Use of designer nucleases for targeted gene and genome editing in plants

The ability to efficiently inactivate or replace genes in model organisms allowed a rapid expansion of our understanding of many of the genetic, biochemical, molecular and cellular mechanisms that support life. With the advent of new techniques for manipulating genes and genomes that are applicable not only to single-celled organisms, but also to more complex organisms such as animals and plants, the speed with which scientists and biotechnologists can expand fundamental knowledge and apply that knowledge to improvements in medicine, industry and agriculture is set to expand in an exponential fashion. At the heart of these advancements will be the use of gene editing tools such as zinc finger nucleases, modified meganucleases, hybrid DNA/ RNA oligonucleotides, TAL effector nucleases and modified CRISPR/Cas9. Each of these tools has the ability to precisely target one specific DNA sequence within a genome and (except for DNA/ RNA oligonucleotides) to create a double-stranded DNA break. DNA repair to such breaks sometimes leads to gene knockouts or gene replacement by homologous recombination if exogenously supplied homologous DNA fragments are made available. Genome rearrangements are also possible to engineer. Creation and use of such genome rearrangements, gene knockouts and gene replacements by the plant science community is gaining significant momentum. To document some of this progress and to explore the technology’s longer term potential, this review highlights present and future uses of designer nucleases to greatly expedite research with model plant systems and to engineer genes and genomes in major and minor crop species for enhanced food production

Climate Change Impacts on Southern Ross Sea Phytoplankton Composition, Productivity, and Export

The Ross Sea, a highly productive region of the Southern Ocean, is expected to experience warming during the next century along with reduced summer sea ice concentrations and shallower mixed layers. This study investigates how these climatic changes may alter phytoplankton assemblage composition, primary productivity, and export. Glider measurements are used to force a one-dimensional biogeochemical model, which includes diatoms and both solitary and colonial forms of Phaeocystis antarctica. Model performance is evaluated with glider observations, and experiments are conducted using projections of physical drivers for mid-21st and late-21st century. These scenarios reveal a 5% increase in primary productivity by midcentury and 14% by late-century and a proportional increase in carbon export, which remains approximately 18% of primary production. In addition, scenario results indicate diatom biomass increases while P. antarctica biomass decreases in the first half of the 21st century. In the second half of the century, diatom biomass remains relatively constant and P. antarctica biomass increases. Additional scenarios examining the independent contributions of expected future changes (temperature, mixed layer depth, irradiance, and surface iron inputs from melting ice) demonstrate that earlier availability of low light due to reduction of sea ice early in the growing season is the primary driver of productivity increases over the next century; shallower mixed layer depths additionally contribute to changes of assemblage composition and export. This study further demonstrates how glider data can be effectively used to facilitate model development and simulation, and inform interpretation of biogeochemical observations in the context of climate change

Neuroimaging the consciousness of self: Review, and conceptual-methodological framework

We review neuroimaging research investigating self-referential processing (SRP), that is, how we respond to stimuli that reference ourselves, prefaced by a lexical-thematic analysis of words indicative of “self-feelings”. We consider SRP as occurring verbally (V-SRP) and non-verbally (NV-SRP), both in the controlled, “top-down” form of introspective and interoceptive tasks, respectively, as well as in the “bottom-up” spontaneous or automatic form of “mind wandering” and “body wandering” that occurs during resting state. Our review leads us to outline a conceptual and methodological framework for future SRP research that we briefly apply toward understanding certain psychological and neurological disorders symptomatically associated with abnormal SRP. Our discussion is partly guided by William James’ original writings on the consciousness of self

The development and validation of a scoring tool to predict the operative duration of elective laparoscopic cholecystectomy

Background: The ability to accurately predict operative duration has the potential to optimise theatre efficiency and utilisation, thus reducing costs and increasing staff and patient satisfaction. With laparoscopic cholecystectomy being one of the most commonly performed procedures worldwide, a tool to predict operative duration could be extremely beneficial to healthcare organisations. Methods: Data collected from the CholeS study on patients undergoing cholecystectomy in UK and Irish hospitals between 04/2014 and 05/2014 were used to study operative duration. A multivariable binary logistic regression model was produced in order to identify significant independent predictors of long (> 90 min) operations. The resulting model was converted to a risk score, which was subsequently validated on second cohort of patients using ROC curves. Results: After exclusions, data were available for 7227 patients in the derivation (CholeS) cohort. The median operative duration was 60 min (interquartile range 45–85), with 17.7% of operations lasting longer than 90 min. Ten factors were found to be significant independent predictors of operative durations > 90 min, including ASA, age, previous surgical admissions, BMI, gallbladder wall thickness and CBD diameter. A risk score was then produced from these factors, and applied to a cohort of 2405 patients from a tertiary centre for external validation. This returned an area under the ROC curve of 0.708 (SE = 0.013, p  90 min increasing more than eightfold from 5.1 to 41.8% in the extremes of the score. Conclusion: The scoring tool produced in this study was found to be significantly predictive of long operative durations on validation in an external cohort. As such, the tool may have the potential to enable organisations to better organise theatre lists and deliver greater efficiencies in care

Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment

BACKGROUND: Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adélie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri]. RESULTS: Phylogenetic dating suggests that early penguins arose ~60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from ~1 million years ago to ~100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology. CONCLUSIONS: Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment

Dynamic framing in the communication of scientific research: texts and interactions

The fields of science education and science communication share the overarching goal of helping non-experts and non-members of the professional science community develop knowledge of the content and processes of scientific research. However, the specific audiences, methods, and aims employed in the two fields have evolved quite differently and as a result, the two fields rarely share findings and theory. Despite this lack of crosstalk, one theoretical construct—framing—has shown substantial analytic power for researchers in both fields. Specifically, both fields have productively made use of the fact that when people approach situations or texts in the world, they do so with a sense of “what is going on here” that guides their actions and sense-making in that situation. In this article, we examine the dynamics of how interactions between scientists, reporters, members of the general public, and various texts give rise to in-the-moment frames that shape each actors interpretation of scientific research. In doing so we couple science communication literature's focus on framings within and across texts with science education's focus on dynamic framing in interactions. We present a case study that follows a single piece of scientific research from scientist to reporter to the general public. Through semi-structured clinical interviews, video-based observation, and qualitative content analysis, we demonstrate that changes in science knowledge as it moves along the pathways of science communication are the aggregate result of dynamic moment-to-moment framings dispersed over people and interactions. The complexity and nuance of the story presented here have implications for how each field—science communication and science education—conceptualizes the process by which the public comes to knowledge of science