A set of microsatellite markers with long core repeat optimized for grape (Vitis spp.) genotyping

BACKGROUND: Individual fingerprinting based on molecular markers has become a popular tool for studies of population genetics and analysis of genetic diversity in germplasm collections, including the solution of synonymy/homonymy and analysis of paternity and kinship. Genetic profiling of individuals is nowadays based on SSR (Simple Sequence Repeat) markers, which have a number of positive features that make them superior to any other molecular marker developed so far. In humans, SSRs with core repeats three to five nucleotides long are preferred because neighbour alleles are more easily separated and distinguished from each other; while in plants, SSRs with shorter repeats, namely two-nucleotides long, are still in use although they suffer lower separation of neighbour alleles and uncomfortable stuttering. RESULTS: New microsatellite markers, containing tri-, tetra-, and penta-nucleotide repeats, were selected from a total of 26,962 perfect microsatellites in the genome sequence of nearly homozogous grapevine PN40024, assembled from reads covering 8.4 X genome equivalents. Long nucleotide repeats were selected for fingerprinting, as previously done in many species including humans. The new grape SSR markers were tested for their reproducibility and information content in a panel of 48 grape cultivars. Allelic segregation was tested in progenies derived from two controlled crosses. CONCLUSION: A list of 38 markers with excellent quality of peaks, high power of discrimination, and uniform genome distribution (1–3 markers/chromosome), is proposed for grape genotyping. The reasons for exclusion are given for those that were discarded. The construction of marker-specific allelic ladders is also described, and their use is recommended to harmonise allelic calls and make the data obtained with different equipment and by different laboratories fully comparable

Genome Wide Binding Site Analysis Reveals Transcriptional Coactivation of Cytokinin-Responsive Genes by DELLA Proteins

[EN] The ability of plants to provide a plastic response to environmental cues relies on the connectivity between signaling pathways. DELLA proteins act as hubs that relay environmental information to the multiple transcriptional circuits that control growth and development through physical interaction with transcription factors from different families. We have analyzed the presence of one DELLA protein at the Arabidopsis genome by chromatin immunoprecipitation coupled to large-scale sequencing and we find that it binds at the promoters of multiple genes. Enrichment analysis shows a strong preference for cis elements recognized by specific transcription factor families. In particular, we demonstrate that DELLA proteins are recruited by type-B ARABIDOPSIS RESPONSE REGULATORS (ARR) to the promoters of cytokinin-regulated genes, where they act as transcriptional co-activators. The biological relevance of this mechanism is underpinned by the necessity of simultaneous presence of DELLAs and ARRs to restrict root meristem growth and to promote photomorphogenesis.This work was funded by grants BIO2007-60923 and BIO2010-15071 from the Spanish Ministry of Economy and Innovation (MAB); grant ERC-2011-StG_20101109 from the European Research Council (JUL); grants BB/J/00426X/1 and BB/E022618/1 from the Biotechnology and Biological Sciences Research Council (SGT); the Professorial Research Fellowship award BB/G023972/1 from the Biotechnology and Biological Sciences Research Council (KH and MJB); and grant FP7-311929 from the European Union (RPB). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Marín-De La Rosa, NA.; Pfeiffer, A.; Hill, K.; Locascio ., AAM.; Bhalerao, R.; Miskolczi, P.; Grønlund, A.... (2015). Genome Wide Binding Site Analysis Reveals Transcriptional Coactivation of Cytokinin-Responsive Genes by DELLA Proteins. PLoS Genetics. 11(7):1-20. https://doi.org/10.1371/journal.pgen.100533712011

Chemokine nitration prevents intratumoral infiltration of antigen-specific T cells

Tumor-promoted constraints negatively affect cytotoxic T lymphocyte (CTL) trafficking to the tumor core and, as a result, inhibit tumor killing. The production of reactive nitrogen species (RNS) within the tumor microenvironment has been reported in mouse and human cancers. We describe a novel RNS-dependent posttranslational modification of chemokines that has a profound impact on leukocyte recruitment to mouse and human tumors. Intratumoral RNS production induces CCL2 chemokine nitration and hinders T cell infiltration, resulting in the trapping of tumor-specific T cells in the stroma that surrounds cancer cells. Preconditioning of the tumor microenvironment with novel drugs that inhibit CCL2 modification facilitates CTL invasion of the tumor, suggesting that these drugs may be effective in cancer immunotherapy. Our results unveil an unexpected mechanism of tumor evasion and introduce new avenues for cancer immunotherapy

Status Update and Interim Results from the Asymptomatic Carotid Surgery Trial-2 (ACST-2)

Objectives: ACST-2 is currently the largest trial ever conducted to compare carotid artery stenting (CAS) with carotid endarterectomy (CEA) in patients with severe asymptomatic carotid stenosis requiring revascularization. Methods: Patients are entered into ACST-2 when revascularization is felt to be clearly indicated, when CEA and CAS are both possible, but where there is substantial uncertainty as to which is most appropriate. Trial surgeons and interventionalists are expected to use their usual techniques and CE-approved devices. We report baseline characteristics and blinded combined interim results for 30-day mortality and major morbidity for 986 patients in the ongoing trial up to September 2012. Results: A total of 986 patients (687 men, 299 women), mean age 68.7 years (SD ± 8.1) were randomized equally to CEA or CAS. Most (96%) had ipsilateral stenosis of 70-99% (median 80%) with contralateral stenoses of 50-99% in 30% and contralateral occlusion in 8%. Patients were on appropriate medical treatment. For 691 patients undergoing intervention with at least 1-month follow-up and Rankin scoring at 6 months for any stroke, the overall serious cardiovascular event rate of periprocedural (within 30 days) disabling stroke, fatal myocardial infarction, and death at 30 days was 1.0%. Conclusions: Early ACST-2 results suggest contemporary carotid intervention for asymptomatic stenosis has a low risk of serious morbidity and mortality, on par with other recent trials. The trial continues to recruit, to monitor periprocedural events and all types of stroke, aiming to randomize up to 5,000 patients to determine any differential outcomes between interventions. Clinical trial: ISRCTN21144362. © 2013 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved

Global urban environmental change drives adaptation in white clover

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale

Identificazione di microsatelliti in Picea abies K. e loro utilizzo come marcatori nello studio della variabilita' genetica in tre popolazioni italiane

Dottorato di ricerca in produttivita' delle piante coltivate. 8. ciclo. A.a. 1992-95. Tutore A. M. Olivieri. Cotutore M. MorganteConsiglio Nazionale delle Ricerche - Biblioteca Centrale - P.le Aldo Moro, 7, Rome; Biblioteca Nazionale Centrale - P.za Cavalleggeri, 1, Florence / CNR - Consiglio Nazionale delle RichercheSIGLEITItal

Physical interaction between ARR1 and DELLAs regulates division at the root meristem and photomorphogenesis.

<p>(<i>A</i>) Root meristem size of <i>35S</i>::<i>ARR1ΔDDK</i>:<i>GR</i> seedlings grown for 4 days with and without GAs. (n = 20; data are mean ± SD, ***p<0.001 in a Student’s t-test with respect to control plants). Arrowheads mark the extension of the meristem. (<i>B</i>) Angle between cotyledons of <i>35S</i>::<i>ARR1ΔDDK</i>:<i>GR</i> seedlings grown for 4 days with and without GAs in darkness. (n = 18; data are mean ± SD; ***p<0.001 in a Student’s t-test with respect to seedlings treated with DEX without GAs). (<i>C</i>) Angle between cotyledons of <i>35S</i>::<i>ARR1ΔDDK</i>:<i>GR</i> seedlings in <i>gai rga</i> double mutant or in an otherwise wild-type background. Seedlings were grown for 4 days in darkness. (n = 15; data are mean ± SD; ***p<0.001 in a Student’s t-test with respect to <i>35S</i>::<i>ARR1ΔDDK</i>:<i>GR GAI RGA</i> seedlings treated with DEX). (<i>D</i>) Angle between cotyledons of wild-type and <i>arr1 arr12</i> seedlings grown for 4 days with and without PAC in darkness. (n = 18; data are mean ± SD; ***p<0.001 in a Student’s t-test with respect to PAC-treated wild-type seedlings). Experiments were performed as indicated in Materials and Methods. Equivalent treatments of wild-type seedlings with DEX did not cause any change in root meristem size and or the angle between cotyledons.</p

Genome-wide occupancy of RGA at target loci.

<p>(<i>A</i>) Genomic location of the statistically significant peaks of GFP-RGA along its target genes. (<i>B</i>) Gene ontology analysis of RGA targets, using ReviGO. (<i>C</i>) Statistically significant over-representation of <i>cis</i> elements for different transcription factor families. The <i>p</i> value for each element is indicated. Bars represent the number of genes with at least one copy of the corresponding <i>cis</i> element in the ChIP peak. Colours indicate induction (red), repression (blue), both (yellow) or no effect (gray) by DELLAs across all published transcriptomic datasets. Please note that each ChIP peak may contain more than one <i>cis</i> element, therefore the sum of all genes in the graph is much larger than the 421 genes associated to ChIP peaks.</p

DELLAs promote ARR1 activity.

<p>(<i>A</i>) Expression in <i>Arabidopsis</i> roots of GFP under the control of the CK- and ARR1-responsive TCS element, after treatments with 0.5 μM <i>trans</i>-zeatin and 1 μM GA₄. (<i>B</i>) Luciferase assays in <i>N</i>. <i>benthamiana</i> leaves agroinfiltrated with HA-ARR1, YFP-GAI, and <i>myc</i>-M5GAI, using the <i>LUC</i> gene under the control of the wild-type and mutant versions of the TCS element, and the constitutively expressed <i>Renilla</i> luciferase (<i>REN</i>) for normalization. The values represent the ratio between both luciferase activities and are the average of three biological replicates. Error bars are the standard deviation. One and two asterisks denote statistical significance (p<0.05 and p<0.005 respectively). The lower panel contains the western-blot analysis of the protein samples corresponding to equal mixtures from the three leaves used for the LUC assays with the wild-type TCS elements.</p