Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control.

Rootless plants in the genus Wolffia are some of the fastest growing known plants on Earth. Wolffia have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for Wolffia australiana (Benth.) Hartog & Plas, which has the smallest genome size in the genus at 357 Mb and has a reduced set of predicted protein-coding genes at about 15,000. Comparison between multiple high-quality draft genome sequences from W. australiana clones confirmed loss of several hundred genes that are highly conserved among flowering plants, including genes involved in root developmental and light signaling pathways. Wolffia has also lost most of the conserved nucleotide-binding leucine-rich repeat (NLR) genes that are known to be involved in innate immunity, as well as those involved in terpene biosynthesis, while having a significant overrepresentation of genes in the sphingolipid pathways that may signify an alternative defense system. Diurnal expression analysis revealed that only 13% of Wolffia genes are expressed in a time-of-day (TOD) fashion, which is less than the typical ∼40% found in several model plants under the same condition. In contrast to the model plants Arabidopsis and rice, many of the pathways associated with multicellular and developmental processes are not under TOD control in W. australiana, where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The Wolffia genome and TOD expression data set thus provide insight into the interplay between a streamlined plant body plan and optimized growth.

Dynamic correction of astigmatism.

For the correction of defocus and astigmatism, mechanical approaches are well known, but there is a need for a non-mechanical, electrically tunable optical system that could provide both focus and astigmatism power correction with an adjustable axis. The optical system presented here is composed of three liquid-crystal-based tunable cylindrical lenses that are simple, low cost, and having a compact structure. Potential applications of the concept device include smart eyeglasses, virtual reality (VR)/ augmented reality (AR) head-mounted displays (HMDs), and optical systems subject to thermal or mechanical distortion. Details of the concept, design method, numerical computer simulations of the proposed device, as well as characterization of a prototype, are provided in this work.

Large area liquid crystal lenses for correction of presbyopia.

Presbyopia is the failure of the eye lens to accommodate. The widely used presbyopia correction method involves wearing bi/trifocal or progressive glasses, which limits the field of view due to division of lens area into sections of different optical power. A large aperture focus tunable liquid crystal lens has the potential to correct human eye accommodation failure and provide a wide field of view. In this paper, we present characterization and demonstration of a segmented phase profile liquid crystal lens, which has the characteristics of a large area (diameter: 20 mm), being flat and thin (<2 mm), and having continuous focus tunability (1.5 D to 0 D), fast response time (<500 ms), low operating voltage (<5 V), and on-axis diffraction-limited performance (for a 5mm aperture). Considering all these properties, our lens provides performance details of an approach for presbyopia correction. We have tested the minimum resolution and visual acuity of 20 subjects using the designed lens and compared the results with a reference glass lens of the same optical power.

Architecture and evolution of a minute plant genome.

It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation. However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. Unexpectedly, we identified at least three rounds of WGD in U. gibba since common ancestry with tomato (Solanum) and grape (Vitis). The compressed architecture of the U. gibba genome indicates that a small fraction of intergenic DNA, with few or no active retrotransposons, is sufficient to regulate and integrate all the processes required for the development and reproduction of a complex organism.

Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies.

Spirodela polyrhiza is a fast-growing aquatic monocot with highly reduced morphology, genome size and number of protein-coding genes. Considering these biological features of Spirodela and its basal position in the monocot lineage, understanding its genome architecture could shed light on plant adaptation and genome evolution. Like many draft genomes, however, the 158-Mb Spirodela genome sequence has not been resolved to chromosomes, and important genome characteristics have not been defined. Here we deployed rapid genome-wide physical maps combined with high-coverage short-read sequencing to resolve the 20 chromosomes of Spirodela and to empirically delineate its genome features. Our data revealed a dramatic reduction in the number of the rDNA repeat units in Spirodela to fewer than 100, which is even fewer than that reported for yeast. Consistent with its unique phylogenetic position, small RNA sequencing revealed 29 Spirodela-specific microRNA, with only two being shared with Elaeis guineensis (oil palm) and Musa balbisiana (banana). Combining DNA methylation data and small RNA sequencing enabled the accurate prediction of 20.5% long terminal repeats (LTRs) that doubled the previous estimate, and revealed a high Solo:Intact LTR ratio of 8.2. Interestingly, we found that Spirodela has the lowest global DNA methylation levels (9%) of any plant species tested. Taken together our results reveal a genome that has undergone reduction, likely through eliminating non-essential protein coding genes, rDNA and LTRs. In addition to delineating the genome features of this unique plant, the methodologies described and large-scale genome resources from this work will enable future evolutionary and functional studies of this basal monocot family.

Design of a large aperture tunable refractive Fresnel liquid crystal lens.

A large aperture tunable lens based on liquid crystals, which is considered for near-to-eye applications, is designed, built, and characterized. Large liquid crystal lenses with high quality are limited by very slow switching speeds due to the large optical path difference (OPD) required. To reduce the switching time of the lens, the thickness is controlled through the application of several phase resets, similar to the design of a Fresnel lens. A main point of the paper is the design of the Fresnel structure to have a minimal effect on the image quality. Our modeling and experimental results demonstrate that minimal image degradation due to the phase resets is observable when the segment spacing is chosen by taking into account human eye resolution. Such lenses have applications related to presbyopia and, in virtual reality systems, to solve the well-known issue of accommodation-convergence mismatch.

A genetic linkage map of black raspberry (Rubus occidentalis) and the mapping of Ag(4) conferring resistance to the aphid Amphorophora agathonica.

KEY MESSAGE: We have constructed a densely populated, saturated genetic linkage map of black raspberry and successfully placed a locus for aphid resistance. Black raspberry (Rubus occidentalis L.) is a high-value crop in the Pacific Northwest of North America with an international marketplace. Few genetic resources are readily available and little improvement has been achieved through breeding efforts to address production challenges involved in growing this crop. Contributing to its lack of improvement is low genetic diversity in elite cultivars and an untapped reservoir of genetic diversity from wild germplasm. In the Pacific Northwest, where most production is centered, the current standard commercial cultivar is highly susceptible to the aphid Amphorophora agathonica Hottes, which is a vector for the Raspberry mosaic virus complex. Infection with the virus complex leads to a rapid decline in plant health resulting in field replacement after only 3-4 growing seasons. Sources of aphid resistance have been identified in wild germplasm and are used to develop mapping populations to study the inheritance of these valuable traits. We have constructed a genetic linkage map using single-nucleotide polymorphism and transferable (primarily simple sequence repeat) markers for F1 population ORUS 4305 consisting of 115 progeny that segregate for aphid resistance. Our linkage map of seven linkage groups representing the seven haploid chromosomes of black raspberry consists of 274 markers on the maternal map and 292 markers on the paternal map including a morphological locus for aphid resistance. This is the first linkage map of black raspberry and will aid in developing markers for marker-assisted breeding, comparative mapping with other Rubus species, and enhancing the black raspberry genome assembly.

Genome-wide mapping of alternative splicing in Arabidopsis thaliana.

Alternative splicing can enhance transcriptome plasticity and proteome diversity. In plants, alternative splicing can be manifested at different developmental stages, and is frequently associated with specific tissue types or environmental conditions such as abiotic stress. We mapped the Arabidopsis transcriptome at single-base resolution using the Illumina platform for ultrahigh-throughput RNA sequencing (RNA-seq). Deep transcriptome sequencing confirmed a majority of annotated introns and identified thousands of novel alternatively spliced mRNA isoforms. Our analysis suggests that at least approximately 42% of intron-containing genes in Arabidopsis are alternatively spliced; this is significantly higher than previous estimates based on cDNA/expressed sequence tag sequencing. Random validation confirmed that novel splice isoforms empirically predicted by RNA-seq can be detected in vivo. Novel introns detected by RNA-seq were substantially enriched in nonconsensus terminal dinucleotide splice signals. Alternative isoforms with premature termination codons (PTCs) comprised the majority of alternatively spliced transcripts. Using an example of an essential circadian clock gene, we show that intron retention can generate relatively abundant PTC(+) isoforms and that this specific event is highly conserved among diverse plant species. Alternatively spliced PTC(+) isoforms can be potentially targeted for degradation by the nonsense mediated mRNA decay (NMD) surveillance machinery or regulate the level of functional transcripts by the mechanism of regulated unproductive splicing and translation (RUST). We demonstrate that the relative ratios of the PTC(+) and reference isoforms for several key regulatory genes can be considerably shifted under abiotic stress treatments. Taken together, our results suggest that like in animals, NMD and RUST may be widespread in plants and may play important roles in regulating gene expression.

Foresight for ethical AI.

There is growing expectation that artificial intelligence (AI) developers foresee and mitigate harms that might result from their creations; however, this is exceptionally difficult given the prevalence of emergent behaviors that occur when integrating AI into complex sociotechnical systems. We argue that Naturalistic Decision Making (NDM) principles, models, and tools are well-suited to tackling this challenge. Already applied in high-consequence domains, NDM tools such as the premortem, and others, have been shown to uncover a reasonable set of risks of underlying factors that would lead to ethical harms. Such NDM tools have already been used to develop AI that is more trustworthy and resilient, and can help avoid unintended consequences of AI built with noble intentions. We present predictive policing algorithms as a use case, highlighting various factors that led to ethical harms and how NDM tools could help foresee and mitigate such harms.

Assembly and operation of an imaging system for long-term monitoring of bioluminescent and fluorescent reporters in plants.

BACKGROUND: Non-invasive reporter systems are powerful tools to query physiological and transcriptional responses in organisms. For example, fluorescent and bioluminescent reporters have revolutionized cellular and organismal assays and have been used to study plant responses to abiotic and biotic stressors. Integrated, cooled charge-coupled device (CCD) camera systems have been developed to image bioluminescent and fluorescent signals in a variety of organisms; however, these integrated long-term imaging systems are expensive. RESULTS: We have developed self-assembled systems for both growing and monitoring plant fluorescence and bioluminescence for long-term experiments under controlled environmental conditions. This system combines environmental growth chambers with high-sensitivity CCD cameras, multi-wavelength LEDs, open-source software, and several options for coordinating lights with imaging. This easy-to-assemble system can be used for short and long-term imaging of bioluminescent reporters, acute light-response, circadian rhythms, delayed fluorescence, and fluorescent-protein-based assays in vivo. CONCLUSIONS: We have developed two self-assembled imaging systems that will be useful to researchers interested in continuously monitoring in vivo reporter systems in various plant species.

Supersplat--spliced RNA-seq alignment.

MOTIVATION: High-throughput sequencing technologies have recently made deep interrogation of expressed transcript sequences practical, both economically and temporally. Identification of intron/exon boundaries is an essential part of genome annotation, yet remains a challenge. Here, we present supersplat, a method for unbiased splice-junction discovery through empirical RNA-seq data. RESULTS: Using a genomic reference and RNA-seq high-throughput sequencing datasets, supersplat empirically identifies potential splice junctions at a rate of approximately 11.4 million reads per hour. We further benchmark the performance of the algorithm by mapping Illumina RNA-seq reads to identify introns in the genome of the reference dicot plant Arabidopsis thaliana and we demonstrate the utility of supersplat for de novo empirical annotation of splice junctions using the reference monocot plant Brachypodium distachyon. AVAILABILITY: Implemented in C++, supersplat source code and binaries are freely available on the web at http://mocklerlab-tools.cgrb.oregonstate.edu/.

Combat-related craniofacial and cervical injuries: a 5-year review from the British military.

BACKGROUND: Recent international publications have noted a sustained increase in the incidence of head, face, and neck (HFN) wounds in comparison with total battle injuries from the 20th to the 21st century. The aim of this review was therefore to perform an analysis of the epidemiology of all HFN injuries sustained by British forces in Iraq and Afghanistan from March 1, 2003, to December 31, 2008. METHODS: Descriptive injury data for this research were obtained from the Joint Theater Trauma Registry and overall battle injury and evacuation figures from the Defense Analytical and Statistical Agency. RESULTS: During this period, 448 servicemen sustained injuries to their HFN. A total of 71% of HFN injuries were sustained in battle. Of all service personnel sustaining HFN injuries, 32% died before the field hospital and a further 6% died subsequently. A total of 73% of injuries required evacuation back to the United Kingdom, whereas 27% of injuries were managed definitively in the theater of operations. HFN injuries altogether were found in 29% of battle injuries between 2006 and 2008. CONCLUSIONS: The individual incidences of head (15%) and face (19%) injuries in relation to total battle injuries, although greater than seen in previous United Kingdom conflicts, were only slightly higher than that seen by US forces. The incidence of neck injury alone in relation to total battle injuries of 11% in United Kingdom forces in comparison with 3% to 5% found in US forces warrants further investigation. This article also provides further evidence to support the existing published opinion of multiple international authors in the requirement to develop innovative methods of protecting the vulnerable HFN regions.

Neurocognitive assessment on a tablet device: Test-retest reliability and practice effects of ANAM Mobile.

New technology has allowed for the transition of computerized neurocognitive assessments to increasingly user-friendly mobile platforms. While this increased portability facilitates neurocognitive assessment in a wider variety of settings, this transition necessitates further examination of the psychometric properties of tests that have been previously validated on alternate platforms. The present study evaluated the test-retest reliability and practice effects for a new version of the Automated Neuropsychological Assessment Metrics (ANAM), ANAM Mobile, designed to be administered on a tablet computer. A total of 108 undergraduate students completed ANAM Mobile and returned after one week for repeated testing. Observed test-retest reliabilities were consistent with previously established estimates across similar time intervals and ranged from .55 (Simple Response Time) to .87 (Matching to Sample). Modest practice effects were observed. Base rates of reliable decline were low and suggested that declines on two or more tests are uncommon among healthy college students. The present study demonstrates that ANAM Mobile subtests have good-to-excellent reliability across a 7-day retest interval with minimal practice effects. Future research should explore within-subject reliability across repeated ANAM administrations on a tablet device and further examine retest reliabilities over varying time courses and in more diverse samples.

Dynamics of a liquid-crystal variable optical prism based on Pancharatnam phase.

We consider the dynamics of a variable optical prism based on Pancharatnam phase. The device basics, using liquid crystals (LCs) as the electro-optical material, have been previously proposed. In this paper, we study the dynamics of discrete changes in the phase profile, and also continuous changes in the phase profile through acquired data and numerical modeling. We show that a design based on LCs whose dielectric anisotropy can change sign (as a function of frequency) allows continuous tuning with reasonable response times.

Biomarkers for moral cognition: Current status and future prospects for neurotransmitters and neuropeptides.

The translational neuroscience of moral cognitions draws together developments throughout the fields of neuroscience pertaining to moral cognitions in order to better the human condition. That condition, seen through this lens, is one in which much of the violence and suffering we endure and inflict upon one another is based on moral cognitions-attitudes, beliefs, judgments-that are thought to result from correct or incorrect perceptions of moral properties. The biology tells a different story; namely, that moral cognitions, like other cognitions and mental states, are predicted and determined by biological mechanisms modulated by genotype, neurotransmitter availability and receptor density, neurophysiology, and individual differences among these as well as biology-environment interactions including nutrition, experience, and microbiome. A wealth of research has demonstrated that moral reasoning and judgments are easily alterable with the application of pharmaceuticals including SSRIs, and simpler treatments and conditions like the amount of time since one's last meal. Public health experts have pushed for analysis of violence and development of interventions treating violence as a public health pandemic. We see this research as a response to that call. Work in this field demonstrates that we are unaware of both the sources and nature of the cognitions on which we base much of our violent behaviors, societally and individually. Animal studies bolster the human subjects research, demonstrating the evolutionary roots of the causal mechanisms beneath our social structures and group formations.

Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff.

Teff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Here, we report a chromosome-scale assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintaining as syntenic gene pairs. TE analysis allows us to estimate that the teff polyploidy event occurred ~1.1 million years ago (mya) and that the two subgenomes diverged ~5.0 mya. Despite this divergence, we detect no large-scale structural rearrangements, homoeologous exchanges, or biased gene loss, in contrast to many other allopolyploids. The two teff subgenomes have partitioned their ancestral functions based on divergent expression across a diverse expression atlas. Together, these genomic resources will be useful for accelerating breeding of this underutilized grain crop and for fundamental insights into polyploid genome evolution.

QSRA: a quality-value guided de novo short read assembler.

BACKGROUND: New rapid high-throughput sequencing technologies have sparked the creation of a new class of assembler. Since all high-throughput sequencing platforms incorporate errors in their output, short-read assemblers must be designed to account for this error while utilizing all available data. RESULTS: We have designed and implemented an assembler, Quality-value guided Short Read Assembler, created to take advantage of quality-value scores as a further method of dealing with error. Compared to previous published algorithms, our assembler shows significant improvements not only in speed but also in output quality. CONCLUSION: QSRA generally produced the highest genomic coverage, while being faster than VCAKE. QSRA is extremely competitive in its longest contig and N50/N80 contig lengths, producing results of similar quality to those of EDENA and VELVET. QSRA provides a step closer to the goal of de novo assembly of complex genomes, improving upon the original VCAKE algorithm by not only drastically reducing runtimes but also increasing the viability of the assembly algorithm through further error handling capabilities.

Target Capture Sequencing Unravels Rubus Evolution.

Rubus (Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of Rubus challenging. Our objectives were to estimate the phylogeny of 94 taxonomically and geographically diverse species and three cultivars using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between major Rubus clades; and examine the historical biogeography of species diversification. Target capture sequencing identified eight major groups within Rubus. Subgenus Orobatus and Subg. Anoplobatus were monophyletic, while other recognized subgenera were para- or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at subgeneric levels, e.g., Subg. Rubus (blackberries) × Subg. Idaeobatus (raspberries) and Subg. Idaeobatus × Subg. Cylactis (Arctic berries) hybrids. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus was most likely distributed in North America. Multiple distribution events occurred during the Miocene (about 20 Ma) from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus. Rubus species diversified greatly in Asia during the Miocene. Rubus taxonomy does not reflect phylogenetic relationships and subgeneric revision is warranted. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the genus Rubus may have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for further Rubus systematics research. In conclusion, the target capture dataset provides high resolution between species though it also gave evidence of gene tree/species tree and cytonuclear discordance. Discordance may be due to hybridization or incomplete lineage sorting, rather than a lack of phylogenetic signal. This study illustrates the importance of using multiple phylogenetic methods when examining complex groups and the utility of software programs that estimate signal conflict within datasets.