Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes

BACKGROUND: Codon usage bias has been widely reported to correlate with GC composition. However, the quantitative relationship between codon usage bias and GC composition across species has not been reported. RESULTS: Based on an informatics method (SCUO) we developed previously using Shannon informational theory and maximum entropy theory, we investigated the quantitative relationship between codon usage bias and GC composition. The regression based on 70 bacterial and 16 archaeal genomes showed that in bacteria, SCUO = -2.06 * GC3 + 2.05*(GC3)(2 )+ 0.65, r = 0.91, and that in archaea, SCUO = -1.79 * GC3 + 1.85*(GC3)(2 )+ 0.56, r = 0.89. We developed an analytical model to quantify synonymous codon usage bias by GC compositions based on SCUO. The parameters within this model were inferred by inspecting the relationship between codon usage bias and GC composition across 70 bacterial and 16 archaeal genomes. We further simplified this relationship using only GC3. This simple model was supported by computational simulation. CONCLUSIONS: The synonymous codon usage bias could be simply expressed as 1+ (p/2)log(2)(p/2) + ((1-p)/2)log(2)((l-p)/2), where p = GC3. The software we developed for measuring SCUO (codonO) is available at

Binomial version of Markov model of fatigue life of composite with two reasons for failure

A model of fatigue damage accumulation in laminate with two reasons for fatigue failure (the distortion of rigid items and the excessive yielding of the plastic part of the composite (matrix)) is offered. The model is based on the use of the Markov chains theory. It is shown how the corresponding transition probability matrix can be filled and how to calculate the mean time to failure, the variance of this time, and the probability distribution function. This model can be used as a nonlinear regression model for fatigue curve approximation and for fatigue damage accumulation description in program fatigue test. Processing of experimental data (fatigue test of carbon‐fiber reinforced laminate for fatigue curve building and for residual fatigue‐life investigation in program test with two levels of stress) shows that the model can be used for satisfactory description of the results of these tests. The specific feature of the model considered in this paper is the use of binomial distribution of failure of rigid items and the number of acts of yielding in the plastic part of the laminate. First Published Online: 14 Oct 201

A resistance gene to Ustilago nuda in barley is located on chromosome 3H

Canadian Journal of Plant Pathology website: http://www.tandfonline.com/loi/tcjp20Loose smut of barley is a common disease which can be controlled using resistant varieties. Information on the chromosome location of loci controlling loose smut resistance and the development of molecular markers to aid in selection for these genes can be beneficial in the resistant variety development process. The objectives of this work were to determine the resistance or susceptibility of doubled haploid barley lines arising from a cross of the varieties ‘Steptoe’ and ‘Morex’ to Ustilago nuda, the causal agent of loose smut of barley, and map the chromosome location of the loose smut resistance locus in ‘Morex’. The reaction to Ustilago nuda of the doubled-haploid barley plants was determined by inoculating spikelets of each line at anthesis by injection of a teliospore suspension using a needle inoculation method. Mature seeds from the inoculated spikelets were grown to determine the percentage of plants that developed with smutted heads. The lines were classified as susceptible if greater than 10% of the plants were smutted. The loose smut resistance locus from the resistant source ‘Morex’ was mapped using an existing DNA marker map of the ‘Steptoe’/‘Morex’ population. The distribution of the resistant and susceptible progeny from the loose smut testing fit a single gene model. The resistance gene was mapped to chromosome 3 (3H)

The rpg4/Rpg5 stem rust resistance locus in barley; resistance genes and cytoskeleton dynamics

Two closely linked resistance genes, rpg4 and Rpg5, conferring resistance to several races of Puccinia graminis, were cloned and characterized. The Rpg5 gene confers resistance to an isolate of Puccinia graminis f. sp. secalis (Pgs), while rpg4 confers resistance to Puccinia graminis f. sp. tritici (Pgt). Rpg5 is a novel gene containing nucleotide binding site-leucine rich repeat domains in combination with a serine threonine protein kinase domain. High-resolution mapping plus allele and recombinant sequencing identified the rpg4 gene, which encodes an actin depolymerizing factor-like protein (ADF2). Resistance against the Pgt races QCCJ, MCCF, TTKSK (aka Ug99) and RCRS requires both Rpg5 and rpg4, while Rpg5 alone confers resistance to Pgs isolate 92-MN-90. The dependency on the actin modifying protein ADF2 indicates cytoskeleton reorganization or redirection plays a role in pathogen-host interactions. Rpg5 may interact with ADF2 to activate or deactivate its function in the resistance response. Alternatively, Rpg5 could initiate signal transduction leading to resistance in response to detecting ADF2 protein modification. Pgt may redirect the actin cytoskeleton by inducing modifications of ADF2. The redirection of actin could possibly enable the pathogen to develop a haustoria-plant cell cytoskeleton interface for acquisition of nutrients

A short history of seminars on "recent research and design progress in aeronautical engineering and its influence on education"

The aeronautical sciences and aerospace industry are by nature international. Coming from this thesis, we decided in 1994 to organise an international meeting, further called the Seminar, devoted to “RECENT RESEARCH AND DESIGN PROGRESS IN AERONAUTICAL ENGINEERING AND ITS INFLUENCE ON EDUCATION”. The objective of that first Seminar and following ones was to organise a multinational forum for discussion and interchange of aeronautical issues and subjects, focusing on their influence on university education. Other goals included promoting international co-operation in the study of the problems in aeronautical science and technology in which there was a common interest and facilitating personal contacts between scientists, university lecturers, and industrial engineers. Our area of interest was aeronautical technology, as it is widely understood. The special focus of our Seminars was concentrated on Aircraft Design, Aircraft Oriented Aerodynamics, Flight Dynamics, Helicopter Dynamics, Computational Fluid Dynamics, Materials and Structures, Control and Flight Tests. All these topics and their influence on the teaching process at a technical university were considered — what we believe is a specific feature of our Seminars. We notice a mutual influence between contemporary research and education; it is impossible to deliver a modern university lecture without conducting one’s own serious research or design, and it is almost impossible to become a serious, successful researcher or designer without being a graduate of a good, contemporary university. The other specific feature of our Seminars is a student session. An international jury of professors and deans from aerospace faculties all over the world observes the sessions and awarded the best student papers diplomas (sometimes with small prizes contributed by different institutions). We believe that the student sessions promote personal contacts between students and foreign lecturers and encourage students to work harder in the future. For all of us, it is the promise of a new generation of engineers, designers and scientists. First published online: 14 Oct 201

Identification and mapping of a leaf rust resistance gene in barley line Q21861

Barley line Q21861 possesses an incompletely dominant gene (RphQ) for resistance to leaf rust caused by Puccinia hordei. To investigate the allelic and linkage relations between RphQ and other known Rph genes, F2 populations from crosses between Q21861 and donors of Rph1 to Rph14 (except for Rph8) were evaluated for leaf rust reaction at the seedling stage. Results indicate that RphQ is either allelic with or closely linked to the Rph2 locus. A doubled haploid population derived from a cross between Q21861 and SM89010 (a leaf rust susceptible line) was used for molecular mapping of the resistance locus. Bulked segregant analysis was used to identify markers linked to RphQ, using random amplified polymorphic DNAs (RAPDs), restriction fragment length polymorphisms (RFLPs), and sequence tagged sites (STSs). Of 600 decamer primers screened, amplified fragments generated by 9 primers were found to be linked to the RphQ locus; however, only 4 of them were within 10 cM of the target. The RphQ locus was mapped to the centromeric region of chromosome 7, with a linkage distance of 3.5 cM from the RFLP marker CDO749. Rrn2, an RFLP clone from the ribosomal RNA intergenic spacer region, was found to be very closely linked with RphQ, based on bulked segregant analysis. An STS marker, ITS1, derived from Rrn2, was also closely linked (1.6 cM) to RphQ

Identification of QTLs Associated with Fusarium Head Blight Resistance in Barley Accession CIho 4196

Fusarium head blight (FHB), incited by Fusarium graminearum Schwabe [teleomorph Gibberella zea (Schwein)], reduces quality of harvested barley (Hordeum vulgare L.) because of blighted kernels and the presence of deoxynivalenol (DON), a mycotoxin produced by the pathogen. CIho 4196, a two-rowed type, is one of the most resistant accessions known in barley; however, it possesses many undesirable agronomic traits. To better understand the genetics of reduced FHB severity and DON accumulation conferred by CIho 4196, a genetic map was generated using a population of recombinant inbred lines derived from a cross between Foster (a six-rowed malting cultivar) and CIho 4196. Quantitative trait loci (QTL) analyses were performed using data obtained from 10 field environments. The possible associations of resistance QTLs and various agronomic and morphological traits in barley also were investigated. The centromeric region of chromosome 2H flanked by the markers ABG461C and MWG882A (bins 6–10) likely (P\u3c0.001) contains two QTLs contributing to lower FHB severity and plant height, and one QTL each for DON accumulation, days to heading, and rachis node number. The QTL for low FHB severity in the bin 8 region explained from 3 to 9% of the variation, while the QTL in the bin 10 region explained from 17 to 60% of the variation. A QTL for DON accumulation that explained 9 to 14% of the variation was found in the bin 2 region of chromosome 4H. This may represent a new QTL not present in other FHB resistant sources. Resistance QTLs in the bin 8 region and bin 10 region of chromosome 2HL were provisionally designated Qrgz-2H-8 and Qrgz-2H-10, respectively. The QTL for DON accumulation in chromosome 4H was provisionally named QDON-4H-2