World Vegetable Center eggplant collection: origin, composition, seed dissemination and utilization in breeding

[EN] Eggplant is the fifth most economically important solanaceous crop after potato, tomato, pepper, and tobacco. Apart from the well-known brinjal eggplant (Solanum melongena L.), two other under-utilized eggplant species, the scarlet eggplant (S. aethiopicum L.) and the gboma eggplant (S. macrocarpon L.) are also cultivated. The taxonomy and identification of eggplant wild relatives is challenging for breeders due to the large number of related species, but recent phenotypic and genetic data and classification in primary, secondary, and tertiary genepools, as well as information on the domestication process and wild progenitors, facilitates their utilization in breeding. The World Vegetable Center (WorldVeg) holds a large public germplasm collection of eggplant, which includes the three cultivated species and more than 30 eggplant wild relatives, with more than 3,200 accessions collected from 90 countries. Over the last 15 years, more than 10,000 seed samples from the Center's eggplant collection have been shared with public and private sector entities, including other genebanks. An analysis of the global occurrences and genebank holdings of cultivated eggplants and their wild relatives reveals that the WorldVeg genebank holds the world's largest public collection of the three cultivated eggplant species. The composition, seed dissemination and utilization of germplasm from the Center's collection are highlighted. In recent years more than 1,300 accessions of eggplant have been characterized for yield and fruit quality parameters. Further screening for biotic and abiotic stresses in eggplant wild relatives is a priority, as is the need to amass more comprehensive knowledge regarding wild relatives' potential for use in breeding. However, as is the case for many other crops, wild relatives are highly under-represented in the global conservation system of eggplant genetic resources.Funding for the World Vegetable Center’s general research activities is provided by core donors: Republic of China (Taiwan), UK aid, United States Agency for International Development (USAID), Australian Centre for International Agricultural Research (ACIAR), Germany, Thailand, Philippines, Korea, and Japan. In addition we like to thank Global Crop Diversity Trust for contribution to meetings and to this open-access publication.Taher, D.; Solberg, S.; Prohens Tomás, J.; Chou, Y.; Rakha, M.; Wu, T. (2017). World Vegetable Center eggplant collection: origin, composition, seed dissemination and utilization in breeding. Frontiers in Plant Science. 8. https://doi.org/10.3389/fpls.2017.01484S1484

gsSKAT: Rapid gene set analysis and multiple testing correction for rareâ variant association studies using weighted linear kernels

Nextâ generation sequencing technologies have afforded unprecedented characterization of lowâ frequency and rare genetic variation. Due to low power for singleâ variant testing, aggregative methods are commonly used to combine observed rare variation within a single gene. Causal variation may also aggregate across multiple genes within relevant biomolecular pathways. Kernelâ machine regression and adaptive testing methods for aggregative rareâ variant association testing have been demonstrated to be powerful approaches for pathwayâ level analysis, although these methods tend to be computationally intensive at highâ variant dimensionality and require access to complete data. An additional analytical issue in scans of large pathway definition sets is multiple testing correction. Gene set definitions may exhibit substantial genic overlap, and the impact of the resultant correlation in test statistics on Type I error rate control for large agnostic gene set scans has not been fully explored. Herein, we first outline a statistical strategy for aggregative rareâ variant analysis using component geneâ level linear kernel score test summary statistics as well as derive simple estimators of the effective number of tests for familyâ wise error rate control. We then conduct extensive simulation studies to characterize the behavior of our approach relative to direct application of kernel and adaptive methods under a variety of conditions. We also apply our method to two caseâ control studies, respectively, evaluating rare variation in hereditary prostate cancer and schizophrenia. Finally, we provide openâ source R code for public use to facilitate easy application of our methods to existing rareâ variant analysis results.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/136750/1/gepi22036.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/136750/2/gepi22036_am.pd

Association between polymorphism in IgG Fc receptor IIIa coding gene and biological response to infliximab in Crohn's disease

AIM: To test the hypothesis of an association between polymorphism in FCGR3A (the gene coding for FcgammaRIIIa, which is expressed on macrophages and natural killer cells, is involved in antibody-dependent cell-mediated cytotoxicity and has recently been associated with a positive response to rituximab, a recombinant immunoglobulin G1 antibody used in non-Hodgkin's lymphomas) and response to infliximab in Crohn's disease. METHODS: FCGR3A-158 polymorphism was determined using an allele-specific polymerase chain reaction assay in 200 Crohn's disease patients who had received infliximab for either refractory luminal (n = 142) or fistulizing (n = 58) Crohn's disease. Clinical and biological responses (according to C-reactive protein levels) were assessed in 200 and 145 patients, respectively. RESULTS: There were 82.9% clinical responders in V/V patients vs. 72.7% in V/F and F/F patients (N.S.). Globally, the decrease in C-reactive protein was significantly higher in V/V patients than in F carriers (P = 0.0078). A biological response was observed in 100% of V/V patients, compared with 69.8% of F carriers (P = 0.0002; relative risk, 1.43; 95% confidence interval, 1.27-1.61). In the sub-group of patients with elevated C-reactive protein before treatment, the multivariate analysis selected the use of immunosuppressive drugs and FCGR3A genotype as independent factors influencing the clinical response to infliximab (P = 0.003). CONCLUSION: Crohn's disease patients with FCGR3A-158 V/V genotype have a better biological and, possibly, clinical response to infliximab

A technique for pediatric total skin electron irradiation

<p>Abstract</p> <p>Background</p> <p>Total skin electron irradiation (TSEI) is a special radiotherapy technique which has generally been used for treating adult patients with mycosis fungoides. Recently, two infants presented with leukemia cutis isolated to the skin requiring TSEI. This work discusses the commissioning and quality assurance (QA) methods for implementing a modified Stanford technique using a rotating harness system to position sedated pediatric patients treated with electrons to the total skin.</p> <p>Methods and Results</p> <p>Commissioning of pediatric TSEI consisted of absolute calibration, measurement of dosimetric parameters, and subsequent verification in a pediatric patient sized cylindrical phantom using radiographic film and optically stimulated luminance (OSL) dosimeters. The depth of dose penetration under TSEI treatment condition was evaluated using radiographic film sandwiched in the phantom and demonstrated a 2 cm penetration depth with the maximum dose located at the phantom surface. Dosimetry measurements on the cylindrical phantom and in-vivo measurements from the patients suggested that, the factor relating the skin and calibration point doses (i.e., the <it>B</it>-factor) was larger for the pediatric TSEI treatments as compared to adult TSEI treatments. Custom made equipment, including a rotating plate and harness, was fabricated and added to a standard total body irradiation stand and tested to facilitate patient setup under sedated condition. A pediatric TSEI QA program, consisting of daily output, energy, flatness, and symmetry measurements as well as in-vivo dosimetry verification for the first cycle was developed. With a long interval between pediatric TSEI cases, absolute dosimetry was also repeated as part of the QA program. In-vivo dosimetry for the first two infants showed that a dose of ± 10% of the prescription dose can be achieved over the entire patient body.</p> <p>Conclusion</p> <p>Though pediatric leukemia cutis and the subsequent need for TSEI are rare, the ability to commission the technique on a modified TBI stand is appealing for clinical implementation and has been successfully used for the treatment of two pediatric patients at our institution.</p

Quit Attempt Correlates among Smokers by Race/Ethnicity

Introduction: Cigarette smoking is the leading preventable cause of premature deaths in the U.S., accounting for approximately 443,000 deaths annually. Although smoking prevalence in recent decades has declined substantially among all racial/ethnic groups, disparities in smoking-related behaviors among racial/ethnic groups continue to exist. Two of the goals of Healthy People 2020 are to reduce smoking prevalence among adults to 12% or less and to increase smoking cessation attempts by adult smokers from 41% to 80%. Our study assesses whether correlates of quit attempts vary by race/ethnicity among adult (≥18 years) smokers in the U.S. Understanding racial/ethnic differences in how both internal and external factors affect quit attempts is important for targeting smoking-cessation interventions to decrease tobacco-use disparities. Methods: We used 2003 Tobacco Use Supplement to the Current Population Survey (CPS) data from 16,213 adults to examine whether the relationship between demographic characteristics, smoking behaviors, smoking policies and having made a quit attempt in the past year varied by race/ethnicity. Results: Hispanics and persons of multiple races were more likely to have made a quit attempt than whites. Overall, younger individuals and those with &gt;high school education, who smoked fewer cigarettes per day and had smoked for fewer years were more likely to have made a quit attempt. Having a smoke-free home, receiving a doctor’s advice to quit, smoking menthol cigarettes and having a greater time to when you smoked your first cigarette of the day were also associated with having made a quit attempt. The relationship between these four variables and quit attempts varied by race/ethnicity; most notably receiving a doctor’s advice was not related to quit attempts among Asian American/Pacific Islanders and menthol use among whites was associated with a lower prevalence of quit attempts while black menthol users were more likely to have made a quit attempt than white non-menthol users. Conclusions: Most correlates of quit attempts were similar across all racial/ethnic groups. Therefore population-based comprehensive tobacco control programs that increase quit attempts and successful cessation among all racial/ethnic groups should be continued and expanded. Additional strategies may be needed to encourage quit attempts among less educated, older, and more addicted smokers

Single fraction radiosurgery using Rapid Arc for treatment of intracranial targets

<p>Abstract</p> <p>Background</p> <p>Stereotactic-Radio-Surgery (SRS) using Conformal-Arc-Therapy (CAT) is a well established irradiation technique for treatment of intracranial targets. Although small safety margins are required because of very high accuracy of patient positioning and exact online localisation, there are still disadvantages like long treatment time, high number of monitor units (MU) and covering of noncircular targets. This planning study analysed whether Rapid Arc (RA) with stereotactic localisation for single-fraction SRS can solve these problems.</p> <p>Methods</p> <p>Ten consecutive patients were treated with Linac-based SRS. Eight patients had one or more brain metastases. The other patients presented a symptomatic vestibularis schwannoma and an atypic meningeoma. For all patients, two plans (CAT/RA) were calculated and analysed.</p> <p>Results</p> <p>Conformity was higher for RA with additional larger low-dose areas. Furthermore, RA reduced the number of MU and the treatment time for all patients. Dose to organs at risk were equal or slightly higher using RA in comparison to CAT.</p> <p>Conclusions</p> <p>RA provides a new alternative for single-fraction SRS irradiation combining advantages of short treatment time with lower number of MU and better conformity in addition to accuracy of stereotactic localisation in selected cases with uncomplicated clinical realization.</p

Comparing the transcriptomes of embryos from domesticated and wild Atlantic salmon (Salmo salar L.) stocks and examining factors that influence heritability of gene expression

Background&nbsp; Due to selective breeding, domesticated and wild Atlantic salmon are genetically diverged, which raises concerns about farmed escapees having the potential to alter the genetic composition of wild populations and thereby disrupting local adaptation. Documenting transcriptional differences between wild and domesticated stocks under controlled conditions is one way to explore the consequences of domestication and selection. We compared the transcriptomes of wild and domesticated Atlantic salmon embryos, by using a custom 44k oligonucleotide microarray to identify perturbed gene pathways between the two stocks, and to document the inheritance patterns of differentially-expressed genes by examining gene expression in their reciprocal hybrids.&nbsp; Results&nbsp; Data from 24 array interrogations were analysed: four reciprocal cross types (W♀&times;W♂, D♀&times;W♂; W♀&times;D♂, D♀&times;D♂)&times;six biological replicates. A common set of 31,491 features on the microarrays passed quality control, of which about 62% were assigned a KEGG Orthology number. A total of 6037 distinct genes were identified for gene-set enrichment/pathway analysis. The most highly enriched functional groups that were perturbed between the two stocks were cellular signalling and immune system, ribosome and RNA transport, and focal adhesion and gap junction pathways, relating to cell communication and cell adhesion molecules. Most transcripts that were differentially expressed between the stocks were governed by additive gene interaction (33 to 42%). Maternal dominance and over-dominance were also prevalent modes of inheritance, with no convincing evidence for a stock effect.&nbsp; Conclusions&nbsp; Our data indicate that even at this relatively early developmental stage, transcriptional differences exist between the two stocks and affect pathways that are relevant to wild versus domesticated environments. Many of the identified differentially perturbed pathways are involved in organogenesis, which is expected to be an active process at the eyed egg stage. The dominant effects are more largely due to the maternal line than to the origin of the stock. This finding is particularly relevant in the context of potential introgression between farmed and wild fish, since female escapees tend to have a higher spawning success rate compared to males

Discovery of blood transcriptomic markers for depression in animal models and pilot validation in subjects with early-onset major depression

Early-onset major depressive disorder (MDD) is a serious and prevalent psychiatric illness in adolescents and young adults. Current treatments are not optimally effective. Biological markers of early-onset MDD could increase diagnostic specificity, but no such biomarker exists. Our innovative approach to biomarker discovery for early-onset MDD combined results from genome-wide transcriptomic profiles in the blood of two animal models of depression, representing the genetic and the environmental, stress-related, etiology of MDD. We carried out unbiased analyses of this combined set of 26 candidate blood transcriptomic markers in a sample of 15–19-year-old subjects with MDD (N=14) and subjects with no disorder (ND, N=14). A panel of 11 blood markers differentiated participants with early-onset MDD from the ND group. Additionally, a separate but partially overlapping panel of 18 transcripts distinguished subjects with MDD with or without comorbid anxiety. Four transcripts, discovered from the chronic stress animal model, correlated with maltreatment scores in youths. These pilot data suggest that our approach can lead to clinically valid diagnostic panels of blood transcripts for early-onset MDD, which could reduce diagnostic heterogeneity in this population and has the potential to advance individualized treatment strategies

An International Comparison of Individual Tree Detection and Extraction using Airborne Laser Scanning

The objective of the “Tree Extraction” project organized by EuroSDR (European Spatial data Research) and ISPRS (International Society of Photogrammetry and Remote Sensing) was to evaluate the quality, accuracy, and feasibility of automatic tree extraction methods mainly based on laser scanner data. In the final report of the project, Kaartinen and Hyyppä (2008) reported a high variation in the quality of the published methods under boreal forest conditions and with varying laser point densities. This paper summarizes the findings beyond the final report after analyzing the results obtained in different tree height classes. Omission / Commission statistics as well as neighborhood relations are taken into account. Additionally four automatic tree detection and extraction techniques were added to the test. Several methods in this experiment were superior to manual processing in the dominant, co-dominant and suppressed tree storeys. In general, as expected, the taller the tree, the better the location accuracy. The accuracy of tree height, after removing gross errors, was better than 0.5m in all tree height classes with the best methods investigated in this experiment. For forest inventory, minimum curvature-based tree detection accompanied by point cloud -based cluster detection for suppressed trees is a solution that deserves attention in the future.Peer reviewe

Effects of osteopontin inhibition on radiosensitivity of MDA-MB-231 breast cancer cells

<p>Abstract</p> <p>Background</p> <p>Osteopontin (OPN) is a secreted glycophosphoprotein that is overexpressed in various tumors, and high levels of OPN have been associated with poor prognosis of cancer patients. In patients with head and neck cancer, high OPN plasma levels have been associated with poor prognosis following radiotherapy. Since little is known about the relationship between OPN expression and radiosensitivity, we investigated the cellular and radiation induced effects of OPN siRNA in human MDA-MB-231 breast cancer cells.</p> <p>Methods</p> <p>MDA-MB-231 cells were transfected with OPN-specific siRNAs and irradiated after 24 h. To verify the OPN knockdown, we measured the OPN mRNA and protein levels using qRT-PCR and Western blot analysis. Furthermore, the functional effects of OPN siRNAs were studied by assays to assess clonogenic survival, migration and induction of apoptosis.</p> <p>Results</p> <p>Treatment of MDA-MB-231 cells with OPN siRNAs resulted in an 80% decrease in the OPN mRNA level and in a decrease in extracellular OPN protein level. Transfection reduced clonogenic survival to 42% (p = 0.008), decreased the migration rate to 60% (p = 0.15) and increased apoptosis from 0.3% to 1.7% (p = 0.04). Combination of OPN siRNA and irradiation at 2 Gy resulted in a further reduction of clonogenic survival to 27% (p < 0.001), decreased the migration rate to 40% (p = 0.03) and increased apoptosis to 4% (p < 0.005). Furthermore, OPN knockdown caused a weak radiosensitization with an enhancement factor of 1.5 at 6 Gy (p = 0.09) and a dose modifying factor (DMF₁₀) of 1.1.</p> <p>Conclusion</p> <p>Our results suggest that an OPN knockdown improves radiobiological effects in MDA-MB-231 cells. Therefore, OPN seems to be an attractive target to improve the effectiveness of radiotherapy.</p