Draft genome sequence of potentially dikaryotic black fungus Aureobasidium melanogenum isolated from aircraft

The Ascomycota yeast Aureobasidium melanogenum strain W12 was isolated from an aircraft polymer-coated surface. The genome size is 53,160,883 bp with a G + C content of 50.13%. The genome contains fatty acid transporters, cutinases, hydroxylases, and lipases potentially used for survival on polymer coatings on aircraft.

A Pilot Study of the Effect of Deployment on the Gut Microbiome and Traveler's Diarrhea Susceptibility

Traveler's diarrhea (TD) is a recurrent and significant issue for many travelers including the military. While many known enteric pathogens exist that are causative agents of diarrhea, our gut microbiome may also play a role in TD susceptibility. To this end, we conducted a pilot study of the microbiome of warfighters prior to- and after deployment overseas to identify marker taxa relevant to TD. This initial study utilized full-length 16S rRNA gene sequencing to provide additional taxonomic resolution toward identifying predictive taxa.16S rRNA analyses of pre- and post-deployment fecal samples identified multiple marker taxa as significantly differentially abundant in subjects that reported diarrhea, including Weissella, Butyrivibrio, Corynebacterium, uncultivated Erysipelotrichaceae, Jeotgallibaca, unclassified Ktedonobacteriaceae, Leptolinea, and uncultivated Ruminiococcaceae. The ability to identify TD risk prior to travel will inform prevention and mitigation strategies to influence diarrhea susceptibility while traveling.

A plasmid containing the human metallothionein II gene can function as an antibody-assisted electrophoretic biosensor for heavy metals

Different forms of heavy metals affect biochemical systems in characteristic ways that cannot be detected with typical metal analysis methods like atomic absorption spectrometry. Further, using living systems to analyze interaction of heavy metals with biochemical systems can be laborious and unreliable. To generate a reliable easy-to-use biologically-based biosensor system, the entire human metallothionein-II (MT-II) gene was incorporated into a plasmid (pUC57-MT) easily replicated in Escherichia coli. In this system, a commercial polyclonal antibody raised against human metal-responsive transcription factor-1 protein (MTF-1 protein) could modify the electrophoretic migration patterns (i.e. cause specific decreases in agarose gel electrophoretic mobility) of the plasmid in the presence or absence of heavy metals other than zinc (Zn). In the study here, heavy metals, MTF-1 protein, and polyclonal anti-MTF-1 antibody were used to assess pUC57-MT plasmid antibody-assisted electrophoretic mobility. Anti-MTF-1 antibody bound both MTF-1 protein and pUC57-MT plasmid in a non-competitive fashion such that it could be used to differentiate specific heavy metal binding. The results showed that antibody-inhibited plasmid migration was heavy metal level-dependent. Zinc caused a unique mobility shift pattern opposite to that of other metals tested, i.e. Zn blocked the antibody ability to inhibit plasmid migration, despite a greatly increased affinity for DNA by the antibody when Zn was present. The Zn effect was reversed/modified by adding MTF-1 protein. Additionally, antibody inhibition of plasmid mobility was resistant to heat pre-treatment and trypsinization, indicating absence of residual DNA extraction-resistant bacterial DNA binding proteins. DNA binding by anti-DNA antibodies may be commonly enhanced by xenobiotic heavy metals and elevated levels of Zn, thus making them potentially effective tools for assessment of heavy metal bioavailability in aqueous solutions and fluid obtained from metal implant sites.

Microelectrode array biosensor for studying carbohydrate-mediated interactions

Carbohydrate-mediated host-pathogen interactions are essential to bacterial and viral pathogenesis, and represent an attractive target for the development of antiadhesives to prevent infection. We present a versatile microelectrode array-based platform to investigate carbohydrate-mediated protein and bacterial binding, with the objective of developing a generalizable method for screening inhibitors of host-microbe interactions. Microelectrode arrays are well suited for interrogating biological binding events, including proteins and whole-cells, and are amenable to electrochemical derivitization, facilitating rapid deposition of biomolecules. In this study, we achieve microelectrode functionalization with carbohydrates via controlled polymerization of pyrrole to individual microelectrodes, followed by physisorption of neoglycoconjugates to the polypyrrole-coated electrodes. Bioactivity of the immobilized carbohydrates was confirmed with carbohydrate-binding proteins (lectins) detected by both fluorescent and electrochemical means. The platform's ability to analyze whole-cell binding was demonstrated using strains of Escherichia coli and Salmonella enterica, and the dose-dependent inhibition of S. enterica by a soluble carbohydrate antiadhesive.

A Comparison of 2-part and 3-part Nanoparticle-Based Sensors

There has long been a drive to produce sensors with ever-increasing sensitivity and selectivity, while also achieving robustness and ease of use. Nanoparticle-based sensing approaches have generated a great deal of attention and excitement, because they possess such qualities. For these assays to function properly, it requires the integration of molecular recognition motifs and materials with outstanding optical properties. Aptamers are DNA or RNA sequences that bind analytes with high specificity, which makes them a suitable choice as recognition elements. Changes in the surface plasmon resonance (SPR) of gold nanoparticles (AuNPS) as a function of interparticle distance, has been used as an optical signal to detect the presence of different species in solution by the naked eye. In this work, we coated gold nanoparticles with short oligonucleotides and aptamers for the design of sensors that can be used under different conditions, including salt concentration, pH and temperatures. Three aptamer sensors were developed using this approach 1) riboflavin, as a general indicator of biological activity, 2) ricin, a toxin that is of broad interest, and 3) theophylline, an adenosine antagonist. Our designs are based on two approaches, the first method consisted of the use of two sets of AuNPs, each coated with a short oligonucleotide complementary to a different part of the sequence of the aptamer of interest. Hybridization of the DNA-coated particles (DNA-AuNPs) with the free aptamer produced aggregates, i.e. 3-part design. The second approach consisted of the use of only two sets of DNA-AuNPs, one coated with an aptamer that contains a thiol group in its 5′ end, and the second set of AuNPs coated with a sequence complementary to part of the aptamer. Hybridization of these two sets of particles produced aggregates, i.e. 2-part design. In both cases, the presence of the analyte promoted a change in the conformation of the aptamer, which caused the dehybridization of the complementary sequences. This conformational change of the aptamer upon binding of the analyte produced the dissociation of the nanoparticle aggregates, which is translated into a change in the color of the suspensions from blue to red. In this presentation, we will compare the advantages and disadvantages associated with a 3-part versus a 2-part nanoparticle-oligonucleotide reporting assay.

Identification of upper respiratory tract pathogens using electrochemical detection on an oligonucleotide microarray

Bacterial and viral upper respiratory infections (URI) produce highly variable clinical symptoms that cannot be used to identify the etiologic agent. Proper treatment, however, depends on correct identification of the pathogen involved as antibiotics provide little or no benefit with viral infections. Here we describe a rapid and sensitive genotyping assay and microarray for URI identification using standard amplification and hybridization techniques, with electrochemical detection (ECD) on a semiconductor-based oligonucleotide microarray. The assay was developed to detect four bacterial pathogens (Bordetella pertussis, Streptococcus pyogenes, Chlamydia pneumoniae and Mycoplasma pneumoniae) and 9 viral pathogens (adenovirus 4, coronavirus OC43, 229E and HK, influenza A and B, parainfluinza types 1, 2, and 3 and respiratory syncytial virus. This new platform forms the basis for a fully automated diagnostics system that is very flexible and can be customized to suit different or additional pathogens. Multiple probes on a flexible platform allow one to test probes empirically and then select highly reactive probes for further iterative evaluation. Because ECD uses an enzymatic reaction to create electrical signals that can be read directly from the array, there is no need for image analysis or for expensive and delicate optical scanning equipment. We show assay sensitivity and specificity that are excellent for a multiplexed format.

Use of semiconductor-based oligonucleotide microarrays for influenza a virus subtype identification and sequencing

In the face of concerns over an influenza pandemic, identification of virulent influenza A virus isolates must be obtained quickly for effective responses. Rapid subtype identification, however, is difficult even in well-equipped virology laboratories or is unobtainable in the field under more austere conditions. Here we describe a genome assay and microarray design that can be used to rapidly identify influenza A virus hemagglutinin subtypes 1 through 15 and neuraminidase subtypes 1 through 9. Also described is an array-based enzymatic assay that can be used to sequence portions of both genes or any other sequence of interest.

TaqMan PCR for detection of Vibrio cholerae O1, O139, non-O1, and non-O139 in pure cultures, raw oysters, and synthetic seawater

Vibrio cholerae is recognized as a leading human waterborne pathogen. Traditional diagnostic testing for Vibrio is not always reliable, because this bacterium can enter a viable but nonculturable state. Therefore, nucleic acid-based tests have emerged as a useful alternative to traditional enrichment testing. In this article, a TaqMan PCR assay is presented for quantitative detection of V. cholerae in pure cultures, oysters, and synthetic seawater. Primers and probe were designed from the nonclassical hemolysin (hlyA) sequence of V. cholerae strains. This probe was applied to DNA from 60 bacterial strains comprising 21 genera. The TaqMan PCR assay was positive for all of the strains of V. cholerae tested and negative for all other species of Vibrio tested. In addition, none of the other genera tested was amplified with the TaqMan primers and probe used in this study. The results of the TaqMan PCR with raw oysters and spiked with V. cholerae serotypes O1 and O139 were comparable to those of pure cultures. The sensitivity of the assay was in the range of 6 to 8 CFU g(-1) and 10 CFU ml(-1) in spiked raw oyster and synthetic seawater samples, respectively. The total assay could be completed in 3 h. Quantification of the Vibrio cells was linear over at least 6 log units. The TaqMan probe and primer set developed in this study can be used as a rapid screening tool for the presence of V. cholerae in oysters and seawater without prior isolation and characterization of the bacteria by traditional microbiological methods.

Bacteria associated with processed crawfish and potential toxin production by Clostridium botulinum type E in vacuum-packaged and aerobically packaged crawfish tails

Refrigerated vacuum-packaged storage has been shown to increase significantly the shelf life of fresh fish and seafood products, but the effect, if any, on the outgrowth and toxin production of Clostridium botulinum type E on cooked crawfish is unknown. Microflora associated with live crawfish reflect the microbial populations of the harvest water and sediments in which they are living. The presence or absence of specific pathogens in either vacuum-packaged or air-permeable bags of cooked crawfish have not been thoroughly evaluated. This study evaluates the potential survival and outgrowth of biological hazards in both vacuum-packaged and air-permeable-packaged cooked crawfish held at 4 and 10 degrees C for 30 days. During shelf-life studies of vacuum-packaged and air-permeable-bagged cooked crawfish, a total of 31 bacterial species were isolated and identified from crawfish samples using both selective and nonselective media. The only pathogens isolated from both vacuum-packed and air-permeable bags of processed crawfish samples during shelf-life studies were strains of Aeromonas hydrophila and Staphylococcus aureus. C. botulinum type E and Clostridium perfringens species were not isolated from any of the uninoculated crawfish samples. Cooked crawfish were inoculated with 10(3) C. botulinum type E spores per g of crawfish tail meat to determine whether cooked crawfish tails would support the growth of C. botulinum type E strains and produce toxin at refrigerated temperatures. Spore-inoculated crawfish tails were vacuum packaged in both a high barrier film and an air-permeable bag and stored at 4 degrees C and 10 degrees C for 30 days. C. botulinum toxin E was not detected in any of the spore-inoculated packages throughout the shelf-life study until day 30. Microbiological data from this study should be useful in the development and implementation of the hazard analysis and critical control point plans for processed crawfish tails.

Reduction of endogenous bacteria associated with catfish fillets using the Grovac process

Fresh catfish (Ictalurus punctatus) fillets are known to be contaminated with a large number of spoilage and pathogenic bacteria. The Grovac method, a new patented (U.S. 5,543,163) process, was evaluated for its efficacy in reducing the number of pathogens and spoilage microorganisms associated with food. This process involves using a processing solution containing ascorbic acid (AA) and sodium chloride (NaCl), vacuum, and tumbling. A total of 51 bacterial isolates were isolated and identified from whole catfish and catfish fillets using both selective and nonselective media, phenotypic tests, and the Vitek identification system. Psychrotrophic foodborne pathogens included: Aeromonas hydrophila, Escherichia coli, Listeria sp., Plesiomonas shigelloides, Proteus sp., Staphylococcus aureus, and Vibrio parahaemolyticus. High aerobic plate counts (2.6 x 10(7) CFU/g) for catfish fillets indicated that fillets were heavily contaminated during processing of catfish. The Grovac process showed that various treatment combinations of AA and NaCl resulted in a 1.2 to 2.3 CFU/g log reduction of microbial counts associated with catfish fillets. The effectiveness of the process may be related to the synergistic effect of tumbling, AA, NaCl, and vacuum. These results suggested that the Grovac process could be used as an alternative processing procedure to reduce microbial populations associated with catfish fillets and may be useful to improve the shelf-life and food safety of the product. Microbiological data from this study will be used for the development of a hazard analysis for the implementation of the hazard analysis critical control point program for processed catfish fillets.

Isolation and Purification of Colicin ECL 12, a Bacteriocin That Inhibits Strains of Escherichia coli O157:H7 †

A swine fecal isolate, identified as Escherichia coli ECL12, was found to produce an antimicrobial substance designated as colicin ECL12. Colicin ECL12 was inhibitory against 20 strains of E. coli O157:H7 previously isolated from both human and bovine feces. Identification of the producer strain was determined phenotypically by biochemical and morphological tests. Colicin ECL12 was sensitive to several proteolytic enzymes. Adsorption of colicin ECL12 to sensitive cells of E. coli O157:H7 was bactericidal, resulting in a 2 log reduction in viable cell counts. Colicin ECL12 was purified from strain ECL12 by cell extraction and ion-exchange chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of colicin ECL12 resolved a single protein with a molecular weight of approximately 65,000.

Isolation and Purification of Enterocin EL1, a Bacteriocin Produced by a Strain of Enterococcus faecium †

A meat isolate, identified as Enterococcus faecium L1, was found to produce a bacteriocin designated enterocin EL1 Enterocin EL1 was active against a narrow spectrum of microorganisms, inhibiting all tested strains of Listeria . Identification of the producer strain was determined phenotypically by biochemical and morphological tests. Enterocin EL1 was heat stable, sensitive to several proteolytic enzymes, and stable from pH 2 to 11. Adsorption of the bacteriocin to producer cells was dependent on ionic interaction of the bacteriocin and the cell surface at various pHs. By changing the pH of the extraction buffer, enterocin EL1 was extracted from E. faecium L1 cells in a concentrated form. Enterocin EL1 isolated by cell extraction was resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis as a protein with an approximate molecular weight of 2,300. Partially purified enterocin EL1 added to sensitive cells of Listeria ivanovii was bactericidal; however, the bacteriocin did not inhibit the producer strain L1.

Inhibition of psychrotrophic organisms by propionicin PLG-1, a bacteriocin produced by Propionibacterium thoenii

Propionibacterium thoenii strain P127, which produces the bacteriocin propionicin PLG-1, was grown in a skim milk medium and produced bacteriocin in that medium. No bacteriocin activity was detected in skim milk medium in which strain P127-1, a bacteriocin-negative variant of strain P127, had been grown. Five psychrotrophic spoilage or pathogenic organisms (one strain each of Listeria monocytogenes, Pseudomonas fluorescens, Vibrio parahaemolyticus, Yersinia enterocolitica, and one strain of Corynebacterium sp.) were incubated for 24 h in laboratory medium, nonfermented skim milk, and skim milk that had been fermented by strain P127 or P127-1. Strains were inhibited only in the skim milk fermented by strain P127, as evidenced by loss in numbers of viable cells after 24 h at 10 degrees C and less growth than in other media after 24 h at optimal growth temperatures. Growth of selected strains was delayed or slowed during prolonged incubation (21 d) at 10 degrees C. Propionicin PLG-1 shows promise as a preservative for food products.

Isolation and purification of propionicin PLG-1, a bacteriocin produced by a strain of Propionibacterium thoenii

Production of propionicin PLG-1 by Propionibacterium thoenii P127 was pH dependent, with maximal activity detected in supernatants of cultures grown at pH 7.0 Propionicin PLG-1 was purified by ion-exchange chromatography and isoelectric focusing. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of propionicin PLG-1 purified through isoelectric focusing resolved a protein band with a molecular weight of 10,000. Propionicin PLG-1 was bactericidal to sensitive cells, demonstrating single-hit kinetics. The producing strain harbored a single plasmid (pLG1) with an approximate size of 250 kb. Preliminary data indicate that both propionicin PLG-1 and immunity to the bacteriocin are encoded on the chromosome. Exposure of strain P127 to acriflavine or to N-methyl-N'-nitro-N-nitrosoguanidine yielded isolates that no longer produced bacteriocin activity and isolates that were cured of the plasmid. However, loss of bacteriocin production was not correlated with loss of the plasmid. Isolates cured of the plasmid were phenotypically identical to plasmid-bearing cells in fermentation patterns, pigment production, and growth characteristics.

Partial Purification and Characterization of a Bacteriocin Produced by Propionibacterium thoenii

A partially purified bacteriocin produced by Propionibacterium thoenii designated propionicin PLG-1 was found to be active against closely related species and exhibited a broad spectrum of activity against other microorganisms. Propionicin PLG-1 was found to be heat labile, sensitive to several proteolytic enzymes, and stable at pH 3 to 9. Propionicin PLG-1 was isolated from solid medium, partially purified by ammonium sulfate precipitation, and purified further by gel filtration. Gel filtration experiments revealed that bacteriocin PLG-1 was present as two different protein aggregates with apparent molecular weights of more than 150,000 and approximately 10,000. Resolution of these protein aggregates by sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed the presence of a protein common to both with an apparent molecular weight of 10,000.