Nonsense-mediated mRNA decay pathway in plants under stress: general gene regulatory mechanism and advances

MAIN CONCLUSION

Nonsense-mediated mRNA decay in eukaryotes is vital to cellular homeostasis. Further knowledge of its putative role in plant RNA metabolism under stress is pivotal to developing fitness-optimizing strategies. Nonsense-mediated mRNA decay (NMD), part of the mRNA surveillance pathway, is an evolutionarily conserved form of gene regulation in all living organisms. Degradation of mRNA-bearing premature termination codons and regulation of physiological RNA levels highlight NMD's role in shaping the cellular transcriptome. Initially regarded as purely a tool for cellular RNA quality control, NMD is now considered to mediate various aspects of plant developmental processes and responses to environmental changes. Here we offer a basic understanding of NMD in eukaryotes by explaining the concept of premature termination codon recognition and NMD complex formation. We also provide a detailed overview of the NMD mechanism and its role in gene regulation. The potential role of effectors, including ABCE1, in ribosome recycling during the translation process is also explained. Recent reports of alternatively spliced variants of corresponding genes targeted by NMD in Arabidopsis thaliana are provided in tabular format. Detailed figures are also provided to clarify the NMD concept in plants. In particular, accumulating evidence shows that NMD can serve as a novel alternative strategy for genetic manipulation and can help design RNA-based therapies to combat stress in plants. A key point of emphasis is its function as a gene regulatory mechanism as well as its dynamic regulation by environmental and developmental factors. Overall, a detailed molecular understanding of the NMD mechanism can lead to further diverse applications, such as improving cellular homeostasis in living organisms.

Microbial remediation and plant-microbe interaction under arsenic pollution

Arsenic contamination in aquatic and terrestrial ecosystem is a serious environmental issue. Both natural and anthropogenic processes can introduce it into the environment. The speciation of the As determine the level of its toxicity. Among the four oxidation states of As (-3, 0, +3, and + 5), As(III) and As(V) are the common species found in the environment, As(III) being the more toxic with adverse impact on the plants and animals including human health. Therefore, it is very necessary to remediate arsenic from the polluted water and soil. Different physicochemical as well as biological strategies can be used for the amelioration of arsenic polluted soil. Among the microbial approaches, oxidation of arsenite, methylation of arsenic, biosorption, bioprecipitation and bioaccumulation are the promising transformation activities in arsenic remediation. The purpose of this review is to discuss the significance of the microorganisms in As toxicity amelioration in soil, factors affecting the microbial remediation, interaction of the plants with As resistant bacteria, and the effect of microorganisms on plant arsenic tolerance mechanism. In addition, the exploration of genetic engineering of the bacteria has a huge importance in bioremediation strategies, as the engineered microbes are more potent in terms of remediation activity along with quick adaptively in As polluted sites.

Genome-Wide Identification of Aquaporin Genes in Adzuki Bean (Vigna angularis) and Expression Analysis under Drought Stress

The adzuki bean Vigna angularis (Wild.) is an important leguminous crop cultivated mainly for food purposes in Asian countries; it represents a source of carbohydrates, digestible proteins, minerals, and vitamins. Aquaporins (AQPs) are crucial membrane proteins involved in the transmembrane diffusion of water and small solutes in all living organisms, including plants. In this study, we used the whole genome sequence of the adzuki bean for in silico analysis to comprehensively identify 40 Vigna angularis aquaporin (VaAQP) genes and reveal how these plants react to drought stress. VaAQPs were compared with AQPs from other closely-related leguminous plants, and the results showed that mustard (Brassica rapa) (59), barrel medic (Medicago truncatula) (46), soybean (Glycine max) (66), and common bean (Phaseolus vulgaris L.) (41) had more AQP genes. Phylogenetic analysis revealed that forty VaAQPs belong to five subfamilies, with the VaPIPs (fifteen) subfamily the largest, followed by the VaNIPs (ten), VaTIPs (ten), VaSIPs (three), and VaXIPs (two) subfamilies. Furthermore, all AQP subcellular locations were found at the plasma membrane, and intron-exon analysis revealed a relationship between the intron number and gene expression, duplication, evolution, and diversity. Among the six motifs identified, motifs one, two, five, and six were prevalent in VaTIP, VaNIP, VaPIP, and VaXIP, while motifs one, three, and four were not observed in VaPIP1-3 and VaPIP1-4. Under drought stress, two of the VaAQPs (VaPIP2-1 and VaPIP2-5) showed significantly higher expression in the root tissue while the other two genes (VaPIP1-1 and VaPIP1-7) displayed variable expression in leaf tissue. This finding revealed that the selected VaAQPs might have unique molecular functions linked with the uptake of water under drought stress or in the exertion of osmoregulation to transport particular substrates rather than water to protect plants from drought. This study presents the first thorough investigation of VaAQPs in adzuki beans, and it reveals the transport mechanisms and related physiological processes that may be utilized for the development of drought-tolerant adzuki bean cultivars.

Exploration of silicate solubilizing bacteria for sustainable agriculture and silicon biogeochemical cycle

Silicon (Si), a quasi-essential element for plants, is abundant in the soil typically as insoluble silicate forms. However, plants can uptake Si only in the soluble form of monosilicic acid. Production of monosilicic acid by rock-weathering mostly depends on temperature, pH, redox-potential, water-content, and microbial activities. In the present review, approaches involved in the efficient exploration of silicate solubilizing bacteria (SSB), its potential applications, and available technological advances are discussed. Present understanding of Si uptake, deposition, and subsequent benefits to plants has also been discussed. In agricultural soils, pH is found to be one of the most critical factors deciding silicate solubilization and the formation of different Si compounds. Numerous studies have predicted the role of Indole-3-Acetic Acid (IAA) and organic acids produced by SSB in silicate solubilization. In this regard, approaches for the isolation and characterization of SSB, quantification of IAA, and subsequent Si solubilization mechanisms are addressed. Phylogenetic evaluation of previously reported SSB showed a highly diverse origin which provides an opportunity to study different mechanisms involved in Si solubilization. Soil biochemistry in concern of silicon availability, microbial activity and silicon mediated changes in plant physiology are addressed. In addition, SSB's role in Si-biogeochemical cycling is summarized. The information presented here will be helpful to explore the potential of SSB more efficiently to promote sustainable agriculture.

Models and evidence of intersectoral cooperation in prevention and health promotion

Background

Inter-sectoral coalitions are regarded as a key principle of health promotion. The study examines the questions of how these are defined, which scientific theories and models are available, and which methods and parameters are used for their evaluation.

Methods

The scoping review in three databases (PubMed, Web of Science, LIVIVO) included studies in English and German published in 1/2010 to 5/2018. The results were analyzed qualitatively. In addition, relevant websites and textbooks in the field of public health, health promotion and social work were subjected to a document analysis in an iterative procedure.

Results

The database searches yielded 186 hits, of which 48 publications were systematically examined. Document analysis revealed 128 materials. Six common terms on inter-sectoral cooperation (network, collaboration, partnership, coalition, cooperation, alliance) were identified. Uniform definitions and unambiguous distinctions do not exist. Overall, only a few of the identified inter-sectoral collaborations are theoretically based, nine publications present models. Only seven studies provide insights into the effectiveness of model/theory-based strategies, whereby these almost exclusively examine output parameters. In particular, there are parameters on structure and process (e.g. team functioning, coalition capacity). Qualitative success factors and barriers were identified (e.g. integration of different actors, development of new financial sources, formalization). Eight validated instruments are identified. Four studies also examine the outcome level and demonstrate intended effects on behavioral parameters.

Conclusions

For research and practice, it is necessary to sharpen the terminology of intersectoral cooperation. Existing models should be systematically used and evaluated. In the future, an evaluation of the outcome of inter-sectoral cooperation and long-term effects will be increasingly necessary.

Key messages

Inter-sectoral coalitions are an evolving field, and both their theoretical foundation and empirical testing are still in their infancy. While success factors are well investigated, evaluations at the outcomes level are particularly necessary.

Eyelid metastasis as presenting feature of disseminated leiomyosarcoma - A rare case report

Soft tissue sarcomas with smooth muscle differentiation are termed leiomyosarcoma. Leiomyosarcoma is an aggressive tumor commonly originating from smooth muscle cells of uterus or retro peritoneal areas. Distant metastasis occurs by hematogenous route to liver and lung. Eyelid metastasis without involvement of other ocular structures is extremely rare. A case of eyelid metastasis which on extensive investigations was proved to be from upper gastrointestinal tract leiomyosarcoma is reported here.

Mixing with applications to inertial-confinement-fusion implosions

Approximate one-dimensional (1D) as well as 2D and 3D simulations are playing an important supporting role in the design and analysis of future experiments at National Ignition Facility. This paper is mainly concerned with 1D simulations, used extensively in design and optimization. We couple a 1D buoyancy-drag mix model for the mixing zone edges with a 1D inertial confinement fusion simulation code. This analysis predicts that National Ignition Campaign (NIC) designs are located close to a performance cliff, so modeling errors, design features (fill tube and tent) and additional, unmodeled instabilities could lead to significant levels of mix. The performance cliff we identify is associated with multimode plastic ablator (CH) mix into the hot-spot deuterium and tritium (DT). The buoyancy-drag mix model is mode number independent and selects implicitly a range of maximum growth modes. Our main conclusion is that single effect instabilities are predicted not to lead to hot-spot mix, while combined mode mixing effects are predicted to affect hot-spot thermodynamics and possibly hot-spot mix. Combined with the stagnation Rayleigh-Taylor instability, we find the potential for mix effects in combination with the ice-to-gas DT boundary, numerical effects of Eulerian species CH concentration diffusion, and ablation-driven instabilities. With the help of a convenient package of plasma transport parameters developed here, we give an approximate determination of these quantities in the regime relevant to the NIC experiments, while ruling out a variety of mix possibilities. Plasma transport parameters affect the 1D buoyancy-drag mix model primarily through its phenomenological drag coefficient as well as the 1D hydro model to which the buoyancy-drag equation is coupled.

Asymmetries in core-collapse supernovae from maps of radioactive 44Ti in Cassiopeia A

Asymmetry is required by most numerical simulations of stellar core-collapse explosions, but the form it takes differs significantly among models. The spatial distribution of radioactive (44)Ti, synthesized in an exploding star near the boundary between material falling back onto the collapsing core and that ejected into the surrounding medium, directly probes the explosion asymmetries. Cassiopeia A is a young, nearby, core-collapse remnant from which (44)Ti emission has previously been detected but not imaged. Asymmetries in the explosion have been indirectly inferred from a high ratio of observed (44)Ti emission to estimated (56)Ni emission, from optical light echoes, and from jet-like features seen in the X-ray and optical ejecta. Here we report spatial maps and spectral properties of the (44)Ti in Cassiopeia A. This may explain the unexpected lack of correlation between the (44)Ti and iron X-ray emission, the latter being visible only in shock-heated material. The observed spatial distribution rules out symmetric explosions even with a high level of convective mixing, as well as highly asymmetric bipolar explosions resulting from a fast-rotating progenitor. Instead, these observations provide strong evidence for the development of low-mode convective instabilities in core-collapse supernovae.

Long-term outcome with lenalidomide and dexamethasone therapy for newly diagnosed multiple myeloma

The combination of lenalidomide and dexamethasone (Len-Dex) is a commonly used initial therapy for newly diagnosed multiple myeloma (MM). Although the initial response rates and toxicity are well known, long-term outcome is not well described. We studied 286 consecutive patients with newly diagnosed MM initially treated with Len-Dex. The median (range) age at diagnosis was 63 (28-92) years, 166 (58%) patients ≤ 65 years and 175 (61%) male. The median estimated duration on Len-Dex was 5.3 months with overall response (≥ partial response) of 72%, including 26% with very good partial response or better. The median overall survival (OS) from the diagnosis was not reached (NR) and the estimated 5-year survival was 71%. The median time to first disease progression, irrespective of transplant status, was 30.2 months. Overall, 143 (50%) patients underwent stem cell transplant. The median OS was NR for patients ≤ 70 years and 5.8 years for the older patients (P=0.01). The 5-year OS estimate for patients in International Staging System stage 1, 2 and 3 were 82, 65, and 44% respectively. There were 21 new second malignancies after MM diagnosis (6.6%). The median survival exceeding 7 years reflects the efficacy of novel agents. The risk of second malignancies doesn't appear to be excessive in this population.

Tooth fragment embedded in the upper lip after dental trauma: a case report presenting an immediate diagnostic approach and complete rehabilitation

Dental traumas are reasonably common, especially in children and adolescents. They are caused by many factors with fall accounting for the most frequent one. Dental trauma requires a special consideration when dental fractures accompany soft tissue lacerations. Dental fragments occasionally penetrate into soft tissue and may cause severe complications. Early diagnosis and surgical removal of these fragments could prevent undesirable foreign body reaction and scarring. This report presents immediate diagnosis and management of a case in which dental fragment was embedded in the lip soft tissue.

SU-E-I-28: Development of Graphic Patient Models for a Real-Time Skin Dose Tracking System (DTS) for Fluoroscopic Interventional Procedures

PURPOSE

To develop a library of graphic human models that closely match patients undergoing interventional fluoroscopic procedures in order to obtain an accurate estimate of their skin dose.

METHODS

A dose tracking system (DTS) has been developed that calculates the dose to the patient's skin in real time during fluoroscopic procedures based on a graphical simulation of the x-ray system and the patient. The calculation is performed using a lookup table containing values of mGy per mAs at a reference point and inverse-square correction using the distance from the source to individual points on the skin. For proper inverse-square correction, the external shape of the graphic should closely match that of the patient. We are in the process of developing a library of 3D human graphic models categorized as a function of basic body type, sex, height and weight. Two different open- source software applications are being used to develop graphic models with varying weights and heights, to 'morph' the shapes for body type and to 'pose' them for proper positioning on the table. The DTS software is being designed such that the most appropriate body graphic can be automatically selected based on input of several basic patient dimensional metrics.

RESULTS

A series of male and female body graphic models have been developed which vary in weight and height. Matching pairs have been constructed with arms at the side and over the head to simulate the usual placement in cardiac procedures. The error in skin dose calculation due to inverse-square correction is expected to be below 5% if the graphic can match the position of the patient's skin surface within 1 cm.

CONCLUSIONS

A library of categorized body shapes should allow close matching of the graphic to the patient shape allowing more accurate determination of skin dose with the DTS. Support for this work was provided in part by NIH grants R43FD0158401, R44FD0158402, R01EB002873 and R01EB008425, and by Toshiba Medical Systems Corporation.

Peripheral giant cell granuloma

Peripheral giant cell granuloma is a benign reactive lesion of gingiva. It manifests as a firm, soft, bright nodule or as a sessile or pedunculate mass. This article reports the management of peripheral giant cell granuloma in a 12-year-old boy by surgical excision.

Risk of intracranial hemorrhage and cerebrovascular accidents in non-small cell lung cancer brain metastasis patients

7671

Background: Brain metastases confer significant morbidity and a poorer survival in non-small cell lung cancer (NSCLC). Vascular endothelial growth factor-targeted antiangiogenic therapies (AAT) have demonstrated benefit for patients with metastatic NSCLC and are expected to directly inhibit the pathophysiology and morbidity of brain metastases, yet patients with brain metastases have been excluded from most clinical trials of AAT for fear of intracranial hemorrhage (ICH). This is a low suspected risk, but needs to be quantitated to plan clinical trials of AAT for NSCLC brain metastases. Methods: Data from MD Anderson Cancer Center Tumor Registry and electronic medical records from January 1998 to March 2006 was interrogated. 2143 patients with metastatic NSCLC registering from Jan 1998 to Sept 2005 were followed till March 2006. 776 patients with and 1367 patients without brain metastases were followed till death, date of ICH, or last date of study, whichever occurred first. Results: The incidence of ICH seemed to be higher in those with brain metastasis compared to those without. However, the rates of symptomatic ICH were not significantly different. All ICH patients with brain metastasis had received radiation therapy for them and were not anticoagulated. Most of the brain metastasis-associated ICH's were asymptomatic, detected during radiologic surveillance. The rates of symptomatic ICH, or cerebrovascular accidents were similar and not significantly different between the two groups. The following table depicts the rates of CVA and/or ICH in metastatic NSCLC patients. Conclusions: In metastatic NSCLC patients, the incidence of spontaneous ICH appeared to be higher in those with brain metastases compared to those without, but was very low in both groups nonetheless without a statistically significant difference. These data suggest minimal risk of clinically significant ICH for NSCLC brain metastasis patients and justifies for them clinical trials of AAT.

No significant financial relationships to disclose.

[Table: see text]

Prognostic quantification of non-small cell lung cancer metastases to the lung

17080

Background: Lung is the most frequent organ site of metastases from non-small cell lung cancer (NSCLC), yet the impact of these metastases on the natural history of the disease has not been well elucidated. Part of the difficulty of evaluating the prognosis of lung metastases in NSCLC patients is the effect of metastases to other organ sites. Here we have studied the survival of patients with lung as the solitary or dominant site of metastases and correlated it with number and maximal size of tumors. Methods: Data from the M.D. Anderson Cancer Center Tumor Registry during 1998 to 2002 was interrogated. Of 1280 patients registering as new patients, 87 were evaluable as having lung as the only site of metastases on initial staging evaluation. Excluding 13 patients who had bronchioloalveolar carcinoma (BAC) or BAC features on histology, the remaining 74 patients’ baseline CT scans were reviewed and scored for 1) the maximal linear measurement of the largest lung tumor and 2) the number of lung nodules that were growing and consistent with lung metastases. Results: In non-BAC patients with lung only metastases, an inverse correlation is seen between maximal linear measurement of a patient’s largest lung metastasis on baseline staging and their subsequent survival. A similar inverse correlation is seen between the number of lung metastases and survival. When patients with subsequent development of other metastatic sites are excluded from the analysis, these correlations are strengthened. Also, in BAC patients with lung only metastases, a trend toward longer survival with fewer metastases was seen, but only 13 patients were evaluable. Formal statistical analysis of these results is pending. Conclusions: The number and size of lung metastases from NSCLC appear to be independent predictors of survival. This might be explained by lead-time bias where fewer lesions represent an earlier stage of metastatic disease, however, increasing number and size of metastases may also be multiplying the source for further metastatic spread of disease. This interpretation of data may justify the local therapy of individual lung metastases in oligometastatic disease by surgery, stereotactic radiosurgery, or radiofrequency ablation.

No significant financial relationships to disclose.

Neoadjuvant chemotherapy improves outcomes of chemoradiation therapy for locally advanced pancreatic cancer

4036

Background: Two-thirds of all pancreatic cancer patients have radiographically detectable metastatic disease at the time of diagnosis. Most of the remaining patients have locally advanced, unresectable disease that is typically treated with either chemoradiation or chemotherapy alone. We explored the possible benefit of the use of consolidative chemoradiation after induction chemotherapy. Methods: Between December 1993 and October 2005, 318 patients with locally advanced, non-metastatic, pancreatic cancer were treated at our institution with concurrent chemoradiation therapy. All patients underwent CT staging and biopsy confirmed adenocarcinoma. 245 patients received chemoradiation (CR) as initial treatment while 73 patients received a median of 2.5 months of induction chemotherapy prior to chemoradiation (CCR). Radiosensitizers included 5FU (42%), gemcitabine (39%) and capecitabine (19%) and most patients (88%) received 30 Gy of radiation therapy. The most common induction chemotherapy regimens were gemcitabine and cisplatin (73%) and gemcitabine alone (15%). Results: All statistics are actuarial and calculated from date of initial treatment. Median follow-up was 5.5 months (range 1–63 months). For all patients, overall survival was 9.0 months and 2-year survival was 8%. Age, gender, histology, grade, radiation fractionation and concurrent chemotherapy regimen had no impact on outcomes on univariate analysis. However, overall survival was 8.5 months in the CR group and 11.9 months in the CCR group (p = 0.0004). Median time to local progression was 6.0 months in the CR group and 8.4 in the CCR group (p = 0.0055). Median time to distant progression was 5.8 months in the CR group and 9.5 months in the CCR group (p=0.0136). Conclusions: In one of the largest series of locally advanced pancreatic cancer patients, the use of induction chemotherapy followed by chemoradiation seems to prolong median survival over initial treatment with chemoradiation. By excluding patients who progress rapidly during induction chemotherapy, this approach presumably selects patients most likely to benefit from a local treatment modality. This strategy merits prospective evaluation.

[Table: see text]