Development of a D genome specific marker resource for diploid and hexaploid wheat

Background: Mapping and map-based cloning of genes that control agriculturally and economically important traits remain great challenges for plants with complex highly repetitive genomes such as those within the grass tribe, Triticeae. Mapping limitations in the Triticeae are primarily due to low frequencies of polymorphic gene markers and poor genetic recombination in certain genetic regions. Although the abundance of repetitive sequence may pose common problems in genome analysis and sequence assembly of large and complex genomes, they provide repeat junction markers with random and unbiased distribution throughout chromosomes. Hence, development of a high-throughput mapping technology that combine both gene-based and repeat junction-based markers is needed to generate maps that have better coverage of the entire genome. Results: In this study, the available genomics resource of the diploid Aegilop tauschii, the D genome donor of bread wheat, were used to develop genome specific markers that can be applied for mapping in modern hexaploid wheat. A NimbleGen array containing both gene-based and repeat junction probe sequences derived from Ae. tauschii was developed and used to map the Chinese Spring nullisomic-tetrasomic lines and deletion bin lines of the D genome chromosomes. Based on these mapping data, we have now anchored 5,171 repeat junction probes and 10,892 gene probes, corresponding to 5,070 gene markers, to the delineated deletion bins of the D genome. The order of the gene-based markers within the deletion bins of the Chinese Spring can be inferred based on their positions on the Ae. tauschii genetic map. Analysis of the probe sequences against the Chinese Spring chromosome sequence assembly database facilitated mapping of the NimbleGen probes to the sequence contigs and allowed assignment or ordering of these sequence contigs within the deletion bins. The accumulated length of anchored sequence contigs is about 155 Mb, representing ~ 3.2 % of the D genome. A specific database was developed to allow user to search or BLAST against the probe sequence information and to directly download PCR primers for mapping specific genetic loci. Conclusions: In bread wheat, aneuploid stocks have been extensively used to assign markers linked with genes/traits to chromosomes, chromosome arms, and their specific bins. Through this study, we added thousands of markers to the existing wheat chromosome bin map, representing a significant step forward in providing a resource to navigate the wheat genome. The database website (http://probes.pw.usda.gov/ATRJM/) provides easy access and efficient utilization of the data. The resources developed herein can aid map-based cloning of traits of interest and the sequencing of the D genome of hexaploid wheat.Keywords: Recombination, Repeat junction markers, Genetic map, NimbleGen array, Molecular markers, Wheat deletion bin

Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii

BACKGROUND: Development of a high quality reference sequence is a daunting task in crops like wheat with large (~17Gb), highly repetitive (>80%) and polyploid genome. To achieve complete sequence assembly of such genomes, development of a high quality physical map is a necessary first step. However, due to the lack of recombination in certain regions of the chromosomes, genetic mapping, which uses recombination frequency to map marker loci, alone is not sufficient to develop high quality marker scaffolds for a sequence ready physical map. Radiation hybrid (RH) mapping, which uses radiation induced chromosomal breaks, has proven to be a successful approach for developing marker scaffolds for sequence assembly in animal systems. Here, the development and characterization of a RH panel for the mapping of D-genome of wheat progenitor Aegilops tauschii is reported. RESULTS: Radiation dosages of 350 and 450 Gy were optimized for seed irradiation of a synthetic hexaploid (AABBDD) wheat with the D-genome of Ae. tauschii accession AL8/78. The surviving plants after irradiation were crossed to durum wheat (AABB), to produce pentaploid RH(1)s (AABBD), which allows the simultaneous mapping of the whole D-genome. A panel of 1,510 RH(1) plants was obtained, of which 592 plants were generated from the mature RH(1) seeds, and 918 plants were rescued through embryo culture due to poor germination (<3%) of mature RH(1) seeds. This panel showed a homogenous marker loss (2.1%) after screening with SSR markers uniformly covering all the D-genome chromosomes. Different marker systems mostly detected different lines with deletions. Using markers covering known distances, the mapping resolution of this RH panel was estimated to be <140kb. Analysis of only 16 RH lines carrying deletions on chromosome 2D resulted in a physical map with cM/cR ratio of 1:5.2 and 15 distinct bins. Additionally, with this small set of lines, almost all the tested ESTs could be mapped. A set of 399 most informative RH lines with an average deletion frequency of ~10% were identified for developing high density marker scaffolds of the D-genome. CONCLUSIONS: The RH panel reported here is the first developed for any wild ancestor of a major cultivated plant species. The results provided insight into various aspects of RH mapping in plants, including the genetically effective cell number for wheat (for the first time) and the potential implementation of this technique in other plant species. This RH panel will be an invaluable resource for mapping gene based markers, developing a complete marker scaffold for the whole genome sequence assembly, fine mapping of markers and functional characterization of genes and gene networks present on the D-genome

Investigation of ATG16L1 rs2241880 Polymorphism with Cancer Risk: A Meta-Analysis

Background and Objectives: Previous studies have investigated the impact of the ATG16L1 rs2241880 (Thr300Ala) polymorphism on individual susceptibility to cancer, but the conclusions are still controversial. To get a more precise evaluation of the correlation between ATG16L1 rs2241880 polymorphism and cancer susceptibility, we performed a meta-analysis of the association of all eligible studies. Materials and Methods: Searches were performed in the Web of Science, PubMed, Scopus and Google Scholar databases up to November 2018. A total of 12 case-control studies from 9 articles comprising 2254 cases and 4974 controls were included. Statistical analysis was achieved by STATA 14.1 and Review Manager 5.3 software. The odds ratios (ORs) with 95% confidence intervals (95% CIs) under five genetic models were used to determine the strength of association among rs2241880 polymorphism and cancer susceptibility. Results: The findings did not support an association between the rs2241880 variant in either the overall study population or the subgroups, based on cancer types and ethnicity in any of the genetic models. As far as we know, our study is the first meta-analysis of the association between rs2241880 polymorphism and cancer risk. Conclusions: In conclusion, the findings of this meta-analysis proposes that the ATG16L1 rs2241880 polymorphism may not play a role in cancer development. Further well-designed studies are necessary to clarify the precise role of the ATG16L1 rs2241880 polymorphism on cancer risk

Performance Enhancement of an Adaptive Dynamic Extensible Processor by Using a Heterogeneous Reconfigurable Functional Unit

International SoC Design Conference : October 15-16 : KoreaIn this paper, we develop a heterogeneous architecture for the reconfigurable functional unit of an extensible processor. To verify the efficiency of our architecture, we applied it to 8 applications of Mibench. The new architecture improves execution time of custom instructions by 20% to 30% on average while supporting more custom instructions. The area and the total wire length are reduced by 15% and 20% respectively. In addition, depending on the custom instructions being run on the unit, average dynamic power consumption is reduced by 9% making this unit more suitable for embedded applications

An efficient Heterogeneous Reconfigurable Functional Unit for an Adaptive Dynamic Extensible Processor

15th Annual IFIP International Conference on Very Large Scale Integration : VLSI-SoC 2007 : October 15-17, 2007 : Atlanta, U.S.A.Replacing functional units of an extensible processor with reconfigurable functional units enhances performance and flexibility of processors to execute custom instructions. That is due to the ability of reconfigurable functional units to perform computations in hardware to increase performance, while retaining much of the flexibility of a software solution. In this paper, we develop a heterogeneous architecture for the reconfigurable functional unit of an extensible processor. To verify the efficiency of our architecture, we applied it to 8 applications of Mibench. Our experiments show that compared to the similar architectures, ours supports a wide range of custom instructions. In addition, use of the new architecture improves execution time of custom instructions by 20% to 30% on average. Moreover, compared with the previous architecture, area is reduced by 15%

An efficient Heterogeneous Reconfigurable Functional Unit for an Adaptive Dynamic Extensible Processor

15th Annual IFIP International Conference on Very Large Scale Integration : VLSI-SoC 2007 : October 15-17, 2007 : Atlanta, U.S.A.Replacing functional units of an extensible processor with reconfigurable functional units enhances performance and flexibility of processors to execute custom instructions. That is due to the ability of reconfigurable functional units to perform computations in hardware to increase performance, while retaining much of the flexibility of a software solution. In this paper, we develop a heterogeneous architecture for the reconfigurable functional unit of an extensible processor. To verify the efficiency of our architecture, we applied it to 8 applications of Mibench. Our experiments show that compared to the similar architectures, ours supports a wide range of custom instructions. In addition, use of the new architecture improves execution time of custom instructions by 20% to 30% on average. Moreover, compared with the previous architecture, area is reduced by 15%

Prediction of shear wave velocity using empirical correlations and artificial intelligence methods

Good understanding of mechanical properties of rock formations is essential during the development and production phases of a hydrocarbon reservoir. Conventionally, these properties are estimated from the petrophysical logs with compression and shear sonic data being the main input to the correlations. This is while in many cases the shear sonic data are not acquired during well logging, which may be for cost saving purposes. In this case, shear wave velocity is estimated using available empirical correlations or artificial intelligent methods proposed during the last few decades. In this paper, petrophysical logs corresponding to a well drilled in southern part of Iran were used to estimate the shear wave velocity using empirical correlations as well as two robust artificial intelligence methods knows as Support Vector Regression (SVR) and Back-Propagation Neural Network (BPNN). Although the results obtained by SVR seem to be reliable, the estimated values are not very precise and considering the importance of shear sonic data as the input into different models, this study suggests acquiring shear sonic data during well logging. It is important to note that the benefits of having reliable shear sonic data for estimation of rock formation mechanical properties will compensate the possible additional costs for acquiring a shear log

Graphene oxide strongly inhibits amyloid beta fibrillation

Since amyloid beta fibrillation (AbF) plays an important role in the development of neurodegenerative diseases, we investigated the effect of graphene oxide (GO) and their protein-coated surfaces on the kinetics of Ab fibrillation in the aqueous solution. We showed that GO and their protein-covered surfaces delay the AbF process via adsorption of amyloid monomers. Also, the large available surface of GO sheets can delay the AbF process by adsorption of amyloid monomers. The inhibitory effect of the GO sheet was increased when we increase the concentration from 10% (in vitro; stimulated media) to 100% (in vivo; stimulated media). Conclusion: our results revealed that GO and their surface proteins inhibit AbF by decreasing the kinetic reaction

Evaluation of Antibacterial Properties of Dental Adhesives Containing Metal Nanoparticles

Statement of problem: Secondary dental caries is a common clinical finding in composite restoration. The development of a bactericidal dental adhesive provides a promising method to reduce the risk of secondary caries. Objectives: This study aimed to assess the antibacterial activity of silver (Ag) and titanium dioxide (TiO2) nanoparticles incorporated into an experimental dentin bonding agent formulation. Materials and Methods: Ag and TiO2 nanoparticles at 0.05, 0.1, 0.2, 0.5, and 1 wt% concentrations were incorporated into the adhesives. The suspensions were sonicated to ensure homogenous dispersion of nanoparticles in the adhesive system. Formulation was composed of acetone, 2,2-bis[4-(2-hydroxy-3-methacryloxypropoxy)phenyl]propane (Bis-GMA), 1,6-bis-[2-methacryloyloxyethyl carbonyl amino]-2,4,4-trimethylhexane (UDMA), trimethylolpropane trimethacrylate (TMPTMA), 2-hydroxyethyl methacrylate (HEMA), and photoinitiator, with polyvinylpyrrolidone (PVP) as the stabilizer. We counted the colony-forming units (CFU%) of two cariogenic bacteria, Streptococcus mutans (S. mutans) and Lactobacillus acidophilus (L. acidophilus), that were exposed to the powdered light cured adhesive specimens. The effects of various concentrations of each nanoparticle were compared by one-way ANOVA, followed by the post hoc Bonferroni test. Results: All samples exhibited definite antibacterial activity (P<0.05) compared to the control specimens. The Ag nanoparticle samples showed higher antibacterial properties compared to the TiO2 nanoparticle samples. Increasing the concentration of nanoparticles resulted in significant differences in bactericidal properties, with the exception of 0.2 to 0.5 wt% Ag nanoparticle specimens exposed to S. mutans and the 0.2 to 0.5 wt% TiO2 nanoparticle specimens exposed to L. acidophilus. Conclusions: These metal-based nanoparticles exhibited dose-dependent bactericidal activities. The Ag nanoparticles had higher antibacterial activity compared to the TiO2 nanoparticles. Incorporation of these nanoparticles into dental adhesives is a promising way to reduce the risk of secondary caries. However, further clinical evaluations should be performed

LAPTM4B gene polymorphism augments the risk of cancer: Evidence from an updated meta-analysis

International audienceLysosome‐associated protein transmembrane‐4 beta (LAPTM4B) has two alleles named as LAPTM4B*1 and LAPTM4B*2 (GenBank No. AY219176 and AY219177). Allele *1 has a single copy of a 19‐bp sequence in the 5` untranslated region (5`UTR), but allele *2 contains tandem repeats of 19‐bp sequence.1 LAPTM4B gene is located on long chromosome 8 (8q22.1) and contains seven exons that encodes two isoforms of tetratransmembrane proteins, LAPTM4B‐24 and LAPTM4B‐35, with molecular weights of 25 kDa and 35 kDa respectively. The LAPTM4B‐35′s primary structure is formed by 317 amino acid residues, and LAPTM4B‐24 comprised 226 amino acids. LAPTM4B, an integral membrane protein, contains several lysosomal‐targeting motifs at the C terminus and colocalizes with late endosomal and lysosomal markers. LAPTM4B is a proto‐oncogene, which becomes up‐regulated in various cancers. Preceding studies have examined the possible link between LAPTM4B polymorphism and susceptibility to several cancers,1-26 but the findings are still inconsistent. Hence, the present meta‐analysis was designed to investigate the impact of LAPTM4B polymorphism on risk of cancer