Efforts to capture high amylose in rice

Screening of wild and cultivated rice in IRRI germplasm collection revealed that majority have intermediate apparent amylose content. It appears that ancient farmers selected rice based on texture of the lower amylose varieties, considering that the majority of rice consumers today prefer intermediate to soft-textured rice. Furthermore, 30% seems to be the natural upper natural limit of amylose levels in wild-type rice. If this is the case, the rich biodiversity of rice has been subjected to the bottleneck of domestication to select for grains that have superior cooking and eating but not nutritional or satiating qualities considering that the majority of rice consumers today eat rice three times a day. On the other hand, the amylose content of available rice mutants with deficient SBEIIb or an over-expressed GBSSI also revealed amylose levels of around 35% which is significantly lower by comparison with other high amylose cereals, whose amylose content ranges from 70–90%. Hence, to produce the high amylose phenotype in rice, one might need to target different sets of enzymes or regulatory pathways. Since increasing the amylose levels in rice might mean a concomitant increase in its resistant starch content and in its levels of satiety, and a decrease in its glycemic response, developing high amylose rice by biotechnology is imperative. This type of rice will be important not only in addressing the growing obesity epidemic which now also affects the developing countries but also as a basis of novel degradable biopolymers and for further elucidating the mechanisms of starch synthesis in the cereal endosperm. In this paper, we also present the status of our research project which aims to silence the expression of SBEIIa, SBEIIb and SSIIa singly or in combination using microRNA and RNAi silencing technologies with the aim of increasing the amylose levels in rice beyond its natural limits

Association between alleles of the waxy gene and traits of grain quality in Philippine Seed Board rice varieties

The association between alleles of the Waxy gene, defined by the number of CT repeats on exon 1, and traits of grain quality was carried out using 47 Philippine Seed Board rice varieties. The major alleles of the Waxy gene in the set of 47 were (CT), (CT) (CT)and (CT)20. Varieties were divided into four clusters based on the metric of each trait of grain quality. (CT) (27-32% amylose content (AC)) and (CT) (22-30% AC) were mainly in clusters 3 and 4 (hard texture), and (CT) (20-24% AC) and (CT) (18- 27% AC) were exclusively in grain quality cluster 1 (soft texture) and 2 (medium texture). (CT) associated negatively with AC in this set. Only six (CT) and one (CT) rices were in cluster 4 (high-AC low-GT) and had high RVA consistency (final viscosity - trough viscosity) > 200 RVU. (CT) seemed to be the preferred source of low-intermediate AC in the Philippine rice breeding program, followed by (CT)

16S rRNA Amplicon Sequencing of Urban Prokaryotic Communities in the South Bronx River Estuary

Biodiversity monitoring is an essential component of restoration efforts. We sequenced 16S rRNA gene amplicons from sediments and waters of Hunts Point Riverside Park and Soundview Park, located in a historically degraded but recovering urban estuary in New York. In total, 16,165 unique amplicon sequence variants were recovered, and Proteobacteria was the dominant phylum

16S rRNA Amplicon Sequencing of Urban Prokaryotic Communities in the South Bronx River Estuary

Biodiversity monitoring is an essential component of restoration efforts. We sequenced 16S rRNA gene amplicons from sediments and waters of Hunts Point Riverside Park and Soundview Park, located in a historically degraded but recovering urban estuary in New York. In total, 16,165 unique amplicon sequence variants were recovered, and Proteobacteria was the dominant phylum

Validation of a liquid chromatography tandem mass spectrometry (LC-MS/MS) method to detect cannabinoids in whole blood and breath.

Background The widespread availability of cannabis raises concerns regarding its effect on driving performance and operation of complex equipment. Currently, there are no established safe driving limits regarding ∆9-tetrahydrocannabinol (THC) concentrations in blood or breath. Daily cannabis users build up a large body burden of THC with residual excretion for days or weeks after the start of abstinence. Therefore, it is critical to have a sensitive and specific analytical assay that quantifies THC, the main psychoactive component of cannabis, and multiple metabolites to improve interpretation of cannabinoids in blood; some analytes may indicate recent use. Methods A liquid chromatography tandem mass spectrometry (LC-MS/MS) method was developed to quantify THC, cannabinol (CBN), cannabidiol (CBD), 11-hydroxy-THC (11-OH-THC), (±)-11-nor-9-carboxy-Δ9-THC (THCCOOH), (+)-11-nor-Δ9-THC-9-carboxylic acid glucuronide (THCCOOH-gluc), cannabigerol (CBG), and tetrahydrocannabivarin (THCV) in whole blood (WB). WB samples were prepared by solid-phase extraction (SPE) and quantified by LC-MS/MS. A rapid and simple method involving methanol elution of THC in breath collected in SensAbues® devices was optimized. Results Lower limits of quantification ranged from 0.5 to 2 μg/L in WB. An LLOQ of 80 pg/pad was achieved for THC concentrations in breath. Calibration curves were linear (R2>0.995) with calibrator concentrations within ±15% of their target and quality control (QC) bias and imprecision ≤15%. No major matrix effects or drug interferences were observed. Conclusions The methods were robust and adequately quantified cannabinoids in biological blood and breath samples. These methods will be used to identify cannabinoid concentrations in an upcoming study of the effects of cannabis on driving

Extracellular superoxide dismutase (SOD3) regulates oxidative stress at the vitreoretinal interface

Oxidative stress is a pathogenic feature in vitreoretinal disease. However, the ability of the inner retina to manage metabolic waste and oxidative stress is unknown. Proteomic analysis of antioxidants in the human vitreous, the extracellular matrix opposing the inner retina, identified superoxide dismutase-3 (SOD3) that localized to a unique matrix structure in the vitreous base and cortex. To determine the role of SOD3, Sod3-/- mice underwent histological and clinical phenotyping. Although the eyes were structurally normal, at the vitreoretinal interface Sod3-/- mice demonstrated higher levels of 3-nitrotyrosine, a key marker of oxidative stress. Pattern electroretinography also showed physiological signaling abnormalities within the inner retina. Vitreous biopsies and epiretinal membranes collected from patients with diabetic vitreoretinopathy (DVR) and a mouse model of DVR showed significantly higher levels of nitrates and/or 3-nitrotyrosine oxidative stress biomarkers suggestive of SOD3 dysfunction. This study analyzes the molecular pathways that regulate oxidative stress in human vitreous substructures. The absence or dysregulation of the SOD3 antioxidant at the vitreous base and cortex results in increased oxidative stress and tissue damage to the inner retina, which may underlie DVR pathogenesis and other vitreoretinal diseases

Association of Accelerometry-Measured Physical Activity and Cardiovascular Events in Mobility-Limited Older Adults: The LIFE (Lifestyle Interventions and Independence for Elders) Study.

BACKGROUND:Data are sparse regarding the value of physical activity (PA) surveillance among older adults-particularly among those with mobility limitations. The objective of this study was to examine longitudinal associations between objectively measured daily PA and the incidence of cardiovascular events among older adults in the LIFE (Lifestyle Interventions and Independence for Elders) study. METHODS AND RESULTS:Cardiovascular events were adjudicated based on medical records review, and cardiovascular risk factors were controlled for in the analysis. Home-based activity data were collected by hip-worn accelerometers at baseline and at 6, 12, and 24 months postrandomization to either a physical activity or health education intervention. LIFE study participants (n=1590; age 78.9±5.2 [SD] years; 67.2% women) at baseline had an 11% lower incidence of experiencing a subsequent cardiovascular event per 500 steps taken per day based on activity data (hazard ratio, 0.89; 95% confidence interval, 0.84-0.96; P=0.001). At baseline, every 30 minutes spent performing activities ≥500 counts per minute (hazard ratio, 0.75; confidence interval, 0.65-0.89 [P=0.001]) were also associated with a lower incidence of cardiovascular events. Throughout follow-up (6, 12, and 24 months), both the number of steps per day (per 500 steps; hazard ratio, 0.90, confidence interval, 0.85-0.96 [P=0.001]) and duration of activity ≥500 counts per minute (per 30 minutes; hazard ratio, 0.76; confidence interval, 0.63-0.90 [P=0.002]) were significantly associated with lower cardiovascular event rates. CONCLUSIONS:Objective measurements of physical activity via accelerometry were associated with cardiovascular events among older adults with limited mobility (summary score >10 on the Short Physical Performance Battery) both using baseline and longitudinal data. CLINICAL TRIAL REGISTRATION:URL: http://www.clinicaltrials.gov. Unique identifier: NCT01072500

Gene flow in environmental Legionella pneumophila leads to genetic and pathogenic heterogeneity within a Legionnaires' disease outbreak

BACKGROUND: Legionnaires’ disease is a severe form of pneumonia caused by the environmental bacterium Legionella pneumophila. Outbreaks commonly affect people with known risk factors, but the genetic and pathogenic complexity of L. pneumophila within an outbreak is not well understood. Here, we investigate the etiology of the major Legionnaires’ disease outbreak that occurred in Edinburgh, UK, in 2012, by examining the evolutionary history, genome content, and virulence of L. pneumophila clinical isolates. RESULTS: Our high resolution genomic approach reveals that the outbreak was caused by multiple genetic subtypes of L. pneumophila, the majority of which had diversified from a single progenitor through mutation, recombination, and horizontal gene transfer within an environmental reservoir prior to release. In addition, we discover that some patients were infected with multiple L. pneumophila subtypes, a finding which can affect the certainty of source attribution. Importantly, variation in the complement of type IV secretion systems encoded by different genetic subtypes correlates with virulence in a Galleria mellonella model of infection, revealing variation in pathogenic potential among the outbreak source population of L. pneumophila. CONCLUSIONS: Taken together, our study indicates previously cryptic levels of pathogen heterogeneity within a Legionnaires’ disease outbreak, a discovery that impacts on source attribution for future outbreak investigations. Furthermore, our data suggest that in addition to host immune status, pathogen diversity may be an important influence on the clinical outcome of individual outbreak infections. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-014-0504-1) contains supplementary material, which is available to authorized users

A high-resolution map of human evolutionary constraint using 29 mammals.

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease