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.

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.

Whole Slide Imaging for Teleconsultation: The Mount Sinai Hospital, Labcorp Dianon, and Philips Collaborative Experience.

BACKGROUND: With the emergence of whole slide imaging (WSI) and widespread access to high-speed Internet, pathology labs are now poised to implement digital pathology as a way to access diagnostic pathology expertise. This paper describes a collaborative partnership between a high-volume reference diagnostic laboratory (Labcorp) and an academic pathology department (Mount Sinai Hospital) in the transition from a traditional glass slide service to a digital platform. Using the standard framework of implementation science, we evaluate the consistency and quality of the Philips IntelliSite Pathology Solution (PIPS) in delivering save and efficient diagnostic services. MATERIALS AND METHODS: Digital and glass slide diagnoses of all consult cases were documented over a 12-month period. The Proctor guideline was used to quantitatively and qualitatively measure (e.g., focus group studies, field notes, and administrative data) implementation success. Lean techniques (e.g., value stream mapping) were applied to measure changes in efficiency with the transition to a digital platform. RESULTS: Our study supports the acceptability, high adoption, appropriateness, feasibility, fidelity, and sustainability of the digital pathology platform. The digital portal also improved the quality of patient care by increasing efficiency, effectiveness, safety, and timeliness. The intraobserver concordance rate was 100%. The digital transition resulted in a reduction in turnaround time from 86 h to an average 35 min and a 20-fold increase in efficiency of the consultation process. CONCLUSION: As the pathology community contemplates digital pathology as a transformational tool in providing broad access to diagnostic expertise across time and space, our study provides an implementation strategy along with evidence that the digital platform is safe, effective, and efficient.

Application of Hyperspectral Imaging to Underwater Habitat Mapping, Southern Adriatic Sea.

Hyperspectral imagers enable the collection of high-resolution spectral images exploitable for the supervised classification of habitats and objects of interest (OOI). Although this is a well-established technology for the study of subaerial environments, Ecotone AS has developed an underwater hyperspectral imager (UHI) system to explore the properties of the seafloor. The aim of the project is to evaluate the potential of this instrument for mapping and monitoring benthic habitats in shallow and deep-water environments. For the first time, we tested this system at two sites in the Southern Adriatic Sea (Mediterranean Sea): the cold-water coral (CWC) habitat in the Bari Canyon and the Coralligenous habitat off Brindisi. We created a spectral library for each site, considering the different substrates and the main OOI reaching, where possible, the lower taxonomic rank. We applied the spectral angle mapper (SAM) supervised classification to map the areal extent of the Coralligenous and to recognize the major CWC habitat-formers. Despite some technical problems, the first results demonstrate the suitability of the UHI camera for habitat mapping and seabed monitoring, through the achievement of quantifiable and repeatable classifications.

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.

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.

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.

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.

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.

Novel use of bovine zeta-crystallin as a conformational DNA probe to characterize a phase transition zone and terminally differentiating fiber cells in the adult canine ocular lens.

Using a novel immunocytochemical staining method, we aimed to characterize the phase transition zone (PTZ) (approximatly 100 microm) in adult ocular lenses and the process of terminal differentiation (denucleation) within normal fiber cells. The binding to DNA of zeta-(zeta) crystallin (Z-DNA-binding protein) and anti-double-stranded (ds-)-B-DNA antibody probes was found to decline gradually throughout denucleating fibers, with a precipitous decrease occurring at about 100 microm (PTZ). Nuclei of superficial fiber cells (in front of the PTZ) showed the highest DNA probe-binding values, followed by middle fibers (MF) and deep fibers (DF). With the use of zeta-crystallin, anti-ds-B-DNA antibody, and anti-single stranded (ss-) DNA antibody probes, it was possible to reveal a loss of reactivity of fiber cell ds-DNA. Ss-DNA antibody binding was seen initially in the MF and reached its highest intensity level in the DF. The pattern of zeta-crystallin probe-DNA reactivity correlates with the loss of anti-B-DNA antibody staining and decreased eosin-protein staining. These data suggest that a reorganization of DNA and intracellular protein supramolecular order in normal adult lenses occurs at a depth of about 100 microm (PTZ).

Mapping IgG epitopes bound by rheumatoid factors from immunized controls identifies disease-specific rheumatoid factors produced by patients with rheumatoid arthritis.

We have mapped the specificity of 28 monoclonal IgM rheumatoid factors (RFs) produced by heterohybridomas derived from five healthy blood donors immunized with mismatched human red blood cells (HID). The HID-RFs did not differ in their binding specificity for IgG epitopes from RFs that we previously analyzed from patients with Waldenström's macroglobulinemia. However, IgM RFs produced by HID differed in their specificity for IgG compared with RFs expressed by patients with rheumatoid arthritis (RA-RFs). Only 1 of 28 HID-RFs bound all IgG subclasses (pan binding pattern) compared with 7 of 19 RA-RFs (p = 0.006). Three HID-RFs bound IgG3 compared with 9 RA-RFs (p = 0.007). Fine specificity differences were also identified between HID- and RA-RFs. Therefore, some RA-RFs show novel specificities for IgG not found among RFs from HID or individuals with Waldenström's macroglobulinemia who do not have joint disease. These Abs with unique specificities may represent disease-specific autoantibodies in patients with RA. Nine of the HID-RFs from the same individual were clonally related, and several contained somatic mutations. Even when the clonally related HID-RFs were considered as one RF for comparison, the reactivity of the HID-RFs differed significantly from RA-RFs in their inability to recognize all IgG subclasses (p = 0.044) and recognize IgG3 (p = 0.041). Interestingly, among the clonally related RFs, considerable differences in the specificity for IgG were also observed, with the RF containing the most somatic mutations in VH and VL showing the most distinctive specificity changes. Therefore, these studies also demonstrate a correlation between somatic mutation and binding specificity.

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.

Mapping studies reveal unique epitopes on IgG recognized by rheumatoid arthritis-derived monoclonal rheumatoid factors.

We have used chimeric IgG antibodies and their genetically engineered variants prepared by a combination of site-directed mutagenesis and exon exchange to define the structure(s) on IgG recognized by monoclonal rheumatoid factor (RF) autoantibodies from rheumatoid arthritis (RA) patients. Nineteen RF produced by EBV-transformed cell lines from the synovium or blood of RA patients were analyzed. Their binding patterns differ significantly from those seen with RF obtained from patients with Waldenstrom's macroglobulinemia (WMac). Half of the RA-derived RF bound IgG1, 2, and 4, but not 3 (Ga specificity), the common pattern in WMac. However, heterogeneity in fine specificity within the Ga reactivity pattern was observed. Moreover, seven others bound all four IgG subclasses, a pattern observed for only one WMac-derived RF from a patient who also had RA. Three RF had subclass specificities unlike any observed with WMac-derived RF. Most RA-derived RF bound IgG at a discontinuous epitope comprised of residues from both the CH2 and CH3 H chain constant regions. However, unlike any WMac-derived RF, one RA-derived RF bound IgG in CH2, another in CH3, and a third at an undetermined site outside of the CH2-CH3 interface. Some RA-derived RF bound aglycosylated IgG4 less well than glycosylated IgG4, suggesting that the carbohydrate moiety was important in establishing their binding epitope in CH2. These studies demonstrate that the repertoire of RF expressed by RA patients contains some unique binding specificities for IgG epitopes not found among our panel of WMac-derived RF. Our results therefore call into question whether WMac-derived RF with their limited diversity are appropriate models for disease-related RF. In addition, RF with their multiple specificities can serve as probes of antibody structure.

Mapping rheumatoid factor binding sites using genetically engineered, chimeric IgG antibodies.

We are using chimeric IgG antibodies consisting of murine variable regions joined to human constant regions as rheumatoid factor (RF) binding substrates to localize and map IgM RF binding sites on IgG. Using chimeric antibodies in a modified RF ELISA, we showed that RFs from rheumatoid arthritis (RA) and Waldenstrom's macroglobulinemia (WMac) patients differ in their binding specificities for IgG3, although some of these RFs share common specificity for IgG1, IgG2, and IgG4. By shuffling constant region domains between IgG3 and IgG4, we showed that sequence variation in the CH3 domain is responsible for WMac-derived RF differentiation of IgG3 and IgG4. By making site-directed mutations in the wild-type IgG3 or IgG4 human gamma constant genes, we showed that His-435 is an essential residue in RF binding to IgG for most WMac RFs. The allotypic polymorphism in IgG3 at 436 is not responsible for differences in previous reports of high-frequency IgG3 binding by WMac RFs. A amino acid loop in the CH2 domain of IgG4 proximal to the CH2-CH3 interface is important in WMac RF binding to IgG; a more distal CH2 loop in CH2 has a more variable effect on WMac RF binding. To evaluate the contribution of the N-linked carbohydrate moiety at Asn-297 to RF binding sites on IgG, we measured RF binding to aglycosylated IgG antibodies produced by mutating the glycosylation signal Asn-297 to another amino acid. Of all four IgG subclasses, only aglycosylated IgG3 was a better RF binding substrate than its glycosylated subclass counterpart.(ABSTRACT TRUNCATED AT 250 WORDS)

The major rheumatoid factor cross-reactive idiotype is dominantly expressed by Staphylococcus aureus Cowan strain I-activated CD5+ control B cells.

Some seropositive (RF+) and seronegative (RF-) rheumatoid arthritis (RA) patients selectively express high concentrations of the major RF cross-reactive idiotype (RCRI) in their sera and generate high frequencies of RCRI+ pokeweed mitogen (PWM)-induced plasma cells from their peripheral blood mononuclear cells (PBM). To determine if normal individuals can express RCRI in vitro, B cells from controls were activated with Staphylococcus aureus Cowan strain I (SAC) bacteria to identify RCRI and RF production. In addition, we studied the relationship of RCRI expression with the subset of B cells bearing CD5. Control CD5+ B cells are responsible for RCRI expression following SAC activation. We also observed that RCRI is dominantly expressed by control SAC-induced B cells in frequencies comparable to that expressed by some RA and juvenile rheumatoid arthritis patients' PBM activated by PWM. Therefore, the frequency of RCRI+ B cells in control and arthritis patients' PBL may be similar, or the selection and/or regulation of RCRI+ B-cell expression in vitro and in vivo may be different in arthritis patients compared to normal individuals.

Endocytosis of the TCR/CD3 complex and the class-I major histocompatibility complex in a human T cell line.

We investigated the expression of the T cell receptor (TCR)/CD3 complex on a CD4-positive human T cell lymphoma cell line treated with phorbol myristate acetate (PMA) and/or CA2+ ionophore using fluorescence flow cytometry and fluorescence microscopic analysis. PMA induced a significant decrease in the expression of the CD3 complex on the cell membranes. Fluorescence microscopy confirmed that the down regulation is due to internalization of the antigens. Ca2+ ionophore treatment had no effect on the internalization of the CD3 complex. Double staining revealed that the vesicles containing the internalized CD3 complex and those containing intra-cytoplasmic class I major histocompatibility complex antigen had similar distribution in the PMA-stimulated cells, implying coexistence of these two antigens in a cytoplasmic perinuclear distribution.

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.

Class II MHC molecules are spontaneously internalized in acidic endosomes by activated B cells.

The antibody response to protein antigens requires specific cooperation between B and T cells. In order to deliver the helper signal, T cells must recognize, in the context of Class II MHC, processed antigen on the membrane of B cells. Processed antigen is in the form of peptides bound in a given site of the Class II MHC molecule; in order to address the question of where, in the B cell, the complex of Class II MHC and processed antigen is formed, we studied the subcellular localization of these two molecules. Since the formation of this complex is the crucial step in antigen processing and presentation, the answer to this question is central to the whole problem of the physiology of antigen handling by B cells. To collect information pertinent to the question, we have compared, in B cells, the intracellular traffic of Class II MHC and of monovalent and divalent anti-immunoglobulin antibodies used as protein ligands of the membrane immunoglobulins. We have done so by two-color immunofluorescence microscopy, and we have detected extensive confluence of Class II MHC molecules with the immunoglobulin ligand, both mono- and bi-valent, in the endosomes of LPS-activated murine B cells. Whereas the ligand clearly reaches the endosomes by internalization from the cell membrane, the Class II MHC molecules could reach the same location either by endocytosis from the membrane or through targeting to the endosomes of newly synthesized Class II MHC molecules. We have collected quantitative evidence for endocytosis of Class II MHC by following, with the fluorescence activated cell sorter, the quenching of the fluorescence of fluoresceinated Fab' anti Class II MHC in LPS-activated murine B cells; this quenching indicates the entry of the label into an acidic intracellular compartment. Together with the results of others, obtained with different methods, our observations support the concept that, at least in mature activated B cells, Class II MHC molecules reach the organelles where they meet processed protein antigens, mainly through the endocytic route. Since activated B cells endocytose their membrane Class II MHC, and not their membrane Class I, our results contribute to the understanding of how B cells present antigens, that have bound to their membrane immunoglobulins, to Class II-restricted helper T cells and not to Class I-restricted cytolytic T cells.