A Reference Genome Assembly of Hybrid-Derived California Wild Radish (Raphanus sativus × raphanistrum)

For agriculturally important plants, pollination and herbivory are 2 ecological factors that play into the success of crop yields. Each is also important in natural environments where invasive plants and their effect on species interactions may alter the native ecology. The California Wild Radish (Raphanus sativus × raphanistrum), a hybrid derived from an agriculturally important crop and a nonnative cultivar, is common in California. Remarkably, it has recently replaced wild populations of both progenitor species. Experiments on phenotypic variation for petal color and antiherbivore defenses suggest both pairs of polymorphisms are maintained as a result of pollinator- and herbivore-mediated natural selection. This species provides an opportunity to understand how natural selection shapes the evolution of ecologically important traits when traits are constrained by 2 opposing forces. Here we provide the genome assembly of the California Wild Radish displaying improvement to currently existing genomes for agronomically important crucifers. This genome sequence provides the tools to dissect the genomic architecture of traits related to herbivory and pollination using natural variation in the wild as well as the ability to infer demographic and selective history in the context of hybridization. Study systems like these will improve our understanding and predictions of evolutionary change for correlated traits.

P–062 Annexin-V MACS method could be a good choice for sperm selection with high PLCZ1 expression and high blastocyst rate in high DFI male factor

Study question

What effect does Annexin-V MACS method have on sperm selection by pLCZ1 expression and blastocyst rate in male DNA fragmentation?

Summary answer

AnnexinV-MACS method could be a good choice for sperm selection with high pLCZ1 expression and high blastocyst rate in high DNA fragmentation male factor.

What is known already

Sperm selection based on morphology and motility in ART techniques, is not enough for choosing the best sperm especially in male factor patients. In Annexin-V magnetic activated cell sorting (MACS) technique, apoptotic sperm are separated from non-apoptotic one by negative selection. So, this method can improved quality of compaction rate in embryo. PLCζ is oocyte activating factors that it starts oscillations of calcium ca2+ in oocyte and it has a significant effect on fertilization and implantation.

Study design, size, duration

Semen samples from 30 male factor infertile couples with high DFI (DFI>30%) were selected and divided into two group (control and experimental) in each patient.

Participants/materials, setting, methods

Control was washed with DGC and experimental one was selected by MACS-DGC. Retrieved eggs in each patient, were divided in 2. Both group were injected by DGC and MACS respectively. Semen parameters and DFI (SCD test) were analyzed before and after processing. After ICSI, rate of fertilization, embryo development and blastocyst formation were evaluated. Real time PCR evaluate expression of PLCζ. Comparison between results of two groups was assessed by SPSS analysis.

Main results and the role of chance

Results showed that, sperm motility and morphology after MACS method (45%, 1.7%) was significantly higher than DGC method (40%, 1.1%) and before washing (35%, 0.9%). Percent of DFI in MACS group (36%) was significantly decreased compared to DGC (45%) and primitive group (55%). The number of oocytes were injected in DGC group was 93 and in MACS group was 111. Fertilization rate in both groups was almost the same (72.07% in MACS vs 73.11 in DGC). Rate of day 3 embryo with good grade in MACS group (72. 5%) was significantly higher than DGC (51.47%) (P < 0.05). The blastocyst rate in MACS-DGC group (69.69%) was significantly increased compared to DGC group (48%). PLCζ gene expression in MACS-DGC was significantly higher than DGC group (p-value=0.046).

Limitations, reasons for caution

This experiment was performed invivo.

Wider implications of the findings: Sperm selection by MACS-DGC method can improve sperm motility, morphology and reduce sperm DFI. No significant difference was observed in fertilization rate, but percent of high-quality embryo on days 3 and 5 was significantly higher by this method,also it can be suggested as a good choice for patients with highDF.

Trial registration number

Not applicable

Ecological convergence of secondary phytochemicals along elevational gradients

Biologists still strive to identify the ecological and evolutionary drivers of phytochemical variation that mediate biotic interactions. We hypothesized that plant species growing at sites characterized by high herbivore pressure would converge to produce highly toxic blends of secondary metabolites, independent of phylogenetic constraints. To address the role of shared evolutionary history and ecological niches in driving variation in plant phytochemistry, we combined targeted metabolomics with insect herbivore bioassays and with a set of growth-related traits of several Cardamine species growing along the entire elevational gradient of the Alps. We observed that Cardamine phytochemical profiles grouped according to previously established growth form categorizations within specific abiotic conditions, independently of phylogenetic relationship. We also showed that novel indices summarizing functional phytochemical diversity better explain plant resistance against chewing and sap-feeding herbivores than classic diversity indices. We conclude that multiple functional axes of phytochemical diversity should be integrated with the functional axis of plant growth forms to study phenotypic convergence along large-scale ecological gradients.

Variation in Below-to Aboveground Systemic Induction of Glucosinolates Mediates Plant Fitness Consequences under Herbivore Attack

Plants defend themselves against herbivore attack by constitutively producing toxic secondary metabolites, as well as by inducing them in response to herbivore feeding. Induction of secondary metabolites can cross plant tissue boundaries, such as from root to shoot. However, whether the potential for plants to systemically induce secondary metabolites from roots to shoots shows genetic variability, and thus, potentially, is under selection conferring fitness benefits to the plants is an open question. To address this question, we induced 26 maternal plant families of the wild species Cardamine hirsuta belowground (BG) using the wound-mimicking phytohormone jasmonic acid (JA). We measured resistance against a generalist (Spodoptera littoralis) and a specialist (Pieris brassicae) herbivore species, as well as the production of glucosinolates (GSLs) in plants. We showed that BG induction increased AG resistance against the generalist but not against the specialist, and found substantial plant family-level variation for resistance and GSL induction. We further found that the systemic induction of several GSLs tempered the negative effects of herbivory on total seed set production. Using a widespread natural system, we thus confirm that BG to AG induction has a strong genetic component, and can be under positive selection by increasing plant fitness. We suggest that natural variation in systemic induction is in part dictated by allocation trade-offs between constitutive and inducible GSL production, as well as natural variation in AG and BG herbivore attack in nature.

Variable effects on growth and defense traits for plant ecotypic differentiation and phenotypic plasticity along elevation gradients

Along ecological gradients, phenotypic differentiation can arise through natural selection on trait diversity and magnitude, and environment-driven plastic changes. The magnitude of ecotypic differentiation versus phenotypic plasticity can vary depending on the traits under study. Using reciprocal transplant-common gardens along steep elevation gradients, we evaluated patterns of ecotypic differentiation and phenotypic plasticity of several growth and defense-related traits for two coexisting but unrelated plant species, Cardamine pratensis and Plantago major. For both species, we observed ecotypic differentiation accompanied by plasticity in growth-related traits. Plants grew faster and produced more biomass when placed at low elevation. In contrast, we observed fixed ecotypic differentiation for defense and resistance traits. Generally, low-elevation ecotypes produced higher chemical defenses regardless of the growing elevation. Yet, some plasticity was observed for specific compounds, such as indole glucosinolates. The results of this study may suggest that ecotypic differentiation in defense traits is maintained by costs of chemical defense production, while plasticity in growth traits is regulated by temperature-driven growth response maximization.

Root JA Induction Modifies Glucosinolate Profiles and Increases Subsequent Aboveground Resistance to Herbivore Attack in Cardamine hirsuta

Alteration and induction of plant secondary metabolites after herbivore attack have been shown in almost all the studied plant species. Induction can be at the local site of damage, or systemic, such as from roots to shoots. In addition to immediate induction, previous herbivore bouts have been shown to "prime" the plants for a stronger and faster response only after a subsequent attack happens. Whereas several studies revealed a link between root herbivory and increased resistance against aboveground (AG) herbivory, the evidence of root defense priming against subsequent AG herbivory is currently lacking. To address this gap, we induced Cardamine hirsuta roots by applying jasmonic acid (JA), and, after a time lag, we subjected both control and JA-treated plants to AG herbivory by the generalist herbivore Spodoptera littoralis. We addressed the effect of root JA addition on AG herbivore resistance by measuring larval weight gain and tested the effect of root induction on abundance and composition of glucosinolates (GSLs) in shoots, prior, and after subsequent herbivory. We observed a strong positive effect of root induction on the resistance against AG herbivory. The overall abundance and identity of GSLs was globally affected by JA induction and by herbivore feeding, independently, and we found a significant correlation between larval growth and the shoot GSL profiles only after AG herbivory, 11 days after induction in roots. Contrary to expectations of priming, we observed that JA induction in roots altered the GSLs profile in the leaves that was maintained through time. This initial modification was sufficient to maintain a lower caterpillar weight gain, even 11 days post-root induction. Altogether, we show that prior root defense induction increases AG insect resistance by modifying and maintaining variation in GSL profiles during insect feeding.

TTY2 genes deletions as genetic risk factor of male infertility

Y chromosome has a number of genes that are expressed in testis and have a role in spermatogenesis. TTY2L12A and TTY2L2A are the members of testis transcript Y2 (TTY2) that are Y linked multi-copy gene families, located on Yp11 and Yq11 loci respectively. The aim of this study was to investigate frequency of TTY2L12A and TTY2L2A deletions in azoospermic patients compared with fertile males. This study was performed on 45 infertile males with idiopathic azoospermia without any AZF micro deletions (group A), 33 infertile males with azoospermia which do not screened for AZF micro deletions (group B) and 65 fertile males (group C), from October 2013 to April 2015 in west of Iran. Polymerase chain reaction (PCR) method was used for detection of TTY2L12A and TTY2L2A gene deletions in studied groups. No deletions were detected in normal fertile males of group C. 1 out of 45 azoospermic males of group A (2.22%) and 3 out of 33 azoospermic males of group B (9.09%) had TTY2L2A deletion (p= 0.409 and p= 0.036 respectively), also 1 out of 45 azoospermic males of group A (2.22%) and 4 out of 33 azoospermic males of group B (12.12%) had TTY2L12A deletion (p= 0.409 and p= 0.011 respectively).  None of azoospermic males in Group A and B had deletions in both genes. Our data showed significant correlation between non-obstructive azoospermia and TTY2L12A and TTY2L2A deletions. Thus, it seems that TTY2L12A and TTY2L2A deletions can consider as one of the genetic risk factors for non-obstructive azoospermia.

Biological Control beneath the Feet: A Review of Crop Protection against Insect Root Herbivores

Sustainable agriculture is certainly one of the most important challenges at present, considering both human population demography and evidence showing that crop productivity based on chemical control is plateauing. While the environmental and health threats of conventional agriculture are increasing, ecological research is offering promising solutions for crop protection against herbivore pests. While most research has focused on aboveground systems, several major crop pests are uniquely feeding on roots. We here aim at documenting the current and potential use of several biological control agents, including micro-organisms (viruses, bacteria, fungi, and nematodes) and invertebrates included among the macrofauna of soils (arthropods and annelids) that are used against root herbivores. In addition, we discuss the synergistic action of different bio-control agents when co-inoculated in soil and how the induction and priming of plant chemical defense could be synergized with the use of the bio-control agents described above to optimize root pest control. Finally, we highlight the gaps in the research for optimizing a more sustainable management of root pests.

An Exploration of the Maternal Experiences of Breast Engorgement and Milk Leakage after Perinatal ‎Loss‎

Introduction and Purpose:

Perinatal loss is one of the toughest events of life. Physiological milk secretion after perinatal loss adds to complicacy of the hardships of the event. The present study is aimed at exploring women’s experience with breast problems and milk leakage after perinatal loss.

Methods:

The Study was carried out through explorative quality approach with 18 participants. Sampling method was purposeful and selecting the participants from widest variety was ensured. Data gathering was through deep semi-structured interview and data analyses were done by conventional content analysis. Reliability and validity of the data were ensured by collecting data from a wide range of participants and frequent revisions.

Findings:

Data analysis indicated four themes including beyond pain, longing being mother, insufficiency of provided information and coping Strategies, and beliefs and values regarding milk leakage and breast engorgement.

Conclusion:

The findings suggested that health care givers needed to inform the patients about probability milk leakage and breast engorgement and remedies to reduce pains and problems of breast engorgement.

SU-E-J-114: Web-Browser Medical Physics Applications Using HTML5 and Javascript

PURPOSE

Since 2010, there has been a great attention about HTML5. Application developers and browser makers fully embrace and support the web of the future. Consumers have started to embrace HTML5, especially as more users understand the benefits and potential that HTML5 can mean for the future.Modern browsers such as Firefox, Google Chrome, and Safari are offering better and more robust support for HTML5, CSS3, and JavaScript. The idea is to introduce the HTML5 to medical physics community for open source software developments. The benefit of using HTML5 is developing portable software systems.

METHODS

The HTML5, CSS, and JavaScript programming languages were used to develop several applications for Quality Assurance in radiation therapy. The canvas element of HTML5 was used for handling and displaying the images, and JavaScript was used to manipulate the data. Sample application were developed to: 1. analyze the flatness and symmetry of the radiotherapy fields in a web browser, 2.analyze the Dynalog files from Varian machines, 3. visualize the animated Dynamic MLC files, 4. Simulation via Monte Carlo, and 5. interactive image manipulation.

RESULTS

The programs showed great performance and speed in uploading the data and displaying the results. The flatness and symmetry program and Dynalog file analyzer ran in a fraction of second. The reason behind this performance is using JavaScript language which is a lower level programming language in comparison to the most of the scientific programming packages such as Matlab. The second reason is that JavaScript runs locally on client side computers not on the web-servers.

CONCLUSIONS

HTML5 and JavaScript can be used to develop useful applications that can be run online or offline on different modern web-browsers. The programming platform can be also one of the modern web-browsers which are mostly open source (such as Firefox).

Proliferation and differentiation potential of cryopreserved human skin-derived precursors

OBJECTIVES

Skin-derived precursors are recognized to be a potentially autologous and accessible source of neural precursor cells for drug screening or cell-based treatments, in many neurological disorders. Thus, it is necessary to investigate appropriate methods for cryopreservation of such human skin-derived precursors (hSKPs). The aim of this study was to evaluate different cryopreservation techniques for retention of hSKPs to discover an optimized protocol.

MATERIALS AND METHODS

We cryopreserved hSKPs treated with 0%, 10%, 20%, 30% and 40% foetal bovine serum (FBS) and three concentrations of dimethylsulphoxide (DMSO) 5%, 10% and 15%, with two different storage periods in liquid nitrogen (2 days: short-term storage; and 2 months: long-term storage). Then, we assessed survival and proliferation levels of the cells after freeze-thaw processes, by viability measurement and colony-forming assay. For detecting hSKPs, we used immunocytochemistry and RT-PCR assessments.

RESULTS

Our findings indicated that hSKPs cryopreserved in 5% DMSO without FBS, had better survival and proliferation potentials compared to other working formulations. With various concentrations of cryoprotectants over different time periods, hSKPs retained their differentiation potentiality and were able to differentiate into neurons (NFM and βΙΙΙ tubulin-positive), glial cells (GFAP-positive) and smooth muscle cells (SMA-positive).

CONCLUSIONS

  Results revealed that in only 5% DMSO, hSKPs could be cryopreserved for long-term storage with considerable survival and proliferation levels, without losing multipotency.

Using an EPID for patient-specific VMAT quality assurance

PURPOSE

A patient-specific quality assurance (QA) method was developed to verify gantry-specific individual multileaf collimator (MLC) apertures (control points) in volumetric modulated arc therapy (VMAT) plans using an electronic portal imaging device (EPID).

METHODS

VMAT treatment plans were generated in an Eclipse treatment planning system (TPS). DICOM images from a Varian EPID (aS1000) acquired in continuous acquisition mode were used for pretreatment QA. Each cine image file contains the grayscale image of the MLC aperture related to its specific control point and the corresponding gantry angle information. The TPS MLC file of this RapidArc plan contains the leaf positions for all 177 control points (gantry angles). In-house software was developed that interpolates the measured images based on the gantry angle and overlays them with the MLC pattern for all control points. The 38% isointensity line was used to define the edge of the MLC leaves on the portal images. The software generates graphs and tables that provide analysis for the number of mismatched leaf positions for a chosen distance to agreement at each control point and the frequency in which each particular leaf mismatches for the entire arc.

RESULTS

Seven patients plans were analyzed using this method. The leaves with the highest mismatched rate were found to be treatment plan dependent.

CONCLUSIONS

This in-house software can be used to automatically verify the MLC leaf positions for all control points of VMAT plans using cine images acquired by an EPID.

Applying graphics processor units to Monte Carlo dose calculation in radiation therapy

We investigate the potential in using of using a graphics processor unit (GPU) for Monte-Carlo (MC)-based radiation dose calculations. The percent depth dose (PDD) of photons in a medium with known absorption and scattering coefficients is computed using a MC simulation running on both a standard CPU and a GPU. We demonstrate that the GPU's capability for massive parallel processing provides a significant acceleration in the MC calculation, and offers a significant advantage for distributed stochastic simulations on a single computer. Harnessing this potential of GPUs will help in the early adoption of MC for routine planning in a clinical environment.

Role of bremsstrahlung radiation in limiting the energy of runaway electrons in tokamaks

Bremsstrahlung radiation of runaway electrons is found to be an energy limit for runaway electrons in tokamaks. The minimum and maximum energy of runaway electron beams is shown to be limited by collisions and bremsstrahlung radiation, respectively. It is also found that a massive injection of a high-Z gas such as xenon can terminate a disruption-generated runaway current before the runaway electrons hit the walls.

Effect of zidovudine resistance mutations on virologic response to treatment with zidovudine-lamivudine-ritonavir: genotypic analysis of human immunodeficiency virus type 1 isolates from AIDS clinical trials group protocol 315.ACTG Protocol 315 Team

The effect of baseline drug resistance mutations on response to zidovudine, lamivudine, and ritonavir was evaluated in zidovudine-experienced persons infected with human immunodeficiency virus type 1 (HIV-1). Presence of the K70R mutation was associated with significantly higher plasma HIV-1 RNA levels at baseline. However, presence of resistance mutations did not affect the increase in plasma HIV-1 RNA during a 5-week drug washout, nor was there any effect on first-phase virus decay rates after initiation of therapy or on the probability of having plasma HIV-1 RNA levels <100 copies/mL at week 48. Polymorphisms at protease codons 10, 36, and 71 were associated with significantly faster second-phase decay rates. Suppression of plasma HIV-1 RNA despite presence of zidovudine resistance mutations implies that the presence of these mutations does not preclude a durable response to treatment with a potent 3-drug regimen.

Emergence of dual resistance to zidovudine and lamivudine in HIV-1-infected patients treated with zidovudine plus lamivudine as initial therapy

Presence of mutations associated with resistance to zidovudine or lamivudine was determined in isolates of HIV-1 obtained after long-term follow-up of 64 infected individuals who received zidovudine, lamivudine, or both drugs as initial antiretroviral therapy. Zidovudine resistance mutations were less frequent in isolates from patients treated with combination lamivudine plus zidovudine compared with zidovudine alone, but these mutations accumulated over time. Phenotypic resistance to both drugs was found in isolates from 3 of 23 patients. In 3 other patients, lamivudine-resistant virus detected at week 12 was replaced by wild-type virus after longer follow-up, which correlated with a return to baseline levels of plasma HIV-1 RNA. These results show that dual resistance to zidovudine and lamivudine develops over time despite the delayed emergence of zidovudine-resistant mutations. These results also suggest a selective advantage in vivo for HIV-1 species that are wild-type at RT codon 184.

Drug resistance and virologic response in NUCA 3001, a randomized trial of lamivudine (3TC) versus zidovudine (ZDV) versus ZDV plus 3TC in previously untreated patients

OBJECTIVE

To study the effect of HIV-1 resistance to lamivudine (3TC) and zidovudine (ZDV), and syncytium-inducing (SI) phenotype on virologic response to treatment with ZDV, 3TC, or ZDV plus 3TC in previously untreated individuals with HIV-1 infection.

DESIGN

A prospective virologic substudy of GlaxoWellcome protocol NUCA 3001.

METHODS

HIV-1 isolates obtained at study entry and at week 12 were expanded in peripheral blood mononuclear cell (PBMC) culture, titered, and assayed for phenotypic and genotypic evidence of resistance to ZDV and 3TC, and for syncytium formation on MT-2 cells.

RESULTS

Phenotypic and genotypic resistance to 3TC was detected in the majority of HIV-1 isolates from patients who received 3TC alone or in combination with ZDV. Despite showing 3TC resistance, subjects who received 3TC in combination with ZDV had significantly greater decreases in plasma HIV-1 RNA levels compared with those who received ZDV alone. Occurrence of the K7OR ZDV resistance mutation was significantly reduced in patients who received the 3TC/ZDV combination as compared with patients on ZDV monotherapy. Plasma HIV-1 RNA returned to near-baseline levels more quickly in patients with SI isolates at study entry.

CONCLUSIONS

Despite the rapid emergence of 3TC resistance, combination therapy with 3TC plus ZDV resulted in greater reduction in plasma HIV-1 RNA levels over 24 weeks as compared to ZDV monotherapy. Prevention of ZDV resistance may contribute to the sustained activity of the combination therapy.