Computing Maximal Covers for Protein Sequences.

A partial cover of a string or sequence of length n, which we model as an array x=x[1..n], is a repeating substring u of x such that "many" positions in x lie within occurrences of u. A maximal cover u*-introduced in 2018 by Mhaskar and Smyth as optimal cover-is a partial cover that, over all partial covers u, maximizes the positions covered. Applying data structures also introduced by Mhaskar and Smyth, our software MAXCOVER for the first time enables efficient computation of u* for any x-in particular, as described here, for protein sequences of Arabidopsis, Caenorhabditis elegans, Drosophila melanogaster, and humans. In this protein context, we also compare an extended version of MAXCOVER with existing software (MUMmer's repeat-match) for the closely related task of computing non-extendible repeating substrings (a.k.a. maximal repeats). In practice, MAXCOVER is an order-of-magnitude faster than MUMmer, with much lower space requirements, while producing more compact output that, nevertheless, yields a more exact and user-friendly specification of the repeats.

Large-scale detection of repetitions.

Combinatorics on words began more than a century ago with a demonstration that an infinitely long string with no repetitions could be constructed on an alphabet of only three letters. Computing all the repetitions (such as ∙∙∙TTT ∙∙∙ or ∙∙∙ CGACGA ∙∙∙ ) in a given string x of length n is one of the oldest and most important problems of computational stringology, requiring time in the worst case. About a dozen years ago, it was discovered that repetitions can be computed as a by-product of the Θ(n)-time computation of all the maximal periodicities or runs in x. However, even though the computation is linear, it is also brute force: global data structures, such as the suffix array, the longest common prefix array and the Lempel-Ziv factorization, need to be computed in a preprocessing phase. Furthermore, all of this effort is required despite the fact that the expected number of runs in a string is generally a small fraction of the string length. In this paper, I explore the possibility that repetitions (perhaps also other regularities in strings) can be computed in a manner commensurate with the size of the output.

A study of the antimicrobial activity of selected synthetic and naturally occurring quinolines.

The antimicrobial activities of 60 naturally occurring and synthetic quinolines were studied. The quinolines were organised into seven structural subgroups and, using an in-house microtitre assay, were tested against a range of gram-positive and gram-negative bacteria, including a hospital isolate of meticillin-resistant Staphylococcus aureus (MRSA). The quinolines exhibiting good bioactivity [i.e. low minimum inhibitory concentration (MIC)] against two S. aureus strains were then assessed for their antimicrobial activity against a range of eight clinically isolated MRSA strains. The study showed that 30 of the tested compounds displayed antimicrobial activity, mostly against gram-positive bacteria. The effects of substituent groups on the bioactivity of these quinolines have also been discussed. The quinoline 4-hydroxy-3-iodo-quinol-2-one (11) exhibited significant antimicrobial activity, being active against the MRSA clinical isolates with MIC values comparable with the antibiotic vancomycin used in the treatment of MRSA infections. In particular, 4-hydroxy-3-iodo-quinol-2-one (11) showed MIC values of 0.097 microg/mL against an Irish hospital MRSA-1 strain and 0.049 microg/mL against a distinct MRSA strain as well as a non-typeable MRSA strain.

A study of the antimicrobial activity of selected naturally occurring and synthetic coumarins.

The antimicrobial activities of 43 naturally occurring and synthetic coumarins were studied. Using a microtitre assay developed in-house, a range of Gram-positive and Gram-negative bacteria, including a hospital isolate of methicillin-resistant Staphylococcus aureus (MRSA),were utilised. The coumarins exhibiting good bioactivity (i.e. a low minimum inhibitory concentration) against two S. aureus strains were then assessed for their antimicrobial activities against a range of eight clinically isolated MRSA strains. The study showed that nearly one-half of the tested compounds displayed antimicrobial activity. Sixteen of these coumarins also possessed resistance-modifying activity, which reversed the resistance mechanism in MRSA allowing the antimicrobial oxacillin to exert an enhanced effect against an MRSA hospital strain. When tested in combination with oxacillin, 8-iodo-5,7-dihydroxycoumarin (32) had a similar activity to vancomycin, which is the current drug of choice for the treatment of MRSA infections.

An investigation of bioactive phytochemicals in the leaves of Melicope vitiflora by electrospray ionisation ion trap mass spectrometry.

The ethyl acetate extract of the leaves of Melicope vitiflora was separated by column chromatography and the resulting fractions tested for their bioactivity towards methicillin-resistant-Staphylococcus aureus (MRSA) and Micrococcus luteus (ML). The bioactive column chromatography fractions were further separated by preparative TLC and dereplication was carried out on them by first subjecting them to electrospray ionisation-ion trap mass spectrometry (ESI-MS(n)). The resulting molecular masses, their fragmentation patterns in addition to the chemnet database (www.chemnetbase.com) were used to aid in the structural elucidation of some of the compounds by permitting comparison with known structures of natural origin. Some molecular masses and the corresponding fragmentations were found that did not correlate with any known compounds thus revealing potentially novel natural products that could be investigated on a larger scale and could ultimately find application as new drugs against MRSA and other multi drug resistant microorganisms. Structures are also proposed for known compounds that have not been previously reported for M. vitiflora.

A study of the analytical behaviour of selected synthetic and naturally occurring quinolines using electrospray ionisation ion trap mass spectrometry, liquid chromatography and gas chromatography and the construction of an appropriate database for quinoline characterisation.

Mass spectral fragmentation of quinoline alkaloids of significance in plants has been investigated using electrospray ionisation ion trap mass spectrometry (ESI-MS(n)) with a view to characterisation of molecules of unknown structure isolated from these natural sources. This investigation has led to the generation of an appropriate database incorporating data from ESI-MS(n) and also from gas liquid chromatography (GLC) and liquid chromatography (HPLC) for these low molecular mass quinolines. This has been put to practical application in the identification of quinoline alkaloids in a plant extract. Thus, an acid extraction of the leaves of Choisya ternata containing such tertiary alkaloids was analysed by liquid chromatography-electrospray ionisation mass spectrometry (HPLC-ESI-MS) and the resulting behaviour of the quinolines was compared with that of the quinoline alkaloids in the database.

Recent studies on the electrospray ionisation mass spectrometric behaviour of selected nitrogen-containing drug molecules and its application to drug analysis using liquid chromatography-electrospray ionisation mass spectrometry.

This review presents recent studies on the electrospray ionisation mass spectrometry (ESI-MS) of selected N-containing drug molecules, their metabolites, formulation degradation products and process impurities taken from both studies in the author's laboratory and the recent literature using the Web of Knowledge database. Molecules of mass less than 500 Da are chosen according to selected structural classes in which they give ESI signals primarily in the positive ion mode as [M+H]+ ions. The structural classes are drugs with amine-containing side chains, drugs with N-containing saturated ring structures, drugs with N-containing unsaturated ring structures and quaternary ammonium drugs. Details are given on the fragmentations, where available, that these ionic species exhibit in-source and in ion-trap, triple quadrupole and time-of flight mass spectrometers. Fragmentation data, again where available, using electron impact mass spectrometry (EI-MS) is included for comparison. A review of applications for the period 2004-2005, again taken from the Web of Knowledge database, of the technique liquid chromatography-electrospray ionisation mass spectrometry (LC-ESI-MS) to the detection and determination of these N-containing drug molecules in biomatrices, pharmaceutical formulations, etc., is then made. Analytical information on, for example, sample concentration techniques, LC separation conditions, recoveries from biological media, degradation products and limits of detection (LODs) are provided. Comparisons, where available, are also made with rival analytical techniques such as gas liquid chromatography-mass spectrometry (GLC-MS), capillary electrophoresis-electrospray ionisation mass spectrometry (CE-ESI-MS) and stripping voltammetry (SV).

Microbial decolourisation and degradation of textile dyes.

Dyes and dyestuffs find use in a wide range of industries but are of primary importance to textile manufacturing. Wastewater from the textile industry can contain a variety of polluting substances including dyes. Increasingly, environmental legislation is being imposed to control the release of dyes, in particular azo-based compounds, into the environment. The ability of microorganisms to decolourise and metabolise dyes has long been known, and the use of bioremediation based technologies for treating textile wastewater has attracted interest. Within this review, we investigate the mechanisms by which diverse categories of microorganisms, such as the white-rot fungi and anaerobic bacterial consortia, bring about the degradation of dyestuffs.

A study of the electrospray ionisation and ion trap fragmentation of hemiterpenoid and dimeric coumarin derivatives.

The electrospray ionisation (ESI) of selected hemiterpenoid and dimeric coumarin derivatives and their subsequent fragmentation using an ion trap mass spectrometer are reported and discussed. Sequential product ion fragmentation experiments (MS(n)) were performed in order to elucidate the degradation pathways for these compounds. The results illustrate that the observed characteristic fragmentation patterns are of considerable utility in the application of ESI mass spectrometry to the characterisation of this class of compounds.

A study of the electrospray ionisation of pharmacologically significant 1,4-benzodiazepines and their subsequent fragmentation using an ion-trap mass spectrometer.

The electrospray ionisation (ESI) of sixteen pharmacologically significant 1,4-benzodiazepines and their subsequent fragmentation using an ion-trap mass spectrometer have been investigated. Sequential product ion fragmentation experiments (MSn) were performed in order to elucidate the degradation pathways for these compounds. Comparisons were also made between these ESI spectra and those obtained under electron impact (EI) conditions. The data presented in this paper provide useful information on the effect of different substituents on the ionisation/fragmentation processes and can be used in the characterisation of this important class of drugs and their metabolites.

A study of the electrospray ionisation of selected coumarin derivatives and their subsequent fragmentation using an ion trap mass spectrometer.

The electrospray ionisation (ESI) of selected coumarin derivatives and their subsequent fragmentation using an ion trap mass spectrometer have been investigated. Sequential product ion fragmentation experiments (MS(n)) were performed in order to elucidate the degradation pathways for these compounds. A comparison was also made between these ESI spectra and those obtained under electron impact (EI) conditions. The data presented in this paper provides useful information on the effect of different substituents on the ionisation/fragmentation processes and can be used in the characterisation of these compounds.

Electrospray ionisation-mass spectrometric characterisation of selected anti-psychotic drugs and their detection and determination in human hair samples by liquid chromatography-tandem mass spectrometry.

Electrospray ionisation quadrupole ion-trap mass spectrometric (ESI-MS) characterisation of the anti-psychotic drugs chlorpromazine, trifluoperazine, flupenthixol, risperidone and the antidepressant/internal standard trimipramine is presented and possible mechanisms for the observed MSn fragmentation patterns proposed. A validated liquid chromatography (LC)-MS-MS method is then applied to the detection and determination of these drugs in the hair of a patient under clinical treatment for schizophrenia. Chlorpromazine, trifluoperazine and flupenthixol are identified and determined in this hair sample following alkaline degradation of the matrix, solvent extraction and LC-MS-MS using trimipramine as internal standard.

The identification and determination of selected 1,4-benzodiazepines by an optimised capillary electrophoresis-electrospray mass spectrometric method.

An optimised capillary electrophoresis-electrospray mass spectrometric method is presented for the identification and determination of diazepam and its metabolites N'-desmethyldiazepam, oxazepam and temazepam. By investigating constituent parts of the capillary electrophoresis-electrospray mass spectrometric interface and optimising their function, a relatively fast and reproducible method is described for the identification and determination of selected 1,4-benzodiazepines. Optimisation of sheath and auxiliary gas flows, capillary tip tapering, capillary tip positioning, sheath liquid composition and flow rate and pressure application during the separation step have led to acceptable relative standard deviation (RSD) values for migration time and peak area, correlation coefficients and limits of detection. This has been achieved as a result of stabilising the electrospray current prior to analysis, a procedure that takes a matter of minutes when using the method described. Sequential product ion fragmentation (MS(n)) characterisation of 15 1,4-benzodiazepines is also presented and mechanisms for the observed fragmentation patterns proposed.

Application of electrospray mass spectrometry in the detection and determination of Remazol textile dyes.

The electrospray (ES) behaviour of selected Remazol textile dyes, their hydrolysis products and the latters' reaction, following elution from a strong anion-exchange cartridge, with 30% concentrated HCl in MeOH, is studied and applied to the direct analysis of dye containing effluent. For unambiguous identification and determination of these textile dyes in effluents, it is necessary to resort to ES utilising MS-MS and MS3. Further, a tabular review of recent applications of HPLC-ES-MS and, to a lesser extent, CE-ES-MS with reference to drug and pesticide analysis is presented.

Determination of 1,4-benzodiazepines and their metabolites by capillary electrophoresis and high-performance liquid chromatography using ultraviolet and electrospray ionisation mass spectrometry.

A study is presented for the separation and determination of fifteen 1,4-benzodiazepine drugs and metabolites by capillary electrophoresis (CE) compared with high-performance liquid chromatography (HPLC). A comparison is made between the CE determination of the compounds by conventional UV detection and LC determination with electrospray ionisation (ESI) ion-trap mass spectrometry. CE is shown to provide superior separation to HPLC but the MS-MS capability of the ion-trap allows for the specific detection and determination of four of the compounds, diazepam, N'-desmethyldiazepam, oxazepam and temazepam in the hair of a patient under clinical treatment with diazepam and temazepam. Selected mixtures of drugs and metabolites are determined by CE and LC and the determination of diazepam and its metabolites by CE-UV-ESI-MS-MS is also presented.

A critical evaluation of the application of capillary electrophoresis to the detection and determination of 1,4-benzodiazepine tranquilizers in formulations and body materials.

Studies of the capillary zone electrophoresis (CZE) and micellar electrokinetic capillary chromatography (MEKC) behaviour of 1,4-benzodiazepines have seen application in subject areas such as the development of pharmaceuticals, therapeutic drug monitoring and forensic toxicology. In the development of pharmaceuticals, pKa determinations by CZE can be used in preclinical studies whereas analytical data on the detection and determination of 1,4-benzodiazepines is of value primarily in raw material/formulation assay and in the analysis of body fluids in clinical studies. The capillary electrophoresis (CE) techniques, which generally have inferior limits of detection (LOD) to rival techniques such as gas chromatography (GC) and high-performance liquid chromatography (HPLC), are particularly applicable in forensic toxicology where reasonably high concentrations of these drugs can be encountered. It is anticipated that, with the interfacing of CZE and capillary electrochromatography (CEC) with mass spectrometry (MS) techniques, the excellent selectivity of CZE and particularly CEC will be effectively combined with the sensitivity of MS and the identification capabilities of tandem mass spectrometry (MS/MS) and MS hyphenated (MSn) techniques.

Capillary electrophoretic determination of trace metals in hair samples and its comparison with high performance liquid chromatography and atomic absorption spectrometry techniques.

Capillary electrophoresis (CE) is compared with high performance liquid chromatography (HPLC) and atomic absorption spectrometry (AA) for the determination of trace concentrations of selected metals in human hair. CE and HPLC methods are based upon the chelation of the metals with 2-(5'-bromo-2'-pyridylazo)-5-diethylamino phenol (5-Br-PADAP) followed by ultraviolet-visible (UV-Vis) detection. Large volume sample stacking (LVSS)-CE using injection times of up to 300 s is applied to the simultaneous determination of Co and Zn providing lower limits of detection (LODs) of 4.2 x 10(-8) mol dm(-3) and 6.0 x 10(-8) mol dm(-3), respectively, than can be achieved by conventional CE. The LVSS procedure could not be applied to hair samples due to a higher run current existing when the sample is introduced into the capillary. Conventional CE with cetyltrimethylammonium bromide (CTAB) present in the run buffer to retain the ligand in solution is used for the determination of metal concentrations in hair samples. Only Zn could be determined in this way as it exists at relatively high levels in hair. Co, Ni and Hg could be detected when spiked hair samples were analysed with estimated LODs of 5.0 x 10(-7) mol dm(-3), 1.0 x 10(-6) mol dm(-3) and 3.0 x 10(-5) mol dm(-3), respectively. HPLC was successfully used to determine Co and Cu in hair samples, with levels of 57.6 ppb and 17.31 ppm being found, respectively, and corresponded closely to results produced by AA. Fe also gave a signal together with unidentified coeluting species. In a separate HPLC study the determination of Ni and Hg as their complexes with hydrogen peroxide and 5-Br-PADAP was also investigated and LODs of 2.0 x 10(-6) mol dm(-3) and 5.0 x 10(-6) mol dm(-3), respectively, were achieved. AA was used as a reference method to determine levels of Co, Cu, Fe, Pb and Zn in hair and the results produced were in order of magnitude agreement with accepted literature values.

Large-volume sample stacking of selected drugs of forensic significance by capillary electrophoresis.

Large-volume sample stacking capillary electrophoresis (LVSS-CE) and conventional capillary electrophoresis (CE) are compared for the separation of drugs of significance to forensic and clinical analyses. LVSS-CE for cations requires the use of an electroosmotic flow (EOF) modifier in conjunction with polarity switching to effect on-column concentration of an analyte and its subsequent migration in the capillary. The run buffer consists of 0.05 mol dm(-3) disodium tetraborate adjusted to pH 2.2 with orthophosphoric acid, and the EOF modifier is 0.002 mol dm(-3) cetyltrimethylammonium bromide. CE investigations used an identical run buffer minus the EOF modifier. LVSS-CE and CE investigations used injection times of 30 s and 3 s, respectively. Both modes of capillary electrophoresis are compared in terms of their limits of detection, efficiency, resolution and reproducibility. LVSS-CE is also applied to the analysis of a spiked urine sample.

Capillary electrophoresis: a new tool in forensic toxicology. Applications and prospects in hair analysis for illicit drugs.

Capillary electrophoresis, the modern approach to instrumental electrophoresis, is probably the most rapidly expanding analytical technique that has appeared in recent years. In the hands of forensic toxicologists, capillary electrophoresis (CE) represents a powerful new analytical tool, which has proved suitable for the investigation of illicit drugs in seized preparations and also in complex biological matrices, among which is hair. CE can be applied according to different separation mechanisms, and among those that are toxicologically relevant are capillary zone electrophoresis and micellar electrokinetic capillary chromatography, which display different selectivities. For the investigation of hair for drugs of abuse, capillary electrophoresis proved effective, providing simultaneous determinations of different drugs without derivatization, with acceptable sensitivity (typically better than 1 ng of drug per mg of hair). The possibility of carrying out determinations of the same analytes, based on different separation mechanisms (capillary zone electrophoresis and micellar electrokinetic chromatography) with the same instrumentation, simply changing the buffer composition, provides an interesting possibility of 'internal' confirmation of the results.