Precise molecular weight determination of PCR products of the rRNA intergenic spacer region using electrospray quadrupole mass spectrometry for differentiation of B. subtilis and B. atrophaeus, closely related species of bacilli

Pharmacokinetics and antibacterial activity of tiamulin after single and multiple oral administrations in geese

Tiamulin is an antibiotic approved exclusively in veterinary medicine, active against G-positive bacteria as well as Mycoplasma spp. and Leptospirae spp. The study was aimed to establish its pharmacokinetics and to evaluate drug effects on resistance in cloacal flora in vivo in geese. Eight healthy geese underwent to a two-phase longitudinal study (60 mg/kg single oral administration vs 60 mg/kg/day for 4 days) with a two-week wash-out period. Blood samples and cloacal swabs were collected at pre-assigned times. Minimal inhibitory concentration (MIC) has been evaluated for each isolated bacterial species. The pharmacokinetic parameters that significantly differed between the groups were Cmax (p = 0.024), AUC0-t (p = 0.031), AUC0-inf (p = 0.038), t1/2kel (p = 0.021), Cl/F (p = 0.036), and Vd/F (p = 0.012). Tiamulin exhibited a slow to moderate terminal half-life (3.13 h single; 2.62 h multiple) and a rapid absorption (1 h single; 0.5 h multiple) in geese, with an accumulation ratio of 1.8 after multiple doses. An in-silico simulation of multiple dosing did not reflect the results of the in vivo multiple dosage study. In both treatments, the MIC values were very high demonstrating a resistance (> 64 μg/ml) against tiamulin that can be present prior the drug administration for some strains, or emerge shortly after the commencing of treatment for some others.

Lysinibacillus louembei sp. nov., a spore-forming bacterium isolated from Ntoba Mbodi, alkaline fermented leaves of cassava from the Republic of the Congo

Investigation of the microbial diversity of Ntoba Mbodi, an African food made from the alkaline fermentation of cassava leaves, revealed the presence of a Gram-positive, catalase-positive, aerobic, motile and rod-shaped endospore-forming bacterium (NM73) with unusual phenotypic and genotypic characteristics. The analysis of the 16S rRNA gene sequence revealed that the isolate was most closely related to Lysinibacillus meyeri WS 4626T (98.93%), Lysinibacillus xylanilyticus XDB9T (96.95%) and Lysinibacillus odysseyi 34hs-1T (96.94%). The DNA-DNA relatedness of the isolate with L. meyeri LMG 26643T, L. xylanilyticus DSM 23493T and L. odysseyi DSM 18869T was 41%, 16% and 15%, respectively. The internal transcribed spacer-PCR profile of the isolate was different from those of closely related bacteria. The cell-wall peptidoglycan type was A4α, L-Lys-D-Asp and the major fatty acids were iso-C15:0, anteiso-C15:0, anteiso-C17:0 and iso-C17:0 and iso-C17:1ω10c. The polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphoaminolipid, aminolipid, two phospholipids and two unknown lipids. The predominant menaquinones were MK-7 and MK-6. Ribose was the only whole-cell sugar detected. The DNA G+C content was 38 mol%. Based on the results of the phenotypic and genotypic characterization, it was concluded that the isolate represents a novel species of the genus Lysinibacillus, for which the name of Lysinibacillus louembei sp. nov. is proposed. NM73T ( = DSM 25583T = LMG 26837T) represents the type strain.

Distinct differentiation of closely related species of Bacillus subtilis group with industrial importance

PCR amplification of 16S rRNA gene by universal primers followed by restriction fragment length polymorphism analysis using RsaI, CfoI and HinfI endonucleases, distinctly differentiated closely related Bacillus amyloliquefaciens, Bacillus licheniformis and Bacillus pumilus from Bacillus subtilis sensu stricto. This simple, economical, rapid and reliable protocol could be an alternative to misleading phenotype-based grouping of these closely related species.

Quantification of both the presence, and oxidation state, of Mn in Bacillus atrophaeus spores and its imparting of magnetic susceptibility to the spores

Bacillus atrophaeus spores were previously reported to have significant magnetic susceptibility in a magnetic field due to the presence of Mn. However, relatively little is known about the total amount and distribution of the oxidation state of Mn associated with this specific strain's spores. Using the instrument, cell tracking velocimetry (CTV) both magnetically induced velocity and settling velocity was quantitatively measured. Visual observations, and calculated diameter using previously reported densities, indicate that the spores are present in the form of clusters of approximately 3-6 µm. Treatment of these clusters with EDTA or pH of 2.0 or below resulted in not only the disruption of the spore clusters, but also a significant decrease in magnetic susceptibility, in some cases by almost two orders of magnitude. Since the magnetic susceptibility of Mn varies significantly between the three typically reported valance states of Mn, Mn(II), Mn(III), and Mn(IV); X-Ray Photoelectron Spectroscopy, XPS, was used to determined the valance states of Mn in the spores. This XPS analysis, which penetrates up to 10 nm into the spore, returned the following fractions: 0.41, 0.38, and 0.21 for the valance states: Mn(II), Mn(III), and Mn(IV), respectively. The total mass of Mn associated with each spore cluster was determined by ICP-MS. A second, completely independent estimate of Mn mass associated with each spore cluster was made, by mathematically solving for the amount of Mn per spore cluster using the experimentally measured magnetophoretic mobility and the magnetic susceptibility of each of the three valence states from the XPS analysis. IPC-MS returned a value of 3.28 × 10(-11) g of Mn per spore cluster while the calculated estimation from mobility and XPS analysis retuned a value of 1.16 × 10(-11) g, which given the complexity of the two techniques, is a reasonable agreement. Finally, a discussion of potential applications of the magnetic properties of these spores is presented.

Development of amplified fragment length polymorphism-derived functional strain-specific markers to assess the persistence of 10 bacterial strains in soil microcosms

To augment the information on commercial microbial products, we investigated the persistence patterns of high-priority bacterial strains from the Canadian Domestic Substance List (DSL). Specific DNA markers for each of the 10 DSL bacterial strains were developed using the amplified fragment length polymorphism (AFLP) technique, and the fates of DSL strains introduced in soil were assessed by real-time quantitative PCR (qPCR). The results indicated that all DNA markers had high specificity at the functional strain level and that detection of the target microorganisms was sensitive at a detection limitation range from 1.3 × 10² to 3.25 × 10⁵ CFU/g of dry soil. The results indicated that all introduced strains showed a trend toward a declining persistence in soil and could be categorized into three pattern types. The first type was long-term persistence exemplified by Pseudomonas stutzeri (ATCC 17587) and Pseudomonas denitrificans (ATCC 13867) strains. In the second pattern, represented by Bacillus subtilis (ATCC 6051) and Escherichia hermannii (ATCC 700368), the inoculated strain populations dropped dramatically below the detection threshold after 10 to 21 days, while in the third pattern there was a gradual decrease, with the population falling below the detectable level within the 180-day incubation period. These patterns indicate a selection effect of a microbial community related to the ecological function of microbial strains introduced in soil. As a key finding, the DSL strains can be quantitatively tracked in soil with high sensitivity and specificity at the functional strain level. This provides the basic evidence for further risk assessment of the priority DSL strains.

Characterization of lactic acid bacteria isolated from Italian Bella di Cerignola table olives: selection of potential multifunctional starter cultures

Lactic acid bacteria (19 isolates) from Bella di Cerignola Italian table olives were investigated for their technological and probiotic properties for the selection of multifunctional starter cultures for table olives. The bacteria were first identified by phenotyping and genotyping, then characterized for the production of biogenic amines, growth at different pH, NaCl concentrations, and temperatures. The potentiality of the bacteria to have some probiotic properties (antimicrobial activity against foodborne pathogens, survival in low pH and in the presence of bile salts, ability to adhere to the mammalian cells model IPEC-J2) was also investigated. Eighteen of the studied isolates were identified as Lactobacillus plantarum and one as Enterococcus faecalis. All bacteria were able to grow at a range of pH between 4.0 and 10.0 as well as in media supplemented with 2.5 to 7.5% of NaCl and 0.3% bile salts and survived in MRS broth acidified at pH 2.5; moreover, they inhibited significantly Escherichia coli O157:H7. The adhesion to IPEC-J2 cells was in general low to moderate (5.3 to 8.3%); however, 2 isolates of L. plantarum (c16 and c19) showed interesting higher adhesion values (up to 16%). Our results suggest that at least 3 isolates could be possible multifunctional starters for Bella di Cerignola olives: L. plantarum 16 and 19 for mainly their probiotic properties and L. plantarum 10 for mainly its technological characteristics. Practical Application: A functional starter is a microorganism exerting benefits on human health (probiotic) and able to guide a fermentation (starter). The main goal of this article was to select a functional starter for table olives.

Frontiers of mass spectrometry in nucleic acids analysis

Nucleic acids research is a highly competitive field of research. A number of well established methods are available. The current output of high throughput ("next generation") sequencing technologies is impressive, and still technologies are continuing to make progress regarding read lengths, bp per second, accuracy and costs. Although in the 1990s MS was considered as an analytical platform for sequencing, it was soon realized that MS will never be competitive. Thus, the focus shifted from de novo sequencing towards other areas of application where MS has proven to be a powerful analytical tool. Potential niches for the application of MS in nucleic acids research include genotyping of genetic markers (single nucleotide polymorphisms, short tandem repeats, and combinations thereof), quality control of synthetic oligonucleotides, metabolic profiling of therapeutics, characterization of modified nucleobases in DNA and RNA molecules, and the study of non covalent interactions among nucleic acids as well as interactions of nucleic acids with drugs and proteins. The diversity of possible applications for MS highlights its significance for nucleic acid research.

Development of quantitative real-time PCR assays for detection and quantification of surrogate biological warfare agents in building debris and leachate

Evaluation of the fate and transport of biological warfare (BW) agents in landfills requires the development of specific and sensitive detection assays. The objective of the current study was to develop and validate SYBR green quantitative real-time PCR (Q-PCR) assays for the specific detection and quantification of surrogate BW agents in synthetic building debris (SBD) and leachate. Bacillus atrophaeus (vegetative cells and spores) and Serratia marcescens were used as surrogates for Bacillus anthracis (anthrax) and Yersinia pestis (plague), respectively. The targets for SYBR green Q-PCR assays were the 16S-23S rRNA intergenic transcribed spacer (ITS) region and recA gene for B. atrophaeus and the gyrB, wzm, and recA genes for S. marcescens. All assays showed high specificity when tested against 5 ng of closely related Bacillus and Serratia nontarget DNA from 21 organisms. Several spore lysis methods that include a combination of one or more of freeze-thaw cycles, chemical lysis, hot detergent treatment, bead beat homogenization, and sonication were evaluated. All methods tested showed similar threshold cycle values. The limit of detection of the developed Q-PCR assays was determined using DNA extracted from a pure bacterial culture and DNA extracted from sterile water, leachate, and SBD samples spiked with increasing quantities of surrogates. The limit of detection for B. atrophaeus genomic DNA using the ITS and B. atrophaeus recA Q-PCR assays was 7.5 fg per PCR. The limits of detection of S. marcescens genomic DNA using the gyrB, wzm, and S. marcescens recA Q-PCR assays were 7.5 fg, 75 fg, and 7.5 fg per PCR, respectively. Quantification of B. atrophaeus vegetative cells and spores was linear (R(2) > 0.98) over a 7-log-unit dynamic range down to 10(1) B. atrophaeus cells or spores. Quantification of S. marcescens (R(2) > 0.98) was linear over a 6-log-unit dynamic range down to 10(2) S. marcescens cells. The developed Q-PCR assays are highly specific and sensitive and can be used for monitoring the fate and transport of the BW surrogates B. atrophaeus and S. marcescens in building debris and leachate.

Rapid discrimination of Bacillus anthracis from other members of the B. cereus group by mass and sequence of “intact” small acid soluble proteins (SASPs) using mass spectrometry

The intentional contamination of buildings, e.g. anthrax in the bioterrorism attacks of 2001, demonstrated that the population can be affected rapidly and lethally if the appropriate treatment is not provided at the right time. Molecular approaches, primarily involving PCR, have proved useful in characterizing "white powders" used in these attacks as well as isolated organisms. However there is a need for a simpler approach, which does not involve temperamental reagents (e.g. enzymes and primers) which could potentially be used by first responders. It is demonstrated here that small acid-soluble proteins (SASPs), located in the core region of Bacillus spores, are reliable biomarkers for identification. The general strategy used in this study was to measure the molecular weight (MW) of an intact SASP by electrospray ionization mass spectrometry (ESI MS) followed by generation of sequence-specific information by ESI MS/MS (tandem mass spectrometry). A prominent SASP of mass 6679 was present in all B. anthracis strains. For B. cereus and B. thuringiensis strains the SASP had a mass of 6712. This represents a two amino acid substitution (serine to alanine; phenylalanine to tyrosine). The only SASP present in the B. anthracis genome consistent with this sequence is encoded by the gene ssB. This protein has a predicted mass of 6810, presumably post-translational processing leads to loss of methionine (mass 131) generating a SASP of mass 6679. This study showed that intact SASPs can be used as a biomarker for identification of B. anthracis; the protocol is simple and rapid. Extrapolation of this approach might prove important for real-time biodetection.

Correlation between diverse cyclic lipopeptides production and regulation of growth and substrate utilization by Bacillus subtilis strains in a particular habitat

The two Bacillus subtilis strains (DM-03 and DM-04) were isolated from two extremely different habitats; one from the traditional fermented food and another one from a petroleum contaminated soil sample. These strains produced quantitatively and qualitatively different cyclic lipopeptides isoforms under laboratory culture conditions. MALDI-TOF mass spectral analysis revealed that lipopeptide profile varied according to the producing B. subtilis strains; iturins and surfactins isoforms were pre-dominant cyclic lipopeptides produced by B. subtilis DM-03 and DM-04 strains, respectively. A comparative study showed that these strains possessed distinct preferences for the carbon and nitrogen substrates, temperature and pH for optimal growth and biosurfactant production. Our study documented that the cyclic lipopeptide isoforms produced by the respective strains played an important role in the utilization of available hydrophobic substrate(s) from their natural habitats and conferred some kind of competitive advantage to the producing B. subtilis strains in their parent ecological niche.

Identification of Bacteria by Polymerase Chain Reaction Followed by Liquid Chromatography−Mass Spectrometry

Bloodstream infections are an important cause of serious morbidity and mortality. Rapid detection and identification of specific pathogens from blood or other clinical specimens could improve the rational use of antimicrobial therapy in clinical medicine and have a great impact on the outcome of patients with systemic infections. Polymerase chain reaction using generic primers was used to amplify genomic DNA of different bacterial strains. The identification was accomplished by measuring the molecular masses of the PCR products using ion-pair reversed-phase high-performance liquid chromatography hyphenated to electrospray ionization mass spectrometry. DNA from 10 bacterial species was amplified by PCR, and the resulting amplification products were analyzed. In all cases, the measured molecular masses of the PCR products matched the theoretical value for the species-specific DNA sequence. However, three pairs of bacteria could not be distinguished since the theoretical difference in amplicon molecular mass was < 1.0 Da (different sequence, same base composition of amplicon). Determination of intra- and interday mass reproducibility resulted in relative standard deviations of 0.0030 and 0.018%, respectively. The limit of detection of the presented method was shown to be 0.5 genome equivalents/PCR. The specificity of the method in a human background was successfully tested by amplifying and analyzing 1000-10000 genome equivalents of Staphylococcus aureus spiked into human plasma.

Strain discrimination among B. anthracis and related organisms by characterization of bclA polymorphisms using PCR coupled with agarose gel or microchannel fluidics electrophoresis

The bclA gene codes for the protein backbone of the exosporium glycoprotein BclA of B. anthracis. BclA has a central collagen-like region formed by polymorphic GXX repeats and conserved amino- and carboxy-termini. It is noted here that the bclA gene is also present in the genome of Bacillus cereus and Bacillus thuringiensis. There is considerable size heterogeneity among the BclA proteins, both for species and strains, due to different numbers of GPT repeats and [GPT]5GDTGTT repeats (BclA repeats). PCR products that included the entire variable region were analyzed by conventional agarose gel electrophoresis and by micro-channel fluidics (MCF) LabChip to assess differences in molecular weight (MW). Both methods provided discrimination at the strain level for B. cereus group organisms. Results obtained by MCF electrophoresis were superior to conventional agarose gel analysis demonstrating improved reproducibility and much faster analysis time. The expression of a carbohydrate-rich exosporium (corresponding to BclA) in other members of the B. cereus group, in addition to B. anthracis, was also demonstrated ultra-structurally. Analysis of sequence variability within the bclA gene CLR revealed even greater potential for strain and species identification.

Rapid phenotypic characterization of Salmonella enterica strains by pyrolysis metastable atom bombardment mass spectrometry with multivariate statistical and artificial neural network pattern recognition

Pyrolysis mass spectrometry was investigated for rapid characterization of bacteria. Spectra of Salmonella were compared to their serovars, pulsed-field gel electrophoresis (PFGE) patterns, antibiotic resistance profiles, and MIC values. Pyrolysis mass spectra generated via metastable atom bombardment were analyzed by multivariate principal component-discriminant analysis and artificial neural networks (ANNs). Spectral patterns developed by discriminant analysis and tested with Leave-One-Out (LOO) cross-validation distinguished Salmonella strains by serovar (97% correct) and by PFGE groups (49%). An ANN model of the same PFGE groups was cross-validated, using the LOO rule, with 92% agreement. Using an ANN, thirty previously unseen spectra were correctly classified by serotype (97%) and at the PFGE level (67%). Attempts by ANN to model spectra grouped by resistance profile-but ignoring PFGE or serotype-failed (10% correct), but ANNs differentiating ten samples of the same serotype/PFGE class were more successful. To assess the information content of PyMS data serendipitously associated with or directly related to resistance character, the ten isolates were grouped into four, three, or two categories. The four categories corresponded to four resistance profiles. The four class and three class ANNs showed much improved but insufficient modeling power. The two-class ANN and a corresponding multivariate model maximized inferential power for a coarse antibiotic-resistance-related distinction. They each cross-validated by LOO at 90%. This is the first direct correlation of pyrolysis metastable atom bombardment mass spectrometry with immunological (e.g. serology) or molecular biology (e.g. PFGE) based techniques.

Mass spectrometry provides accurate characterization of two genetic marker types in Bacillus anthracis

Epidemiological and forensic analyses of bioterrorism events involving Bacillus anthracis could be improved if both variable number tandem repeats (VNTRs) and single nucleotide polymorphisms (SNPs) could be combined on a single analysis platform. Here we present the use of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) to characterize 24 alleles from 6 VNTR loci and 11 alleles from 7 SNP loci in B. anthracis. The results obtained with ESI-FTICR-MS were consistent with independent results obtained from traditional approaches using electrophoretic detection of fluorescent products. However, ESI-FTICR-MS improves on the traditional approaches because it does not require fluorescent labeling of PCR products, minimizes post-PCR processing, obviates electrophoresis, and provides unambiguous base composition of both SNP and VNTR PCR products. In addition, ESI-FTICR-MS allows both marker types to be examined simultaneously and at a rate of approximately 1 sample per min. This technology represents a significant advance in our ability to rapidly characterize B. anthracis isolates using VNTR and SNP loci.

Analysis of nucleic acids by FTICR MS

Fourier transform ion cyclotron resonance (FTICR) mass spectrometry represents a unique platform with which to study nucleic acids and non-covalent complexes containing nucleic acids moieties. In particular, systems in which very high mass measurement accuracy is required, very complex mixtures are to be analyzed, or very limited amounts of sample are available may be uniquely suited to interrogation by FTICR mass spectrometry. Although the FTICR platform is now broadly deployed as an integral component of many high-end proteomics-based research efforts, momentum is still building for the application of the platform towards nucleic acid-based analyses. In this work, we review fundamental aspects of nucleic acid analysis by FTICR, focusing primarily on the analysis of DNA oligonucleotides but also describing applications related to the characterization of RNA constructs. The goal of this review article is to give the reader a sense of the breadth and scope of the status quo of FTICR analysis of nucleic acids and to summarize a few recently published reports in which researchers have exploited the performance attributes of FTICR to characterize nucleic acids in support of basic and applied research disciplines including genotyping, drug discovery, and forensic analyses.

Genotyping and toxigenic potential of Bacillus subtilis and Bacillus pumilus strains occurring in industrial and artisanal cured sausages

Artisanal and industrial sausages were analyzed for their aerobic, heat-resistant microflora to assess whether new emerging pathogens could be present among Bacillus strains naturally contaminating cured meat products. Sixty-four isolates were characterized by randomly amplified polymorphic DNA (RAPD)-PCR and fluorescent amplified fragment length polymorphism (fAFLP). The biotypes, identified by partial 16S rRNA gene sequence analysis, belonged to Bacillus subtilis, Bacillus pumilus, and Bacillus amyloliquefaciens species. Both RAPD-PCR and fAFLP analyses demonstrated that a high genetic heterogeneity is present in the B. subtilis group even in strains harvested from the same source, making it possible to isolate 56 different biotypes. Moreover, fAFLP analysis made it possible to distinguish B. subtilis from B. pumilus strains. The strains were characterized for their toxigenic potential by molecular, physiological, and immunological techniques. Specific PCR analyses revealed the absence of DNA sequences related to HBL, BcET, NHE, and entFM Bacillus cereus enterotoxins and the enzymes sphingomyelinase Sph and phospholipase PI-PLC in all strains; also, the immunological analyses showed that Bacillus strains did not react with NHE- and HBL-specific antibodies. However, some isolates were found to be positive for hemolytic and lecithinase activity. The absence of toxigenic potential in Bacillus strains from the sausages analyzed indicates that these products can be considered safe under the processing conditions they were produced; however, great care should be taken when the ripening time is shortened, particularly in the case of traditional sausages, which could contain high amounts of Bacillus strains and possibly some B. cereus cells.

Genotyping of starter cultures of Bacillus subtilis and Bacillus pumilus for fermentation of African locust bean (Parkia biglobosa) to produce Soumbala

Bacillus spp. are the predominant microorganisms in fermented African locust bean called Soumbala in Burkina Faso. Ten strains selected as potential starter cultures were characterised by PCR amplification of the16S-23S rDNA intergenic transcribed spacer (ITS-PCR), restriction fragment length polymorphism of the ITS-PCR (ITS-PCR RFLP), pulsed field gel electrophoresis (PFGE) and sequencing of the 968-1401 region of the 16S rDNA. In previous studies, the isolates were identified by phenotyping as Bacillus subtilis and Bacillus pumilus. The phenotyping was repeated as a reference in the present study. The ITS-PCR and ITS-PCR RLFP allowed a typing at species level. The PFGE was more discriminative and allowed a typing at strain level. Full agreement with the phenotyping was observed in all cases. The sequencing of the 16S rDNA allowed the identification at species level with an identity from 97% to 100% comparing the sequences to those from the GenBank databases. The desired cultures of B. subtilis and B. pumilus from African locust bean fermentation were distinguished by ITS-PCR and ITS-PCR RLFP from Bacillus cereus and Bacillus sphaericus which sometimes occur in the beginning of the fermentation.

Carbohydrates and glycoproteins of Bacillus anthracis and related bacilli: targets for biodetection

The spore is the form released in a bioterrorism attack. There is a real need for definition of new targets for Bacillus anthracis that might be incorporated into emerging biodetection technologies. Particularly of interest are macromolecules found in B. anthracis that are (1) spore-specific, (2) readily accessible on the spore surface and (3) distinct from those present in related organisms. One of the few biochemical methods to identify the spores of B. anthracis is based on the presence of rhamnose and 3-O-methyl rhamnose as determined by gas chromatography-mass spectrometry. Related organisms additionally contain 2-O-methyl rhamnose and fucose. Carbohydrates and glycoproteins of the B. cereus group of organisms and the related B. subilis group are reviewed here. It is hypothesized that the spore-specific carbohydrate is a component of the newly described glycoprotein of the exosporium of B. anthracis. Further work to define the protein and carbohydrate components of the glycoprotein of B. anthracis could be highly useful in developing new technologies for rapid biodetection.

Mass spectrometry and tandem mass spectrometry, alone or after liquid chromatography, for analysis of polymerase chain reaction products in the detection of genomic variation

The availability of the sequences of entire bacterial and human genomes has opened up tremendous opportunities in biomedical research. The next stage in genomics will include utilizing this information to obtain a clearer understanding of molecular diversity among pathogens (helping improved identification and detection) and among normal and diseased people (e.g. aiding cancer diagnosis). To delineate such differences it may sometimes be necessary to sequence multiple representative genomes. However, often it may be adequate to delineate structural differences between genes among individuals. This may be readily achieved by high-throughput mass spectrometry analysis of polymerase chain reaction products.

The use of MassARRAY technology for high throughput genotyping

This chapter will explore the role of mass spectrometry (MS) as a detection method for genotyping applications and will illustrate how MS evolved from an expert-user-technology to a routine laboratory method in biological sciences. The main focus will be time-of-flight (TOF) based devices and their use for analyzing single-nucleotide-polymorphisms (SNPs, pronounced snips). The first section will describe the evolution of the use of MS in the field of bioanalytical sciences and the protocols used during the early days of bioanalytical MALDI TOF mass spectrometry. The second section will provide an overview on intraspecies sequence diversity and the nature and importance of SNPs for the genomic sciences. This is followed by an exploration of the special and advantageous features of mass spectrometry as the key technology in modern bioanalytical sciences in the third chapter. Finally, the fourth section will describe the MassARRAY technology as an advanced system for automated high-throughput analysis of SNPs.

Restriction fragment length polymorphism of rRNA operons for discrimination and intergenic spacer sequences for cataloging of Bacillus subtilis sub-groups

Restriction fragment length polymorphism of rRNA operons (RFLP) and 16S-23S rRNA intergenic region (ISR) sequences of Bacillus subtilis subsp. subtilis, B. subtilis subsp. spizizenii, and B. atrophaeus were compared. ISR sequences of the B. subtilis subspecies were extremely similar (W23 versus 168 rrn H, J, G,W; 96.8%; rrn D, E; 98.4%; rrnB; 97.9%) and, therefore, not useful for their differentiation. However, RFLP of rRNA operons of the B. subtilis subspecies were distinct in terms of numbers and organization within the genome (e.g. the 168 sub-group generally contained 8.3- and 8.0-kb fragments absent in the W23 sub-group). The more distantly related B. atrophaeus was distinct from both B. subtilis subspecies in terms of ISR sequence and rRNA operon number and organization. RFLP of rRNA operons discriminates the two sub-groups of Bacillus subtilis that are indistinguishable by ISR sequence. However, ISR sequence defines the relatedness of B. subtilis to other species (e.g. B. atrophaeus) within the genus Bacillus.

Variation in 16S-23S rRNA intergenic spacer regions among Bacillus subtilis 168 isolates

The genome of the Bacillus subtilis 168-type strain contains 10 ribosomal RNA (rRNA) operons. In the intergenic spacer region (ISR) between the 16S and 23S rRNA genes, five rRNA operons, rrnI-H-G and rrnJ-W, lack a trinucleotide signature region. Precise determination of molecular weight (MW), using electrospray mass spectrometry (MS), of the polymerase chain reaction (PCR) products from a segment of the ISR from the 168-type strain and B. subtilis 168-like strain 23071 demonstrated 114 and 111 basepair (bp) PCR products (due to the presence or absence of the insert in the operons) as predicted from sequence. However, PCR of the ISR segment for five other B. subtilis 168 isolates generated only a 114 bp PCR product, suggesting the presence of the trinucleotide signature region in all rRNA operons for these strains. Additional genetic variability between the seven B. subtilis 168 isolates was demonstrated by restriction fragment length polymorphism (RFLP) of the rRNA operons, with three distinct patterns found upon Southern blot analysis. The 168-type strain and three others (23066, 23067, and 23071) exhibited the same Southern pattern. Thus, operon deletion is not responsible for the absence of a 111 bp product on MS analysis for strains 23066 and 23067. Restriction analysis confirmed the presence of the trinucleotide signature region in the ISR of all rRNA operons for five B. subtilis 168 isolates; sequencing of rrnW/H from a representative strain also upheld this finding. These results help provide a better understanding of variations in sequence, operon number and chromosomal organization, both within a genome and among isolates of B. subtilis subgroup 168. It is also hypothesized that the presence of the trinucleotide insert in certain rRNA operons may play a role in rRNA maturation and protein synthesis.

Electrophoretic mobility anomalies associated with PCR amplification of the intergenic spacer region between 16S and 23S ribosomal RNA genes of Fusobacterium necrophorum

PCR amplification of the intergenic spacer region (ISR) between 16S and 23S rRNA genes among subspecies of the anaerobic bacterium Fusobacterium necrophorum gave identical patterns, with two forms of ISR identified. However, extra bands resulting from anomalous electrophoretic mobility of amplified DNA fragments with certain primer combinations were encountered. Therefore, PCR assays relying solely on banding patterns may be unreliable, and supporting sequence analysis is essential for correct culture identification.