A saturated genetic linkage map of autotetraploid alfalfa (Medicago sativa L.) developed using genotyping-by-sequencing is highly syntenous with the Medicago truncatula genome.

A genetic linkage map is a valuable tool for quantitative trait locus mapping, map-based gene cloning, comparative mapping, and whole-genome assembly. Alfalfa, one of the most important forage crops in the world, is autotetraploid, allogamous, and highly heterozygous, characteristics that have impeded the construction of a high-density linkage map using traditional genetic marker systems. Using genotyping-by-sequencing (GBS), we constructed low-cost, reasonably high-density linkage maps for both maternal and paternal parental genomes of an autotetraploid alfalfa F1 population. The resulting maps contain 3591 single-nucleotide polymorphism markers on 64 linkage groups across both parents, with an average density of one marker per 1.5 and 1.0 cM for the maternal and paternal haplotype maps, respectively. Chromosome assignments were made based on homology of markers to the M. truncatula genome. Four linkage groups representing the four haplotypes of each alfalfa chromosome were assigned to each of the eight Medicago chromosomes in both the maternal and paternal parents. The alfalfa linkage groups were highly syntenous with M. truncatula, and clearly identified the known translocation between Chromosomes 4 and 8. In addition, a small inversion on Chromosome 1 was identified between M. truncatula and M. sativa. GBS enabled us to develop a saturated linkage map for alfalfa that greatly improved genome coverage relative to previous maps and that will facilitate investigation of genome structure. GBS could be used in breeding populations to accelerate molecular breeding in alfalfa

The roles of aldehyde dehydrogenases (ALDHs) in the PDH bypass of Arabidopsis

<p>Abstract</p> <p>Background</p> <p>Eukaryotic aldehyde dehydrogenases (ALDHs, EC 1.2.1), which oxidize aldehydes into carboxylic acids, have been classified into more than 20 families. In mammals, Family 2 ALDHs detoxify acetaldehyde. It has been hypothesized that plant Family 2 ALDHs oxidize acetaldehyde generated via ethanolic fermentation, producing acetate for acetyl-CoA biosynthesis via acetyl-CoA synthetase (ACS), similar to the yeast pathway termed the "pyruvate dehydrogenase (PDH) bypass". Evidence for this pathway in plants has been obtained from pollen.</p> <p>Results</p> <p>To test for the presence of the PDH bypass in the sporophytic tissue of plants, Arabidopsis plants homozygous for mutant alleles of all three Family 2 ALDH genes were fed with ¹⁴C-ethanol along with wild type controls. Comparisons of the incorporation rates of ¹⁴C-ethanol into fatty acids in mutants and wild type controls provided direct evidence for the presence of the PDH bypass in sporophytic tissue. Among the three Family 2 ALDHs, one of the two mitochondrial ALDHs (ALDH2B4) appears to be the primary contributor to this pathway. Surprisingly, single, double and triple ALDH mutants of Arabidopsis did not exhibit detectable phenotypes, even though a Family 2 ALDH gene is required for normal anther development in maize.</p> <p>Conclusion</p> <p>The PDH bypass is active in sporophytic tissue of plants. Blocking this pathway via triple ALDH mutants does not uncover obvious visible phenotypes.</p

Comparative gene expression profiles between heterotic and non-heterotic hybrids of tetraploid Medicago sativa

<p>Abstract</p> <p>Background</p> <p>Heterosis, the superior performance of hybrids relative to parents, has clear agricultural value, but its genetic control is unknown. Our objective was to test the hypotheses that hybrids expressing heterosis for biomass yield would show more gene expression levels that were different from midparental values and outside the range of parental values than hybrids that do not exhibit heterosis.</p> <p>Results</p> <p>We tested these hypotheses in three <it>Medicago sativa </it>(alfalfa) genotypes and their three hybrids, two of which expressed heterosis for biomass yield and a third that did not, using Affymetrix <it>M. truncatula </it>GeneChip arrays. Alfalfa hybridized to approximately 47% of the <it>M. truncatula </it>probe sets. Probe set signal intensities were analyzed using MicroArray Suite v.5.0 (MAS) and robust multi-array average (RMA) algorithms. Based on MAS analysis, the two heterotic hybrids performed similarly, with about 27% of genes showing differential expression among the parents and their hybrid compared to 12.5% for the non-heterotic hybrid. At a false discovery rate of 0.15, 4.7% of differentially expressed genes in hybrids (~300 genes) showed nonadditive expression compared to only 0.5% (16 genes) in the non-heterotic hybrid. Of the nonadditively expressed genes, approximately 50% showed expression levels that fell outside the parental range in heterotic hybrids, but only one of 16 showed a similar profile in the non-heterotic hybrid. Genes whose expression differed in the parents were three times more likely to show nonadditive expression than genes whose parental transcript levels were equal.</p> <p>Conclusion</p> <p>The higher proportions of probe sets with expression level that differed from the parental midparent value and that were more extreme than either parental value in the heterotic hybrids compared to a non-heterotic hybrid were also found using RMA. We conclude that nonadditive expression of transcript levels may contribute to heterosis for biomass yield in alfalfa.</p

Efficacy of relacin combined with sodium hypochlorite against Enterococcus faecalis biofilms

Objective: Relacin is a synthetic molecule that targets RelA, an essential protein in a conserved bacterial stress response system. It was shown to inhibit bacterial growth. The aims of this study were to evaluate the antimicrobial effect of relacin combined with sodium hypochlorite (NaOCl) on Enterococcus faecalis biofilms and to evaluate the cytotoxicity of relacin. Material and Methods: 48-h E. faecalis OG1RF biofilms were treated by various concentrations of relacin in order to determine its inhibitory concentration. Then, the 48-h biofilms were treated either with 1-min NaOCl (0.01%, 0.05%) alone, or in combination of relacin. As a means of comparison, the biofilms of ΔrelA were also treated by 1-min NaOCl (0.01%, 0.05%, 0.25%). The treatment efficacy was determined by agar plate count assays. The cytotoxicity of relacin was examined on human gingival epithelial cells Ca9-22 and murine fibroblasts NIH-3T3 by a methyl thiazolyltetrazolium (MTT) assay and a lactate dehydrogenase assay. Statistical analysis was performed by one-way or two-way analysis of variance (ANOVA) with Bonferroni’s post-hoc test and an independent Student’s t-test. A significance level of p&lt;0.05 was used. Results: Relacin inhibited the growth of OG1RF biofilms partially at 8 mM and fully at 14 mM. The relacin (14 mM) and NaOCl combined treatment resulted in significantly higher treatment efficacy than NaOCl treatment alone. At 0.05% NaOCl, the combined treatment resulted in 5.65 (±0.19) log reduction in biofilm viability. The ΔrelA biofilms were more susceptible to NaOCl treatment than the wild type biofilms at 0.25% NaOCl. Relacin at 14 mM was not toxic to host epithelial cells and fibroblasts. Conclusions: The combination of relacin with a low concentration of NaOCl was effective and not cytotoxic

Robust Calibrate Proxy Loss for Deep Metric Learning

The mainstream researche in deep metric learning can be divided into two genres: proxy-based and pair-based methods. Proxy-based methods have attracted extensive attention due to the lower training complexity and fast network convergence. However, these methods have limitations as the poxy optimization is done by network, which makes it challenging for the proxy to accurately represent the feature distrubtion of the real class of data. In this paper, we propose a Calibrate Proxy (CP) structure, which uses the real sample information to improve the similarity calculation in proxy-based loss and introduces a calibration loss to constraint the proxy optimization towards the center of the class features. At the same time, we set a small number of proxies for each class to alleviate the impact of intra-class differences on retrieval performance. The effectiveness of our method is evaluated by extensive experiments on three public datasets and multiple synthetic label-noise datasets. The results show that our approach can effectively improve the performance of commonly used proxy-based losses on both regular and noisy datasets

Research on Community Detection Algorithm Based on the UIR-Q

Aiming at the current problems of community detection algorithm in which user’s property is not used; the community structure is not stable and the efficiency of the algorithm is low, this paper proposes a community detection algorithm based on the user influence and its parallelization method. In terms of the concept of user influence in the subject communication and the PageRank algorithm, this paper uses the properties of nodes of users in social networks to form the user influence factors. Then, the user with the biggest influence is set as the initial node of new community and and the local modularity is introduced into detecting the community structure.  in order to make the result of community detection quick and efficient. Many experiments show that the improved algorithm can efficiently detect the community structure with large scale users and the results are stable. Therefore, this algorithm will have a wide applied prospect

H∞ model reduction for discrete-time Markovian jump systems with deficient mode information

This paper investigates the problem of H∞ model reduction for a class of discrete-time Markovian jump linear systems (MJLSs) with deficient mode information, which simultaneously involves the exactly known, partially unknown, and uncertain transition probabilities. By fully utilizing the properties of the transition probability matrices, together with the convexification of uncertain domains, a new H∞ performance analysis criterion for the underlying MJLSs is first derived, and then two approaches, namely, the convex linearisation approach and iterative approach, for the H∞ model reduction synthesis are proposed. Finally, a simulation example is provided to illustrate the effectiveness of the proposed design methods