroxidase (LiP) from
B. adusta
also showed low activity with most of the dyes, but the specific activities increased 8- to 100-fold when veratryl alcohol was included in the reaction mixture, reaching levels of 3.9 to 9.6 U/mg. The
B. adusta
and
Pleurotus eryngii
MnP isoenzymes are unusual because of their ability to oxidize aromatic compounds like 2,6-dimethoxyphenol and veratryl alcohol in the absence of Mn
2+
. These MnP isoenzymes also decolorized the azo dyes and the phthalocyanine complexes in an Mn
2+
-independent manner. The reactions with the dyes were characterized by apparent

K
m

values ranging from 4 to 16 μM and specific activities ranging from 3.2 to 10.9 U/mg. Dye oxidation by these peroxidases was not increased by adding veratryl alcohol as it was in LiP reactions. Moreover, the reaction was inhibited by the presence of Mn
2+
, which in the case of Reactive Black 5, an azo dye which is not oxidized by the Mn
3+
-lactate complex, was found to act as a noncompetitive inhibitor of dye oxidation by
B. adusta
MnP1.
Monitoring Impact of a Pesticide Treatment on Bacterial Soil Communities by Metabolic and Genetic Fingerprinting in Addition to Conventional Testing Procedures
Authors: Engelen Bert , Meinken Kristin , von Wintzingerode Friedrich , Heuer Holger , Malkomes Hans-Peter , Backhaus Horst 
Published: December 2019

ABSTRACT

Herbogil (dinoterb), a reference herbicide, the mineral oil Oleo (paraffin oil used as an additive to herbicides), and Goltix (metamitron) were taken as model compounds for the study of impacts on microbial soil communities. After the treatment of soil samples, effects on metabolic sum parameters were determined by monitoring substrate-induced respiration (SIR) and dehydrogenase activity, as well as carbon and nitrogen mineralization. These conventional ecotoxicological testing procedures are used in pesticide registration. Inhibition of biomass-related activities and stimulation of nitrogen mineralization were the most significant effects caused by the application of Herbogil. Even though Goltix and Oleo were used at a higher dosage (10 times higher), the application of Goltix resulted in smaller effects and the additive Oleo was the least-active compound, with minor stimulation of test parameters at later observation times. The results served as a background for investigation of the power of “fingerprinting” methods in microbial ecology. Changes in catabolic activities induced by treatments were analyzed by using the 95 carbon sources provided by the BIOLOG system. Variations in the complex metabolic fingerprints demonstrated inhibition of many catabolic pathways after the application of Herbogil. Again, the effects of the other compounds were expressed at much lower levels and comprised stimulations as well as inhibitions. Testing for significance by a multivariate
t
test indicated that the sensitivity of this method was similar to the sensitivities of the conventional testing procedures. The variation of sensitive carbon sources, as determined by factor weights at different observation times, indicated the dynamics of the community shift induced by the Herbogil treatment in more detail. DNA extractions from soil resulted in a collection of molecules representing the genetic composition of total bacterial communities. Distinct and highly reproducible community patterns, or genetic fingerprints, resulting from application of the different herbicides were obtained by the sequence-specific separation of partial 16S rDNA amplification products in temperature gradient gel electrophoresis. Significant pattern variations were quantified. For detailed analysis, application-responsive bands from the Herbogil and Oleo treatments were sequenced and their tentative phylogenetic positions were identified. Data interpretation and the potentials and biases of the additional observation windows on microbial communities are discussed.
One Hundred Seventy-Fold Increase in Excretion of an FV Fragment-Tumor Necrosis Factor Alpha Fusion Protein (sFV/TNF-α) from
Escherichia coli
Caused by the Synergistic Effects of Glycine and Triton X-100
Authors: Yang Junbao , Moyana Terence , MacKenzie Samuel , Xia Qun , Xiang Jim 
Published: December 2019

ABSTRACT

To target tumor necrosis factor alpha (TNF-α) to tumor cells, recombinant DNA techniques were used to construct and express the fused gene V
K
LV
H
–TNF-α, which encodes the secreted form of single-chain fusion protein sFV/TNF-α in
Escherichia coli
. sFV/TNF-α was secreted into the culture medium and purified by affinity chromatography. The production of the fusion protein in the culture medium under the optimal conditions of 30°C and 37 μmol of isopropyl-β-
d
-thiogalactopyranoside (IPTG) per liter was 16- and 5-fold higher than that under the standard conditions of 37°C and 1 mmol of IPTG per liter. Fusion protein excretion into culture medium with 2% glycine, 1% Triton X-100, or both of these two chemicals was either 14-, 38-, or 170-fold higher, respectively than that without the two chemicals. The final yield of sFV/TNF-α was estimated to be 50 mg/liter. The loss of integrity of the cellular membrane may be a potential mechanism for enhancement of fusion protein production and excretion by treatment with glycine and Triton X-100. This study thus provides a practical, large-scale method for more efficient production of the heterologous fusion protein sFV/TNF-α in
E. coli
by using glycine and Triton X-100.