Ribosome inactivation by Escherichia coli GTPase RsgA inhibits T4 phage

IntroductionBacteria must combat phages, and myriad bacterial anti-phage systems have been discovered that reduce host metabolism, for example, by depleting energetic compounds like ATP and NAD+. Hence, these systems indirectly inhibit protein production. Surprisingly, direct reduction of ribosome activity has not been demonstrated to thwart phage.MethodsHere, by producing each of the 4,287 Escherichia coli proteins and selecting for anti-phage activity that leads to enhanced growth, we investigated the role of host proteins in phage inhibition.Results and discussionWe identified that E. coli GTPase RsgA inhibits lytic phage T4 by inactivating ribosomes

Microperimetry hill of vision and volumetric measures of retinal sensitivity

Purpose: Mean retinal sensitivity is the main output measure used in microperimetry. It is, however, of limited use in patients with poor vision because averaging is weighted toward zero in those with significant scotomas creating an artificial floor effect. In contrast, volumetric measures avoid these issues and are displayed graphically as a hill of vision. Methods: An open-source program was created to manipulate raw sensitivity threshold data files obtained from MAIA microperimetry. Thin plate spline interpolated heat maps and three-dimensional hill of vision plots with an associated volume were generated. Retrospective analyses of microperimetry volumes were undertaken in patients with a range of retinal diseases to assess the qualitative benefits of three-dimensional visualization and volumetric measures. Simulated pathology was applied to radial grid patterns to investigate the performance of volumetric sensitivity in nonuniform grids. Results: Volumetric analyses from microperimetry in RPGR-related retinitis pigmentosa, choroideremia, Stargardt disease, and age-related macular degeneration were analyzed. In simulated nonuniform testing grids, volumetric sensitivity was able to detect differences in retinal sensitivity where mean sensitivity could not. Conclusions: Volumetric measures do not suffer from averaging issues and demonstrate superior performance in nonuniform testing grids. Additionally, volume measures enable detection of localized retinal sensitivity changes that might otherwise be undetectable in a mean change. Translational Relevance: As microperimetry has become an outcome measure in several gene-therapy clinical trials, three-dimensional visualization and volumetric sensitivity enables a complementary analysis of baseline disease characteristics and subsequent response to treatment, both as a signal of safety and efficacy

Double Red Blood Cell Donation Eligibility and Interest

Introduction: The process of double RBC donation by apheresis (DRBC), which facilitates the donation of two units of red blood cells (RBC) in a single donation session, was estimated to account for approximately 4% of blood donations in 2005, and is believed to be growing at a rate of 40% per year. Blood shortages in this country could be corrected by converting as few as 10% of current single unit whole blood donors to DRBC donors. Advantages of DRBC donation may include reduction in donor-related exposures in recipients, improved cost-effectiveness of the donation process, and improved convenience for donors. The safety profile of DRBC has been found to be equal to, and in some cases better than that of single unit whole blood donation, especially in young donors (/o). DRBC donors have been shown to restore 92% of RBC volume in 4 weeks without iron supplementation, and to have no significant differences in hemoglobin, serum iron, or ferritin when compared with single unit whole blood donors six months after donation. Our study seeks to quantify the number of current single unit whole blood donors who are both eligible for and interested in DRBC donation.https://scholarworks.uvm.edu/comphp_gallery/1031/thumbnail.jp

Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture

Marine sediments contain a high diversity of micro- and macro-organisms which are important in the functioning of biogeochemical cycles. Traditionally, anthropogenic perturbation has been investigated by identifying macro-organism responses along gradients. Environmental DNA (eDNA) analyses have recently been advocated as a rapid and cost-effective approach to measuring ecological impacts and efforts are underway to incorporate eDNA tools into monitoring. Before these methods can replace or complement existing methods, robustness and repeatability of each analytical step has to be demonstrated. One area that requires further investigation is the selection of sediment DNA extraction method. Environmental DNA sediment samples were obtained along a disturbance gradient adjacent to a Chinook (Oncorhynchus tshawytscha) salmon farm in Otanerau Bay, New Zealand. DNA was extracted using four extraction kits (Qiagen DNeasy PowerSoil, Qiagen DNeasy PowerSoil Pro, Qiagen RNeasy PowerSoil Total RNA/DNA extraction/elution and Favorgen FavorPrep Soil DNA Isolation Midi Kit) and three sediment volumes (0.25, 2, and 5 g). Prokaryotic and eukaryotic communities were amplified using primers targeting the 16S and 18S ribosomal RNA genes, respectively, and were sequenced on an Illumina MiSeq. Diversity and community composition estimates were obtained from each extraction kit, as well as their relative performance in established metabarcoding biotic indices. Differences were observed in the quality and quantity of the extracted DNA amongst kits with the two Qiagen DNeasy PowerSoil kits performing best. Significant differences were observed in both prokaryotes and eukaryotes (p < 0.001) richness among kits. A small proportion of amplicon sequence variants (ASVs) were shared amongst the kits (~3%) although these shared ASVs accounted for the majority of sequence reads (prokaryotes: 59.9%, eukaryotes: 67.2%). Differences were observed in the richness and relative abundance of taxonomic classes revealed with each kit. Multivariate analysis showed that there was a significant interaction between “distance” from the farm and “kit” in explaining the composition of the communities, with the distance from the farm being a stronger determinant of community composition. Comparison of the kits against the bacterial and eukaryotic metabarcoding biotic index suggested that all kits showed similar patterns along the environmental gradient. Overall, we advocate for the use of Qiagen DNeasy PowerSoil kits for use when characterizing prokaryotic and eukaryotic eDNA from marine farm sediments. We base this conclusion on the higher DNA quality values and richness achieved with these kits compared to the other kits/amounts investigated in this study. The additional advantage of the PowerSoil Kits is that DNA extractions can be performed using an extractor robot, offering additional standardization and reproducibility of results.publishedVersio

The Role of PemIK (PemK/PemI) Type II TA System from Klebsiella pneumoniae Clinical Strains in Lytic Phage Infection

[Abstract] Since their discovery, toxin-antitoxin (TA) systems have captivated the attention of many scientists. Recent studies have demonstrated that TA systems play a key role in phage inhibition. The aim of the present study was to investigate the role of the PemIK (PemK/PemI) type II TA system in phage inhibition by its intrinsic expression in clinical strains of Klebsiella pneumoniae carrying the lncL plasmid, which harbours the carbapenemase OXA-48 and the PemK/PemI TA system. Furthermore, induced expression of the system in an IPTG-inducible plasmid in a reference strain of K. pneumoniae ATCC10031 was also studied. The results showed that induced expression of the whole TA system did not inhibit phage infection, whereas overexpression of the pemK toxin prevented early infection. To investigate the molecular mechanism involved in the PemK toxin-mediated inhibition of phage infection, assays measuring metabolic activity and viability were performed, revealing that overexpression of the PemK toxin led to dormancy of the bacteria. Thus, we demonstrate that the PemK/PemI TA system plays a role in phage infection and that the action of the free toxin induces a dormant state in the cells, resulting in inhibition of phage infections.This study was funded by grant PI19/00878 awarded to M. Tomás within the State Plan for R+D+I 2013-2016 (National Plan for Scientific Research, Technological Development and Innovation 2008-2011) and co-financed by the ISCIII-Deputy General Directorate for Evaluation and Promotion of Research—European Regional Development Fund "A way of Making Europe" and Instituto de Salud Carlos III FEDER, Spanish Network for the Research in Infectious Diseases (REIPI, RD16/0016/0001, RD16/0016/0006 and RD16/CIII/0004/0002) and by the Study Group on Mechanisms of Action and Resistance to Antimicrobials, GEMARA (SEIMC, http://www.seimc.org/). M. Tomás was financially supported by the Miguel Servet Research Programme (SERGAS and ISCIII). I. Bleriot was financially supported by pFIS program (ISCIII, FI20/00302). O. Pacios and M. López was financially supported by a grant IN606A-2020/035 and IN606B-2018/008, respectively (GAIN, Xunta de Galicia) and M. Gonzalez-Bardanca was financially supported by the Rio Hortega program (ISCIII, CM20/00198)Xunta de Galicia; IN606A-2020/035Xunta de Galicia; IN606B-2018/00

Metabolic Syndrome Is Associated with Greater Histologic Severity, Higher Carbohydrate, and Lower Fat Diet in Patients with NAFLD

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73077/1/j.1572-0241.2006.00719.x.pd

Movement Interventions for Children with Autism and Developmental Disabilities: An Evidence-Based Practice Project

This review explored the following question: Are the comprehensive treatment models Makoto Therapy, Brain Gym, and Interactive Metronome effective interventions for improving occupational performance including improving executive function, academic performance, and physical coordination in children and adolescents with Autism Spectrum Disorder (ASD)? Because current research on Interactive Metronome, Brain Gym®, and Makoto Therapy fails to address children and adolescents with autism spectrum disorder, presents multiple flaws in research design, and does not measure occupational outcomes such as occupational performance, we recommend that these interventions should not be used as comprehensive treatment models in occupational therapy. We recommend that more occupational-based, methodologically-sound research involving youth with ASD be conducted before implementing these interventions in occupational therapy practice

Do residents’ perceptions of being well-placed and objective presence of local amenities match? A case study in West Central Scotland, UK

Background:&lt;p&gt;&lt;/p&gt; Recently there has been growing interest in how neighbourhood features, such as the provision of local facilities and amenities, influence residents’ health and well-being. Prior research has measured amenity provision through subjective measures (surveying residents’ perceptions) or objective (GIS mapping of distance) methods. The latter may provide a more accurate measure of physical access, but residents may not use local amenities if they do not perceive them as ‘local’. We believe both subjective and objective measures should be explored, and use West Central Scotland data to investigate correspondence between residents’ subjective assessments of how well-placed they are for everyday amenities (food stores, primary and secondary schools, libraries, pharmacies, public recreation), and objective GIS-modelled measures, and examine correspondence by various sub-groups.&lt;p&gt;&lt;/p&gt; Methods:&lt;p&gt;&lt;/p&gt; ArcMap was used to map the postal locations of ‘Transport, Health and Well-being 2010 Study’ respondents (n = 1760), and the six amenities, and the presence/absence of each of them within various straight-line and network buffers around respondents’ homes was recorded. SPSS was used to investigate whether objective presence of an amenity within a specified buffer was perceived by a respondent as being well-placed for that amenity. Kappa statistics were used to test agreement between measures for all respondents, and by sex, age, social class, area deprivation, car ownership, dog ownership, walking in the local area, and years lived in current home.&lt;p&gt;&lt;/p&gt; Results:&lt;p&gt;&lt;/p&gt; In general, there was poor agreement (Kappa &lt;0.20) between perceptions of being well-placed for each facility and objective presence, within 800 m and 1000 m straight-line and network buffers, with the exception of pharmacies (at 1000 m straight-line) (Kappa: 0.21). Results varied between respondent sub-groups, with some showing better agreement than others. Amongst sub-groups, at 800 m straight-line buffers, the highest correspondence between subjective and objective measures was for pharmacies and primary schools, and at 1000 m, for pharmacies, primary schools and libraries. For road network buffers under 1000 m, agreement was generally poor.&lt;p&gt;&lt;/p&gt; Conclusion:&lt;p&gt;&lt;/p&gt; Respondents did not necessarily regard themselves as well-placed for specific amenities when these amenities were present within specified boundaries around their homes, with some exceptions; the picture is not clear-cut with varying findings between different amenities, buffers, and sub-groups

Explaining asymmetry between weakening and recovery of the AMOC in a coupled climate model

The Atlantic meridional overturning circulation (AMOC) is projected to weaken in the coming century due to anthropogenic climate change. Various studies have considered AMOC weakening and collapse, with less research focusing on the processes and timescales of the recovery phase. This study uses a coupled climate model to explore the roles of salinity and temperature in AMOC recovery after a weakening. The North Atlantic and Arctic region was hosed with freshwater for 200 years. The mean Atlantic salinity increased strongly during recovery, and remained elevated for ~ 600 years post hosing. The behaviour of the AMOC was well reconstructed by applying “rotated geostrophy” to meridional density gradient profiles between 50°N and 30°S. This makes it possible to determine the role of overturning, gyre, and surface fluxes in the North and South Atlantic. Changes at 50°N dominate the weakening and early recovery. The magnitude of the overshoot to high AMOC transports in the recovery phase was related to density changes in the South Atlantic