bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and Functional Analysis of the Gene Encoding Methionine-γ-Lyase in
Brevibacterium linens
Authors: Amarita Felix , Yvon Mireille , Nardi Michele , Chambellon Emilie , Delettre Jerôme , Bonnarme Pascal 
Published: December 2004

ABSTRACT

The enzymatic degradation of
l
-methionine and subsequent formation of volatile sulfur compounds (VSCs) is believed to be essential for flavor development in cheese.
l
-Methionine-γ-lyase (MGL) can convert
l
-methionine to methanethiol (MTL), α-ketobutyrate, and ammonia. The
mgl
gene encoding MGL was cloned from the type strain
Brevibacterium linens
ATCC 9175 known to produce copious amounts of MTL and related VSCs. The disruption of the
mgl
gene, achieved in strain ATCC 9175, resulted in a 62% decrease in thiol-producing activity and a 97% decrease in total VSC production in the knockout strain. Our work shows that
l
-methionine degradation via γ-elimination is a key step in the formation of VSCs in
B. linens
.
PCR Analysis of the Distribution of Unicellular Cyanobacterial Diazotrophs in the Arabian Sea
Authors: Mazard Sophie L. , Fuller Nicholas J. , Orcutt Karen M. , Bridle Oliver , Scanlan Dave J. 
Published: December 2004

ABSTRACT

An oligonucleotide primer, NITRO821R, targeting the 16S rRNA gene of unicellular cyanobacterial N
2
fixers was developed based on newly derived sequences from
Crocosphaera
sp. strain WH 8501 and
Cyanothece
sp. strains WH 8902 and WH 8904 as well as several previously described sequences of
Cyanothece
sp. and sequences of intracellular cyanobacterial symbionts of the marine diatom
Climacodium frauenfeldianum
. This oligonucleotide is specific for the targeted organisms, which represent a well-defined phylogenetic lineage, and can detect as few as 50 cells in a standard PCR when it is used as a reverse primer together with the cyanobacterium- and plastid-specific forward primer CYA359F (U. Nübel, F. Garcia-Pichel, and G. Muyzer, Appl. Environ. Microbiol.
63:
3327-3332, 1997). Use of this primer pair in the PCR allowed analysis of the distribution of marine unicellular cyanobacterial diazotrophs along a transect following the 67°E meridian from Victoria, Seychelles, to Muscat, Oman (0.5°S to 26°N) in the Arabian Sea. These organisms were found to be preferentially located in warm (>29°C) oligotrophic subsurface waters between 0 and 7°N, but they were also found at a station north of Oman at 26°N, 56°35′E, where similar water column conditions prevailed. Slightly cooler oligotrophic waters (<29°C) did not contain these organisms or the numbers were considerably reduced, suggesting that temperature is a key factor in dictating the abundance of this unicellular cyanobacterial diazotroph lineage in marine environments.
Bacterial Diversity in a Nonsaline Alkaline Environment: Heterotrophic Aerobic Populations
Authors: Tiago Igor , Chung Ana Paula , Veríssimo António 
Published: December 2004

ABSTRACT

Heterotrophic populations were isolated and characterized from an alkaline groundwater environment generated by active serpentinization, which results in a Ca(OH)
2
-enriched, extremely diluted groundwater with pH 11.4. One hundred eighty-five strains were isolated in different media at different pH values during two sampling periods. To assess the degree of diversity present in the environment and to select representative strains for further characterization of the populations, we screened the isolates by using random amplified polymorphic DNA-PCR profiles and grouped them based on similarities determined by fatty acid methyl ester analysis. Phenotypic characterization, determinations of G+C content, phylogenetic analyses by direct sequencing of 16S rRNA genes, and determinations of pH tolerance were performed with the selected isolates. Although 38 different populations were identified and characterized, the vast majority of the isolates were gram positive with high G+C contents and were affiliated with three distinct groups, namely, strains closely related to the species
Dietzia natrolimnae
(32% of the isolates), to
Frigoribacterium
/
Clavibacter
lineages (29% of the isolates), and to the type strain of
Microbacterium kitamiense
(20% of the isolates). Other isolates were phylogenetically related to strains of the genera
Agrococcus
,
Leifsonia
,
Kytococcus
,
Janibacter
,
Kocuria
,
Rothia
,
Nesterenkonia
,
Citrococcus
,
Micrococcus
,
Actinomyces
,
Rhodococcus
,
Bacillus
, and
Staphylococcus
. Only five isolates were gram negative: one was related to the
Sphingobacteria
lineage and the other four were related to the
α-Proteobacteria
lineage. Despite the pH of the environment, the vast majority of the populations were alkali tolerant, and only two strains were able to grow at pH 11.
Novel Type of Heme-Dependent Oxygenase Catalyzes Oxidative Cleavage of Rubber (Poly-cis-1,4-Isoprene)
Authors: Braaz Reinhard , Fischer Peter , Jendrossek Dieter 
Published: December 2004

ABSTRACTAn extracellular protein with strong absorption at 406 nm was purified from cell-free culture fluid of latex-grownXanthomonassp. strain 35Y. This protein was identical to the gene product of a recently characterized gene cloned fromXanthomonassp., as revealed by determination ofm/zvalues and sequencing of selected isolated peptides obtained after trypsin fingerprint analysis. The purified protein degraded both natural rubber latex and chemosynthetic poly(cis-1,4-isoprene) in vitro by oxidative cleavage of the double bonds of poly(cis-1,4-isoprene). 12-Oxo-4,8-dimethyltrideca-4,8-diene-1-al (m/z236) was identified and unequivocally characterized as the major cleavage product, and there was a homologous series of minor metabolites that differed from the major degradation product only in the number of repetitive isoprene units between terminal functions, CHO-CH2— and —CH2-COCH3. An in vitro enzyme assay for oxidative rubber degradation was developed based on high-performance liquid chromatography analysis and spectroscopic detection of product carbonyl functions after derivatization with dinitrophenylhydrazone. Enzymatic cleavage of rubber by the purified protein was strictly dependent on the presence of oxygen; it did not require addition of any soluble cofactors or metal ions and was optimal around pH 7.0 at 40°C. Carbon monoxide and cyanide inhibited the reaction; addition of catalase had no effect, and peroxidase activity could not be detected. The purified protein was specific for natural rubber latex and chemosynthetic poly(cis-1,4-isoprene). Analysis of the amino acid sequence deduced from the cloned gene (roxA[rubber oxygenase]) revealed the presence of two heme-binding motifs (CXXCH) for covalent attachment of heme to the protein. Spectroscopic analysis confirmed the presence of heme, and approximately 2 mol of heme per mol of RoxA was found.
Cadmium-Responsive Thiols in the Ectomycorrhizal Fungus
Paxillus involutus
Authors: Courbot Mikael , Diez Laurent , Ruotolo Roberta , Chalot Michel , Leroy Pierre 
Published: December 2004

ABSTRACT

Molecular and cellular mechanisms underlying the sustained metal tolerance of ectomycorrhizal fungi are largely unknown. Some of the main mechanisms involved in metal detoxification appear to involve the chelation of metal ions in the cytosol with thiol-containing compounds, such as glutathione, phytochelatins, or metallothioneins. We used an improved high-performance liquid chromatography method for the simultaneous measurement of thiol-containing compounds from cysteine and its derivatives (γ-glutamylcysteine, glutathione) to higher-molecular-mass compounds (phytochelatins). We found that glutathione and γ-glutamylcysteine contents increased when the ectomycorrhizal fungus
Paxillus involutus
was exposed to cadmium. An additional compound with a 3-kDa molecular mass, most probably related to a metallothionein, increased drastically in mycelia exposed to cadmium. The relative lack of phytochelatins and the presence of a putative metallothionein suggest that ectomycorrhizal fungi may use a different means to tolerate heavy metals, such as Cd, than do their plant hosts.
Shear Rate Moderates Community Diversity in Freshwater Biofilms
Authors: Rickard Alexander H. , McBain Andrew J. , Stead Amy T. , Gilbert Peter 
Published: December 2004

ABSTRACT

The development of freshwater multispecies biofilms at solid-liquid interfaces occurs both in quiescent waters and under conditions of high shear rates. However, the influence of hydrodynamic shear rates on bacterial biofilm diversity is poorly understood. We hypothesized that different shear rates would significantly influence biofilm diversity and alter the relative proportions of coaggregating and autoaggregating community isolates. In order to study this hypothesis, freshwater biofilms were developed at five shear rates (<0.1 to 305 S
−1
) in a rotating concentric cylinder reactor fed with untreated potable water. Eubacterial diversity was assessed by denaturing gradient gel electrophoresis (DGGE) and culturing on R2A agar. Fifty morphologically distinct biofilm strains and 16 planktonic strains were isolated by culturing and identified by partial 16S rRNA gene sequencing, and their relatedness was determined by the construction of a neighbor-joining phylogenetic tree. Phylogenetic and DGGE analyses showed an inverse relationship between shear rate and bacterial diversity. An in vitro aggregation assay was used to assess the relative proportions of coaggregating and autoaggregating species from each biofilm. The highest proportion of autoaggregating bacteria was present at high shear rates (198 to 305 S
−1
). The intermediate shear rate (122 S
−1
) selected for the highest proportion of coaggregating bacteria (47%, or 17 of a possible 36 coaggregation interactions). Under static conditions (<0.1 S
−1
), 41 (33%) of a possible 125 coaggregation interactions were positive. Few coaggregation (3.3%) or autoaggregation (25%) interactions occurred between the 16 planktonic strains. In conclusion, these data show that shear rates affect biofilm diversity as well as the relative proportions of aggregating bacteria.
Shedding Patterns of Verocytotoxin-ProducingEscherichia coliStrains in a Cohort of Calves and Their Dams on a Scottish Beef Farm
Authors: Shaw D. J. , Jenkins C. , Pearce M. C. , Cheasty T. , Gunn G. J. , Dougan G. , Smith H. R. , Woolhouse M. E. J. , Frankel G. 
Published: December 2004

ABSTRACTRectal fecal samples were taken once a week from 49 calves on the same farm. In addition, the dams of the calves were sampled at the time of calf birth and at the end of the study. Strains of verocytotoxin-producingEscherichia coli(VTEC) were isolated from these samples by using PCR and DNA probe hybridization tests and were characterized with respect to serotype, verocytotoxin gene (vtx) type, and the presence of the intimin (eae) and hemolysin (ehxA) genes. A total of 170 VTEC strains were isolated during 21 weeks from 130 (20%) of 664 samples from calves and from 40 (47%) of 86 samples from their dams. The characteristics of the calf strains differed from those strains isolated from the dams with respect to verocytotoxin 2 and the presence of theeaegene. In addition, no calf shed the same VTEC serogroup (excluding O?) as its dam at birth or at the end of the study. The most frequently detected serogroups in calves were serogroup O26 and provisional serogroup E40874 (VTEC O26 was found in 25 calves), whereas in dams serogroup O91 and provisional serogroup E54071 were the most common serogroups. VTEC O26 shedding appeared to be associated with very young calves and declined as the calves aged, whereas VTEC O2 shedding was associated with housing of the animals. VTEC O26 strains from calves were characterized by the presence of thevtx1,eae, andehxAgenes, whereasvtx2was associated with VTEC O2 and provisional serogroup E40874. The high prevalence of VTEC O26 and of VTEC strains harboring theeaegene in this calf cohort is notable because of the association of the O26 serogroup and the presence of theeaegene with human disease. No association between calf diarrhea and any of the VTEC serogroups was identified.
Cyclo(l-Leucyl-l-Prolyl) Produced byAchromobacter xylosoxidansInhibits Aflatoxin Production byAspergillus parasiticus
Authors: Yan Pei-Sheng , Song Yuan , Sakuno Emi , Nakajima Hiromitsu , Nakagawa Hiroyuki , Yabe Kimiko 
Published: December 2004

ABSTRACTAflatoxins are potent carcinogenic and toxic substances that are produced primarily byAspergillus flavusandAspergillus parasiticus. We found that a bacterium remarkably inhibited production of norsolorinic acid, a precursor of aflatoxin, byA. parasiticus. This bacterium was identified asAchromobacter xylosoxidansbased on its 16S ribosomal DNA sequence and was designatedA. xylosoxidansNFRI-A1.A. xylosoxidansstrains commonly showed similar inhibition. The inhibitory substance(s) was excreted into the medium and was stable after heat, acid, or alkaline treatment. Although the bacterium appeared to produce several inhibitory substances, we finally succeeded in purifying a major inhibitory substance from the culture medium using Diaion HP20 column chromatography, thin-layer chromatography, and high-performance liquid chromatography. The purified inhibitory substance was identified as cyclo(l-leucyl-l-prolyl) based on physicochemical methods. The 50% inhibitory concentration for aflatoxin production byA. parasiticusSYS-4 (= NRRL2999) was 0.20 mg ml−1, as determined by the tip culture method. High concentrations (more than 6.0 mg ml−1) of cyclo(l-leucyl-l-prolyl) further inhibited fungal growth. Similar inhibitory activities were observed with cyclo(d-leucyl-d-prolyl) and cyclo(l-valyl-l-prolyl), whereas cyclo(d-prolyl-l-leucyl) and cyclo(l-prolyl-d-leucyl) showed weaker activities. Reverse transcription-PCR analyses showed that cyclo(l-leucyl-l-prolyl) repressed transcription of the aflatoxin-related genesaflR,hexB,pksL1, anddmtA. This is the first report of a cyclodipeptide that affects aflatoxin production.
Effects of Climate on Incidence of
Campylobacter
spp. in Humans and Prevalence in Broiler Flocks in Denmark
Authors: Patrick Mary Evans , Christiansen Lasse Engbo , Wainø Michael , Ethelberg Steen , Madsen Henrik , Wegener Henrik Caspar 
Published: December 2004

ABSTRACT

Campylobacter
infections are increasing and pose a serious public health problem in Denmark. Infections in humans and broiler flocks show similar seasonality, suggesting that climate may play a role in infection. We examined the effects of temperature, precipitation, relative humidity, and hours of sunlight on
Campylobacter
incidence in humans and broiler flocks by using lag dependence functions, locally fitted linear models, and cross validation methods. For humans, the best model included average temperature and sunlight 4 weeks prior to infection; the maximum temperature lagged at 4 weeks was the best single predictor. For broilers, the average and maximum temperatures 3 weeks prior to slaughter gave the best estimate; the average temperature lagged at 3 weeks was the best single predictor. The combined effects of temperature and sunlight or the combined effects of temperature and relative humidity predicted the incidence in humans equally well. For broiler flock incidence these factors explained considerably less. Future research should focus on elements within the broiler environment that may be affected by climate, as well as the interaction of microclimatic factors on and around broiler farms. There is a need to quantify the contribution of broilers as a source of campylobacteriosis in humans and to further examine the effect of temperature on human incidence after this contribution is accounted for. Investigations should be conducted into food consumption and preparation practices and poultry sales that may vary by season.
Novel, Attached, Sulfur-Oxidizing Bacteria at Shallow Hydrothermal Vents Possess Vacuoles Not Involved in Respiratory Nitrate Accumulation
Authors: Kalanetra Karen M. , Huston Sherry L. , Nelson Douglas C. 
Published: December 2004

ABSTRACT

Novel, vacuolate sulfur bacteria occur at shallow hydrothermal vents near White Point, Calif. There, these filaments are attached densely to diverse biotic and abiotic substrates and extend one to several centimeters into the surrounding environment, where they are alternately exposed to sulfidic and oxygenated seawater. Characterizations of native filaments collected from this location indicate that these filaments possess novel morphological and physiological properties compared to all other vacuolate bacteria characterized to date. Attached filaments, ranging in diameter from 4 to 100 μm or more, were composed of cylindrical cells, each containing a thin annulus of sulfur globule-filled cytoplasm surrounding a large central vacuole. A near-complete 16S rRNA gene sequence was obtained and confirmed by fluorescent in situ hybridization to be associated only with filaments having a diameter of 10 μm or more. Phylogenetic analysis indicates that these wider, attached filaments form within the gamma proteobacteria a monophyletic group that includes all previously described vacuolate sulfur bacteria (the genera
Beggiatoa
,
Thioploca
, and
Thiomargarita
) and no nonvacuolate genera. However, unlike for all previously described vacuolate bacteria, repeated measurements of cell lysates from samples collected over 2 years indicate that the attached White Point filaments do not store internal nitrate. It is possible that these vacuoles are involved in transient storage of oxygen or contribute to the relative buoyancy of these filaments.
Isolation and Characterization of Novel Marine-Derived Actinomycete Taxa Rich in Bioactive Metabolites
Authors: Magarvey Nathan A. , Keller Jessica M. , Bernan Valerie , Dworkin Martin , Sherman David H. 
Published: December 2004

ABSTRACT

A unique selective enrichment procedure has resulted in the isolation and identification of two new genera of marine-derived actinobacteria. Approximately 90% of the microorganisms cultured by using the presented method were from the prospective new genera, a result indicative of its high selectivity. In this study, 102 actinomycetes were isolated from subtidal marine sediments collected from the Bismarck Sea and the Solomon Sea off the coast of Papua New Guinea. A combination of physiological parameters, chemotaxonomic characteristics, distinguishing 16S rRNA gene sequences, and phylogenetic analysis based on 16S rRNA genes provided strong evidence for the two new genera (represented by strains of the PNG1 clade and strain UMM518) within the family
Micromonosporaceae
. Biological activity testing of fermentation products from the new marine-derived actinomycetes revealed that several had activities against multidrug-resistant gram-positive pathogens, malignant cells, and vaccinia virus replication.
Analysis of Proteasome-Dependent Proteolysis in
Haloferax volcanii
Cells, Using Short-Lived Green Fluorescent Proteins
Authors: Reuter Christopher J. , Maupin-Furlow Julie A. 
Published: December 2004

ABSTRACT

Proteasomes are energy-dependent proteases that are central to the quality control and regulated turnover of proteins in eukaryotic cells. Dissection of this proteolytic pathway in archaea, however, has been hampered by the lack of substrates that are easily detected in whole cells. In the present study, we developed a convenient reporter system by functional expression of a green fluorescent protein variant with C-terminal fusions in the haloarchaeon
Haloferax volcanii
. The levels of this reporter protein correlated with whole-cell fluorescence that was readily detected in culture. Accumulation of the reporter protein was dependent on the sequence of the C-terminal amino acid fusion, as well as the presence of an irreversible, proteasome-specific inhibitor (
clasto
-lactacystin β-lactone). This inhibitor was highly specific for
H. volcanii
20S proteasomes, with a

K
i

of ∼40 nM. In contrast, phenylmethanesulfonyl fluoride did not influence the levels of fluorescent reporter protein or inhibit 20S proteasomes. Together, these findings provide a powerful tool for the elucidation of protein substrate recognition motifs and the identification of new genes which may be involved in the proteasome pathway of archaea.
Nucleotide Sequences, Genetic Organization, and Distribution of pEU30 and pEL60 from
Erwinia amylovora
Authors: Foster Gayle C. , McGhee Gayle C. , Jones Alan L. , Sundin George W. 
Published: December 2004

ABSTRACT

The nucleotide sequences, genetic organization, and distribution of plasmids pEU30 (30,314 bp) and pEL60 (60,145 bp) from the plant pathogen
Erwinia amylovora
are described. The newly characterized pEU30 and pEL60 plasmids inhabited strains isolated in the western United States and Lebanon, respectively. The gene content of pEU30 resembled plasmids found in plant-associated bacteria, while that of pEL60 was most similar to IncL/M plasmids inhabiting enteric bacteria.
Reevaluation and Reduction of a PCR Bias Caused by Reannealing of Templates
Authors: Kurata Shinya , Kanagawa Takahiro , Magariyama Yukio , Takatsu Kyoko , Yamada Kazutaka , Yokomaku Toyokazu , Kamagata Yoichi 
Published: December 2004

ABSTRACT
We reevaluated the bias toward a 1:1 ratio of products in multitemplate PCR used in ecological studies and showed that the template reannealing at the annealing step would not cause the bias; however, the preferential homoduplex formation during temperature decrease from denaturation to annealing step would cause the bias.
Role for Compatible Solutes Glycine Betaine and
l
-Carnitine in Listerial Barotolerance
Authors: Smiddy Mary , Sleator Roy D. , Patterson Margaret F. , Hill Colin , Kelly Alan L. 
Published: December 2004

ABSTRACT

Increased listerial barotolerance at elevated osmolarity is attributed, in part, to the presence of accumulated betaine and
l
-carnitine. The percentage of listerial survival following exposure to 400 MPa for 5 min increased from 0.008 to 0.02% with added
l
-carnitine (5 mM) and to 0.05% with added betaine (5 mM). Furthermore, listerial cells incapable of transporting compatible solutes fail to adapt to high pressure at elevated osmolarity.
Resistance of Solid-Phase U(VI) to Microbial Reduction during In Situ Bioremediation of Uranium-Contaminated Groundwater
Authors: Ortiz-Bernad Irene , Anderson Robert T. , Vrionis Helen A. , Lovley Derek R. 
Published: December 2004

ABSTRACT
Speciation of solid-phase uranium in uranium-contaminated subsurface sediments undergoing uranium bioremediation demonstrated that although microbial reduction of soluble U(VI) readily immobilized uranium as U(IV), a substantial portion of the U(VI) in the aquifer was strongly associated with the sediments and was not microbially reducible. These results have important implications for in situ uranium bioremediation strategies.
Effects of Expression of
hemA
and
hemB
Genes on Production of Porphyrin in
Propionibacterium freudenreichii
Authors: Piao Yongzhe , Kiatpapan Pornpimon , Yamashita Mitsuo , Murooka Yoshikatsu 
Published: December 2004

ABSTRACT

The genus
Propionibacterium
has a wide range of probiotic activities that are exploited in dairy and fermentation systems such as cheeses, propionic acid, and tetrapyrrole compounds. In order to improve production of tetrapyrrole compounds, we expressed the
hemA
gene, which encodes δ-aminolevulinic acid (ALA) synthase from
Rhodobacter sphaeroides
, and the
hemB
gene, which encodes porphobilinogen (PBG) synthase from
Propionibacterium freudenreichii
subsp.
shermanii
IFO12424, either monocistronically or polycistronically in strain IFO12426. The recombinant strains accumulated larger amounts of ALA and PBG, with resultant 28- to 33-fold-higher production of porphyrinogens, such as uroporphyrinogen and coproporphyrinogen, than those observed in strain IFO12426, which harbored the shuttle vector pPK705.