Insights Into the Genetics of the Zhonghua 11 Resistance to Meloidogyne graminicola and Its Molecular Determinism in Rice.

Meloidogyne graminicola is a widely spread nematode pest of rice that reduces crop yield up to 20% on average in Asia, with devastating consequences for local and global rice production. Due to the ban on many chemical nematicides and the recent changes in water management practices in rice agriculture, an even greater impact of M. graminicola can be expected in the future, stressing the demand for the development of new sustainable nematode management solutions. Recently, a source of resistance to M. graminicola was identified in the Oryza sativa japonica rice variety Zhonghua 11 (Zh11). In the present study, we examine the genetics of the Zh11 resistance to M. graminicola and provide new insights into its cellular and molecular mechanisms. The segregation of the resistance in F2 hybrid populations indicated that two dominant genes may be contributing to the resistance. The incompatible interaction of M. graminicola in Zh11 was distinguished by a lack of swelling of the root tips normally observed in compatible interactions. At the cellular level, the incompatible interaction was characterised by a rapid accumulation of reactive oxygen species in the vicinity of the nematodes, accompanied by extensive necrosis of neighbouring cells. The expression profiles of several genes involved in plant immunity were analysed at the early stages of infection during compatible (susceptible plant) and incompatible (resistant plant) interactions. Notably, the expression of OsAtg4 and OsAtg7, significantly increased in roots of resistant plants in parallel with the cell death response, suggesting that autophagy is activated and may contribute to the resistance-mediated hypersensitive response. Similarly, transcriptional regulation of genes involved in hormonal pathways in Zh11 indicated that salicylate signalling may be important in the resistance response towards M. graminicola. Finally, the nature of the resistance to M. graminicola and the potential exploitation of the Zh11 resistance for breeding are discussed.

Discovery of new genetic determinants of morphological plasticity in rice roots and shoots under phosphate starvation using GWAS.

Phosphorus is an essential nutrient for plants that is often in short supply. In rice (Oryza sativa L.), inorganic phosphate (Pi) deficiency leads to various physiological disorders that consequently affect plant productivity. In this study, a large-scale phenotyping experiment using 160 Vietnamese rice landraces was performed under greenhouse conditions, by employing an alpha lattice design with three replicates, to identify quantitative trait loci (QTLs) associated with plant growth inhibition caused by Pi deficiency. Rice plantlets were grown for six weeks in the PVC sand column (16 cm diameter × 80 cm height) supplied with Pi-deficient medium (10 µM P) or full-Pi Yoshida medium (320 µM P). The effects of Pi deficiency on the number of crown roots, root length, shoot length, root weight, shoot weight and total weight were studied. From 36 significant markers identified using a genome-wide association study, 21 QTLs associated with plant growth inhibition under Pi starvation were defined. In total, 158 candidate genes co-located with the defined QTLs were identified. Interestingly, one QTL (qRST9.14) was associated with all three weight-traits. The co-located gene GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE 13 was found to be potentially involved in Pi transport. Understanding the molecular mechanisms of Pi-starvation responses, and identifying the potential QTLs responsible for low-Pi stress tolerance, will provide valuable information for developing new varieties tolerant of low-Pi conditions.

Genome-wide Association Study of a Panel of Vietnamese Rice Landraces Reveals New QTLs for Tolerance to Water Deficit During the Vegetative Phase.

BACKGROUND: Drought tolerance is a major challenge in breeding rice for unfavorable environments. In this study, we used a panel of 180 Vietnamese rice landraces genotyped with 21,623 single-nucleotide polymorphism markers to perform a genome-wide association study (GWAS) for different drought response and recovery traits during the vegetative stage. These landraces originate from different geographical locations and are adapted to different agrosystems characterized by contrasted water regimes. Vietnamese landraces are often underrepresented in international panels used for GWAS, but they can contain original genetic determinants related to drought resistance. RESULTS: The panel of 180 rice varieties was phenotyped under greenhouse conditions for several drought-related traits in an experimental design with 3 replicates. Plants were grown in pots for 4 weeks and drought-stressed by stopping irrigation for an additional 4 weeks. Drought sensitivity scores and leaf relative water content were measured throughout the drought stress. The recovery capacity was measured 2 weeks after plant rewatering. Several QTLs associated with these drought tolerance traits were identified by GWAS using a mixed model with control of structure and kinship. The number of detected QTLs consisted of 14 for leaf relative water content, 9 for slope of relative water content, 12 for drought sensitivity score, 3 for recovery ability and 1 for relative crop growth rate. This set of 39 QTLs actually corresponded to a total of 17 different QTLs because 9 were simultaneously associated with two or more traits, which indicates that these common loci may have pleiotropic effects on drought-related traits. No QTL was found in association with the same traits in both the indica and japonica subpanels. The possible candidate genes underlying the quantitative trait loci are reviewed. CONCLUSIONS: Some of the identified QTLs contain promising candidate genes with a function related to drought tolerance by osmotic stress adjustment.

Internal model control for industrial wireless plant using WirelessHART hardware-in-the-loop simulator.

The emergence of wireless technologies such as WirelessHART and ISA100 Wireless for deployment at industrial process plants has urged the need for research and development in wireless control. This is in view of the fact that the recent application is mainly in monitoring domain due to lack of confidence in control aspect. WirelessHART has an edge over its counterpart as it is based on the successful Wired HART protocol with over 30 million devices as of 2009. Recent works on control have primarily focused on maintaining the traditional PID control structure which is proven not adequate for the wireless environment. In contrast, Internal Model Control (IMC), a promising technique for delay compensation, disturbance rejection and setpoint tracking has not been investigated in the context of WirelessHART. Therefore, this paper discusses the control design using IMC approach with a focus on wireless processes. The simulation and experimental results using real-time WirelessHART hardware-in-the-loop simulator (WH-HILS) indicate that the proposed approach is more robust to delay variation of the network than the PID.

Surviving with trisomy 13: Provider and parent perspectives and the role of the pediatric palliative care program.

Trisomy 13 typically denotes an overall poor prognosis in the setting of multisystem anomalies. Through a provider and parent perspective, this case illustrates the benefit of hope, communication, and teamwork through the integration of a palliative care team in the care of a medically complex child with trisomy 13, resulting in enhance survival and perceived quality of life for patient and family. © 2016 Wiley Periodicals, Inc.

Impact of Race/Ethnicity on Pain Management Outcomes in a Community-Based Teaching Hospital Following Inpatient Palliative Care Consultation.

OBJECTIVE: To examine race/ethnicity differences in pain management outcomes following inpatient palliative care consultation. METHODS: We conducted a retrospective study based on data from a community-based teaching hospital in Fresno, CA, USA, from April 2014 to July 2015. One hundred sixty-one patients with life-limiting diagnoses and palliative care pain-related consultations were included. The patients were categorized into four racial groups: Caucasians, African-Americans, Hispanics, and Asians/Others. Demographics and baseline pain scores using the Visual Analogue Scale (VAS) were obtained. The outcome measures included the length of stay, time to consult, and pain scores at admission, 24 hours before the consultation, 24-48 hours after consultation, and at discharge. RESULTS: The initial median pain scores were not significantly different between the groups, however, the Asians had slightly higher pain scores compared to the other groups. African-Americans, Caucasians, and Hispanics had significant differences in pain outcomes after consultation compared to 24 hours prior to consultation (p = 0.01, p < 0.01 and p = 0.02, respectively). Caucasians and Hispanics had significant differences in pain outcomes after palliative consultation compared to initial admission assessment (p < 0.01). The differences between discharge and admission pain scores were significant only for Asians, Caucasians, and Hispanics (p = 0.04, p < 0.01, p < 0.01, respectively) but not African-Americans. There were no significant pain score differences across the racial groups following consultations. CONCLUSION: There were no significant differences in pain reduction amongst the racial groups, suggesting that pain can adequately be managed in individual racial groups after inpatient palliative care consultations.

Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam.

BACKGROUND: Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. RESULTS: The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. CONCLUSIONS: Some of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development.

OsMADS26 Negatively Regulates Resistance to Pathogens and Drought Tolerance in Rice.

Functional analyses of MADS-box transcription factors in plants have unraveled their role in major developmental programs (e.g. flowering and floral organ identity) as well as stress-related developmental processes, such as abscission, fruit ripening, and senescence. Overexpression of the rice (Oryza sativa) MADS26 gene in rice has revealed a possible function related to stress response. Here, we show that OsMADS26-down-regulated plants exhibit enhanced resistance against two major rice pathogens: Magnaporthe oryzae and Xanthomonas oryzae. Despite this enhanced resistance to biotic stresses, OsMADS26-down-regulated plants also displayed enhanced tolerance to water deficit. These phenotypes were observed in both controlled and field conditions. Interestingly, alteration of OsMADS26 expression does not have a strong impact on plant development. Gene expression profiling revealed that a majority of genes misregulated in overexpresser and down-regulated OsMADS26 lines compared with control plants are associated to biotic or abiotic stress response. Altogether, our data indicate that OsMADS26 acts as an upstream regulator of stress-associated genes and thereby, a hub to modulate the response to various stresses in the rice plant.

Characterization of a panel of Vietnamese rice varieties using DArT and SNP markers for association mapping purposes.

BACKGROUND: The development of genome-wide association studies (GWAS) in crops has made it possible to mine interesting alleles hidden in gene bank resources. However, only a small fraction of the rice genetic diversity of any given country has been exploited in the studies with worldwide sampling conducted to date. This study presents the development of a panel of rice varieties from Vietnam for GWAS purposes. RESULTS: The panel, initially composed of 270 accessions, was characterized for simple agronomic traits (maturity class, grain shape and endosperm type) commonly used to classify rice varieties. We first genotyped the panel using Diversity Array Technology (DArT) markers. We analyzed the panel structure, identified two subpanels corresponding to the indica and japonica sub-species and selected 182 non-redundant accessions. However, the number of usable DArT markers (241 for an initial library of 6444 clones) was too small for GWAS purposes. Therefore, we characterized the panel of 182 accessions with 25,971 markers using genotyping by sequencing. The same indica and japonica subpanels were identified. The indica subpanel was further divided into six populations (I1 to I6) using a model-based approach. The japonica subpanel, which was more highly differentiated, was divided into 4 populations (J1 to J4), including a temperate type (J2). Passport data and phenotypic traits were used to characterize these populations. Some populations were exclusively composed of glutinous types (I3 and J2). Some of the upland rice varieties appeared to belong to indica populations, which is uncommon in this region of the world. Linkage disequilibrium decayed faster in the indica subpanel (r2 below 0.2 at 101 kb) than in the japonica subpanel (r2 below 0.2 at 425 kb), likely because of the strongest differentiation of the japonica subpanel. A matrix adapted for GWAS was built by eliminating the markers with a minor allele frequency below 5% and imputing the missing data. This matrix contained 21,814 markers. A GWAS was conducted on time to flowering to prove the utility of this panel. CONCLUSIONS: This publicly available panel constitutes an important resource giving access to original allelic diversity. It will be used for GWAS on root and panicle traits.

Predictors of discharge to acute care after inpatient rehabilitation in severely affected stroke patients.

OBJECTIVE: This study aimed to determine the predictors of discharge to acute care after inpatient rehabilitation in severely affected stroke patients. DESIGN: This was a retrospective study using data from the Uniform Data System for Medical Rehabilitation (UDSMR) between 2008 and 2009. The main outcome variable was discharge location, which included discharge to acute care or discharge to the community after inpatient rehabilitation. The study sample included 223 of the most severely affected stroke patients (Case-Mix Group 0110 of Medicare reimbursement classification), of whom 86 were discharged to acute care from after the inpatient medical rehabilitation setting; 137 similarly classified stroke patients were discharged to the community after inpatient medical rehabilitation. The variables examined were Functional Independence Measure ratings, co-morbid medical conditions, and four groups of stroke-related neurologic deficits (hemiparesis, dysphagia, language deficits, and other stroke-related neurologic deficits). The groups were devised based on International Classification of Diseases, 9th Revision codes. RESULTS: There were no significant demographic differences between the two groups-those discharged to the acute care hospital and those discharged to the community. There was a difference in admission Functional Independence Measure ratings, whereby patients discharged to acute care were significantly lower (P < 0.05) on admission motor and cognitive function than were patients discharged to the community. When controlling for 19 groups of co-morbid medical conditions and 4 groups of stroke-related neurologic deficits, there was no significant difference between patients being discharged to an acute care hospital and those discharged to the community. CONCLUSIONS: In the current study, controlling for impairment (stroke), severity of condition, demographic variables, inpatient rehabilitation admission day of the week and discharge day of the week, prehospitalization living setting, prehospitalization living with (alone, family, other), payer (secondary insurance coverage), onset days, co-morbid medical conditions, and classification of stroke-related neurologic deficits, the only variable predictive of discharge to the acute care hospital from an inpatient rehabilitation facility is function at admission, mainly the admission motor Functional Independence Measure rating. If clinicians routinely assess the functional status of patients during the preadmission screening process, it may aid in identifying whether the patient is at an increased risk of being readmitted to the acute care hospital.

Pesticide mixtures, endocrine disruption, and amphibian declines: are we underestimating the impact?

Amphibian populations are declining globally at an alarming rate. Pesticides are among a number of proposed causes for these declines. Although a sizable database examining effects of pesticides on amphibians exists, the vast majority of these studies focus on toxicological effects (lethality, external malformations, etc.) at relatively high doses (parts per million). Very few studies focus on effects such as endocrine disruption at low concentrations. Further, most studies examine exposures to single chemicals only. The present study examined nine pesticides (four herbicides, two fungicides, and three insecticides) used on cornfields in the midwestern United States. Effects of each pesticide alone (0.1 ppb) or in combination were examined. In addition, we also examined atrazine and S-metolachlor combined (0.1 or 10 ppb each) and the commercial formulation Bicep II Magnum, which contains both of these herbicides. These two pesticides were examined in combination because they are persistent throughout the year in the wild. We examined larval growth and development, sex differentiation, and immune function in leopard frogs (Rana pipiens). In a follow-up study, we also examined the effects of the nine-compound mixture on plasma corticosterone levels in male African clawed frogs (Xenopus laevis). Although some of the pesticides individually inhibited larval growth and development, the pesticide mixtures had much greater effects. Larval growth and development were retarded, but most significantly, pesticide mixtures negated or reversed the typically positive correlation between time to metamorphosis and size at metamorphosis observed in controls: exposed larvae that took longer to metamorphose were smaller than their counterparts that metamorphosed earlier. The nine-pesticide mixture also induced damage to the thymus, resulting in immunosuppression and contraction of flavobacterial meningitis. The study in X. laevis revealed that these adverse effects may be due to an increase in plasma levels of the stress hormone corticosterone. Although it cannot be determined whether all the pesticides in the mixture contribute to these adverse effects or whether some pesticides are effectors, some are enhancers, and some are neutral, the present study revealed that estimating ecological risk and the impact of pesticides on amphibians using studies that examine only single pesticides at high concentrations may lead to gross underestimations of the role of pesticides in amphibian declines.