Cloning Grnas to Enable Crispr-Mediated Human Gene Knockouts

The human genome encodes over 80 members of the tripartite motif (TRIM) protein family. Many of the TRIM proteins are upregulated in cells responding to interferon-beta (IFNβ). Interestingly, screens have shown that approximately half of the TRIM proteins act on interferon signal transduction pathways in positive and negative feedback loops. Cell lines are being created that can be used as tools for identifying the step of IFN signaling acted upon by TRIM proteins. To create tools for this goal, we have cloned guide RNAs targeting IFNB, IFNAR1, IRF3, and IRF7 genes into the pSpCas9(BB)-2A-EGFP vector using recombination techniques. Success of cloning was confirmed by restriction digests and DNA sequencing. Human cells (293T) were successfully transfected and are currently being cultured to attain monoclonal EGFP+ lines. Screening for loss of gene expression in clonal lines will assessed by immunoblotting as well as tested functionally using luciferase reporter assays

The Relationship Between Holistic Admissions Criteria and Program Ranking Among Occupational Therapy Entry-Level Programs

Holistic admissions criteria are one strategy to be more inclusive of students with a variety of experiences, cultures, and beliefs. The purpose of this study is to evaluate the relationship between holistic admissions criteria and occupational therapy program ranking. We used a retrospective cross-sectional cohort descriptive study design of occupational therapy programs in the United States to understand whether top performing programs employ holistic admissions criteria. Secondary descriptive analysis from the top and bottom 50 ranked occupational therapy programs in 2020 U.S. News & World Report (Morse et al., 2020) was completed. We used a nominal scale to classify programs into two groups based on use of holistic measures. Overall, 54.95% (n = 61) of the programs used holistic admissions criteria. Of these, 36 were among the top 50 ranked programs, and 25 were among the bottom 50 ranked schools. Occupational therapy programs using holistic admissions criteria were not statistically different from the programs that did not use holistic admissions criteria on their overall ranking (χ2 = 0.55, p = 0.46). The bottom- and top-ranked programs were not statistically different regarding use of holistic admissions criteria, which suggests that implementation of holistic admission criteria is not associated with program ranking. Therefore, this research should encourage universities to implement holistic admissions criteria, as it is not associated with lowered program ranking, but has been associated with increasing both diversity and academic performance in other health professional programs (Glazer et al., 2014; Witzburg & Sondheimer, 2013; Price & Mills, 2010)

The next generation of training for arabidopsis researchers: Bioinformatics and Quantitative Biology

It has been more than 50 years since Arabidopsis (Arabidopsis thaliana) was first introduced as a model organism to understand basic processes in plant biology. A well-organized scientific community has used this small reference plant species to make numerous fundamental plant biology discoveries (Provart et al., 2016). Due to an extremely well-annotated genome and advances in high-throughput sequencing, our understanding of this organism and other plant species has become even more intricate and complex. Computational resources, including CyVerse,3 Araport,4 The Arabidopsis Information Resource (TAIR),5 and BAR,6 have further facilitated novel findings with just the click of a mouse. As we move toward understanding biological systems, Arabidopsis researchers will need to use more quantitative and computational approaches to extract novel biological findings from these data. Here, we discuss guidelines, skill sets, and core competencies that should be considered when developing curricula or training undergraduate or graduate students, postdoctoral researchers, and faculty. A selected case study provides more specificity as to the concrete issues plant biologists face and how best to address such challenges

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

Rate Effects on Timing, Key Velocity, and Finger Kinematics in Piano Performance

We examined the effect of rate on finger kinematics in goal-directed actions of pianists. In addition, we evaluated whether movement kinematics can be treated as an indicator of personal identity. Pianists' finger movements were recorded with a motion capture system while they performed melodies from memory at different rates. Pianists' peak finger heights above the keys preceding keystrokes increased as tempo increased, and were attained about one tone before keypress. These rate effects were not simply due to a strategy to increase key velocity (associated with tone intensity) of the corresponding keystroke. Greater finger heights may compensate via greater tactile feedback for a speed-accuracy tradeoff that underlies the tendency toward larger temporal variability at faster tempi. This would allow pianists to maintain high temporal accuracy when playing at fast rates. In addition, finger velocity and accelerations as pianists' fingers approached keys were sufficiently unique to allow pianists' identification with a neural-network classifier. Classification success was higher in pianists with more extensive musical training. Pianists' movement “signatures” may reflect unique goal-directed movement kinematic patterns, leading to individualistic sound

Sediment reworking by the burrowing polychaete Hediste diversicolor modulated by environmental and biological factors across the temperate North Atlantic. A tribute to Gaston Desrosiers

International audienceParticle mixing and irrigation of the seabed by benthic fauna (bioturbation) have major impacts on ecosystem functions such as remineralization of organic matter and sediment-water exchange. As a tribute to Prof. Gaston Desrosiers by the Nereis Park association, eighteen laboratories carried out a collaborative experiment to acquire a global snapshot of particle reworking by the polychaete Hediste diversicolor at 16 sites surrounding the Northern Atlantic. Organisms and soft sediments were collected during May – July at different geographical locations and, using a common laboratory protocol, particulate fluorescent tracers (‘luminophores’) were used to quantify particle transport over a 10-day period. Particle mixing was quantified using the maximum penetration depth of tracers (MPD), particle diffusive coefficients (Db), and non-local transport coefficients (r). Non-local coefficients (reflecting centimeter scale transport steps) ranged from 0.4 to 15 yr−1, and were not correlated across sites with any measured biological (biomass, biovolume) or environmental parameters (temperature, grain size, organic matter). Maximum penetration depths (MPD) averaged ~10.7 cm (6.5–14.5 cm), and were similar to the global average bioturbation depth inferred from short-lived radiochemical tracers. MPD was also not correlated with measures of size (individual biomass), but increased with grain size and decreased with temperature. Biodiffusion (Db) correlated inversely with individual biomass (size) and directly with temperature over the environmental range (Q10 ~ 1.7; 5–21 °C). The transport data were comparable in magnitude to rates reported for localized H. diversicolor populations of similar size, and confirmed some but not all correlations between sediment reworking and biological and environmental variables found in previous studies. The results imply that measures of particle reworking activities of a species from a single location can be generally extrapolated to different populations at similar conditions

Benthic pH gradients across a range of shelf sea sediment types linked to sediment characteristics and seasonal variability

This study used microelectrodes to record pH profiles in fresh shelf sea sediment cores collected across a range of different sediment types within the Celtic Sea. Spatial and temporal variability was captured during repeated measurements in 2014 and 2015. Concurrently recorded oxygen microelectrode profiles and other sedimentary parameters provide a detailed context for interpretation of the pH data. Clear differences in profiles were observed between sediment type, location and season. Notably, very steep pH gradients exist within the surface sediments (10–20 mm), where decreases greater than 0.5 pH units were observed. Steep gradients were particularly apparent in fine cohesive sediments, less so in permeable sandier matrices. We hypothesise that the gradients are likely caused by aerobic organic matter respiration close to the sediment–water interface or oxidation of reduced species at the base of the oxic zone (NH4+, Mn2+, Fe2+, S−). Statistical analysis suggests the variability in the depth of the pH minima is controlled spatially by the oxygen penetration depth, and seasonally by the input and remineralisation of deposited organic phytodetritus. Below the pH minima the observed pH remained consistently low to maximum electrode penetration (ca. 60 mm), indicating an absence of sub-oxic processes generating H+ or balanced removal processes within this layer. Thus, a climatology of sediment surface porewater pH is provided against which to examine biogeochemical processes. This enhances our understanding of benthic pH processes, particularly in the context of human impacts, seabed integrity, and future climate changes, providing vital information for modelling benthic response under future climate scenarios