Two-laboratory collaborative study on identification of mycobacteria: molecular versus phenotypic methods

Previous studies have indicated that the conventional tests used for the identification of mycobacteria may (i) frequently result in erroneous identification and (ii) underestimate the diversity within the genus Mycobacterium. To address this issue in a more systematic fashion, a study comparing phenotypic and molecular methods for the identification of mycobacteria was initiated. Focus was given to isolates which were difficult to identify to species level and which yielded inconclusive results by conventional tests performed under day-to-day routine laboratory conditions. Traditional methods included growth rate, colonial morphology, pigmentation, biochemical profiles, and gas-liquid chromatography of short-chain fatty acids. Molecular identification was done by PCR-mediated partial sequence analysis of the gene encoding the 16S rRNA. A total of 34 isolates was included in this study; 13 of the isolates corresponded to established species, and 21 isolates corresponded to previously uncharacterized taxa. For five isolates, phenotypic and molecular analyses gave identical results. For five isolates, minor discrepancies were present; four isolates remained unidentified after biochemical testing. For 20 isolates, major discrepancies between traditional and molecular typing methods were observed. Retrospective analysis of the data revealed that the discrepant results were without exception due to erroneous biochemical test results or interpretations. In particular, phenotypic identification schemes were compromised with regard to the recognition of previously undescribed taxa. We conclude that molecular typing by 16S rRNA sequence determination is not only more rapid (12 to 36 h versus 4 to 8 weeks) but also more accurate than traditional typing.     

Effect of nutrient seed coating on the emergence of wheat and oats

A series of experiments was conducted under controlled soil moisture and temperature conditions in a growth chamber to examine the effect of a range of nutrient seed coatings on the emergence to wheat (Triticum aestivum L. cv. Kite) and oats (Avena sativa L. cv. Blackbutt) sown in a coarse sandy loam soil. Final emergence of oats was not reduced by a coating containing 10 kg P ha^–1 (as monocalcium phosphate [MCP]) whereas the same coating reduced wheat emergence by 15%. The emergence of both wheat and oats was severely reduced by urea coatings (supplying 10 kg N ha^–1) to 33 and 13% respectively; this injury was lessened markedly by the inclusion of phenyl phosphorodiamidate (PPD) in the urea coatings at 1% (w/w) (emergence increased to 66 and 56% respectively).Low soil moisture (67% of field capacity [FC]) resulted in almost no emergence of wheat coated with urea (± bentonites of different pH). In soil at FC, the addition of bentonite of pH 5 (B5) to urea coatings permitted greater emergence (54%) than when bentonite of pH 9 (B9) was added (32%) which, in turn, permitted greater emergence than urea coating alone (10%). When PPD and bentonite (B5 or B9) were combined either singly or together with urea in seed coatings, PPD was more effective than either of the bentonites in reducing injury and masked the slight positive effect of B5.Coatings containing various combinations of N and P sources (at 3.6 and at 8 kg ha^–1 respectively) all reduced the emergence of wheat compared to raw seed (91% emergence). When applied alone, MCP was least damaging (74%); the combination of MCP with ammonium sulfate (AS) caused somewhat more injury (68%) whilst combination with calcium nitrate (CN) caused most injury (29%). In contrast, CN alone caused relatively little damage (73%) whilst AS alone was more damaging (50%). There was no significant regression found between percentage emergence and either the calculated partial salt index or the pH of the nutrient coatings. Further work is needed to examine the mechanisms of injury due to nutrient seed coatings so that safe but effective formulations can be developed.     

An improved version of ISICS: A program for calculating K-, L- and M-shell cross sections from PWBA and ECPSSR theory using a personal computer

The formatting of the M-shell atomic parameters imbedded in file XCSC.H in ISICS has been corrected. The problem only affected cross section calculations for Uranium and heavier elements. The corrected version of ISICS has been re-compiled and is now available.

New version program summary

Program title: ISICSCatalogue identifier: ADDS_v3_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADDS_v3_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 4645No. of bytes in distributed program, including test data, etc.: 106 731Distribution format: tar.gzProgramming language: C++Computer: 80486 or higher-level PCsOperating system: WINDOWS 98 through WINDOWS XPClassification: 16.7Does the new version supersede the previous version?: YesNature of problem: Ionization and X-ray production cross section calculations for ion-atom collisions.Solution method: Numerical integration of form factor using a logarithmic transform and Gaussian quadrature, plus exact integration limits.Reasons for new version: The formatting of the M-shell atomic parameters involving cross section calculations for Uranium and heavier elements needed to be corrected.Summary of revisions: The affected file XCSC.H in ISICS has been corrected and ISICS has been recompiled.Restrictions: The consumed CPU time increases with the atomic shell (K, L, M), but execution is still very fast.Running time: This depends on which shell and the number of different energies to be used in the calculation. For example, to calculate K-shell cross sections for protons striking carbon for 19 different proton energies it took less than 10 s; to calculate M-shell cross sections for protons on gold for 21 proton energies it took 4.2 min.     

The mitochondrial genome integrity gene, MGI1, of Kluyveromyces lactis encodes the beta-subunit of F1-ATPase

In a previous report, we found that mutations at the mitochondrial genome integrity locus, MGI1, can convert Kluyveromyces lactis into a petite-positive yeast. In this report, we describe the isolation of the MGI1 gene and show that it encodes the beta-subunit of the mitochondrial F1-ATPase. The site of mutation in four independently isolated mgi1 alleles is at Arg435, which has changed to Gly in three cases and Ile in the fourth isolate. Disruption of MGI1 does not lead to the production of mitochondrial genome deletion mutants, indicating that an assembled F1 complex is needed for the "gain-of-function" phenotype found in mgi1 point mutants. The location of Arg435 in the beta-subunit, as deduced from the three-dimensional structure of the bovine F1-ATPase, together with mutational sites in the previously identified mgi2 and mgi5 alleles, suggests that interaction of the beta- and alpha- (MGI2) subunits with the gamma-subunit (MGI5) is likely to be affected by the mutations.     

Incremental Linear Discriminant Analysis Using Sufficient Spanning Sets and Its Applications

This paper presents an incremental learning solution for Linear Discriminant Analysis (LDA) and its applications to object recognition problems. We apply the sufficient spanning set approximation in three steps i.e. update for the total scatter matrix, between-class scatter matrix and the projected data matrix, which leads an online solution which closely agrees with the batch solution in accuracy while significantly reducing the computational complexity. The algorithm yields an efficient solution to incremental LDA even when the number of classes as well as the set size is large. The incremental LDA method has been also shown useful for semi-supervised online learning. Label propagation is done by integrating the incremental LDA into an EM framework. The method has been demonstrated in the task of merging large datasets which were collected during MPEG standardization for face image retrieval, face authentication using the BANCA dataset, and object categorisation using the Caltech101 dataset.     

ISICS2011, an updated version of ISICS: A program for calculation K-, L-, and M-shell cross sections from PWBA and ECPSSR theories using a personal computer

In this new version of ISICS, called ISICS2011, a few omissions and incorrect entries in the built-in file of electron binding energies have been corrected; operational situations leading to un-physical behavior have been identified and flagged.

New version program summary

Program title: ISICS2011Catalogue identifier: ADDS_v5_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADDS_v5_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 6011No. of bytes in distributed program, including test data, etc.: 130 587Distribution format: tar.gzProgramming language: CComputer: 80486 or higher-level PCsOperating system: WINDOWS XP and all earlier operating systemsClassification: 16.7Catalogue identifier of previous version: ADDS_v4_0Journal reference of previous version: Comput. Phys. Commun. 180 (2009) 1716.Does the new version supersede the previous version?: YesNature of problem: Ionization and X-ray production cross section calculations for ion–atom collisions.Solution method: Numerical integration of form factor using a logarithmic transform and Gaussian quadrature, plus exact integration limits.Reasons for new version: General need for higher precision in output format for projectile energies; some built-in binding energies needed correcting; some anomalous results occur due to faulty read-in data or calculated parameters becoming un-physical; erroneous calculations could result for the L and M shells when restricted K-shell options are inadvertently chosen; to achieve general compatibility with ISICSoo, a companion C++ version that is portable to Linux and MacOS platforms, has been submitted for publication in the CPC Program Library approximately at the same time as this present new standalone version of ISICS [1].Summary of revisions: The format field for projectile energies in the output has been expanded from two to four decimal places in order to distinguish between closely spaced energy values. There were a few entries in the executable binding energy file that needed correcting; K shell of Eu, M shells of Zn, M1 shell of Kr. The corrected values were also entered in the ENERGY.DAT file. In addition, an alternate data file of binding energies is included, called ENERGY_GW.DAT, which is more up-to-date [2]. Likewise, an alternate atomic parameters data file is now included, called FLOURE_JC.DAT, which is more up-to-date [3] fluorescence yields for the K and L shells and Coster–Kronig parameters for the L shell. Both data files can be read in using the -f usage option. To do this, the original energy file should be renamed and saved (e.g., ENERGY_BB.DAT) and the new file (ENERGY_GW.DAT ) should be duplicated as ENERGY.DAT to be read in using the -f option. Similarly for reading in an alternate FLOURE.DAT file. As with previous versions, the user can also simply input different values of any input quantity by invoking the “specify your own parameters” option from the main menu. You can also use this option to simply check the values of the built-in values of the parameters. If it still happens that a zero binding energy for a particular sub-shell is read in, the program will not completely abort, but will calculate results for the other sub-shells while setting the affected sub-shell output to zero. In calculating the Coulomb deflection factor, if the quantity inside the radical sign of the parameter zs becomes zero or negative, to prevent the program from aborting, the PWBA cross sections are still calculated while the ECPSSR cross sections are set to zero. This situation can happen for very low energy collisions, such as were noticed for helium ions on copper at energies of E?11.2 keV. It was observed during the engineering of ISICSoo [1] that erroneous calculations could result for the L- and M-shell cases when restricted K-shell R or HSR scaling options were inappropriately chosen. The program has now been fixed so that these inappropriate options are ignored for the L and M shells. In the previous versions, the usage for inputting a batch data file was incorrectly stated in the Users Manual as -Bxxx; the correct designation is -Fxxx, or alternatively, -Ixxx, as indicated on the usage screen in running the program.A revised Users Manual is also available.Restrictions: The consumed CPU time increases with the atomic shell (K, L, M), but execution is still very fast.Running time: This depends on which shell and the number of different energies to be used in the calculation. The running time is not significantly changed from the previous version.References:

• [1] 

  M. Batic, M.G. Pia, S. Cipolla, Comput. Phys. Commun. (2011), submitted for publication.

• [2] 

  http://www.jlab.org/~gwyn/ebindene.html.

• [3] 

  J. Campbell, At. Data Nucl. Data Tables 85 (2003) 291.

     

Uncouplers can shuttle between localized energy-coupling sites during photophosphorylation by chromatophores of Rhodopseudomonas capsulata N22

Two models of the action of uncoupler molecules in inhibiting photophosphorylation in bacterial chromatophores are considered: either uncoupler molecules shuttle rapidly between energy-coupling sites, or uncoupler molecules that are bound to particular sites in the chromatophores for a time that is comparable with the turnover time of the photophosphorylation apparatus may uncouple by a co-operative "substoichiometric' mechanism. It is found that the titre of uncoupler necessary to cause complete uncoupling is lowered if the rate of photophosphorylation is initially decreased by partially restricting electron flow with an appropriate titre of antimycin A. This result indicates that uncoupler molecules shuttle rapidly between energy coupling in which the energized intermediate between electron transport and phosphorylation is delocalized over the entire chromatophore membrane and those in which it is not. If the rate of photophosphorylation is partially restricted with the covalent H+-translocating ATP synthase inhibitor dicyclohexylcarbodi-imide, the titre of uncoupler necessary to effect complete inhibition of photophosphorylation is also decreased relative to that in which the covalent H+-ATP synthase inhibitor is absent. This important result appears to be inconsistent with models of electron-transport phosphorylation in which the "energized state' of the chromatophore membrane that is set up by electron transport and utilized in photophosphorylation is delocalized over the entire chromatophore membrane.     

Analysis of the role of inhibition in shaping responses to sinusoidally amplitude-modulated signals in the inferior colliculus

Neurons in the central nucleus of the inferior colliculus (ICc) typically respond with phase-locked discharges to low rates of sinusoidal amplitude-modulated (SAM) signals and fail to phase-lock to higher SAM rates. Previous studies have shown that comparable phase-locking to SAM occurs in the dorsal nucleus of the lateral lemniscus (DNLL) and medial superior olive (MSO) of the mustache bat. The studies of MSO and DNLL also showed that the restricted phase-locking to low SAM rates is created by the coincidence of phase-locked excitatory and inhibitory inputs that have slightly different latencies. Here we tested the hypothesis that responses to SAM in the mustache bat IC are shaped by the same mechanism that shapes responses to SAM in the two lower nuclei. We recorded responses from ICc neurons evoked by SAM signals before and during the iontophoretic application of several pharmacological agents: bicuculline, a competitive antagonist for gamma-aminobutyric acid-A (GABAA) receptors; strychnine, a competitive antagonist for glycine receptors; the GABAB receptor blocker, phaclofen, and the N-methyl-D-aspartate (NMDA) receptor blocker, (-)-2-amino-5-phosphonopentanoic acid (AP5). The hypothesis that inhibition shapes responses to SAM signals in the ICc was not confirmed. In >90% of the ICc neurons tested, the range of SAM rates to which they phase-locked was unchanged after blocking inhibition with bicuculline, strychnine or phaclofen, applied either individually or in combination. We also considered the possibility that faster alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptors follow high temporal rates of incoming excitation but that the slower NMDA receptors could follow only lower rates. Thus at higher SAM rates, NMDA receptors might generate a sustained excitation that "smears" the phase-locked excitation generated by the AMPA receptors. The NMDA hypothesis, like the inhibition hypothesis, was also not confirmed. In none of the cells that we tested did the application of AP5 by itself, or in combination with bicuculline, cause an increase in the range of SAM rates that evoked phase-locking. These results illustrate that the same response property, phase-locking restricted to low SAM rates, is formed in more than one way in the auditory brain stem. In the MSO and DNLL, the mechanism is coincidence of phase-locked excitation and inhibition, whereas in ICc the same response feature is formed by a different but unknown mechanism.     

Bordetella pertussis adenylate cyclase toxin: proCyaA and CyaC proteins synthesised separately in Escherichia coli produce active toxin in vitro

We analyzed the role of Fyn tyrosine kinase in cell cycle progression of B lymphocyte progenitor (pro B cell). Whereas there were no substantial defects in the intramarrow B cell genesis in the fyn(-) mouse, and long-term proliferation of fyn(-) pro B cells was maintained in vitro under a serum containing culture condition, the cell cycle was arrested at G2/M upon serum deprivation. Morphological analyses demonstrated that the cytokinesis of fyn(-) pro B cells was retarded in the presence of serum and that the entry of fyn(-) pro B cells into late telophase was completely blocked under the serum-free condition. In contrast, the earlier phases of mitosis of fyn(-) pro B cells proceeded normally without FCS. This failure to initiate late telophase resulted in the accumulation of elliptical binucleated cells that might be the outcome of the nuclear division without cytokinesis. Consistent with this defect in the progression of cytokinesis, Fyn was localized in the midspace of dividing pro B cells at anaphase. These results suggested that Fyn localizes at the midspace of dividing pro B cells and regulates the progression of cytokinesis.