Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing.

BACKGROUND: Knowledge on population structure and genetic diversity in vegetable crops is essential for association mapping studies and genomic selection. Genotyping by sequencing (GBS) represents an innovative method for large scale SNP detection and genotyping of genetic resources. Herein we used the GBS approach for the genome-wide identification of SNPs in a collection of Capsicum spp. accessions and for the assessment of the level of genetic diversity in a subset of 222 cultivated pepper (Capsicum annum) genotypes. RESULTS: GBS analysis generated a total of 7,568,894 master tags, of which 43.4% uniquely aligned to the reference genome CM334. A total of 108,591 SNP markers were identified, of which 105,184 were in C. annuum accessions. In order to explore the genetic diversity of C. annuum and to select a minimal core set representing most of the total genetic variation with minimum redundancy, a subset of 222 C. annuum accessions were analysed using 32,950 high quality SNPs. Based on Bayesian and Hierarchical clustering it was possible to divide the collection into three clusters. Cluster I had the majority of varieties and landraces mainly from Southern and Northern Italy, and from Eastern Europe, whereas clusters II and III comprised accessions of different geographical origins. Considering the genome-wide genetic variation among the accessions included in cluster I, a second round of Bayesian (K = 3) and Hierarchical (K = 2) clustering was performed. These analysis showed that genotypes were grouped not only based on geographical origin, but also on fruit-related features. CONCLUSIONS: GBS data has proven useful to assess the genetic diversity in a collection of C. annuum accessions. The high number of SNP markers, uniformly distributed on the 12 chromosomes, allowed the accessions to be distinguished according to geographical origin and fruit-related features. SNP markers and information on population structure developed in this study will undoubtedly support genome-wide association mapping studies and marker-assisted selection programs.

Comparative next-generation mapping of the Phytophthora infestans resistance gene Rpi-dlc2 in a European accession of Solanum dulcamara.

Phytophthora infestans, the causal agent of late blight, remains the main threat to potato production worldwide. Screening of 19 accessions of Solanum dulcamara with P. infestans isolate Ipo82001 in detached leaf assays revealed strong resistance in an individual belonging to accession A54750069-1. This plant was crossed with a susceptible genotype, and an F(1) population consisting of 63 individuals was obtained. This population segregated for resistance in 1:1 ratio, both in detached leaf assays and in an open-field experiment. Presence of the formerly mapped Rpi-dlc1 gene as the cause of the observed segregating resistance could be excluded. Subsequently, AFLP analyses using 128 primer combinations enabled identification of five markers linked to a novel resistance gene named Rpi-dlc2. AFLP markers did not show sequence similarity to the tomato and potato genomes, hampering comparative genetic positioning of the gene. For this reason we used next-generation mapping (NGM), an approach that exploits direct sequencing of DNA (in our case: cDNA) pools from bulked segregants to calculate the genetic distance between SNPs and the locus of interest. Plotting of these genetic distances on the tomato and potato genetic map and subsequent PCR-based marker analysis positioned the gene on chromosome 10, in a region overlapping with the Rpi-ber/ber1 and -ber2 loci from S. berthaultii. Pyramiding of Rpi-dlc2 and Rpi-dlc1 significantly increased resistance to P. infestans, compared with individuals containing only one of the genes, showing the usefulness of this strategy to enhance resistance against Phytophthora.

Trajectory of parental hope when a child has difficult-to-treat cancer: a prospective qualitative study.

OBJECTIVE: This prospective and longitudinal study was designed to further our understanding of parental hope when a child is being treated for a malignancy resistant to treatment over three time points during the first year after diagnosis using a qualitative approach to inquiry. METHODS: We prospectively recruited parents of pediatric cancer patients with a poor prognosis who were treated in the Hematology/Oncology Program at a large children's hospital for this longitudinal grounded theory study. Parents were interviewed at three time points: within 3 months of the initial diagnosis, at 6 months, and at 9 months. Data collection and analysis took place concurrently using line-by-line coding. Constant comparison was used to examine relationships within and across codes and categories. RESULTS: Two overarching categories defining hope as a positive inner source were found across time, but their frequency varied depending on how well the child was doing and disease progression: future-oriented hope and present-oriented hope. Under future-oriented hope, we identified the following: hope for a cure and treatment success, hope for the child's future, hope for a miracle, and hope for more quality time with child. Under present-oriented hope, we identified hope for day-to-day/moment-to-moment, hope for no pain and suffering, and hope for no complications. CONCLUSIONS: For parents of children with a diagnosis of cancer with a poor prognosis, hope is an internal resource that can be present and future focused. These views fluctuated over time in response to changes in the child's well-being and disease progression.

Multitraits evaluation of a Solanum pennellii introgression tomato line challenged by combined abiotic stress.

Rising daily temperatures and water shortage are two of the major concerns in agriculture. In this work, we analysed the tolerance traits in a tomato line carrying a small region of the Solanum pennellii wild genome (IL12-4-SL) when grown under prolonged conditions of single and combined high temperature and water stress. When exposed to stress, IL12-4-SL showed higher heat tolerance than the cultivated line M82 at morphological, physiological, and biochemical levels. Moreover, under stress IL12-4-SL produced more flowers than M82, also characterized by higher pollen viability. In both lines, water stress negatively affected photosynthesis more than heat alone, whereas the combined stress did not further exacerbate the negative impacts of drought on this trait. Despite an observed decrease in carbon fixation, the quantum yield of PSII linear electron transport in IL12-4-SL was not affected by stress, thereby indicating that photochemical processes other than CO2 fixation acted to maintain the electron chain in oxidized state and prevent photodamage. The ability of IL12-4-SL to tolerate abiotic stress was also related to the intrinsic ability of this line to accumulate ascorbic acid. The data collected in this study clearly indicate improved tolerance to single and combined abiotic stress for IL12-4-SL, making this line a promising one for cultivation in a climate scenario characterized by frequent and long-lasting heatwaves and low rainfall.

A novel synthetic peptide from a tomato defensin exhibits antibacterial activities against Helicobacter pylori.

Defensins are a class of cysteine-rich proteins, which exert broad spectrum antimicrobial activity. In this work, we used a bioinformatic approach to identify putative defensins in the tomato genome. Fifteen proteins had a mature peptide that includes the well-conserved tetradisulfide array. We selected a representative member of the tomato defensin family; we chemically synthesized its γ-motif and tested its antimicrobial activity. Here, we demonstrate that the synthetic peptide exhibits potent antibacterial activity against Gram-positive bacteria, such as Staphylococcus aureus A170, Staphylococcus epidermidis, and Listeria monocytogenes, and Gram-negative bacteria, including Salmonella enterica serovar Paratyphi, Escherichia coli, and Helicobacter pylori. In addition, the synthetic peptide shows minimal (<5%) hemolytic activity and absence of cytotoxic effects against THP-1 cells. Finally, SolyC exerts an anti-inflammatory activity in vitro, as it downregulates the level of the proinflammatory cytokines TNF-α and IFN-γ.

Decade-long monitoring of seismic velocity changes at the Irpinia fault system (southern Italy) reveals pore pressure pulsations.

Several studies have monitored crustal seismic velocity changes and attempted to relate them to the stress state and physical properties in volume embedding fault systems. The aim is to provide constraints on fault system dynamics and earthquake triggering mechanisms. Here, we reconstruct the spatiotemporal (4D) seismic velocity images of volume embedding the Irpinia fault system (IFS, South Italy), which originated the 1980 Ms 6.9 multi-segmented ruptures. By inverting data from more than ten years of continuous seismicity monitoring, we retrieved time-constant velocity anomalies, whose shapes correlate well with crustal lithology, while time-changing (up to 20%) velocity anomalies are mapped in the central region. Here, the Vp-to-Vs changes at depths of 1-5 km and 8-12 km correlate well with groundwater recharge and geodetic displacement during the same time interval. This correlation provides evidence for the existence of pulsating, pore pressure changes induced by groundwater recharge processes in a deep volume (8-12 km of depth), fractured and saturated with a predominant gas phase (likely CO2). We suggest that tomographic measurements of the Vp-to-Vs spatiotemporal changes are a suitable proxy to track the pore pressure evolution at depth in highly sensitive regions of fault systems.

Blood and plasma kinetics of cis(Z)-clopenthixol and fluphenazine in psychiatric patients after intramuscular injection of their decanoic esters.

Whole blood and plasma concentrations of active neuroleptic drugs were measured in eight schizophrenic outpatients who had received cis(Z)-clopenthixol decanoate in Viscoleo or fluphenazine decanoate in sesame oil by intramuscular injection. Whole blood and plasma concentrations were very similar, though there was a slight tendency for blood concentrations to be higher than plasma concentrations. Maximum concentrations appeared at 1 week after administration of cis(Z)-clopenthixol decanoate, whereas the highest concentrations after fluphenazine decanoate were seen at the end of the 3-week dosage interval. Some between-individual variation and a limited within-individual variation was seen.

Assessment of pain in advanced cancer patients.

This study tested the feasibility of standardized pain assessment instruments in a population of patients with far advanced cancer at the time of admission to a specialty hospital. As pain is a symptom, pain control must be based on patients' self-report. Cognitive impairment and severe physical illness, however, limited the ability to use these tools. Almost one-half (44.8%) of the patients were unable to use the McGill-Melzack Pain Questionnaire, the Memorial Pain Assessment Card, or the Faces Pain Rating Scale. Patients with far advanced cancer fall into three groups: those who report pain, those who report no pain, and those who are unable to state whether or not they have pain. This study demonstrates the need to undertake pain assessment while the patient is able to respond and to monitor behaviors that could be indicative of changes in pain.

Cancer in the older adult: understanding age-related changes.

As the population ages, nurses will be working with increased numbers of elderly cancer patients. It is imperative that nurses gain an understanding of the aging process and an appreciation of the cancer experience in the older adult. By aggravating or influencing cancer-related symptoms and their treatments, or by inducing non-cancer related symptoms, concurrent health problems may inadvertently be thought to be associated with malignancy progression. An in-depth investigation of a patient's history may reveal a vast number of actual and potential health problems; the areas that pose special concerns for the elderly are nutrition, pain, and psychosocial aspects, such as depression and confusion.

Clues from joint inversion of tsunami and geodetic data of the 2011 Tohoku-oki earthquake.

The 2011 Tohoku-oki (Mw 9.1) earthquake is so far the best-observed megathrust rupture, which allowed the collection of unprecedented offshore data. The joint inversion of tsunami waveforms (DART buoys, bottom pressure sensors, coastal wave gauges, and GPS-buoys) and static geodetic data (onshore GPS, seafloor displacements obtained by a GPS/acoustic combination technique), allows us to retrieve the slip distribution on a non-planar fault. We show that the inclusion of near-source data is necessary to image the details of slip pattern (maximum slip ~48 m, up to ~35 m close to the Japan trench), which generated the large and shallow seafloor coseismic deformations and the devastating inundation of the Japanese coast. We investigate the relation between the spatial distribution of previously inferred interseismic coupling and coseismic slip and we highlight the importance of seafloor geodetic measurements to constrain the interseismic coupling, which is one of the key-elements for long-term earthquake and tsunami hazard assessment.