Genome-wide DNA-(de)methylation is associated with Noninfectious Bud-failure exhibition in Almond (Prunus dulcis [Mill.] D.A.Webb).

Noninfectious bud-failure (BF) remains a major threat to almond production in California, particularly with the recent rapid expansion of acreage and as more intensive cultural practices and modern cultivars are adopted. BF has been shown to be inherited in both vegetative and sexual progeny, with exhibition related to the age and propagation history of scion clonal sources. These characteristics suggest an epigenetic influence, such as the loss of juvenility mediated by DNA-(de)methylation. Various degrees of BF have been reported among cultivars as well as within sources of clonal propagation of the same cultivar. Genome-wide methylation profiles for different clones within almond genotypes were developed to examine their association with BF levels and association with the chronological time from initial propagation. The degree of BF exhibition was found to be associated with DNA-(de)methylation and clonal age, which suggests that epigenetic changes associated with ageing may be involved in the differential exhibition of BF within and among almond clones. Research is needed to investigate the potential of DNA-(de)methylation status as a predictor for BF as well as for effective strategies to improve clonal selection against age related deterioration. This is the first report of an epigenetic-related disorder threatening a major tree crop

Application of genomic and quantitative genetic tools to identify candidate resistance genes for brown rot resistance in peach.

The availability of a complete peach genome assembly and three different peach genome sequences created by our group provide new opportunities for application of genomic data and can improve the power of the classical Quantitative Trait Loci (QTL) approaches to identify candidate genes for peach disease resistance. Brown rot caused by Monilinia spp., is the most important fungal disease of stone fruits worldwide. Improved levels of peach fruit rot resistance have been identified in some cultivars and advanced selections developed in the UC Davis and USDA breeding programs. Whole genome sequencing of the Pop-DF parents lead to discovery of high-quality SNP markers for QTL genome scanning in this experimental population. Pop-DF created by crossing a brown rot moderately resistant cultivar 'Dr. Davis' and a brown rot resistant introgression line, 'F8,1-42', derived from an initial almond × peach interspecific hybrid, was evaluated for brown rot resistance in fruit of harvest maturity over three seasons. Using the SNP linkage map of Pop-DF and phenotypic data collected with inoculated fruit, a genome scan for QTL identified several SNP markers associated with brown rot resistance. Two of these QTLs were placed on linkage group 1, covering a large (physical) region on chromosome 1. The genome scan for QTL and SNP effects predicted several candidate genes associated with disease resistance responses in other host-pathogen systems. Two potential candidate genes, ppa011763m and ppa026453m, may be the genes primarily responsible for M. fructicola recognition in peach, activating both PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI) responses. Our results provide a foundation for further genetic dissection, marker assisted breeding for brown rot resistance, and development of peach cultivars resistant to brown rot

OATP1B1 and tumour OATP1B3 modulate exposure, toxicity, and survival after irinotecan-based chemotherapy

Background: Treatment of advanced and metastatic colorectal cancer with irinotecan is hampered by severe toxicities. The active metabolite of irinotecan, SN-38, is a known substrate of drug-metabolising enzymes, including UGT1A1, as well as OATP and ABC drug transporters.Methods:Blood samples (n=127) and tumour tissue (n=30) were obtained from advanced cancer patients treated with irinotecan-based regimens for pharmacogenetic and drug level analysis and transporter expression. Clinical variables, toxicity, and outcomes data were collected.Results:SLCO1B1 521C was significantly associated with increased SN-38 exposure (P\u3c0.001), which was additive with UGT1A1∗28. ABCC5 (rs562) carriers had significantly reduced SN-38 glucuronide and APC metabolite levels. Reduced risk of neutropenia and diarrhoea was associated with ABCC2-24C/T (odds ratio (OR)=0.22, 0.06-0.85) and CES1 (rs2244613; OR=0.29, 0.09-0.89), respectively. Progression-free survival (PFS) was significantly longer in SLCO1B1 388G/G patients and reduced in ABCC2-24T/T and UGT1A1∗28 carriers. Notably, higher OATP1B3 tumour expression was associated with reduced PFS.Conclusions:Clarifying the association of host genetic variation in OATP and ABC transporters to SN-38 exposure, toxicity and PFS provides rationale for personalising irinotecan-based chemotherapy. Our findings suggest that OATP polymorphisms and expression in tumour tissue may serve as important new biomarkers

A fruit quality gene map of Prunus

<p>Abstract</p> <p>Background</p> <p><it>Prunus </it>fruit development, growth, ripening, and senescence includes major biochemical and sensory changes in texture, color, and flavor. The genetic dissection of these complex processes has important applications in crop improvement, to facilitate maximizing and maintaining stone fruit quality from production and processing through to marketing and consumption. Here we present an integrated fruit quality gene map of <it>Prunus </it>containing 133 genes putatively involved in the determination of fruit texture, pigmentation, flavor, and chilling injury resistance.</p> <p>Results</p> <p>A genetic linkage map of 211 markers was constructed for an intraspecific peach (<it>Prunus persica</it>) progeny population, Pop-DG, derived from a canning peach cultivar 'Dr. Davis' and a fresh market cultivar 'Georgia Belle'. The Pop-DG map covered 818 cM of the peach genome and included three morphological markers, 11 ripening candidate genes, 13 cold-responsive genes, 21 novel EST-SSRs from the ChillPeach database, 58 previously reported SSRs, 40 RAFs, 23 SRAPs, 14 IMAs, and 28 accessory markers from candidate gene amplification. The Pop-DG map was co-linear with the <it>Prunus </it>reference T × E map, with 39 SSR markers in common to align the maps. A further 158 markers were bin-mapped to the reference map: 59 ripening candidate genes, 50 cold-responsive genes, and 50 novel EST-SSRs from ChillPeach, with deduced locations in Pop-DG via comparative mapping. Several candidate genes and EST-SSRs co-located with previously reported major trait loci and quantitative trait loci for chilling injury symptoms in Pop-DG.</p> <p>Conclusion</p> <p>The candidate gene approach combined with bin-mapping and availability of a community-recognized reference genetic map provides an efficient means of locating genes of interest in a target genome. We highlight the co-localization of fruit quality candidate genes with previously reported fruit quality QTLs. The fruit quality gene map developed here is a valuable tool for dissecting the genetic architecture of fruit quality traits in <it>Prunus </it>crops.</p

Carbon storage and DNA absorption in allophanic soils and paleosols

Andisols and andic paleosols dominated by the nanocrystalline mineral allophane sequester large amounts of carbon (C), attributable mainly to its chemical bonding with charged hydroxyl groups on the surface of allophane together with its physical protection in nanopores within and between allophane nanoaggregates. C near-edge X-ray absorption fine structure (NEXAFS) spectra for a New Zealand Andisol (Tirau series) showed that the organic matter (OM) mainly comprises quinonic, aromatic, aliphatic, and carboxylic C. In different buried horizons from several other Andisols, C contents varied but the C species were similar, attributable to pedogenic processes operating during developmental upbuilding, downward leaching, or both. The presence of OM in natural allophanic soils weakened the adsorption of DNA on clay; an adsorption isotherm experiment involving humic acid (HA) showed that HA-free synthetic allophane adsorbed seven times more DNA than HA-rich synthetic allophane. Phosphorus X-ray absorption near-edge structure (XANES) spectra for salmonsperm DNA and DNA-clay complexes indicated that DNA was bound to the allophane clay through the phosphate group, but it is not clear if DNA was chemically bound to the surface of the allophane or to OM, or both. We plan more experiments to investigate interactions among DNA, allophane (natural and synthetic), and OM. Because DNA shows a high affinity to allophane, we are studying the potential to reconstruct late Quaternary palaeoenvironments by attempting to extract and characterise ancient DNA from allophanic paleosol

Geotecnologias para suporte à agricultura de precisão em agroecossistemas de terras baixas.

Neste documento são apresentadas as atividades realizadas durante o primeiro ano do projeto e se discute a aplicação de geotecnologias relacionadas às atividades de pesquisa desenvolvidas nas UPs do projeto AP2, na Estação Experimental Terras Baixas (ETB) da Embrapa Clima Temperado, envolvendo o uso de imagens orbitais de baixo custo, manuseio de GPS para efetivar modelos digitais de elevação e processamento dos dados segundo malha regular, sendo disponibilizados resultados preliminares obtidos pela equipe do arroz irrigado.bitstream/item/78794/1/documento-336-.pd

A critical evaluation of the microstructural gradient along the build direction in electron beam melted Ti-6Al-4V alloy

It is generally recognised that electron beam melted (EBM) Ti-6Al-4V alloys exhibit a microstructural gradient along the build direction, but there have been some inconsistent experimental observations and debate as to the origin and magnitude of this effect. Here we present an unambiguous evaluation of this microstructural gradient and associated mechanical property along the EBM build direction on purpose-built round bar RB samples with build height of 380 mm and rectangular plate RP samples with build height of 120 mm. Columnar prior β grain width was found to increase (from 86 ± 38 to 154 ± 56 µm in RB and from 79 ± 34 to 122 ± 56 µm in RP samples) with the build height and the similar increase was also observed for α lath width (from 0.58 ± 24 to 0.87 ± 33 µm in RB and from 1.50 ± 45 to 1.80 ± 49 µm in RP samples). These observations can be attributed to the thermal gradient in the powder bed that produced a cooling rate gradient along the build height. The measured α lath width variation along the build height followed a log-normal distribution. The graded microstructure resulted in a decrease in micro-hardness which correlated very well with the mean α lath width by following a Hall-Petch relation

Four new species of Hydnellum (Thelephorales, Basidiomycota) with a note on Sarcodon illudens

Four new Hydnellum species are described. Hydnellum roseoviolaceum sp. nov. grows in dry pine heaths on acidic, sandy soil. It is close to H. fuligineoviolaceum, another pine-associated species, but differs by smaller spores, an initially rose-coloured instead of violet flesh in fresh basidiomata and a mild taste. Hydnellum scabrosellum sp. nov. grows in coniferous forests on calcareous soil. It shares a general morphology with H. scabrosum, which also is its closest relative. It differs by having smaller and slenderer basidiomata and by the yellowish ochraceous colour of flesh and spines in dried specimens compared to the whitish or reddish brown colour seen in H. scabrosum. Hydnellum fagiscabrosum sp. nov. is another species with morphological and phylogenetic affinities to H. scabrosum. However, it is associated with trees from Fagales whereas H. scabrosum is associated with Pinaceae. Hydnellum nemorosum sp. nov. is yet another species that associates with broadleaved trees. It seems to be a rare species, morphologically reminiscent of H. fuligineoviolaceum, H. ioeides and H. scabrosum, but it is phylogenetically close to H. fennicum . Sequences from the type specimens of H. glaucopus, H. lepidum, H. scabrosum, Sarcodon illudens and S. regalis are included in the analyses. Specimens given the provisional name "Sarcodon pseudoglaucopus" in Sweden are now shown to be referable to S. illudens. The analyses further showed that S. illudens is close to H. lepidum. The new combination Hydnellum illudens is proposed. Sarcodon regalis and H. lepidum are shown to be conspecific and, although their basionyms were simultaneously published, the name S. regalis was only validated in a later publication. Hydnellum lepidum therefore takes priority and S. regalis becomes a synonym

‘Sons of athelings given to the earth’: Infant Mortality within Anglo-Saxon Mortuary Geography

FOR 20 OR MORE YEARS early Anglo-Saxon archaeologists have believed children are underrepresented in the cemetery evidence. They conclude that excavation misses small bones, that previous attitudes to reporting overlook the very young, or that infants and children were buried elsewhere. This is all well and good, but we must be careful of oversimplifying compound social and cultural responses to childhood and infant mortality. Previous approaches have offered methodological quandaries in the face of this under-representation. However, proportionally more infants were placed in large cemeteries and sometimes in specific zones. This trend is statistically significant and is therefore unlikely to result entirely from preservation or excavation problems. Early medieval cemeteries were part of regional mortuary geographies and provided places to stage events that promoted social cohesion across kinship systems extending over tribal territories. This paper argues that patterns in early Anglo-Saxon infant burial were the result of female mobility. Many women probably travelled locally to marry in a union which reinforced existing social networks. For an expectant mother, however, the safest place to give birth was with experience women in her maternal home. Infant identities were affected by personal and legal association with their mother’s parental kindred, so when an infant died in childbirth or months and years later, it was their mother’s identity which dictated burial location. As a result, cemeteries central to tribal identities became places to bury the sons and daughters of a regional tribal aristocracy