Resequencing the Vrs1 gene in Spanish barley landraces revealed reversion of six-rowed to two-rowed spike

Six-rowed spike 1 (Vrs1) is a gene of major importance for barley breeding and germplasm management as it is the main gene determining spike row-type (2-rowed vs. 6-rowed). This is a widely used DUS trait, and has been often associated to phenotypic traits beyond spike type. Comprehensive re-sequencing Vrs1 revealed three two-rowed alleles (Vrs1.b2; Vrs1.b3; Vrs1.t1) and four six-rowed (vrs1.a1; vrs1.a2; vrs1.a3; vrs1.a4) in the natural population. However, the current knowledge about Vrs1 alleles and its distribution among Spanish barley subpopulations is still underexploited. We analyzed the gene in a panel of 215 genotypes, made of Spanish landraces and European cultivars. Among 143 six-rowed accessions, 57 had the vrs1.a1 allele, 83 were vrs1.a2, and three showed the vrs1.a3 allele. Vrs1.b3 was found in most two-rowed accessions, and a new allele was observed in 7 out of 50 two-rowed Spanish landraces. This allele, named Vrs1.b5, contains a ‘T’ insertion in exon 2, originally proposed as the causal mutation giving rise to the six-row vrs1.a2 allele, but has an additional upstream deletion that results in the change of 15 amino acids and a potentially functional protein. We conclude that eight Vrs1 alleles (Vrs1.b2, Vrs1.b3, Vrs1.b5, Vrs1.t1, vrs1.a1, vrs1.a2, vrs1.a3, vrs1.a4) discriminate two and six-rowed barleys. The markers described will be useful for DUS identification, plant breeders, and other crop scientists.This work was supported by the Spanish Ministry of Economy, Industry and Competitiveness grants AGL2010-21929, AGL2013-48756-R, RFP2012-00015-00-00, RTA2012-00033-C03-02, and EUI2009-04075 (national code for Plant-KBBE project ExpResBar). CPC was funded by the Spanish Ministry of Economy, Industry and Competitiveness grant no. BES-2011-045905 (linked to project AGL2010-21929). TK and SS were supported by a research fund by the Ministry of Agriculture, Forestry, and Fisheries of Japan (Genomics for Agricultural Innovation grants no. TRS1002). SS was supported by a Grant-in-Aid from the Japan Society for the Promotion of Science (JSPS) Postdoctoral Fellow for Research Abroad and a Grant-in-Aid for Young Scientists (B) (no. 16 K18635)

Candidate genes underlying QTL for flowering time and their interactions in a wide spring barley (Hordeum vulgare L.) cross

Response to vernalization and photoperiod are the main determinants controlling the time to flowering in temperate cereals. While the individual genes that determine a plant's response to these environmental signals are well characterized, the combinatorial effect on flowering time of allelic variants for multiple genes remains unresolved. This study investigated the genetic control of flowering-time in a biparental population of spring barley, derived from a wide cross between a late-flowering European and an early-flowering North-American cultivar. While the major flowering time genes are not segregating in the Beka × Logan cross, large variation in flowering was observed. We identified five QTL, with both parents found to contribute early alleles. The catalog of QTL discovered aligns with several candidate genes affecting flowering time in barley. The combination of particular alleles at HvCEN, HvELF3 and HvFT1 in Logan are responsible for the earliness of this cultivar. Interestingly, earliness for flowering could be further enhanced, with Beka found to contribute three early alleles, including a QTL co-locating with a HvFD-like gene, suggesting that there are diverse aspects of the flowering-time pathway that have been manipulated in these two cultivars. Epistatic interactions between flowering-time QTL or candidate genes were observed in field data and confirmed under controlled conditions. The results of this study link photoperiod-dependent flowering-time genes with earliness per se genes into a single model, thus providing a unique framework that can be used by geneticists and breeders to optimize flowering time in barley.This work was supported by the Spanish Ministry of Economy and Competitiveness (grant numbers AGL2010-21929 and AGL2013-48756-R), the Spanish Ministry of Economy and Competitiveness, the Agencia Estatal de Investigación, and the European Regional Development Fund (grant number AGL2016–80967-R), and Government of Aragon (Research Group A08_20R)

On the Nature and Genesis of EUV Waves: A Synthesis of Observations from SOHO, STEREO, SDO, and Hinode

A major, albeit serendipitous, discovery of the SOlar and Heliospheric Observatory mission was the observation by the Extreme Ultraviolet Telescope (EIT) of large-scale Extreme Ultraviolet (EUV) intensity fronts propagating over a significant fraction of the Sun's surface. These so-called EIT or EUV waves are associated with eruptive phenomena and have been studied intensely. However, their wave nature has been challenged by non-wave (or pseudo-wave) interpretations and the subject remains under debate. A string of recent solar missions has provided a wealth of detailed EUV observations of these waves bringing us closer to resolving their nature. With this review, we gather the current state-of-art knowledge in the field and synthesize it into a picture of an EUV wave driven by the lateral expansion of the CME. This picture can account for both wave and pseudo-wave interpretations of the observations, thus resolving the controversy over the nature of EUV waves to a large degree but not completely. We close with a discussion of several remaining open questions in the field of EUV waves research.Comment: Solar Physics, Special Issue "The Sun in 360",2012, accepted for publicatio

Fuzzy-stochastic FEM-based homogenization framework for materials with polymorphic uncertainties in the microstructure

Uncertainties in the macroscopic response of heterogeneous materials result from two sources: the natural variability in the microstructure's geometry and the lack of sufficient knowledge regarding the microstructure. The first type of uncertainty is denoted aleatoric uncertainty and may be characterized by a known probability density function. The second type of uncertainty is denoted epistemic uncertainty. This kind of uncertainty cannot be described using probabilistic methods. Models considering both sources of uncertainties are called polymorphic. In the case of polymorphic uncertainties, some combination of stochastic methods and fuzzy arithmetic should be used. Thus, in the current work, we examine a fuzzy‐stochastic finite element method–based homogenization framework for materials with random inclusion sizes. We analyze an experimental radii distribution of inclusions and develop a stochastic representative volume element. The stochastic finite element method is used to obtain the material response in the case of random inclusion radii. Due to unavoidable noise in experimental data, an insufficient number of samples, and limited accuracy of the fitting procedure, the radii distribution density cannot be obtained exactly; thus, it is described in terms of fuzzy location and scale parameters. The influence of fuzzy input on the homogenized stress measures is analyzed

Photonic Biosensor Assays to Detect and Distinguish Subspecies of Francisella tularensis

The application of photonic biosensor assays to diagnose the category-A select agent Francisella tularensis was investigated. Both interferometric and long period fiber grating sensing structures were successfully demonstrated; both these sensors are capable of detecting the optical changes induced by either immunological binding or DNA hybridization. Detection was made possible by the attachment of DNA probes or immunoglobulins (IgG) directly to the fiber surface via layer-by-layer electrostatic self-assembly. An optical fiber biosensor was tested using a standard transmission mode long period fiber grating of length 15 mm and period 260 μm, and coated with the IgG fraction of antiserum to F. tularensis. The IgG was deposited onto the optical fiber surface in a nanostructured film, and the resulting refractive index change was measured using spectroscopic ellipsometry. The presence of F. tularensis was detected from the decrease of peak wavelength caused by binding of specific antigen. Detection and differentiation of F. tularensis subspecies tularensis (type A strain TI0902) and subspecies holarctica (type B strain LVS) was further accomplished using a single-mode multi-cavity fiber Fabry-Perot interferometric sensor. These sensors were prepared by depositing seven polymer bilayers onto the fiber tip followed by attaching one of two DNA probes: (a) a 101-bp probe from the yhhW gene unique to type-A strains, or (b) a 117-bp probe of the lpnA gene, common to both type-A and type-B strains. The yhhW probe was reactive with the type-A, but not the type-B strain. Probe lpnA was reactive with both type-A and type-B strains. Nanogram quantities of the target DNA could be detected, highlighting the sensitivity of this method for DNA detection without the use of PCR. The DNA probe reacted with 100% homologous target DNA, but did not react with sequences containing 2-bp mismatches, indicating the high specificity of the assay. These assays will fill an important void that exists for rapid, culture-free, and field-compatible diagnosis of F. tularensis

Six-month color change and water sorption of 9 new-generation flowable composites in 6 staining solutions

Abstract Color match and water sorption are two factors that affect restorative materials. Discoloration is essential in the lifespan of restorations. The aim of this study was to evaluate color change and water sorption of nine flowable composites at multiple time points over 6 months. 60 samples of each composite were divided into two groups (Color Change and Water Sorption/Solubility). Each Color Change group was divided into six subgroups, which were immersed in distilled water (DW), coffee (CF), Coca-Cola (CC), red wine (RW), tea (TE) and orange juice (OJ). The color was measured at the baseline, 1, 2, 3 and 4 weeks, and 3 and 6 months and color change values (ΔE) were calculated. Each Water Sorption [WS]/Solubility [WL] group was tested according to ISO 4049:2009. The data were evaluated using two-way ANOVA, Fisher’s post-hoc test and Pearson’s correlation test. The composite with the lowest ΔE differed for each solution: Filtek™ Bulk Fill in DW (∆E = 0.73 (0.17–1.759)); Vertise Flow in CF (∆E = 14.75 (7.91–27.41)), in TE (∆E = 7.27 (2.81–24.81)) and OJ (∆E = 3.17 (0.87–9.92)); Tetric EvoFlow® in CC (∆E = 1.27 (0.45–4.02)); and Filtek™ Supreme XTE in RW (∆E = 8.88 (5.23–19.59)). RW caused the most discoloration (∆E = 23.62 (4.93–51.36)). Vertise Flow showed the highest water sorption (WS = 69.10 ± 7.19). The Pearson test showed statistically significant positive correlations between water sorption and solubility and between water sorption and ∆E; the positive solubility-∆E correlation was not statistically significant. The findings suggest that water sorption is one factor associated with the ability of composites to discolor; however, discoloration is a multifactorial problem

Characterization and Whole Genome Analysis of Human Papillomavirus Type 16 E1-1374^63nt Variants

Background. The variation of the most common Human papillomavirus (HPV) type found in cervical cancer, the HPV16, has been extensively investigated in almost all viral genes. The E1 gene variation, however, has been rarely studied. The main objective of the present investigation was to analyze the variability of the E6 and E1 genes, focusing on the recently identified E1-1374^63nt variant. Methodology/Principal Findings. Variation within the E6 of 786 HPV16 positive cervical samples was analyzed using high-resolution melting, while the E1-1374^63nt duplication was assayed by PCR. Both techniques were supplemented with sequencing. The E1-1374^63nt duplication was linked with the E-G350 and the E-C109/G350 variants. In comparison to the referent HPV16, the E1-1374^63nt E-G350 variant was significantly associated with lower grade cervical lesions (p=0.029), while the E1-1374^63nt E-C109/G350 variant was equally distributed between high and low grade lesions. The E1-1374^63nt variants were phylogenetically closest to E-G350 variant lineage (A2 sub-lineage based on full genome classification). The major differences between E1-1374^63nt variants were within the LCR and the E6 region. On the other hand, changes within the E1 region were the major differences from the A2 sub-lineage, which has been historically but inconclusively associated with high grade cervical disease. Thus, the shared variations cannot explain the particular association of the E1-1374^63nt variant with lower grade cervical lesions. Conclusions/Significance. The E1 region has been thus far considered to be well conserved among all HPVs and therefore uninteresting for variability studies. However, this study shows that the variations within the E1 region could possibly affect cervical disease, since the E1-1374^63nt E-G350 variant is significantly associated with lower grade cervical lesions, in comparison to the A1 and A2 sub-lineage variants. Furthermore, it appears that the silent variation 109T>C of the E-C109/G350 variant might have a significant role in the viral life cycle and warrants further study

Responsive Hydrogels for Label-Free Signal Transduction within Biosensors

Hydrogels have found wide application in biosensors due to their versatile nature. This family of materials is applied in biosensing either to increase the loading capacity compared to two-dimensional surfaces, or to support biospecific hydrogel swelling occurring subsequent to specific recognition of an analyte. This review focuses on various principles underpinning the design of biospecific hydrogels acting through various molecular mechanisms in transducing the recognition event of label-free analytes. Towards this end, we describe several promising hydrogel systems that when combined with the appropriate readout platform and quantitative approach could lead to future real-life applications

Augmented serum level of major histocompatibility complex class I-related chain A (MICA) protein and reduced NKG2D expression on NK and T cells in patients with cervical cancer and precursor lesions

<p>Abstract</p> <p>Background</p> <p>Cervical cancer is the second most common cancer in women worldwide. NK and cytotoxic T cells play an important role in the elimination of virus-infected and tumor cells through NKG2D activating receptors, which can promote the lysis of target cells by binding to the major histocompatibility complex class I-related chain A (MICA) proteins. Increased serum levels of MICA have been found in patients with epithelial tumors. The aim of this study was to compare the levels of soluble MICA (sMICA) and NKG2D-expressing NK and T cells in blood samples from patients with cervical cancer or precursor lesions with those from healthy donors.</p> <p>Methods</p> <p>Peripheral blood with or without heparin was collected to obtain mononuclear cells or sera, respectively. Serum sMICA levels were measured by ELISA and NKG2D-expressing immune cells were analyzed by flow cytometry. Also, a correlation analysis was performed to associate sMICA levels with either NKG2D expression or with the stage of the lesion.</p> <p>Results</p> <p>Significant amounts of sMICA were detected in sera from nearly all patients. We found a decrease in the number of NKG2D-expressing NK and T cells in both cervical cancer and lesion groups when compared to healthy donors. Pearson analysis showed a negative correlation between sMICA and NKG2D-expressing T cells; however, we did not find a significant correlation when the analysis was applied to sMICA and NKG2D expression on NK cells.</p> <p>Conclusion</p> <p>Our results show for the first time that high sMICA levels are found in sera from patients with both cervical cancer and precursor lesions when compared with healthy donors. We also observed a diminution in the number of NKG2D-expressing NK and T cells in the patient samples; however, a significant negative correlation between sMICA and NKG2D expression was only seen in T cells.</p