Identification of Mycoplasmas using a fluorophore-free microarray and infrared chemical imaging (IRCI).

A novel application of mid-infrared chemical imaging (IRCI) for the fluorophore-free detection and identification of mycoplasma species is reported for the first time. The PCR-amplified biotinylated targets hybridized to microarray probes were treated with streptavidin-gold nanoparticles followed by silver enhancement. This modification has the potential to expand the implementation of DNA microarray techniques in laboratories involved in the detection of cell substrates, other biological products, and clinical materials for the presence of mycoplasmas.

Effect of dehydrated storage on the survival of Francisella tularensis in infant formula.

Francisella tularensis is a Gram-negative bacterium that can cause gastrointestinal or oropharyngeal tularemia in humans from ingestion of contaminated food or water. Despite the potential for accidental or intentional contamination of foods with F. tularensis, there are few studies on the long-term survivability of this organism in food matrices. Infant formula has previously been implicated as a vehicle for the transmission of a variety of bacterial pathogens in infants. In this study, we investigated the survival of F. tularensis in dehydrated infant formula under various storage conditions. F. tularensis was stored for up to 12 weeks in dehydrated infant formula in an ambient air, dry or nitrogen atmosphere. Viable counts of fresh F. tularensis at 12 weeks in infant formula revealed a 4.15, 3.37 and 3.72-log decrease in ambient air, dry and nitrogen atmosphere, respectively. D-values were calculated (in weeks) as 3.99, 4.68 and 4.47 in air, dry and nitrogen atmosphere, respectively.

Application of a novel hydrophilic infrared-transparent membrane to the differentiation between microcolonies of Enterobacter sakazakii and Klebsiella pneumoniae.

A proof-of-concept study is reported for the differentiation between microcolonies of Enterobacter sakazakii and Klebsiella pneumoniae by means of a novel sample preparation for infrared (IR) analysis. A disposable, IR-transparent, microporous (0.2-microm pores), hydrophobic, polyethylene (PE) membrane (51 microm thick) was plasma treated under an oxygen atmosphere and used to (i) filter (or print microarrays of) dilute aqueous foodborne bacterial suspensions and (ii) subsequently grow bacterial microcolonies when the treated, hydrophilic PE membrane was placed over brain heart infusion agar medium and incubated. Because this unique membrane is transparent to IR light, isolated microcolonies (200 microm) of bacterial cells grown on this PE substrate for the first time could be directly fingerprinted by IR microspectroscopy in the transmission mode. Hence, time-consuming bacterial cell transfer from culture plates to an IR sample holder for subsequent measurement by IR spectroscopy was eliminated. Multivariate analysis of the observed IR spectra for microcolonies allowed the rapid differentiation between E. sakazakii and K. pneumoniae.

Molecular identification of Yersinia enterocolitica isolated from pasteurized whole milk using DNA microarray chip hybridization.

A DNA microarray chip of four virulence genes and 16S ribosomal DNA gene conserved region among all Gram negative species, including Yersinia, as a positive control was developed and evaluated using 22 Yersinia enterocolitica isolates. Eight different oligonucleotide probes (oligoprobes) with an average size of 22 bp, complementary to the unique sequences of each gene, were designed and immobilized on the surface of chemically modified slides. Multiplex PCR was used to simultaneously amplify DNA target regions of all five genes, and single stranded DNA (ssDNA) samples for microarray analysis were prepared by using a primer extension of amplicons in the presence of one primer of all genes. The presence of genes in Y. enterocolitica was established by hybridization of the fluorescently labeled ssDNA representing different samples of the microarray gene-specific oligoprobes and confirmed by PCR. Results of the study showed specificity of genotyping Y. enterocolitica using multiple microarray-based assays. Final validation of the chip's ability to identify Y. enterocolitica genes from adulterated pasteurized whole milk was confirmed and successful. The limit of chip detection of virulence genes in pasteurized whole milk was found to be 1000 CFU per hybridization.

Genotyping of Clostridium perfringens toxins using multiple oligonucleotide microarray hybridization.

A microarray-based method for characterization of six Clostridium perfringens toxin genes: iA (iota toxin), cpa (alpha toxin), cpe (enterotoxin E), etxD (epsilon toxin), cpb1 (beta toxin 1),and cpb2 (beta toxin 2) was developed and evaluated using 17 C. perfringens isolates. Three individual oligonucleotide probes (oligoprobes), complementary to the unique sequences of each toxin gene, were designed and immobilized on a surface of aldehyde-coated glass slides. Multiplex PCR was used to simultaneously amplify DNA target regions of all six genes. Single-stranded DNA (ssDNA) samples for microarray analysis were prepared by following a primer extension of amplicons in the presence of one primer. Fluorescent moieties (Cy3) were incorporated into the ssDNA by chemical modification of guanine bases. The presence of toxin genes in C. perfringens was established by hybridization of the fluorescently labeled ssDNA representing different samples to the microarray gene-specific oligoprobes. Results of the study showed sensitivity and specificity of genotyping C. perfringens using multiple microarray-based assays.

Application of a disposable transparent filtration membrane to the infrared spectroscopic discrimination among bacterial species.

This study describes the application of filtration, infrared spectroscopy, and multivariate analysis to the identification of 10 foodborne bacterial species. The bacteria were applied by filtration to a disposable optical membrane that is transparent to infrared radiation. The filtration step was rapid (2 min). Observed cellular infrared spectra were unique and were used to discriminate among the different species. A dataset for the 10 bacterial species investigated was successfully used to correctly identify unknowns included in the dataset.

Characterization of site-directed mutants in manganese-stabilizing protein (MSP) of Synechocystis sp. PCC6803 unable to grow photoautotrophically in the absence of cytochrome c-550.

To investigate the interaction between the manganese-stabilizing protein (MSP) and cytochrome c-550 (cyt. c-550) of the photosystem II (PSII) complex in the cyanobacterium Synechocystis sp. PCC6803, three site-directed amino acid substitution mutants in MSP (MSP-D159N, MSP-R163L, MSP-D 159N/R 163L) were created by single and double amino acid substitution mutagenesis. The modified psbO genes encoding the mutants forms of MSP were used to transform a single-deletion mutant deltapsO strain lacking MSP as well as a double-deletion strain deltapsbO:deltapsbV lacking both MSP and cyt. c-550. The mutant forms of MSP were expressed in each case and all permitted autotrophic growth in strains expressing cyt. c-550. However, when the MSP mutations were introduced into a strain which lacks cyt. c-550 (deltapsbV), the two single amino acid substitution mutants (deltapsbV:MSP-D159N and deltapsbV:MSP-R 163L) failed to grow photoautotrophically. These strains exhibited coupled O2-evolving activity of 68-77% compared to the wild-type control using CO2 as an electron acceptor and maximal uncoupled O2-evolution rates of 42-57% using 2,6-dichloro-p-benzoquinone (DCBQ) as an artificial electron acceptor. Interestingly, when the two amino acid substitutions were together in the absence of cyt. c-550 (deltapsbV:MSP-D159N/R163L), the mutant grew photoautotrophically and the oxygen-evolving activities were higher than in the single mutants. This indicates that the MSP-D159N mutant suppresses the non-autotrophic phenotype of MSP-R163L (or vice versa) in the absence of cyt. c-550. The possibilities of a direct (ionic) or indirect interaction between D159 and R163 of MSP are discussed.

Deoxyribonuclease activity in Selenomonas ruminantium, Streptococcus bovis, and Bacteroides ovatus.

Six Selenomonas ruminantium strains (132c, JW13, SRK1, 179f, 5521c1, and 5934e), Streptococcus bovis JB1, and Bacteroides ovatus V975 were examined for nuclease activity as well as the ability to utilize nucleic acids, ribose, and 2-deoxyribose. Nuclease activity was detected in sonicated cells and culture supernatants for all bacteria except S. ruminantium JW13 and 179f sonicated cells. S. ruminantium strains were able to utilize several deoxyribonucleosides, while S. bovis JB1 and B. ovatus V975 showed little or no growth on all deoxyribonucleosides. When S. ruminantium strains 5934e, 132c, JW13, and SRK1 were incubated in medium that contained 15 mm ribose, the major end products were acetate, propionate, and lactate. S. ruminantium 5521c1 and S. bovis JB1 did not grow on ribose, and none of the S. ruminantium strains or S. bovis JB1 grew on 15 mm 2-deoxyribose. In contrast, B. ovatus V975 was able to grow on ribose and 2-deoxyribose. In conclusion, all S. ruminantium strains, S. bovis JB1, and B. ovatus V975 had nuclease activity. However, not all bacteria were able to utilize deoxyribonucleosides, ribose, or 2-deoxyribose.

Fermentation of fenugreek fiber, psyllium husk, and wheat bran by Bacteroides ovatus V975.

The objective of this study was to evaluate the ability of the human colonic bacterium Bacteroides ovatus V975 to ferment fenugreek fiber (Fenufibers), psyllium husk (Metamucil), and wheat bran (Wheat Chex). Strain V975 was incubated in basal medium that contained 0.1 g of each fiber source for 0, 24, or 48 h. Little digestion of either fiber source was detected over 48 h, and little acetate or succinate was produced. From the lack of significant fiber digestion and fermentation by B. ovatus, it seems that all three fiber sources could be used as dietary supplements to increase roughage in the human diet.

Complete nucleotide sequence of a cryptic plasmid from the ruminal bacterium Selenomonas ruminantium HD4 and identification of two predicted open reading frames.

A cryptic plasmid (pSR1) isolated from Selenomonas ruminantium HD4 was previously cloned into the HindIII site of pBR322 and a restriction map was constructed using HindIII, ClaI, BamHI, and PvuII (S. A. Martin and R. G. Dean, Appl. Environ. Microbiol. 55(12), 3035-3038, 1989). Analysis of the nucleotide sequence of pSR1 revealed two major open reading frames (ORFs) located in the minus strand at different frames. Analysis of ORF-1 revealed that it has 325 amino acids with a predicted MW of 36,588, and ORF-2 has 379 amino acids with a predicted MW of 42,651. The ORF-1 amino acids showed 30 to 32% sequence homology to the hypothetical protein YtqA in Bacillus subtilis and another hypothetical protein in the thermophilic bacterium Aquifex aeolicus. ORF-2 showed limited homology (23%) to the hypothetical protein ICFG in the photosynthetic cyanobacteria Synechocystis PCC6803.

Photoassembly of the photosystem II (Mn)4 cluster in site-directed mutants impaired in the binding of the manganese-stabilizing protein.

Photoactivation is the light-dependent ligation of Mn2+ into the H2O oxidation complex of photosystem II (PSII) and culminates in the formation of an enzymatically active complex containing Ca2+ and four Mn>/=3+. Previous kinetic analysis demonstrated that the genetic removal of the extrinsic manganese-stabilizing protein (MSP) increases the quantum yield of photoactivation 4-fold relative to that of the wild type, consistent with the hypothesis that MSP hinders access of Mn2+ to a site of photoligation [Burnap, R. L., et al. (1996) Biochemistry35, 874-882]. In this report, several Synechocystis sp. PCC6803 mutants with defined amino acid substitutions in the N-terminal region of MSP or the e-loop of intrinsic PSII protein CP47 [Putnam-Evans, C., et al. (1996) Biochemistry 35, 4046-4053] were characterized in terms of the binding of MSP to the intrinsic portion of the PSII complex and in terms of photoactivation kinetics. The charge-pair switch mutation, Arg384Arg385 --> Glu384Glu385 in the lumenal e-loop of CP47 (CP47 RR384385EE), exhibited the most severe impairment of MSP binding, whereas the Arg384Arg385 --> Gly384Gly385 (CP47 RR384385GG) mutation caused a more moderate impairment in binding. Single-substitution mutations at the highly conserved Asp9 or Asp10 positions in the amino-terminal region of MSP also resulted in a reduced binding affinity, but not as severe as that in CP47 RR384385EE. The relative quantum yield of photoactivation of hydroxylamine-extracted mutant PSII was generally found to correlate with the degree of MSP binding impairment, with the CP47 RR384385 mutants exhibiting the highest quantum yields. A two-locus, double-mutant construct involving deletion of MSP in the CP47 RR384385EE background was found to be only slightly more impaired in H2O oxidation activity than either of the corresponding single-locus mutant derivatives, indicating that mutations at these genetically separate loci encode physically interacting products affecting the same reaction parameter during H2O oxidation. Taken together, the results reinforce the concept that MSP interacts with the e-loop of CP47 at Arg384Arg385 and that disruption of this interaction causes significant alterations of the site of H2O oxidation in terms of assembly and enzymatic activity of the Mn cluster.

Identification and nucleotide sequence analysis of a transfer-related region in the streptococcal conjugative transposon Tn5252.

To obtain a functional map of Tn5252, a 47.5-kb streptococcal conjugative transposon, a series of defined deletion and insertion mutations were introduced within the transposon. Interruptions at several regions were found to affect the conjugal transposition functions of the element in filter-mating experiments. The nucleotide sequence of the left terminus of Tn5252 showed two open reading frames, ORF1 and ORF2, adjoining the att site. The organization of this region and the structure of the predicted integrase encoded by ORF1 were found to be similar to those of other site-specific recombination systems.