Cyanobacteria of the genus Nostoc are capable of forming symbioses with a wide range of organism, including a diverse assemblage of cyanolichens. Only certain lineages of Nostoc appear to be able to ...form a close, stable symbiosis, raising the question whether symbiotic competence is determined by specific sets of genes and functionalities.
We present the complete genome sequencing, annotation and analysis of two lichen Nostoc strains. Comparison with other Nostoc genomes allowed identification of genes potentially involved in symbioses with a broad range of partners including lichen mycobionts. The presence of additional genes necessary for symbiotic competence is likely reflected in larger genome sizes of symbiotic Nostoc strains. Some of the identified genes are presumably involved in the initial recognition and establishment of the symbiotic association, while others may confer advantage to cyanobionts during cohabitation with a mycobiont in the lichen symbiosis.
Our study presents the first genome sequencing and genome-scale analysis of lichen-associated Nostoc strains. These data provide insight into the molecular nature of the cyanolichen symbiosis and pinpoint candidate genes for further studies aimed at deciphering the genetic mechanisms behind the symbiotic competence of Nostoc. Since many phylogenetic studies have shown that Nostoc is a polyphyletic group that includes several lineages, this work also provides an improved molecular basis for demarcation of a Nostoc clade with symbiotic competence.
Bacteria are a major source of natural products that provide rich opportunities for both chemical and biological investigation. Although the vast majority of known bacterial metabolites derive from ...free-living organisms, increasing evidence supports the widespread existence of chemically prolific bacteria living in symbioses. A strategy based on bioinformatic prediction, symbiont cultivation, isotopic enrichment, and advanced analytics was used to characterize a unique polyketide, nosperin, from a lichen-associated Nostoc sp. cyanobacterium. The biosynthetic gene cluster and the structure of nosperin, determined from 30 μg of compound, are related to those of the pederin group previously known only from nonphotosynthetic bacteria associated with beetles and marine sponges. The presence of this natural product family in such highly dissimilar associations suggests that some bacterial metabolites may be specific to symbioses with eukaryotes and encourages exploration of other symbioses for drug discovery and better understanding of ecological interactions mediated by complex bacterial metabolites.
A Fortran-77 program for calculating test statistics to compare weighted histogram with an unweighted histogram and two histograms with weighted entries is presented. The code calculates test ...statistics for cases of histograms with normalized weights of events and unnormalized weights of events.
Program title: CHICOM
Catalogue identifier: AEKE_v1_0
Program summary URL:
http://cpc.cs.qub.ac.uk/summaries/AEKE_v1_0.html
Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland
Licensing provisions: Standard CPC license,
http://cpc.cs.qub.ac.uk/licence/licence.html
No. of lines in distributed program, including test data, etc.: 758
No. of bytes in distributed program, including test data, etc.: 4496
Distribution format: tar.gz
Programming language: Fortran-77
Computer: Any Unix/Linux workstation or PC with a Fortran-77 compiler
Operating system: Unix/Linux
Classification: 4.13, 11.9, 16.4, 19.4
External routines: FPLSOR (M103) 1 and BRENT 2 (FPLSOR is included in the distribution file, BRENT must be obtained by the user)
Nature of problem: The program calculates test statistics for comparing two weighted histograms and an unweighted histogram with a weighted one
Solution method: Calculation of test statistics is done according to formulas presented in Ref. 3.
Running time: 0.001 s for 5 bins histogram
References:
1
CERN Program Library,
http://cernlib.web.cern.ch/cernlib/.
2
W.H. Press, S.A. Teukolsky, W.T. Vetterling, B.P. Flannery, Numerical Recipes in Fortran 77 the Art of Scientific Computing, second edition, Cambridge University Press, 1997.
3
N.D. Gagunashvili, Nucl. Instr. Meth. A 614 (2010) 287–296.
► Program code of tests for comparing two weighted histograms and unweighted histogram with weighted histogram is presented. ► Tests are generalization of classical chi-square test that is used for comparing histograms with unweighted entries. ► Program calculates test statistics for comparing histograms with normalized weights as well as with unnormalized.
A Fortran-77 program for goodness of fit tests for histograms with weighted entries as well as with unweighted entries is presented. The code calculates test statistics for case of histogram with ...normalized weights of events and in case of unnormalized weights of events.
Program title: CHIWEI
Catalogue identifier: AEKQ_v1_0
Program summary URL:
http://cpc.cs.qub.ac.uk/summaries/AEKQ_v1_0.html
Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland
Licensing provisions: Standard CPC licence,
http://cpc.cs.qub.ac.uk/licence/licence.html
No. of lines in distributed program, including test data, etc.: 356
No. of bytes in distributed program, including test data, etc.: 2979
Distribution format: tar.gz
Programming language: Fortran-77
Computer: Any Unix/Linux workstation or PC with a Fortran-77 compiler
Operating system: Unix/Linux
Classification: 4.13, 11.9, 16.4, 19.4
External routines: FPLSOR (M103) 1 (included in the distribution file)
Nature of problem: The program calculates goodness of fit test statistics for weighted histograms.
Solution method: Calculation of test statistics is done according to formulas presented in Ref. 2.
Running time: 0.0001 seconds for 5 bins histogram.
References:
1
CERN Program Library,
http://cernlib.web.cern.ch/cernlib/.
2
N.G. Gagunashvili, Nucl. Instrum. Meth. A 596 (2008) 439.
A goodness-of-fit test for fitting of a parametric model to data obtained from a detector with finite resolution and limited acceptance is proposed. The parameters of the model are found by ...minimization of a statistic that is used for comparing experimental data and simulated reconstructed data. Numerical examples are presented to illustrate and validate the fitting procedure.
In this report, we present a European family with six individuals affected with Moyamoya disease (MMD). We detected two novel missense variants in the Moyamoya susceptibility gene
, c.12553A>G ...(p.(Lys4185Glu)) and c.12562G>A (p.(Ala4188Thr)). Cosegregation of the variants with MMD, as well as a previous report of a variant affecting the same amino acid residue in unrelated MMD patients, supports the role of
in the pathogenesis of MMD.
Chi-square tests for comparing weighted histograms Gagunashvili, N.D.
Nuclear instruments & methods in physics research. Section A, Accelerators, spectrometers, detectors and associated equipment,
03/2010, Letnik:
614, Številka:
2
Journal Article
Recenzirano
Odprti dostop
Weighted histograms in Monte Carlo simulations are often used for the estimation of probability density functions. They are obtained as a result of random experiments with random events that have ...weights. In this paper, the bin contents of a weighted histogram are considered as a sum of random variables with a random number of terms. Generalizations of the classical chi-square test for comparing weighted histograms are proposed. Numerical examples illustrate an application of the tests for the histograms with different statistics of events and different weighted functions. The proposed tests can be used for the comparison of experimental data histograms with simulated data histograms as well as for the two simulated data histograms.
A procedure based on a Mixture Density Model for correcting experimental data for distortions due to finite resolution and limited detector acceptance is presented. Addressing the case that the ...solution is known to be non-negative, in the approach presented here, the true distribution is estimated by a weighted sum of probability density functions with positive weights and with the width of the densities acting as a regularization parameter responsible for the smoothness of the result. To obtain better smoothing in less populated regions, the width parameter is chosen inversely proportional to the square root of the estimated density. Furthermore, the non-negative garrote method is used to find the most economic representation of the solution. Cross-validation is employed to determine the optimal values of the resolution and garrote parameters. The proposed approach is directly applicable to multidimensional problems. Numerical examples in one and two dimensions are presented to illustrate the procedure.
A new algorithm for extraction of asymmetries from polarized lepton–nucleon scattering data is proposed. The algorithm is stable to set-up acceptance and/or luminosity monitor acceptance variations. ...A statistical test for checking the data quality is proposed.
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