Identification of single nucleotide polymorphisms from the transcriptome of an organism with a whole genome duplication

BACKGROUND: The common ancestor of salmonid fishes, including rainbow trout (Oncorhynchus mykiss), experienced a whole genome duplication between 20 and 100 million years ago, and many of the duplicated genes have been retained in the trout genome. This retention complicates efforts to detect allelic variation in salmonid fishes. Specifically, single nucleotide polymorphism (SNP) detection is problematic because nucleotide variation can be found between the duplicate copies (paralogs) of a gene as well as between alleles. RESULTS: We present a method of differentiating between allelic and paralogous (gene copy) sequence variants, allowing identification of SNPs in organisms with multiple copies of a gene or set of genes. The basic strategy is to: 1) identify windows of unique cDNA sequences with homology to each other, 2) compare these unique cDNAs if they are not shared between individuals (i.e. the cDNA is homozygous in one individual and homozygous for another cDNA in the other individual), and 3) give a “SNP score” value between zero and one to each candidate sequence variant based on six criteria. Using this strategy we were able to detect about seven thousand potential SNPs from the transcriptomes of several clonal lines of rainbow trout. When directly compared to a pre-validated set of SNPs in polyploid wheat, we were also able to estimate the false-positive rate of this strategy as 0 to 28% depending on parameters used. CONCLUSIONS: This strategy has an advantage over traditional techniques of SNP identification because another dimension of sequencing information is utilized. This method is especially well suited for identifying SNPs in polyploids, both outbred and inbred, but would tend to be conservative for diploid organisms

Omega-3 polyunsaturated fatty acids: Their potential role in blood pressure prevention and management

Omega-3 polyunsaturated fatty acids (PUFAs) from fish and fish oils appear to protect against coronary heart disease: their dietary intake is in fact inversely associated to cardiovascular disease morbidity/mortality in population studies. Recent evidence suggests that at least part of their heart protective effect is mediated by a relatively small but significant decrease in blood pressure level. In fact, omega-3 PUFAs exhibit wide-ranging biological actions that include regulating both vasomotor tone and renal sodium excretion, partly competing with omega-6 PUFAs for common metabolic enzymes and thereby decreasing the production of vasocostrincting rather than vasodilating and anti-inflammatory eicosanoids. PUFAs also reduce angiotensin-converting enzyme (ACE) activity, angiotensin II formation, TGF-beta expression, enhance eNO generation and activate the parasympathetic nervous system. The final result is improved vasodilation and arterial compliance of both small and large arteries. Preliminary clinical trials involving dyslipidemic patients, diabetics and elderly subjects, as well as normotensive and hypertensive subjects confirm this working hypothesis. Future research will clarify if PUFA supplementation could improve the antihypertensive action of specific blood pressure lowering drug classes and of statins

High-speed high-efficiency resonant cavity enhanced photodiodes

In this paper, we review our research efforts on RCE high-speed high-efficiency p-i-n and Schottky photodiodes. Using a microwave compatible planar fabrication process, we have designed and fabricated GaAs based RCE photodiodes. For RCE Schottky photodiodes, we have achieved a peak quantum efficiency of 50% along with a 3-dB bandwidth of 100 GHz. The tunability of the detectors via a recess etch is also demonstrated. For p-i-n type photodiodes, we have fabricated and tested widely tunable devices with near 100% quantum efficiencies, along with a 3-dB bandwidth of 50 GHz. Both of these results correspond to the fastest RCE photodetectors published in scientific literature

Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Oncorhynchus kisutch) Breeding Population Using a High-Density SNP Array

The estimation of linkage disequilibrium between molecular markers within a population is critical when establishing the minimum number of markers required for association studies, genomic selection, and inferring historical events influencing different populations. This work aimed to evaluate the extent and decay of linkage disequilibrium in a coho salmon breeding population using a high-density SNP array. Linkage disequilibrium was estimated between a total of 93,502 SNPs found in 64 individuals (33 dams and 31 sires) from the breeding population. The markers encompass all 30 coho salmon chromosomes and comprise 1,684.62 Mb of the genome. The average density of markers per chromosome ranged from 48.31 to 66 per 1 Mb. The minor allele frequency averaged 0.26 (with a range from 0.22 to 0.27). The overall average linkage disequilibrium among SNPs pairs measured as r2 was 0.10. The Average r2 value decreased with increasing physical distance, with values ranging from 0.21 to 0.07 at a distance lower than 1 kb and up to 10 Mb, respectively. An r2 threshold of 0.2 was reached at distance of approximately 40 Kb. Chromosomes Okis05, Okis15 and Okis28 showed high levels of linkage disequilibrium (>0.20 at distances lower than 1 Mb). Average r2 values were lower than 0.15 for all chromosomes at distances greater than 4 Mb. An effective population size of 43 was estimated for the population 10 generations ago, and 325, for 139 generations ago. Based on the effective number of chromosome segments, we suggest that at least 74,000 SNPs would be necessary for an association mapping study and genomic predictions. Therefore, the SNP panel used allowed us to capture high-resolution information in the farmed coho salmon population. Furthermore, based on the contemporary Ne, a new mate allocation strategy is suggested to increase the effective population size

Reviewing research priorities in weed ecology, evolution and management: A horizon scan

Weedy plants pose a major threat to food security, biodiversity, ecosystem services and consequently to human health and wellbeing. However, many currently used weed management approaches are increasingly unsustainable. To address this knowledge and practice gap, in June 2014, 35 weed and invasion ecologists, weed scientists, evolutionary biologists and social scientists convened a workshop to explore current and future perspectives and approaches in weed ecology and management. A horizon scanning exercise ranked a list of 124 pre-submitted questions to identify a priority list of 30 questions. These questions are discussed under seven themed headings that represent areas for renewed and emerging focus for the disciplines of weed research and practice. The themed areas considered the need for transdisciplinarity, increased adoption of integrated weed management and agroecological approaches, better understanding of weed evolution, climate change, weed invasiveness and finally, disciplinary challenges for weed science. Almost all the challenges identified rested on the need for continued efforts to diversify and integrate agroecological, socio-economic and technological approaches in weed management. These challenges are not newly conceived, though their continued prominence as research priorities highlights an ongoing intransigence that must be addressed through a more system-oriented and transdisciplinary research agenda that seeks an embedded integration of public and private research approaches. This horizon scanning exercise thus set out the building blocks needed for future weed management research and practice; however, the challenge ahead is to identify effective ways in which sufficient research and implementation efforts can be directed towards these needs

Photometry of Particles Ejected From Active Asteroid (101955) Bennu

AbstractNear‐Earth asteroid (101955) Bennu is an active asteroid experiencing mass loss in the form of ejection events emitting up to hundreds of millimeter‐ to centimeter‐scale particles. The close proximity of the Origins, Spectral Interpretations, Resource Identification, and Security–Regolith Explorer spacecraft enabled monitoring of particles for a 10‐month period encompassing Bennu's perihelion and aphelion. We found 18 multiparticle ejection events, with masses ranging from near zero to hundreds of grams (or thousands with uncertainties) and translational kinetic energies ranging from near zero to tens of millijoules (or hundreds with uncertainties). We estimate that Bennu ejects ~104 g per orbit. The largest event took place on 6 January 2019 and consisted of ~200 particles. The observed mass and translational kinetic energy of the event were between 459 and 528 g and 62 and 77 mJ, respectively. Hundreds of particles not associated with the multiparticle ejections were also observed. Photometry of the best‐observed particles, measured at phase angles between ~70° and 120°, was used to derive a linear phase coefficient of 0.013 ± 0.005 magnitudes per degree of phase angle. Ground‐based data back to 1999 show no evidence of past activity for Bennu; however, the currently observed activity is orders of magnitude lower than observed at other active asteroids and too low be observed remotely. There appears to be a gentle decrease in activity with distance from the Sun, suggestive of ejection processes such as meteoroid impacts and thermal fracturing, although observational bias may be a factor

Formulation of a mmaA4 Gene Deletion Mutant of Mycobacterium bovis BCG in Cationic Liposomes Significantly Enhances Protection against Tuberculosis

A new vaccination strategy is urgently needed for improved control of the global tuberculosis (TB) epidemic. Using a mouse aerosol Mycobacterium tuberculosis challenge model, we investigated the protective efficacy of a mmaA4 gene deletion mutant of Mycobacterium bovis BCG (ΔmmaA4BCG) formulated in dimethyl dioctadecyl ammonium bromide (DDA) – D(+) trehalose 6,6 dibenenate (TDB) (DDA/TDB) adjuvant. In previous studies, deletion of the mmaA4 gene was shown to reduce the suppression of IL-12 production often seen after mycobacterial infections. While the non-adjuvanted ΔmmaA4BCG strain did not protect mice substantially better than conventional BCG against a tuberculous challenge in four protection experiments, the protective responses induced by the ΔmmaA4BCG vaccine formulated in DDA/TDB adjuvant was consistently increased relative to nonadjuvanted BCG controls. Furthermore, the ΔmmaA4BCG-DDA/TDB vaccine induced significantly higher frequencies of multifunctional (MFT) CD4 T cells expressing both IFNγ and TNFα (double positive) or IFNγ, TNFα and IL-2 (triple positive) than CD4 T cells derived from mice vaccinated with BCG. These MFT cells were characterized by having higher IFNγ and TNFα median fluorescence intensity (MFI) values than monofunctional CD4 T cells. Interestingly, both BCG/adjuvant and ΔmmaA4BCG/adjuvant formulations induced significantly higher frequencies of CD4 T cells expressing TNFα and IL-2 than nonadjuvanted BCG or ΔmmaA4BCG vaccines indicating that BCG/adjuvant mixtures may be more effective at inducing central memory T cells. Importantly, when either conventional BCG or the mutant were formulated in adjuvant and administered to SCID mice or immunocompromised mice depleted of IFNγ, significantly lower vaccine-derived mycobacterial CFU were detected relative to immunodeficient mice injected with non-adjuvanted BCG. Overall, these data suggest that immunization with the ΔmmaA4BCG/adjuvant formulation may be an effective, safe, and relatively inexpensive alternative to vaccination with conventional BCG

OSIRIS-REx Encounters Bennu: Initial Assessment from the Approach Phase

The OSIRIS-REx spacecraft launched on September 8, 2016, on a seven-year journey to return samples from asteroid (101955) Bennu. This presentation summarizes the scientific results from the Approach and Preliminary Survey phases. Bennu observations are set to begin on August 17, 2018,when the asteroid is bright enough for detection by the PolyCam. PolyCam and MapCam collect data to survey the asteroid environment for any hazards and characterize the asteroid point-source photometric properties. Resolved images acquired during final approach, starting in late October 2018, allow the creation of a shape model using stereophotoclinometry (SPC), needed by both the navigation team and science planners. The OVIRS and OTES spectrometers characterize the point- source spectral properties over a full rotation period, providing a first look at any features and thermophysical properties. TAGSAM is released from the launch container and deployed into the sampling configuration then returned to the stow position.Preliminary Survey follows the Approach Phase in early December 2018. This phase consists of a series of hyperbolic trajectories that cross over the North and South poles and the equator of Bennu at a close-approach distance of 7 km. Images from these Preliminary Survey passes provide data to complete the 75-cm resolution SPC global shape model and solve for the rotation state. Once the shape model is complete, the asteroid coordinate system is defined for co-registration of all data products. These higher-resolution images also constrain the photometric properties and allow for an initial assessment of the geology. In Preliminary Survey the team also obtains the first OLA data, providing a measure of the surface topography. OVIRS and OTES collect data as "ride-along" instruments, with the spacecraft pointing driven by imaging constraints. These data provide a first look at the spectral variation across the surface of Bennu. Radio science measurements, combined with altimetry and imagery, determine Bennu's mass, a prerequisite to placing the spacecraft into orbit in late December 2018. Together, data from the Approach and Preliminary Survey phases set the stage for the extensive mapping planned for 2019. These dates are the baseline plan. Any contingency or unexpected discovery may change this mission profile