bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation and Use of a Homologous Histone H4 Promoter and a Ribosomal DNA Region in a Transformation Vector for the Oil-Producing FungusMortierella alpina
Authors: Mackenzie Donald A. , Wongwathanarat Prasert , Carter Andrew T. , Archer David B. 
Published: July 2002

ABSTRACTMortierella alpinawas transformed successfully to hygromycin B resistance by using a homologous histone H4 promoter to drive gene expression and a homologous ribosomal DNA region to promote chromosomal integration. This is the first description of transformation in this commercially important oleaginous organism. Two pairs of histone H3 and H4 genes were isolated from this fungus. Each pair consisted of one histone H3 gene and one histone H4 gene, transcribed divergently from an intergenic promoter region. The pairs of encoded histone H3 or H4 proteins were identical in amino acid sequence. At the DNA level, each histone H3 or H4 open reading frame showed 97 to 99% identity to its counterpart but the noncoding regions had little sequence identity. Unlike the histone genes from other filamentous fungi, all fourM. alpinagenes lacked introns. During normal vegetative growth, transcripts from the two histone H4 genes were produced at approximately the same level, indicating that either histone H4 promoter could be used in transformation vectors. The generation of stable, hygromycin B-resistant transformants required the incorporation of a homologous ribosomal DNA region into the transformation vector to promote chromosomal integration.
Decarboxylation of Substituted Cinnamic Acids by Lactic Acid Bacteria Isolated during Malt Whisky Fermentation
Authors: van Beek Sylvie , Priest Fergus G. 
Published: July 2002

ABSTRACTSeven strains ofLactobacillusisolated from malt whisky fermentations and representingLactobacillus brevis,L. crispatus,L. fermentum,L. hilgardii,L. paracasei,L. pentosus, andL. plantarumcontained genes for hydroxycinnamic acid (p-coumaric acid) decarboxylase. With the exception ofL. hilgardii, these bacteria decarboxylatedp-coumaric acid and/or ferulic acid, with the production of 4-vinylphenol and/or 4-vinylguaiacol, respectively, although the relative activities on the two substrates varied between strains. The addition ofp-coumaric acid or ferulic acid to cultures ofL. pentosusin MRS broth induced hydroxycinnamic acid decarboxylase mRNA within 5 min, and the gene was also induced by the indigenous components of malt wort. In a simulated distillery fermentation, a mixed culture ofL. crispatusandL. pentosusin the presence ofSaccharomyces cerevisiaedecarboxylated addedp-coumaric acid more rapidly than the yeast alone but had little activity on added ferulic acid. Moreover, we were able to demonstrate the induction of hydroxycinnamic acid decarboxylase mRNA under these conditions. However, in fermentations with no additional hydroxycinnamic acid, the bacteria lowered the final concentration of 4-vinylphenol in the fermented wort compared to the level seen in a pure-yeast fermentation. It seems likely that the combined activities of bacteria and yeast decarboxylatep-coumaric acid and then reduce 4-vinylphenol to 4-ethylphenol more effectively than either microorganism alone in pure cultures. Although we have shown that lactobacilli participate in the metabolism of phenolic compounds during malt whisky fermentations, the net result is a reduction in the concentrations of 4-vinylphenol and 4-vinylguaiacol prior to distillation.
An Improved Spectrophotometric Method To Study the Transport, Attachment, and Breakthrough of Bacteria through Porous Media
Authors: Deshpande P. A. , Shonnard D. R. 
Published: July 2002

ABSTRACT

This study reports an improved spectrophotometric method for studying bacterial (
Pseudomonas fluorescens
UPER-1) transport and attachment in saturated porous media (silica sand). While studying the effect of ionic strength by the traditional packed-column spectrophotometric method, we encountered an artifact. The absorbance of a well-stirred bacterial suspension was found to decrease with time in the presence of high concentrations of sodium and potassium phosphate salts (≥10
−2
M) as the cells continued to age in a resting stage. Our results show that collision efficiency and a bed ripening index will be in error by as much as 20% if breakthrough is measured by the traditional spectrophotometric technique. We present an improved experimental technique that will minimize the artifact and should substantially advance the understanding of bacteria transport in porous media.
Effects of Acid Adaptation of
Escherichia coli
O157:H7 on Efficacy of Acetic Acid Spray Washes To Decontaminate Beef Carcass Tissue
Authors: Berry Elaine D. , Cutter Catherine N. 
Published: July 2002

ABSTRACT

Exposure to low pH and organic acids in the bovine gastrointestinal tract may result in the induced acid resistance of
Escherichia coli
O157:H7 and other pathogens that may subsequently contaminate beef carcasses. The effect of acid adaptation of
E. coli
O157:H7 on the ability of acetic acid spray washing to reduce populations of this organism on beef carcass tissue was examined. Stationary-phase acid resistance and the ability to induce acid tolerance were determined for a collection of
E. coli
O157:H7 strains by testing the survival of acid-adapted and unadapted cells in HCl-acidified tryptic soy broth (pH 2.5). Three
E. coli
O157:H7 strains that were categorized as acid resistant (ATCC 43895) or acid sensitive (ATCC 43890) or that demonstrated inducible acid tolerance (ATCC 43889) were used in spray wash studies. Prerigor beef carcass surface tissue was inoculated with bovine feces containing either acid-adapted or unadapted
E. coli
O157:H7. The beef tissue was subjected to spray washing treatments with water or 2% acetic acid or left untreated. For strains ATCC 43895 and 43889, larger populations of acid-adapted cells than of unadapted cells remained on beef tissue following 2% acetic acid treatments and these differences remained throughout 14 days of 4°C storage. For both strains, numbers of acid-adapted cells remaining on tissue following 2% acetic acid treatments were similar to numbers of both acid-adapted and unadapted cells remaining on tissue following water treatments. For strain ATCC 43890, there was no difference between populations of acid-adapted and unadapted cells remaining on beef tissue immediately following 2% acetic acid treatments. These data indicate that adaptation to acidic conditions by
E. coli
O157:H7 can negatively influence the effectiveness of 2% acetic acid spray washing in reducing the numbers of this organism on carcasses.
Distribution of Aldoxime Dehydratase in Microorganisms
Authors: Kato Yasuo , Ooi Ryoko , Asano Yasuhisa 
Published: July 2002

ABSTRACT
The distribution of phenylacetaldoxime-degrading and pyridine-3-aldoxime-degrading ability was examined with intact cells of 975 microorganisms, including 45 genera of bacteria, 11 genera of actinomyces, 22 genera of yeasts, and 37 genera of fungi, by monitoring the decrease of the aldoximes by high-pressure liquid chromatography. The abilities were found to be widely distributed in bacteria, actinomyces, fungi, and some yeasts: 98 and 107 strains degraded phenylacetaldoxime and pyridine-3-aldoxime, respectively. All of the active strains exhibited not only the aldoxime-dehydration activity to form nitrile but also nitrile-hydrolyzing activity. On the other hand, all of 19 nitrile-degrading microorganisms (13 species, 7 genera) were found to exhibit aldoxime dehydration activity. It is shown that aldoxime dehydratase and nitrile-hydrolyzing activities are widely distributed among 188 aldoxime and 19 nitrile degraders and that the enzymes were induced by aldoximes or nitriles.
Hydroxylated Metabolites of 2,4-Dichlorophenol Imply a Fenton-Type Reaction in
Gloeophyllum striatum
Authors: Schlosser Dietmar , Fahr Kristina , Karl Wolfgang , Wetzstein Heinz-Georg 
Published: July 2002

ABSTRACT

While degrading 2,4-dichlorophenol, two strains of
Gloeophyllum striatum
, a basidiomycetous fungus causing brown rot decay of wood, simultaneously produced 4-chlorocatechol and 3,5-dichlorocatechol. These metabolites were identified by comparing high-performance liquid chromatography retention times and mass spectral data with those of chemically synthesized standards. Under similar conditions, 3-hydroxyphthalic hydrazide was generated from phthalic hydrazide, a reaction assumed to indicate hydroxyl radical formation. Accordingly, during chemical degradation of 2,4-dichlorophenol by Fenton's reagent, identical metabolites were formed. Both activities, the conversion of 2,4-[U-
14
C]dichlorophenol into
14
CO
2
and the generation of 3-hydroxyphthalic hydrazide, were strongly inhibited by the hydroxyl radical scavenger mannitol and in the absence of iron. These results provide new evidence in favor of a Fenton-type degradation mechanism operative in
Gloeophyllum
.
Chromosomal Integration of
tcb
Chlorocatechol Degradation Pathway Genes as a Means of Expanding the Growth Substrate Range of Bacteria To Include Haloaromatics
Authors: Klemba Michael , Jakobs Barbara , Wittich Rolf-Michael , Pieper Dietmar 
Published: July 2002

ABSTRACT

The
tcbR-tcbCDEF
gene cluster, coding for the chlorocatechol
ortho
-cleavage pathway in
Pseudomonas
sp. strain P51, has been cloned into a Tn
5
-based minitransposon. The minitransposon carrying the
tcb
gene cluster and a kanamycin resistance gene was transferred to
Pseudomonas putida
KT2442, and chromosomal integration was monitored by selection either for growth on 3-chlorobenzoate or for kanamycin resistance. Transconjugants able to utilize 3-chlorobenzoate as a sole carbon source were obtained, although at a >100-fold lower frequency than kanamycin-resistant transconjugants. The vast majority of kanamycin-resistant transconjugants were not capable of growth on 3-chlorobenzoate. Southern blot analysis revealed that many transconjugants selected directly on 3-chlorobenzoate contained multiple chromosomal copies of the
tcb
gene cluster, whereas those selected for kanamycin resistance possessed a single copy. Subsequent selection of kanamycin resistance-selected single-copy transconjugants for growth on 3-chlorobenzoate yielded colonies capable of utilizing this carbon source, but no amplification of the
tcb
gene cluster was apparent. Introduction of two copies of the
tcb
gene cluster without prior 3-chlorobenzoate selection resulted in transconjugants able to grow on this carbon source. Expression of the
tcb
chlorocatechol catabolic operon in
P. putida
thus represents a useful model system for analysis of the relationship among gene dosage, enzyme expression level, and growth on chloroaromatic substrates.
Response of Atmospheric Methane Consumption by Maine Forest Soils to Exogenous Aluminum Salts
Authors: Nanba K. , King Gary M. 
Published: July 2002

ABSTRACT

Atmospheric methane consumption by Maine forest soils was inhibited by additions of environmentally relevant levels of aluminum. Aluminum chloride was more inhibitory than nitrate or sulfate salts, but its effect was comparable to that of a chelated form of aluminum. Inhibition could be explained in part by the lower soil pH values which resulted from aluminum addition. However, significantly greater inhibition by aluminum than by mineral acids at equivalent soil pH values indicated that inhibition also resulted from direct effects of aluminum per se. The extent of inhibition by exogenous aluminum increased with increasing methane concentration for soils incubated in vitro. At methane concentrations of >10 ppm, inhibition could be observed when aluminum chloride was added at concentrations as low as 10 nmol g (fresh weight) of soil
−1
. These results suggest that widespread acidification of soils and aluminum mobilization due to acid precipitation may exacerbate inhibition of atmospheric methane consumption due to changes in other parameters and increase the contribution of methane to global warming.
Novel Bacterial and Archaeal Lineages from an In Situ Growth Chamber Deployed at a Mid-Atlantic Ridge Hydrothermal Vent
Authors: Reysenbach Anna-Louise , Longnecker Krista , Kirshtein Julie 
Published: July 2002

ABSTRACT

The phylogenetic diversity was determined for a microbial community obtained from an in situ growth chamber placed on a deep-sea hydrothermal vent on the Mid-Atlantic Ridge (23°22′ N, 44°57′ W). The chamber was deployed for 5 days, and the temperature within the chamber gradually decreased from 70 to 20°C. Upon retrieval of the chamber, the DNA was extracted and the small-subunit rRNA genes (16S rDNA) were amplified by PCR using primers specific for the
Archaea
or
Bacteria
domain and cloned. Unique rDNA sequences were identified by restriction fragment length polymorphisms, and 38 different archaeal and bacterial phylotypes were identified from the 85 clones screened. The majority of the archaeal sequences were affiliated with the
Thermococcales
(71%) and
Archaeoglobales
(22%) orders. A sequence belonging to the
Thermoplasmales
confirms that thermoacidophiles may have escaped enrichment culturing attempts of deep-sea hydrothermal vent samples. Additional sequences that represented deeply rooted lineages in the low-temperature eurarchaeal (marine group II) and crenarchaeal clades were obtained. The majority of the bacterial sequences obtained were restricted to the
Aquificales
(18%), the ɛ subclass of the
Proteobacteria
(ɛ-
Proteobacteria
) (40%), and the genus
Desulfurobacterium
(25%). Most of the clones (28%) were confined to a monophyletic clade within the ɛ-
Proteobacteria
with no known close relatives. The prevalence of clones related to thermophilic microbes that use hydrogen as an electron donor and sulfur compounds (S
0
, SO
4
, thiosulfate) indicates the importance of hydrogen oxidation and sulfur metabolism at deep-sea hydrothermal vents. The presence of sequences that are related to sequences from hyperthermophiles, moderate thermophiles, and mesophiles suggests that the diversity obtained from this analysis may reflect the microbial succession that occurred in response to the shift in temperature and possible associated changes in the chemistry of the hydrothermal fluid.
Modeling of Combined Processing Steps for Reducing
Escherichia coli
O157:H7 Populations in Apple Cider
Authors: Uljas Heidi E. , Schaffner Donald W. , Duffy Siobain , Zhao Lihui , Ingham Steven C. 
Published: July 2002

ABSTRACT

Probabilistic models were used as a systematic approach to describe the response of
Escherichia coli
O157:H7 populations to combinations of commonly used preservation methods in unpasteurized apple cider. Using a complete factorial experimental design, the effect of pH (3.1 to 4.3), storage temperature and time (5 to 35°C for 0 to 6 h or 12 h), preservatives (0, 0.05, or 0.1% potassium sorbate or sodium benzoate), and freeze-thaw (F-T; −20°C, 48 h and 4°C, 4 h) treatment combinations (a total of 1,600 treatments) on the probability of achieving a 5-log
10
-unit reduction in a three-strain
E. coli
O157:H7 mixture in cider was determined. Using logistic regression techniques, pH, temperature, time, and concentration were modeled in separate segments of the data set, resulting in prediction equations for: (i) no preservatives, before F-T; (ii) no preservatives, after F-T; (iii) sorbate, before F-T; (iv) sorbate, after F-T; (v) benzoate, before F-T; and (vi) benzoate, after F-T. Statistical analysis revealed a highly significant (
P
< 0.0001) effect of all four variables, with cider pH being the most important, followed by temperature and time, and finally by preservative concentration. All models predicted 92 to 99% of the responses correctly. To ensure safety, use of the models is most appropriate at a 0.9 probability level, where the percentage of false positives, i.e., falsely predicting a 5-log
10
-unit reduction, is the lowest (0 to 4.4%). The present study demonstrates the applicability of logistic regression approaches to describing the effectiveness of multiple treatment combinations in pathogen control in cider making. The resulting models can serve as valuable tools in designing safe apple cider processes.
Insertion or Deletion of the Cheo Box Modifies Radiation Inducibility of
Clostridium
Promoters
Authors: Nuyts S. , Van Mellaert L. , Barbé S. , Lammertyn E. , Theys J. , Landuyt W. , Bosmans E. , Lambin P. , Anné J. 
Published: July 2002

ABSTRACT

Radiation-inducible promoters are being used in many viral vector systems to obtain spatial and temporal control of gene expression. It was previously proven that radiation-induced gene expression can also be obtained in a bacterial vector system using anaerobic apathogenic clostridia. The effect of radiation inducibility was detected using mouse tumor necrosis factor alpha (mTNF-α) as a model protein under regulation of the radiation-inducible
recA
promoter. In this report, experiments are described in which this
recA
promoter was modified in order to increase radiation responsiveness. Incorporation of an extra Cheo box in the
recA
promoter region resulted in an increase in mTNF-α secretion from 44% for the wild-type promoter to 412% for the promoter with an extra Cheo box after a single irradiation dose of 2 Gy. Deletion of the Cheo box in the promoter region eliminated radiation inducibility. These results prove that the Cheo box in the
recA
promoter is indeed the radiation-responsive element. We also tested whether we could induce the constitutive endo-β-1,4-glucanase promoter (
eglA
) via ionizing irradiation by introducing a Cheo box in the promoter region. While the use of the constitutive promoter did not lead to an increase in mTNF-α secretion after irradiation, the introduction of a Cheo box resulted in a 242% increase in mTNF-α secretion. Reverse transcriptase PCR of RNA samples isolated from irradiated and nonirradiated bacterial cultures demonstrated that the increase in secretion was the result of enhanced transcription of the mTNF-α gene.
Generation of Metal-Binding Staphylococci through Surface Display of Combinatorially Engineered Cellulose-Binding Domains
Authors: Wernérus Henrik , Lehtiö Janne , Teeri Tuula , Nygren Per-Åke , Ståhl Stefan 
Published: July 2002

ABSTRACT

Ni
2+
-binding staphylococci were generated through surface display of combinatorially engineered variants of a fungal cellulose-binding domain (CBD) from
Trichoderma reesei
cellulase Cel7A. Novel CBD variants were generated by combinatorial protein engineering through the randomization of 11 amino acid positions, and eight potentially Ni
2+
-binding CBDs were selected by phage display technology. These new variants were subsequently genetically introduced into chimeric surface proteins for surface display on
Staphylococcus carnosus
cells. The expressed chimeric proteins were shown to be properly targeted to the cell wall of
S. carnosus
cells, since full-length proteins could be extracted and affinity purified. Surface accessibility for the chimeric proteins was demonstrated, and furthermore, the engineered CBDs, now devoid of cellulose-binding capacity, were shown to be functional with regard to metal binding, since the recombinant staphylococci had gained Ni
2+
-binding capacity. Potential environmental applications for such tailor-made metal-binding bacteria as bioadsorbents in biofilters or biosensors are discussed.
Variation in Resistance to High Hydrostatic Pressure and
rpoS
Heterogeneity in Natural Isolates of
Escherichia coli
O157:H7
Authors: Robey Marianne , Benito Amparo , Hutson Roger H. , Pascual Cristina , Park Simon F. , Mackey Bernard M. 
Published: July 2002

ABSTRACT

Several natural isolates of
Escherichia coli
O157:H7 have previously been shown to exhibit stationary-phase-dependent variation in their resistance to inactivation by high hydrostatic pressure. In this report we demonstrate that loss of the stationary-phase-inducible sigma factor RpoS resulted in decreased resistance to pressure in
E. coli
O157:H7 and in a commensal strain. Furthermore, variation in the RpoS activity of the natural isolates of O157:H7 correlated with the pressure resistance of those strains. Heterogeneity was noted in the
rpoS
alleles of the natural isolates that may explain the differences in RpoS activity. These results are consistent with a role for
rpoS
in mediating resistance to high hydrostatic pressure in
E. coli
O157:H7.
Denaturing Gradient Gel Electrophoresis Analysis of the 16S rRNA Gene V1 Region To Monitor Dynamic Changes in the Bacterial Population during Fermentation of Italian Sausages
Authors: Cocolin Luca , Manzano Marisa , Cantoni Carlo , Comi Giuseppe 
Published: July 2002

ABSTRACT

In this study, a PCR-denaturing gradient gel electrophoresis (DGGE) protocol was used to monitor the dynamic changes in the microbial population during ripening of natural fermented sausages. The method was first optimized by using control strains from international collections, and a natural sausage fermentation was studied by PCR-DGGE and traditional methods. Total microbial DNA and RNA were extracted directly from the sausages and subjected to PCR and reverse transcription-PCR, and the amplicons obtained were analyzed by DGGE. Lactic acid bacteria (LAB) were present together with other organisms, mainly members of the family
Micrococcaceae
and meat contaminants, such as
Brochothrix thermosphacta
and
Enterococcus
sp., during the first 3 days of fermentation. After 3 days, LAB represented the main population, which was responsible for the acidification and proteolysis that determined the characteristic organoleptic profile of the Friuli Venezia Giulia fermented sausages. The PCR-DGGE protocol for studying sausage fermentation proved to be a good tool for monitoring the process in real time, and it makes technological adjustments possible when they are required.
Toxicity Analysis of N- and C-Terminus-Deleted Vegetative Insecticidal Protein from
Bacillus thuringiensis
Authors: Selvapandiyan A. , Arora N. , Rajagopal R. , Jalali S. K. , Venkatesan T. , Singh S. P. , Bhatnagar Raj K. 
Published: July 2002

ABSTRACT

A vegetative insecticidal protein (VIP)-encoding gene from a local isolate of
Bacillus thuringiensis
has been cloned, sequenced, and expressed in
Escherichia coli
. The expressed protein shows insecticidal activity against several lepidopteran pests but is ineffective against
Agrotis ipsilon
. Comparison of the amino acid sequence with those of reported VIPs revealed a few differences. Analysis of insecticidal activity with N- and C-terminus deletion mutants suggests a differential mode of action of VIP against different pests.