Application of numerical methods to simulate the unsteady flow of lean liquor solution through a porous medium made up of porous ore particles

Unsaturated flow of liquid in a bed of uniform and spherical ore particles is studied numerically and experimentally. An unsteady and two-dimensional model is developed based on the mass conservation equations of the liquid phase in the bed and in the particles. The model equations are solved using a fully implicit finite difference method giving the distribution of the degree of saturation in the particles and in the bed and the vertical velocity of flow in the bed, as well as, the effect of periodic infiltration on the above distributions. To calibrate the computational model, several column tests are performed using periodic infiltration of water on 40 cm high columns composed of ore having particles smaller than 25 mm. The numerical analysis shows that (a) the results obtained from numerical modelling under the same operating conditions as used for column tests, are in good agreement with those from the experimental procedure, (b) the degree of saturation of the bed and the time required to reach steady state conditions depend on the inflow of water and intrinsic permeability of the bed and (c) the velocity fluctuations and the fluctuations of the degree of saturation in the bed depend on the inflow of water, period of infiltration, height, and intrinsic permeability of the bed

Molecular characterization and similarity relationships among sunflower (Helianthus annuus L.) inbred lines using some mapped simple sequence repeats

Information about the genetic diversity and relationships among breeding lines and varieties is not only useful for germplasm conservation and inbred line identification, but also for the selection of parental lines for quantitative trait loci (QTL) mapping as well as hybrid breeding in crops, including sunflower. In order to develop mapping populations, genetic distances among twenty eight sunflower genotypes were evaluated using simple sequence repeat (SSR) markers. One hundred and two markers were generated by 38 SSR loci and the mean for the number of allele per locus was 2.32. Polymorphism information content (PIC) values ranged from 0.09 (locus ha3555) to 0.62 (locus ORS598) with an average of 0.41. Jaccard's coefficient similarity matrix for the studied sunflower  genotypes varied from 0.25 to 0.9 indicating a broad genetic base. The maximum similarity (0.9) was observed between genotypes RT931 and ENSAT-R5, while the lowest similarity (0.25) was between genotypes LC1064C and LR64. Based on unweighted pair group method with arithmetic mean (UPGMA) clustering algorithm, the studied genotypes were clustered in four groups. However, some genotypes have the same specific characters that influence their clustering, and as a result, the results of the principal coordinate analysis (PCoA) largely corresponded to those obtained through cluster analysis.Key words: Cluster analysis, genetic diversity, principal coordinate analysis, sunflower, simple sequence repeat

Genetic control of protein, oil and fatty acids content under partial drought stress and late sowing conditions in sunflower (Helianthus annuus)

The purpose of the present study was to map quantitative trait locus (QTLs) associated with percentage of seed protein, oil and fatty acids content under different conditions in a population of recombinant inbred lines (RILs) of sunflower. Three independent field experiments were conducted with well-, partial-irrigated and late-sowing conditions in randomized complete block design with three replications. High significant variation among genotypes is observed for the studied traits in all conditions. Several specific and non-specific QTLs for the aforementioned traits were detected. Under late-sowing condition, a specific QTL of palmitic acid content on linkage group 6 (PAC-LS.6) is located between ORS1233 and SSL66_1 markers. Common chromosomic regions are observed for percentage of seed oil and stearic acid content on linkage group 10 (PSO-PI.10 and SAC-WI.10) and 15 (PSO-PI.15 and SAC-LS.15). Overlapping occurs for QTLs of oleic and linoleic acids content on linkage groups 10, 11 and 16. Seven QTLs associated with palmitic, stearic, oleic and linoleic acids content are identified on linkage group 14. These common QTLs are linked to HPPD homologue, HuCL04260C001. Coincidence of the position for some detected QTLs and candidate genes involved in enzymatic and non-enzymatic antioxidants would be useful for the function of the respective genes in fatty acid stability.Key words: Sunflower, quantitative trait locus, simple sequence repeats, oil content, protein content, fatty acids

Electrophoretic Analysis of Total and Membrane Proteins of Xanthomonas campestris Pathovars, the Causal Agents of the Leaf Streak of Cereals and Grasses in Iran

Forty‐five Iranian isolates of Xanthomonas campestris obtained from wheat, barley and grasses were compared with reference strains using polyacrylamide gel electrophoresis (PAGE) of the whole‐cell and membrane proteins. The PAGE profiles of the whole‐cell and membrane proteins of the Iranian isolates obtained from barley, with the exception of IBLS 11 and IBLS 12, were identical and clearly distinguishable from those of the other isolates. The barley group isolates, which were pathogenic only to barley, were similar to UPB 458 (NCPPB 2389), the reference strain of pathovar hordei. The isolates obtained from wheat and grasses, as well as IBLS 11 and IBLS 12, which can infect wheat, barley and some wild grasses, had similar banding patterns: only IBLS 40 isolated from Hordeum sp. displayed the same profile as the barley group. Reference strains UPB 443 (NCPPB 2821) and UPB 513, which correspond to pathovars undulosa and translucens , respectively, were related to the wheat group. IBLS45, isolated from Bromus sp., had a banding pattern that differed from those observed for strains of the barley and wheat groups. The results suggest that this method can be useful for discriminating different pathovars of X. campestris attacking cereals and grasses, and sodium dodecyl sulphate (SDS)‐PAGE of membrane proteins was not more sensitive than SDS‐PAGE of total proteins for differentiating the isolates

Genetic analysis of partial resistance to bacterial leaf streak ( Xanthomonas campestris pv. cerealis ) in wheat

Genetic variability of partial resistance to bacterial leaf streak was investigated in hexaploid winter wheat (Triticum aestivum. ), using 16 parental genotypes and 48 pure lines (F10) derived from a composite cross programme. Two experiments were undertaken in a controlled growth chamber. Seeds of all genotypes were grown under controlled conditions using a randomized block design with three replications. Each replication consisted of a row of 20 seedlings of each parent and pure line. An Iranian strain of bacterial leaf streak was used for the inoculation of 12‐day‐old seedlings. In a third experiment, eight genotypes from parents and F10 pure lines representing a large variability for partial resistance were inoculated with four other Iranian strains of bacterial leaf streak. A large genetic variability was observed amongst the 64 genotypes for partial resistance to the disease. Partial resistance heritability estimates were rather high (70%), indicating that the resistance factors may be transmitted by crossing. Amongst all genotypes investigated, ‘DC2‐30‐N2’ and ‘IBPT‐66’ displayed the highest partial resistance to the disease. Significant correlations between strains in the third experiment show that a genotype resistant or susceptible to one strain will have similar reactions with other strains. No significant genetic gain was observed for partial resistance in the best pure line of the 48 lines studied, when compared with the best parental line. Increasing the number of pure lines is likely to result in the identification of genotypes that might prove to be more resistant

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Linearization and optimization of robot dynamics via inertial parameter design

In this article, the concept of linearity number (LN) is introduced to measure the ''linearity'' of the equations of motion of a serial manipulator. This number is computable in closed-form and is an average quantitative index of the degree of linearity of the robot over a specified region in the joint space. The definition is flexible, allowing the user to create custom-made definitions according to his or her specific needs. Using the concept of LN and the developed computer package CADLOR, one can design the kinematic and/or inertial parameters of the robot such that the robot is completely linear (or as linear as possible) and obtain the corresponding equations of motion in closed-form. Three manipulators are used to illustrate the linearization algorithm. The relation between LN and the performance of a linear controller is demonstrated by a case study in which the first 3 links of a PUMA 560 type robot is considered. (C) 1996 John Wiley & Sons, Inc