Sex Differences with Aging in the Fatigability of Dynamic Contractions

This study determined the sex difference with aging in fatigability of the elbow flexor muscles during a dynamic fatiguing task, and explored the associated mechanisms. We compared fatigability of the elbow flexor muscles in 18 young (20.2 ± 1 years: 9 men) and 36 old adults (73.5 ± 1 years: 16 men) during and in recovery from repeated dynamic contractions (~ 60°/s) with a load equivalent to 20% of maximal voluntary isometric contraction (MVIC) torque until failure. Transcranial magnetic stimulation (TMS) was used to assess supraspinal fatigue (an increase in the superimposed twitch, SIT) and the peak rate of muscle relaxation. Time to failure was briefer for the men than the women (6.1 ± 2.1 vs. 9.7 ± 5.5 min, respectively; P = 0.02) with no difference between young and old adults (7.2 ± 2.9 vs. 8.4 ± 5.2 min, respectively, P = 0.45) and no interaction (P \u3e 0.05). The relative decline in peak relaxation rate with fatigability was similar for young and old adults (P = 0.11), but greater for men than women (P = 0.046). Supraspinal fatigue increased for all groups and was associated with the time to failure (P \u3c 0.05). Regression analysis however, indicated that the time to failure was best predicted by the peak relaxation rate (baseline values and slowing with fatigability) (r2 = 0.55). Rate-limiting contractile mechanisms (e.g. excitation–contraction coupling) were responsible for the increased fatigability of the elbow flexors of men compared with women for a dynamic fatiguing task of slow angular velocity, and this sex difference was maintained with aging. The age difference in fatigability for the dynamic task was diminished for both sexes relative to what is typically observed with isometric fatiguing contractions

FY 17 Preliminary Education & General Budget Continuing the Discussion Presentation Slides

Slides from presentations regarding the University of Maine\u27s education and general budget for the 2017 fiscal year and fiscal planning. The first set of slides are regarding the preliminary budget, the second are of the final budget discussion, the third are of a multi-year financial analysis FY 2017-2021, and the fourth set are of unified budget with proposed recommendations

Identification of Klebsiella capsule synthesis loci from whole genome data.

Klebsiella pneumoniae is a growing cause of healthcare-associated infections for which multi-drug resistance is a concern. Its polysaccharide capsule is a major virulence determinant and epidemiological marker. However, little is known about capsule epidemiology since serological typing is not widely accessible and many isolates are serologically non-typeable. Molecular typing techniques provide useful insights, but existing methods fail to take full advantage of the information in whole genome sequences. We investigated the diversity of the capsule synthesis loci (K-loci) among 2503 K. pneumoniae genomes. We incorporated analyses of full-length K-locus nucleotide sequences and also clustered protein-encoding sequences to identify, annotate and compare K-locus structures. We propose a standardized nomenclature for K-loci and present a curated reference database. A total of 134 distinct K-loci were identified, including 31 novel types. Comparative analyses indicated 508 unique protein-encoding gene clusters that appear to reassort via homologous recombination. Extensive intra- and inter-locus nucleotide diversity was detected among the wzi and wzc genes, indicating that current molecular typing schemes based on these genes are inadequate. As a solution, we introduce Kaptive, a novel software tool that automates the process of identifying K-loci based on full locus information extracted from whole genome sequences (https://github.com/katholt/Kaptive). This work highlights the extensive diversity of Klebsiella K-loci and the proteins that they encode. The nomenclature, reference database and novel typing method presented here will become essential resources for genomic surveillance and epidemiological investigations of this pathogen

KSHV SOX mediated host shutoff: the molecular mechanism underlying mRNA transcript processing.

Onset of the lytic phase in the KSHV life cycle is accompanied by the rapid, global degradation of host (and viral) mRNA transcripts in a process termed host shutoff. Key to this destruction is the virally encoded alkaline exonuclease SOX. While SOX has been shown to possess an intrinsic RNase activity and a potential consensus sequence for endonucleolytic cleavage identified, the structures of the RNA substrates targeted remained unclear. Based on an analysis of three reported target transcripts, we were able to identify common structures and confirm that these are indeed degraded by SOX in vitro as well as predict the presence of such elements in the KSHV pre-microRNA transcript K12-2. From these studies, we were able to determine the crystal structure of SOX productively bound to a 31 nucleotide K12-2 fragment. This complex not only reveals the structural determinants required for RNA recognition and degradation but, together with biochemical and biophysical studies, reveals distinct roles for residues implicated in host shutoff. Our results further confirm that SOX and the host exoribonuclease Xrn1 act in concert to elicit the rapid degradation of mRNA substrates observed in vivo, and that the activities of the two ribonucleases are co-ordinated

The depression in visual impairment trial (DEPVIT): trial design and protocol

<b>Background</b> The prevalence of depression in people with a visual disability is high but screening for depression and referral for treatment is not yet an integral part of visual rehabilitation service provision. One reason for this may be that there is no good evidence about the effectiveness of treatments in this patient group. This study is the first to evaluate the effect of depression treatments on people with a visual impairment and co morbid depression.<p></p> <b>Methods/design</b> The study is an exploratory, multicentre, individually randomised waiting list controlled trial. Participants will be randomised to receive Problem Solving Therapy (PST), a ‘referral to the GP’ requesting treatment according to the NICE’s ‘stepped care’ recommendations or the waiting list arm of the trial. The primary outcome measure is change (from randomisation) in depressive symptoms as measured by the Beck’s Depression Inventory (BDI-II) at 6 months. Secondary outcomes include change in depressive symptoms at 3 months, change in visual function as measured with the near vision subscale of the VFQ-48 and 7 item NEI-VFQ at 3 and 6 months, change in generic health related quality of life (EQ5D), the costs associated with PST, estimates of incremental cost effectiveness, and recruitment rate estimation.<p></p> <b>Discussion</b> Depression is prevalent in people with disabling visual impairment. This exploratory study will establish depression screening and referral for treatment in visual rehabilitation clinics in the UK. It will be the first to explore the efficacy of PST and the effectiveness of NICE’s ‘stepped care’ approach to the treatment of depression in people with a visual impairment.<p></p&gt

Completing bacterial genome assemblies with multiplex MinION sequencing

AbstractIllumina sequencing platforms have enabled widespread bacterial whole genome sequencing. While Illumina data is appropriate for many analyses, its short read length limits its ability to resolve genomic structure. This has major implications for tracking the spread of mobile genetic elements, including those which carry antimicrobial resistance determinants. Fully resolving a bacterial genome requires long-read sequencing such as those generated by Oxford Nanopore Technologies (ONT) platforms. Here we describe our use of the ONT MinION to sequence 12 isolates of Klebsiella pneumoniae on a single flow cell. We assembled each genome using a combination of ONT reads and previously available Illumina reads, and little to no manual intervention was needed to achieve fully resolved assemblies using the Unicycler hybrid assembler. Assembling only ONT reads with Canu was less effective, resulting in fewer resolved genomes and higher error rates even following error correction with Nanopolish. We demonstrate that multiplexed ONT sequencing is a valuable tool for high-throughput bacterial genome finishing. Specifically, we advocate the use of Illumina sequencing as a first analysis step, followed by ONT reads as needed to resolve genomic structure.Data summarySequence read files for all 12 isolates have been deposited in SRA, accessible through these NCBI BioSample accession numbers: SAMEA3357010, SAMEA3357043, SAMN07211279, SAMN07211280, SAMEA3357223, SAMEA3357193, SAMEA3357346, SAMEA3357374, SAMEA3357320, SAMN07211281, SAMN07211282, SAMEA3357405.A full list of SRA run accession numbers (both Illumina reads and ONT reads) for these samples are available in Table S1.Assemblies and sequencing reads corresponding to each stage of processing and analysis are provided in the following figshare project: https://figshare.com/projects/Completing_bacterial_genome_assemblies_with_multiplex_MinION_sequencing/23068Source code is provided in the following public GitHub repositories: https://github.com/rrwick/Bacterial-genome-assemblies-with-multiplex-MinION-sequencinghttps://github.com/rrwick/Porechophttps://github.com/rrwick/Fast5-to-FastqImpact StatementLike many research and public health laboratories, we frequently perform large-scale bacterial comparative genomics studies using Illumina sequencing, which assays gene content and provides the high-confidence variant calls needed for phylogenomics and transmission studies. However, problems often arise with resolving genome assemblies, particularly around regions that matter most to our research, such as mobile genetic elements encoding antibiotic resistance or virulence genes. These complexities can often be resolved by long sequence reads generated with PacBio or Oxford Nanopore Technologies (ONT) platforms. While effective, this has proven difficult to scale, due to the relatively high costs of generating long reads and the manual intervention required for assembly. Here we demonstrate the use of barcoded ONT libraries sequenced in multiplex on a single ONT MinION flow cell, coupled with hybrid assembly using Unicycler, to resolve 12 large bacterial genomes. Minor manual intervention was required to fully resolve small plasmids in five isolates, which we found to be underrepresented in ONT data. Cost per sample for the ONT sequencing was equivalent to Illumina sequencing, and there is potential for significant savings by multiplexing more samples on the ONT run. This approach paves the way for high-throughput and cost-effective generation of completely resolved bacterial genomes to become widely accessible.</jats:sec

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.

The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platforms generate long reads that can produce complete genome assemblies, but the sequencing is more expensive and error-prone. There is significant interest in combining data from these complementary sequencing technologies to generate more accurate "hybrid" assemblies. However, few tools exist that truly leverage the benefits of both types of data, namely the accuracy of short reads and the structural resolving power of long reads. Here we present Unicycler, a new tool for assembling bacterial genomes from a combination of short and long reads, which produces assemblies that are accurate, complete and cost-effective. Unicycler builds an initial assembly graph from short reads using the de novo assembler SPAdes and then simplifies the graph using information from short and long reads. Unicycler uses a novel semi-global aligner to align long reads to the assembly graph. Tests on both synthetic and real reads show Unicycler can assemble larger contigs with fewer misassemblies than other hybrid assemblers, even when long-read depth and accuracy are low. Unicycler is open source (GPLv3) and available at github.com/rrwick/Unicycler