Engineering strategies to decode and enhance the genomes of coral symbionts

© 2017 Levin, Voolstra, Agrawal, Steinberg, Suggett and van Oppen. Elevated sea surface temperatures from a severe and prolonged El Niño event (2014-2016) fueled by climate change have resulted in mass coral bleaching (loss of dinoflagellate photosymbionts, Symbiodinium spp., from coral tissues) and subsequent coral mortality, devastating reefs worldwide. Genetic variation within and between Symbiodinium species strongly influences the bleaching tolerance of corals, thus recent papers have called for genetic engineering of Symbiodinium to elucidate the genetic basis of bleaching-relevant Symbiodinium traits. However, while Symbiodinium has been intensively studied for over 50 years, genetic transformation of Symbiodinium has seen little success likely due to the large evolutionary divergence between Symbiodinium and other model eukaryotes rendering standard transformation systems incompatible. Here, we integrate the growing wealth of Symbiodinium next-generation sequencing data to design tailored genetic engineering strategies. Specifically, we develop a testable expression construct model that incorporates endogenous Symbiodinium promoters, terminators, and genes of interest, as well as an internal ribosomal entry site from a Symbiodinium virus. Furthermore, we assess the potential for CRISPR/Cas9 genome editing through new analyses of the three currently available Symbiodinium genomes. Finally, we discuss how genetic engineering could be applied to enhance the stress tolerance of Symbiodinium, and in turn, coral reefs

News and views: Response to 'Non-metric dental traits and hominin phylogeny' by Carter et al., with additional information on the Arizona State University Dental Anthropology System and phylogenetic 'place' of Australopithecus sediba

Here we respond to Carter and colleagues’ (2013) remarks concerning our Science article (Irish et al., 2013). The goals for that article were to: 1) further characterize Australopithecus sediba by describing 22 Arizona State University Dental Anthropology System (ASUDAS) traits, 2) compare the traits in A. sediba with those previously recorded in other hominin samples, and 3) present initial phylogenetic analyses using these data. Given the subset of traits, out of 125 possible (below), and small A. sediba sample, our conclusion was that the results “further define [the species’] position relative to other genera,” but that “the phylogenetic place of A. sediba has not been settled” (Irish et al., 2013: 1233062–12330624). These goals were met, as a basis for more comprehensive study. Below we summarize and reply to the eight objections of Carter et al. (2013), while: 1) demonstrating that there is a strong theoretical basis for using the ASUDAS in phylogenetic analyses, 2) presenting results (which corroborate previous cladistic analyses) that are congruent using different methodological approaches, and 3) introducing new results using a second outgroup, Pan troglodytes, that fully uphold our original analysis

Preliminary interpretation of Titan plasma interaction as observed by the Cassini Plasma Spectrometer: Comparisons with Voyager 1

The Cassini Plasma Spectrometer (CAPS) instrument observed the plasma environment at Titan during the Cassini orbiter's TA encounter on October 26, 2004. Titan was in Saturn's magnetosphere during the Voyager 1 flyby and also during the TA encounter. CAPS measurements from this encounter are compared with measurements made by the Voyager 1 Plasma Science Instrument (PLS). The comparisons focus on the composition and nature of ambient and pickup ions. They lead to: A) the major ion components of Saturn's magnetosphere in the vicinity of Titan are H+, H-2(+) and O+/CH4+ ions; B) finite gyroradius effects are apparent in ambient O+ ions as the result of their absorption by Titan's extended atmosphere; C) the principal pickup ions are composed of H+, H-2(+), N+/CH2+, CH4+, and N-2(+); D) the pickup ions are in narrow energy ranges; and E) there is clear evidence of the slowing down of background ions due to pickup ion mass loading

A 3D computed tomography based tool for orthopedic surgery planning

Series : Lecture notes in computational vision and biomechanics, vol. 19The preparation of a plan is essential for a surgery to take place in the best way possible and also for shortening patient’s recovery times. In the orthopedic case, planning has an accentuated significance due to the close relation between the degree of success of the surgery and the patient recovering time. It is important that surgeons are provided with tools that help them in the planning task, in order to make it more reliable and less time consuming. In this paper, we present a 3D Computed Tomography based solution and its implementation as an OsiriX plugin for orthopedic surgery planning. With the developed plugin, the surgeon is able to manipulate a three-dimensional isosurface rendered from the selected imaging study (a CT scan). It is possible to add digital representations of physical implants (surgical templates), in order to evaluate the feasibility of a plan. These templates are STL files generated from CAD models. There is also the feature to extract new isosurfaces of different voxel values and slice the final 3D model according to a predefined plane, enabling a 2D analysis of the planned solution. Finally, we discuss how the proposed application assists the surgeon in the planning process in an alternative way, where it is possible to three-dimensionally analyze the impact of a surgical intervention on the patient.(undefined

Modern Modal Testing: A Cautionary Tale

Over the past 50 years, great advances have been achieved in both analytical modal analysis (i.e. finite element models and analysis) and experimental modal analysis (i.e. modal testing) in aerospace and other fields. With the advent of more powerful computers, higher performance instrumentation and data acquisition systems, and powerful linear modal extraction tools, analysts and test engineers have a breadth and depth of technical resources only dreamed of by our predecessors. However, some observed recent trends indicate that hard lessons learned are being forgotten or ignored, and possibly fundamental concepts are not being understood. These trends have the potential of leading to the degradation of the quality of and confidence in both analytical and test results. These trends are a making of our own doing, and directly related to having ever more powerful computers, programmatic budgetary pressures to limit analysis and testing, and technical capital loss due to the retirement of the senior component of a bimodal workforce. This paper endeavors to highlight some of the most important lessons learned, common pitfalls to hopefully avoid, and potential steps that may be taken to help reverse this trend

Shared Agency with Parents for Educational Goals: Ethnic Differences and Implications for College Adjustment

This study proposed and confirmed three ways in which college students can perceive shared agency and two ways in which they can perceive non-shared agency with parents when pursuing educational goals in college. Differences and similarities were examined among participants from four ethnic backgrounds (N = 515; 67% female): East Asian American, Southeast Asian American, Filipino/Pacific Islander American, and European American. Results indicated that Asian American youth reported higher levels of non-shared agency with parents (i.e., parental directing and noninvolvement), lower levels of shared agency (i.e., parental accommodation, support, or collaboration), and poorer college adjustment compared to European Americans. However, ethnic similarities were found whereby perceived shared agency in education with parents was associated with college adjustment. Multiple mediation analyses also indicated that our model of shared and non-shared agency with parents explained differences in college adjustment between Asian and European Americans, though more strongly for comparisons between European and East Asian Americans. Our results suggest that parents continue to be important in the education of older youth but that continued directing of youth’s education in college can be maladaptive

Antiepileptic drugs’ tolerability and safety – a systematic review and meta-analysis of adverse effects in dogs

<p>Various anti-epileptic drugs (AEDs) are used for the management of idiopathic epilepsy (IE) in dogs. Their safety profile is an important consideration for regulatory bodies, owners and prescribing clinicians. However, information on their adverse effects still remains limited with most of it derived from non-blinded non-randomized uncontrolled trials and case reports.</p><p><span>This poster won third place, which was presented at the Veterinary Evidence Today conference, Edinburgh November 1-3, 2016. </span></p><br /> <img src="https://www.veterinaryevidence.org/rcvskmod/icons/oa-icon.jpg" alt="Open Access" /

Downregulation of Mcl-1 has anti-inflammatory pro-resolution effects and enhances bacterial clearance from the lung

Phagocytes not only coordinate acute inflammation and host defense at mucosal sites, but also contribute to tissue damage. Respiratory infection causes a globally significant disease burden and frequently progresses to acute respiratory distress syndrome, a devastating inflammatory condition characterized by neutrophil recruitment and accumulation of protein-rich edema fluid causing impaired lung function. We hypothesized that targeting the intracellular protein myeloid cell leukemia 1 (Mcl-1) by a cyclin-dependent kinase inhibitor (AT7519) or a flavone (wogonin) would accelerate neutrophil apoptosis and resolution of established inflammation, but without detriment to bacterial clearance. Mcl-1 loss induced human neutrophil apoptosis, but did not induce macrophage apoptosis nor impair phagocytosis of apoptotic neutrophils. Neutrophil-dominant inflammation was modelled in mice by either endotoxin or bacteria (Escherichia coli). Downregulating inflammatory cell Mcl-1 had anti-inflammatory, pro-resolution effects, shortening the resolution interval (R(i)) from 19 to 7 h and improved organ dysfunction with enhanced alveolar–capillary barrier integrity. Conversely, attenuating drug-induced Mcl-1 downregulation inhibited neutrophil apoptosis and delayed resolution of endotoxin-mediated lung inflammation. Importantly, manipulating lung inflammatory cell Mcl-1 also accelerated resolution of bacterial infection (R(i); 50 to 16 h) concurrent with enhanced bacterial clearance. Therefore, manipulating inflammatory cell Mcl-1 accelerates inflammation resolution without detriment to host defense against bacteria, and represents a target for treating infection-associated inflammation

Pseudomonas aeruginosa Adaptation to Lungs of Cystic Fibrosis Patients Leads to Lowered Resistance to Phage and Protist Enemies

Pathogenic life styles can lead to highly specialized interactions with host species, potentially resulting in fitness trade-offs in other ecological contexts. Here we studied how adaptation of the environmentally transmitted bacterial pathogen, Pseudomonas aeruginosa, to cystic fibrosis (CF) patients affects its survival in the presence of natural phage (14/1, ΦKZ, PNM and PT7) and protist (Tetrahymena thermophila and Acanthamoebae polyphaga) enemies. We found that most of the bacteria isolated from relatively recently intermittently colonised patients (1-25 months), were innately phage-resistant and highly toxic for protists. In contrast, bacteria isolated from long time chronically infected patients (2-23 years), were less efficient in both resisting phages and killing protists. Moreover, chronic isolates showed reduced killing of wax moth larvae (Galleria mellonella) probably due to weaker in vitro growth and protease expression. These results suggest that P. aeruginosa long-term adaptation to CF-lungs could trade off with its survival in aquatic environmental reservoirs in the presence of microbial enemies, while lowered virulence could reduce pathogen opportunities to infect insect vectors; factors that are both likely to result in poorer environmental transmission. From an applied perspective, phage therapy could be useful against chronic P. aeruginosa lung infections that are often characterized by multidrug resistance: chronic isolates were least resistant to phages and their poor growth will likely slow down the emergence of beneficial resistance mutations

Role of Caveolae in Cardiac Protection

Myocardial ischemia/reperfusion injury is a major cause of morbidity and mortality. The molecular signaling pathways involved in cardiac protection from myocardial ischemia/reperfusion injury are complex. An emerging idea in signal transduction suggests the existence of spatially organized complexes of signaling molecules in lipid-rich microdomains of the plasma membrane known as caveolae. Caveolins—proteins abundant in caveolae—provide a scaffold to organize, traffic, and regulate signaling molecules. Numerous signaling molecules involved in cardiac protection are known to exist within caveolae or interact directly with caveolins. Over the last 4 years, our laboratories have explored the hypothesis that caveolae are vitally important to cardiac protection from myocardial ischemia/reperfusion injury. We have provided evidence that (1) caveolae and the caveolin isoforms 1 and 3 are essential for cardiac protection from myocardial ischemia/reperfusion injury, (2) stimuli that produce preconditioning of cardiac myocytes, including brief periods of ischemia/reperfusion and exposure to volatile anesthetics, alter the number of membrane caveolae, and (3) cardiac myocyte-specific overexpression of caveolin-3 can produce innate cardiac protection from myocardial ischemia/reperfusion injury. The work demonstrates that caveolae and caveolins are critical elements of signaling pathways involved in cardiac protection and suggests that caveolins are unique targets for therapy in patients at risk of myocardial ischemia