Crystallization of a Mos1 transposase-inverted-repeat DNA complex: biochemical and preliminary crystallographic analyses

A complex formed between Mos1 transposase and its inverted-repeat DNA has been crystallized. The crystals diffract to 3.25 Å resolution and exhibit monoclinic (P2(1)) symmetry, with unit-cell parameters a = 120.8, b = 85.1, c = 131.6 Å, β = 99.3°. The X-ray diffraction data display noncrystallographic twofold symmetry and characteristic dsDNA diffraction at ∼3.3 Å. Biochemical analyses confirmed the presence of DNA and full-length protein in the crystals. The relationship between the axis of noncrystallographic symmetry, the unit-cell axes and the DNA diffraction pattern are discussed. The data are consistent with the previously proposed model of the paired-ends complex containing a dimer of the transposase

Two mechanisms for optic flow and scale change processing of looming

Published in final edited form as: J Vis. ; 11(3): . doi:10.1167/11.3.5.The detection of looming, the motion of objects in depth, underlies many behavioral tasks, including the perception of self-motion and time-to-collision. A number of studies have demonstrated that one of the most important cues for looming detection is optic flow, the pattern of motion across the retina. Schrater et al. have suggested that changes in spatial frequency over time, or scale changes, may also support looming detection in the absence of optic flow (P. R. Schrater, D. C. Knill, & E. P. Simoncelli, 2001). Here we used an adaptation paradigm to determine whether the perception of looming from optic flow and scale changes is mediated by single or separate mechanisms. We show first that when the adaptation and test stimuli were the same (both optic flow or both scale change), observer performance was significantly impaired compared to a dynamic (non-motion, non-scale change) null adaptation control. Second, we found no evidence of cross-cue adaptation, either from optic flow to scale change, or vice versa. Taken together, our data suggest that optic flow and scale changes are processed by separate mechanisms, providing multiple pathways for the detection of looming.We thank Jonathan Victor and the anonymous reviewers of the paper for feedback and suggestions regarding the stimuli used here. This work was supported by NIH grant R01NS064100 to LMV. (R01NS064100 - NIH)Accepted manuscrip

Deficit of temporal dynamics of detection of a moving object during egomotion in a stroke patient: a psychophysical and MEG study

To investigate the temporal dynamics underlying object motion detection during egomotion, we used psychophysics and MEG with a motion discrimination task. The display contained nine spheres moving for 1 second, eight moved consistent with forward observer translation, and one (the target) with independent motion within the scene (approaching or receding). Observers's task was to detect the target. Seven healthy subjects (7HS) and patient PF with an infarct involving the left occipital-temporal cortex participated in both the psychophysical and MEG study. Psychophysical results showed that PF was severely impaired on this task. He was also impaired on the discrimination of radial motion (with even poorer performance on contraction) and 2D direction as well as on detecting motion discontinuity. We used anatomically constrained MEG and dynamic Granger causality to investigate the direction and dynamics of connectivity between the functional areas involved in the object-motion task and compared the results of 7HS and PF. The dynamics of the causal connections among the motion responsive cortical areas (MT, STS, IPS) during the first 200 ms of the stimulus was similar in all subjects. However, in the later part of the stimulus (>200 ms) PF did not show significant causal connections among these areas. Also the 7HS had a strong, probably attention modulatory connection, between MPFC and MT, which was completely absent in PF. In PF and the 7HS, analysis of onset latencies revealed two stages of activations: early after motion onset (200–400 ms) bilateral activations in MT, IPS, and STS, followed (>500 ms) by activity in the postcentral sulcus and middle prefrontal cortex (MPFC). We suggest that the interaction of these early and late onset areas is critical to object motion detection during self-motion, and disrupted connections among late onset areas may have contributed to the perceptual deficits of patient PF.Published versio

TiB_2 and ZrB_2 diffusion barriers in GaAs Ohmic contact technology

The transition metal diboride compounds, ZrB_2 and TiB_2, interposed between Ni/Ge/Au Ohmic contact metallization on n‐type GaAs wafers and an overlying thick Au contact layer, have been investigated to evaluate their effectiveness in stabilizing the Ohmic contact by limiting the in‐diffusion of Au. All of the metal layers were e‐beam deposited except the ZrB_2 which was rf‐diode sputtered. The barrier layer thicknesses were 50 and 100 nm for the TiB_2 and the ZrB_2, respectively. Postdeposition alloying of the contacts was performed at 400, 425, or 450 °C. Auger electron spectroscopy depth profiling of the resultant Ohmic contacts demonstrates that the barrier layers effectively preclude penetration of Au to the Ohmic contact structure. Specific contact resistivities for such contacts are in the low 10^(−7) Ω cm^2 range; although some degradation of the contact resistivity is observed after long term annealing, the values of resistivities do not exceed 1.5×10^(−6) Ω cm^2 after 92 h at 350 °C

A two-fluid model describing the finite-collisionality, stationary Alfvén wave in anisotropic plasma

The stationary inertial Alfvén (StIA) wave (Knudsen, 1996) was predicted for cold, collisionless plasma. The model was generalized (Finnegan et al., 2008) to include nonzero values of electron and ion collisional resistivity and thermal pressure. Here, the two-fluid model is further generalized to include anisotropic thermal pressure. A bounded range of values of parallel electron drift velocity is found that excludes periodic stationary Alfvén wave solutions. This exclusion region depends on the value of the local Alfvén speed VA, plasma beta perpendicular to the magnetic field β⊥ and electron temperature anisotropy

Impact of SARS-CoV-2 (COVID-19) pandemic on patients with lysosomal storage disorders and restoration of services: experience from a specialist centre

This study aims to evaluate the impact of the COVID-19 pandemic on the lysosomal disorders unit (LSDU) at Royal Free London NHS Foundation Trust (RFL), a highly specialised national service for diagnosis and management of adults with lysosomal storage disorders (LSD). Review of home care enzyme replacement therapy (ERT) and emergency care, and COVID-19 shielding categories as per UK government guidance. New clinical pathways were developed to manage patients safely during the pandemic; staff well-being initiatives are described. LSDU staff were redeployed and/or had additional roles to support increased needs of hospitalised COVID-19 patients. During the first lockdown in March 2020, 286 of 602 LSD patients were shielding; 72 of 221 had home care ERT infusions interrupted up to 12 weeks. During the pandemic, there was a 3% reduction in home care nursing support required, with patients learning to self-cannulate or require support for cannulation only. There were no increased adverse clinical events during this period. Twenty-one contracted COVID-19 infection, with one hospitalised and no COVID-19 related deaths. In 2020, virtual clinics were increased by 88% (video and/or telephone) compared to 2019. RFL well-being initiatives supported all staff. We provide an overview of the impact of the COVID-19 pandemic on staff and patients attending a highly specialised rare disease service. As far as we are aware, this is the first detailed narrative on the challenges and subsequent rapid adaptations made, both as part of a large organisation and as a specialist centre. Lessons learnt could be translated to other rare disease services and ensure readiness for any future pandemic

Analysing the impact of iron dysmetabolism on regional metal ion distribution in the brain

An Iron Overload and an H-Ferritin Deficient Mouse Model were used to examine the impact of disrupted iron metabolism on the brain. Brain sections were imaged and compared using Synchrotron μXRF spectroscopy. Quantitative measurement of the relative metal ion concentrations for iron, copper and zinc were made across selected regions of interest in the brain. It was generally found that metal ion concentrations of iron and zinc decreased in specific regions in the Iron Overload condition compared with the control, with copper increasing in only one region. Few regions differed in metal ion concentration between the H-Ferritin Deficient Model and the control. The three conditions exhibited similar / identical results for metal ion concentrations in many brain regions, indicating the validity of the method used for comparison between samples. It is clear that there exists a complex relationship between these trace metal

Supporting Student Knowledge Using Formative Assessment and Universal Design for Learning Expression

This article demonstrates an approach for teachers to use outcomes from activities using the universal design for learning expression principle to evaluate student knowledge in content areas. Based on the student’s level of explanation using a variety of expression methods, teachers can determine whether students need additional support for re-teaching a concept or whether students are ready for additional practice or challenge. Various levels of technology can be used for formatively assessing student understanding, from no technology (e.g., paper and pencil) to mid- or high-technology tools found in most classrooms, including computers and tablets

Species classifier choice is a key consideration when analysing low-complexity food microbiome data

peer-reviewedBackground The use of shotgun metagenomics to analyse low-complexity microbial communities in foods has the potential to be of considerable fundamental and applied value. However, there is currently no consensus with respect to choice of species classification tool, platform, or sequencing depth. Here, we benchmarked the performances of three high-throughput short-read sequencing platforms, the Illumina MiSeq, NextSeq 500, and Ion Proton, for shotgun metagenomics of food microbiota. Briefly, we sequenced six kefir DNA samples and a mock community DNA sample, the latter constructed by evenly mixing genomic DNA from 13 food-related bacterial species. A variety of bioinformatic tools were used to analyse the data generated, and the effects of sequencing depth on these analyses were tested by randomly subsampling reads. Results Compositional analysis results were consistent between the platforms at divergent sequencing depths. However, we observed pronounced differences in the predictions from species classification tools. Indeed, PERMANOVA indicated that there was no significant differences between the compositional results generated by the different sequencers (p = 0.693, R2 = 0.011), but there was a significant difference between the results predicted by the species classifiers (p = 0.01, R2 = 0.127). The relative abundances predicted by the classifiers, apart from MetaPhlAn2, were apparently biased by reference genome sizes. Additionally, we observed varying false-positive rates among the classifiers. MetaPhlAn2 had the lowest false-positive rate, whereas SLIMM had the greatest false-positive rate. Strain-level analysis results were also similar across platforms. Each platform correctly identified the strains present in the mock community, but accuracy was improved slightly with greater sequencing depth. Notably, PanPhlAn detected the dominant strains in each kefir sample above 500,000 reads per sample. Again, the outputs from functional profiling analysis using SUPER-FOCUS were generally accordant between the platforms at different sequencing depths. Finally, and expectedly, metagenome assembly completeness was significantly lower on the MiSeq than either on the NextSeq (p = 0.03) or the Proton (p = 0.011), and it improved with increased sequencing depth. Conclusions Our results demonstrate a remarkable similarity in the results generated by the three sequencing platforms at different sequencing depths, and, in fact, the choice of bioinformatics methodology had a more evident impact on results than the choice of sequencer did.This research was funded by Science Foundation Ireland in the form of a centre grant (APC Microbiome Institute grant number SFI/12/RC/2273). Research in the Cotter laboratory is also funded by Science Foundation Ireland through the PI award “Obesibiotics” (11/PI/1137). Orla O’Sullivan is funded by Science Foundation Ireland through a Starting Investigator Research Grant award (13/SIRG/2160)