Small coastal streams - Critical reservoirs of genetic diversity for trout (Salmo trutta L.) in the face of increasing anthropogenic stressors

This is the final version. Available on open access from Wiley via the DOI in this recordWe used microsatellite markers to investigate levels and structuring of genetic diversity in trout (Salmo trutta L.) sampled from 16 rivers along the south coast of Cornwall in southwest England. This region is characterized by many small coastal streams with a few larger catchments. At a regional level, genetic structuring of contemporary populations has been influenced by a combination of events, including the last Ice Age and also more recent human activities over the last millennium. All populations are shown to have gone through strong genetic bottlenecks, coinciding with increased exploitation of mineral resources within catchments, beginning during the Medieval period. At more local levels, contemporary human-induced habitat fragmentation, such as weir and culvert construction, has disproportionally affected trout populations in the smaller catchments within the study area. However, where small catchments are relatively unaffected by such activities, they can host trout populations with diversity levels comparable to those found in larger rivers in the region. We also predict significant future loses of diversity and heterozygosity in the trout populations inhabiting small, isolated catchments. Our study highlights how multiple factors, especially the activity of humans, have and continue to affect the levels and structuring of genetic diversity in trout over long timescales.European Union 2007‐2013 Atlantic Area Programme INTERREG III B initiativeAtlantic Salmon TrustSalmonid Management Around the Channel (SAMARCH) projec

Sperm competition as an under-appreciated factor in domestication

Humans created an environment that increased selective pressures on subgroups of those species that became domestic. We propose that the domestication process may in some cases have been facilitated by changes in mating behaviour and resultant sperm competition. By adapting to sperm competition, proto-domestic animals could potentially have outcompeted their wild counterparts in human-constructed niches. This could have contributed to the restriction of gene flow between the proto-domesticates and their wild counterparts, thereby promoting the fixation of other domestication characteristics. Further to this novel perspective for domestication, we emphasise the general potential of postcopulatory sexual selection in the restriction of gene flow between populations, and urge more studies

Inter-laboratory proficiency testing scheme for tumour next-generation sequencing in Ontario: A pilot study

Background A pilot inter-laboratory proficiency scheme for 5 Ontario clinical laboratories testing tumour samples for the Ontario-wide Cancer Targeted Nucleic Acid Evaluation (OCTANE) study was undertaken to assess proficiency in the identification and reporting of next-generation sequencing (NGS) test results in solid tumour testing from archival formalin-fixed, paraffin-embedded (FFPE) tissue. Methods One laboratory served as the reference centre and provided samples to 4 participating laboratories. An analyte-based approach was applied: each participating laboratory received 10 FFPE tissue specimens profiled at the reference centre, with tumour site and histology provided. Laboratories performed testing per their standard NGS tumour test protocols. Items returned for assessment included genes and variants that would be typically reported in routine clinical testing and variant call format (VCF) files to allow for assessment of NGS technical quality. Results Two main aspects were assessed: Technical quality and accuracy of identification of exonic variants Site-specific reporting practices Technical assessment included evaluation of exonic variant identification, quality assessment of the VCF files to evaluate base calling, variant allele frequency, and depth of coverage for all exonic variants. Concordance at 100% was observed from all sites in the technical identification of 98 exonic variants across the 10 cases. Variability between laboratories in the choice of variants considered clinically reportable was significant. Of the 38 variants reported as clinically relevant by at least 1 site, only 3 variants were concordantly reported by all participating centres as clinically relevant. Conclusions Although excellent technical concordance for NGS tumour profiling was observed across participating institutions, differences in the reporting of clinically relevant variants were observed, highlighting reporting as a gap where consensus on the part of Ontario laboratories is needed

The Acute Physiological and Perceptual Responses to Blood-flow Restriction Applied During Un-resisted Knee Exercise: A Potential Treatment Adjunct for Physiotherapists

Purpose: Blood-flow restriction [BfR] training involves the temporary, artificial reduction of blood flow through a limb. Evidence suggests that BfR combined with low-intensity resistance exercise can minimise the loss of thigh muscle size and strength during periods of impaired weight-bearing. However, evidence is scarce as to the specific utility of adding BfR to un-resisted or ‘no-load’ exercise during injury rehabilitation. Therefore, this case series examined the effects of applying BfR during a no-load lower-limb knee exercise completed by athletes recovering from significant lower limb injuries. Methods: Three professional rugby players provided consent to incorporate BfR training into their injury rehabilitation programmes. (Case one; four weeks post tibia and fibula fracture. Case two; five weeks post Achilles tendon rupture. Case three; immediately following MRI diagnosis of an osseous stress injury of the knee). During the control exercise session, players performed three sets of a seated, un-resisted, single-leg knee-extension exercise. At subsequent sessions, a 21.5 cm wide blood-pressure cuff was used to superimpose BfR over the same exercise. BfR was applied intermittently or continuously across the upper thigh via 100 mmHg or 120 mmHg cuff pressure. Near infra-red spectroscopy [NIRS] monitored tissue oxygen saturation [SmO2] and total haemoglobin mass [tHb] of the vastus lateralis muscle before and during the exercise of each lower-limb. The relative change in SmO2 and tHb generated during each exercise session was then calculated. Session rate of perceived exertion [RPE] was monitored via a 10-point visual scale. Descriptive statistics were then used to indicate trends among these variables. Results: BfR training was delivered four to five times per week for periods of 4 to 12 weeks. NIRS data from thirty BfRT sessions (five sessions per leg, per player) were obtained. Mean resting values for vastus lateralis SmO2 and tHb were 54.3% and 12.72 g/dL respectively. During the control exercise session, SmO2 increased by a mean of 4.68 points, whilst tHb decreased slightly (-0.04 g/dL). In contrast, the addition of continuous BfR at 120 mmHg generated a mean drop in SmO2 of 22.31 points, whilst tHb increased (+0.23 g/dL). No adverse events or pain occurred during any exercise session. The control session generated a mean session RPE of 0.94 out of 10. Session RPE during BfR training ranged between 3.6 and 4.9. Conclusion(s): In a case series of injured athletes, data indicated that adding BfR to a ‘no-load’ knee extension exercise generated oxygen desaturation of the vastus lateralis muscle and increased perceptual exertion. Lower-limb BfR training was delivered in a safe, tolerable way as part of a multi-modal, intensive injury rehabilitation programme. Implications: BfR training may provide Physiotherapists with a novel Method of generating exercise-induced physiological stress within muscle tissue during exercise, without the need to add any external resistance. Achieving sufficient physiological stress during the very early stages of injury rehabilitation via no-load BfR training may promote a muscular response that limits the longitudinal muscle disuse atrophy seen during periods of impaired weight-bearing. Further research is warranted to substantiate this and to explore the utility of no-load BfR training within non-athletic, clinical populations. Funding acknowledgements: This study was funded via a PhD studentship awarded by Manchester Metropolitan University

A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales

This is the final version. Available on open access from Wiley via the DOI in this recordThe rivers of southern England and northern France which drain into the English Channel contain several genetically unique groups of trout (Salmo trutta L.) that have suffered dramatic declines in numbers over the past 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 95 single nucleotide polymorphism (SNP) loci for trout from this region and investigate their applicability and variability in both target (i.e., southern English) and non-target trout populations from northern Britain and Ireland. In addition, we present three case studies which demonstrate the utility and resolution of these genetic markers at three levels of spatial separation:(a) between closely related populations in nearby rivers, (b) within a catchment and (c) when determining parentage and familial relationships between fish sampled from a single site, using both empirical and simulated data. The SNP loci will be useful for population genetic and assignment studies on brown trout within the UK and beyond.European Union Interreg France (Channel) England programmeWestcountry Rivers Trus

Bio-optical Properties of Cyanobacteria Blooms in Western Lake Erie

There is a growing use of remote sensing observations for detecting and quantifying freshwater cyanobacteria populations, yet the inherent optical properties of these communities in natural settings, fundamental to bio-optical algorithms, are not well known. Toward bridging this knowledge gap, we measured a full complement of optical properties in western Lake Erie during cyanobacteria blooms in the summers of 2013 and 2014. Our measurements focus attention on the optical uniqueness of cyanobacteria blooms, which have consequences for remote sensing and bio-optical modeling. We found the cyanobacteria blooms in the western basin during our field work were dominated by Microcystis, while the waters in the adjacent central basin were dominated by Planktothrix. Chlorophyll concentrations ranged from 1 to over 135 μg/L across the study area with the highest concentrations associated with Microcystis in the western basin. We observed large, amorphous colonial Microcystis structures in the bloom area characterized by high phytoplankton absorption and high scattering coefficients with a mean particle backscatter ratio at 443 nm \u3e 0.03, which is higher than other plankton types and more comparable to suspended inorganic sediments. While our samples contained mixtures of both, our analysis suggests high contributions to the measured scatter and backscatter coefficients from cyanobacteria. Our measurements provide new insights into the optical properties of cyanobacteria blooms, and indicate that current semi-analytic models are likely to have problems resolving a closed solution in these types of waters as many of our observations are beyond the range of existing model components. We believe that different algorithm or model approaches are needed for these conditions, specifically for phytoplankton absorption and particle backscatter components. From a remote sensing perspective, this presents a challenge not only in terms of a need for new algorithms, but also for determining when to apply the best algorithm for a given situation. These results are new in the sense that they represent a complete description of the optical properties of freshwater cyanobacteria blooms, and are likely to be representative of bloom conditions for other systems containing Microcystis cells and colonies

Asymmetric Genome Organization in an RNA Virus Revealed via Graph-Theoretical Analysis of Tomographic Data

Cryo-electron microscopy permits 3-D structures of viral pathogens to be determined in remarkable detail. In particular, the protein containers encapsulating viral genomes have been determined to high resolution using symmetry averaging techniques that exploit the icosahedral architecture seen in many viruses. By contrast, structure determination of asymmetric components remains a challenge, and novel analysis methods are required to reveal such features and characterize their functional roles during infection. Motivated by the important, cooperative roles of viral genomes in the assembly of single-stranded RNA viruses, we have developed a new analysis method that reveals the asymmetric structural organization of viral genomes in proximity to the capsid in such viruses. The method uses geometric constraints on genome organization, formulated based on knowledge of icosahedrally-averaged reconstructions and the roles of the RNA-capsid protein contacts, to analyse cryo-electron tomographic data. We apply this method to the low-resolution tomographic data of a model virus and infer the unique asymmetric organization of its genome in contact with the protein shell of the capsid. This opens unprecedented opportunities to analyse viral genomes, revealing conserved structural features and mechanisms that can be targeted in antiviral drug desig

Oligodendrocyte Death in Pelizaeus-Merzbacher Disease Is Rescued by Iron Chelation.

Pelizaeus-Merzbacher disease (PMD) is an X-linked leukodystrophy caused by mutations in Proteolipid Protein 1 (PLP1), encoding a major myelin protein, resulting in profound developmental delay and early lethality. Previous work showed involvement of unfolded protein response (UPR) and endoplasmic reticulum (ER) stress pathways, but poor PLP1 genotype-phenotype associations suggest additional pathogenetic mechanisms. Using induced pluripotent stem cell (iPSC) and gene-correction, we show that patient-derived oligodendrocytes can develop to the pre-myelinating stage, but subsequently undergo cell death. Mutant oligodendrocytes demonstrated key hallmarks of ferroptosis including lipid peroxidation, abnormal iron metabolism, and hypersensitivity to free iron. Iron chelation rescued mutant oligodendrocyte apoptosis, survival, and differentiationin vitro, and post-transplantation in vivo. Finally, systemic treatment of Plp1 mutant Jimpy mice with deferiprone, a small molecule iron chelator, reduced oligodendrocyte apoptosis and enabled myelin formation. Thus, oligodendrocyte iron-induced cell death and myelination is rescued by iron chelation in PMD pre-clinical models.H.N. acknowledges postdoctoral fellowship support from the European Leukodystrophy Association, and career transition fellowship support from National Multiple Sclerosis Society. M.C. acknowledges funding support from Career Development Grant awarded by Cerebral Palsy Alliance Research Foundation Inc. This work was supported by funding from the National Multiple Sclerosis Foundation (to M.W., D.H. R.), the European Leukodystrophy Association and the New York Stem Cell Foundation (to M.W.), and Action Medical Research, the Adelson Medical Research Foundation, the National Institute for Health Research Cambridge Biomedical Research Centre and the European Research Council (to D.H. R)

OCTANE (ontario-wide cancer targeted nucleic acid evaluation): A platform for intraprovincial, national, and international clinical data-sharing

Cancer is a genetic disease resulting from germline or somatic genetic aberrations. Rapid progress in the field of genomics in recent years is allowing for increased characterization and understanding of the various forms of the disease. The Ontario-wide Cancer Targeted Nucleic Acid Evaluation (octane) clinical trial, open at cancer centres across Ontario, aims to increase access to genomic sequencing of tumours and to facilitate the collection of clinical data related to enrolled patients and their clinical outcomes. The study is designed to assess the clinical utility of next-generation sequencing (ngs) in cancer patient care, including enhancement of treatment options available to patients. A core aim of the study is to encourage collaboration between cancer hospitals within Ontario while also increasing international collaboration in terms of sharing the newly generated data. The single-payer provincial health care system in Ontario provides a unique opportunity to develop a province-wide registry of ngs testing and a repository of genomically characterized, clinically annotated samples. It also provides an important opportunity to use province-wide real-world data to evaluate outcomes and the cost of ngs for patients with advanced cancer. The octane study is attempting to translate knowledge to help deliver precision oncology in a Canadian environment. In this article, we discuss the background to the study and its implementation, current status, and future directions