IMPLEMENTATION OF GENOME-WIDE SELECTION IN WHEAT

With the expected development of thousands of molecular markers in most crops, the marker-assisted selection theory has recently shifted from the use of a few markers targeted in QTL regions (or derived from candidate or validated genes) to the use of many more markers covering the whole genome. These genome-wide markers are already used for association analysis between polymorphisms for anonymous markers and qualitative or quantitative traits. The condition for success is that a sufficient level of linkage disequilibrium (LD) exists between the adjacent markers used for genotyping and the true genes or QTLs. This LD is known to vary among species and type of genetic material. In selfing species, particularly among breeding lines, LD has been reported to range up to 1 cM or more. In such conditions, uncharacterized markers can be used to predict the breeding value of a trait without referring to actual QTLs. We present an example applying DArT markers to the INRA wheat breeding material in an attempt to implement whole genome selection as an alternative to phenotypic selection. This study assesses different models (GBLUP, Ridge Regression BLUP, Bayesian Ridge Regression and Lasso) and their ability to predict the yields of genotypes evaluated in a multi-site network from 2000 to 2009 in a highly unbalanced design. The prediction coefficients obtained by cross-validation techniques are encouraging, given the small size of the training population

Gastric aspiration, epithelial injury and chronic lung allograft rejection

Introduction For patients with a variety of end stage lung diseases, lung transplantation has become an effective therapy. Chronic allograft rejection occurs in over 50% of patients 5 years post transplantation however. Although alloimmune-mediated injury directed against endothelial and epithelial structures were traditionally thought to be the major culprit, non-alloimmunologic inflammation after bile acid aspiration has been implicated in cystic fibrosis (CF) lung injury, after transplantation. Hypothesis Reflux with aspiration of bile acid is present in the lower airways of people with cystic fibrosis associated lung injury before and after transplantation. Bile acid challenge would cause cytoxicity and release of inflammatory mediators from patient derived primary epithelial cells (PBECs), before and after transplantation. Methods PBECs from lung transplantation patients, explanted CF patient cultures and a goblet cell line were used to perform proof of concept experiments. In these experiments the effect of individual primary and secondary bile acids, porcine pepsin, different patient derived gastric juices (whole or filtered and dialysed) samples and an artificial bile acid mixture were evaluated. Cell death, Interleukin 8 (IL-8), Interleukin 6 (IL-6) and Granulocyte Macrophage Colony Stumulating Factor (GMCSF) production were measured by Titer blue and multiplex ELISA. Results Epithelial cells can be cultured successfully from the bronchial brushings of lung transplant recipient, CF patient explanted lungs and a Goblet cell line. In work connected with this study my research group has demonstrated that the lungs of people with advanced CF lung disease removed at the time of transplantation contained significant levels of bile acids higher than expected based on normal serum levels. I therefore tested the effects of bile acids on PBECs from lung transplant and CF patients. Challengesof ≥10mol/l was associated with significant cell death. Potentially physiological challenges with 1, 5 and 10 mol/l bile acids led to a significant release of pro-neutrophilic cytokines from lung transplant PBECs and CF PBECs .The goblet cell line HT-29 MTX was resistant to bile acids. Conclusion Aspiration of bile acids in CF lungs before and after transplantation may cause cell damage and inflammation. This injury may benefit from medical and surgical treatments for reflux, which may benefit the lung allograft generally.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Scalable Synthesis of Few-Layered 2D Tungsten Diselenide (2H-WSe2) Nanosheets Directly Grown on Tungsten (W) Foil Using Ambient-Pressure Chemical Vapor Deposition for Reversible Li-Ion Storage

We report a facile two-furnace APCVD synthesis of 2H-WSe2. A systematic study of the process parameters is performed to show the formation of the phase-pure material. Extensive characterization of the bulk and exfoliated material confirm that 2H-WSe2 is layered (i.e., 2D). X-ray diffraction (XRD) confirms the phase, while high-resolution scanning electron microscopy (HRSEM), high-resolution transmission electron microscopy (HRTEM), and atomic force microscopy (AFM) clarify the morphology of the material. Focused ion beam scanning electron microscopy (FIB-SEM) estimates the depth of the 2H-WSe2 formed on W foil to be around 5-8 μm, and Raman/UV-vis measurements prove the quality of the exfoliated 2H-WSe2. Studies on the redox processes of lithium-ion batteries (LiBs) show an increase in capacity up to 500 cycles. On prolonged cycling, the discharge capacity up to the 50th cycle at 250 mA/g of the material shows a stable value of 550 mAh/g. These observations indicate that exfoliated 2H-WSe2 has promising applications as an LiB electrode material

Graphene FET Sensors for Alzheimer’s Disease Protein Biomarker Clusterin Detection

We report on the fabrication and characterisation of graphene field-effect transistor (GFET) biosensors for the detection of Clusterin, a prominent protein biomarker of Alzheimer’s disease (AD). The GFET sensors were fabricated on Si/SiO2 substrate using photolithographic patterning and metal lift-off techniques with evaporated chromium and sputtered gold contacts. Raman Spectroscopy was performed on the devices to determine the quality of the graphene. The GFETs were annealed to improve their performance before the channels were functionalized by immobilising the graphene surface with linker molecules and anti-Clusterin antibodies. Concentration of linker molecules was also independently verified by absorption spectroscopy using the highly collimated micro-beam light of Diamond B23 beamline. The detection was achieved through the binding reaction between the antibody and varying concentrations of Clusterin antigen from 1 to 100 pg/mL, as well as specificity tests using human chorionic gonadotropin (hCG), a glycoprotein risk biomarker of certain cancers. The GFETs were characterized using direct current (DC) 4-probe electrical resistance (4-PER) measurements, which demonstrated a limit of detection of the biosensors to be ∼ 300 fg/mL (4 fM). Comparison with back-gated Dirac voltage shifts with varying concentration of Clusterin show 4-PER measurements to be more accurate, at present, and point to a requirement for further optimisation of the fabrication processes for our next generation of GFET sensors. Thus, we have successfully fabricated a promising set of GFET biosensors for the detection of Clusterin protein biomarker. The developed GFET biosensors are entirely generic and also have the potential to be applied to a variety of other disease detection applications such as Parkinson’s, cancer, and cardiovascular.</jats:p

Evolutionary relationships between Rhynchosporium lolii sp. nov. and other Rhynchosporium species on grass.

Copyright: 2013 King et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedThe fungal genus Rhynchosporium (causative agent of leaf blotch) contains several host-specialised species, including R. commune (colonising barley and brome-grass), R. agropyri (couch-grass), R. secalis (rye and triticale) and the more distantly related R. orthosporum (cocksfoot). This study used molecular fingerprinting, multilocus DNA sequence data, conidial morphology, host range tests and scanning electron microscopy to investigate the relationship between Rhynchosporium species on ryegrasses, both economically important forage grasses and common wild grasses in many cereal growing areas, and other plant species. Two different types of Rhynchosporium were found on ryegrasses in the UK. Firstly, there were isolates of R. commune that were pathogenic to both barley and Italian ryegrass. Secondly, there were isolates of a new species, here named R. lolii, that were pathogenic only to ryegrass species. R. lolii was most closely related to R. orthosporum, but exhibited clear molecular, morphological and host range differences. The species was estimated to have diverged from R. orthosporum ca. 5735 years before the present. The colonisation strategy of all of the different Rhynchosporium species involved extensive hyphal growth in the sub-cuticular regions of the leaves. Finally, new species-specific PCR diagnostic tests were developed that could distinguish between these five closely related Rhynchosporium species.Peer reviewedFinal Published versio

Structure and expression analysis of rice paleo duplications

Having a well-known history of genome duplication, rice is a good model for studying structural and functional evolution of paleo duplications. Improved sequence alignment criteria were used to characterize 10 major chromosome-to-chromosome duplication relationships associated with 1440 paralogous pairs, covering 47.8% of the rice genome, with 12.6% of genes that are conserved within sister blocks. Using a micro-array experiment, a genome-wide expression map has been produced, in which 2382 genes show significant differences of expression in root, leaf and grain. By integrating both structural (1440 paralogous pairs) and functional information (2382 differentially expressed genes), we identified 115 paralogous gene pairs for which at least one copy is differentially expressed in one of the three tissues. A vast majority of the 115 paralogous gene pairs have been neofunctionalized or subfunctionalized as 88%, 89% and 96% of duplicates, respectively, expressed in grain, leaf and root show distinct expression patterns. On the basis of a Gene Ontology analysis, we have identified and characterized the gene families that have been structurally and functionally preferentially retained in the duplication showing that the vast majority (>85%) of duplicated have been either lost or have been subfunctionalized or neofunctionalized during 50–70 million years of evolution

Genome wide association mapping for arabinoxylan content in a collection of tetraploid wheats

BACKGROUND: Arabinoxylans (AXs) are major components of plant cell walls in bread wheat and are important in bread-making and starch extraction. Furthermore, arabinoxylans are components of soluble dietary fibre that has potential health-promoting effects in human nutrition. Despite their high value for human health, few studies have been carried out on the genetics of AX content in durum wheat. RESULTS: The genetic variability of AX content was investigated in a set of 104 tetraploid wheat genotypes and regions attributable to AX content were identified through a genome wide association study (GWAS). The amount of arabinoxylan, expressed as percentage (w/w) of the dry weight of the kernel, ranged from 1.8% to 5.5% with a mean value of 4.0%. The GWAS revealed a total of 37 significant marker-trait associations (MTA), identifying 19 quantitative trait loci (QTL) associated with AX content. The highest number of MTAs was identified on chromosome 5A (seven), where three QTL regions were associated with AX content, while the lowest number of MTAs was detected on chromosomes 2B and 4B, where only one MTA identified a single locus. Conservation of synteny between SNP marker sequences and the annotated genes and proteins in Brachypodium distachyon, Oryza sativa and Sorghum bicolor allowed the identification of nine QTL coincident with candidate genes. These included a glycosyl hydrolase GH35, which encodes Gal7 and a glucosyltransferase GT31 on chromosome 1A; a cluster of GT1 genes on chromosome 2B that includes TaUGT1 and cisZog1; a glycosyl hydrolase that encodes a CelC gene on chromosome 3A; Ugt12887 and TaUGT1genes on chromosome 5A; a (1,3)-β-D-glucan synthase (Gsl12 gene) and a glucosyl hydrolase (Cel8 gene) on chromosome 7A. CONCLUSIONS: This study identifies significant MTAs for the AX content in the grain of tetraploid wheat genotypes. We propose that these may be used for molecular breeding of durum wheat varieties with higher soluble fibre content.Ilaria Marcotuli, Kelly Houston, Robbie Waugh, Geoffrey B. Fincher, Rachel A. Burton, Antonio Blanco, Agata Gadalet