Y-chromosome haplotypes are associated with variation in size and age at maturity in male Chinook salmon.

Variation in size and age at maturity is an important component of life history that is influenced by both environmental and genetic factors. In salmonids, large size confers a direct reproductive advantage through increased fecundity and egg quality in females, while larger males gain a reproductive advantage by monopolizing access to females. In addition, variation in size and age at maturity in males can be associated with different reproductive strategies; younger smaller males may gain reproductive success by sneaking among mating pairs. In both sexes, there is a trade-off between older age and increased reproductive success and increased risk of mortality by delaying reproduction. We identified four Y-chromosome haplogroups that showed regional- and population-specific variation in frequency using RADseq data for 21 populations of Alaska Chinook salmon. We then characterized the range-wide distribution of these haplogroups using GT-seq assays. These haplogroups exhibited associations with size at maturity in multiple populations, suggesting that lack of recombination between X and Y-chromosomes has allowed Y-chromosome haplogroups to capture different alleles that influence size at maturity. Ultimately, conservation of life history diversity in Chinook salmon may require conservation of Y-chromosome haplotype diversity.

Resolving allele dosage in duplicated loci using genotyping-by-sequencing data: A path forward for population genetic analysis.

Whole-genome duplications have occurred in the recent ancestors of many plants, fish and amphibians. Signals of these whole-genome duplications still exist in the form of paralogous loci. Recent advances have allowed reliable identification of paralogs in genotyping-by-sequencing (GBS) data such as that generated from restriction-site-associated DNA sequencing (RADSeq); however, excluding paralogs from analyses is still routine due to difficulties in genotyping. This exclusion of paralogs may filter a large fraction of loci, including loci that may be adaptively important or informative for population genetic analyses. We present a maximum-likelihood method for inferring allele dosage in paralogs and assess its accuracy using simulated GBS, empirical RADSeq and amplicon sequencing data from Chinook salmon. We accurately infer allele dosage for some paralogs from a RADSeq data set and show how accuracy is dependent upon both read depth and allele frequency. The amplicon sequencing data set, using RADSeq-derived markers, achieved sufficient depth to infer allele dosage for all paralogs. This study demonstrates that RADSeq locus discovery combined with amplicon sequencing of targeted loci is an effective method for incorporating paralogs into population genetic analyses.

Radial head prosthesis: results overview.

BACKGROUND/PURPOSE: Radial head replacement is frequently used in treatment of radial head fractures or sequela. Impossibility to restore a correct anatomy, acute elbow traumatic instability and failure of osteosynthesis hardware are the most common indications. The authors describe their case studies and results on the implantation of various radial head prostheses. MATERIALS: Between June 2005 and June 2016, 28 radial head prostheses were implanted in the same number of patients with an average follow-up of 49 months (6-104). Indications for implantation were: Mason type III and IV radial head fractures and post-traumatic arthritis due to failure of previous treatments. Monopolar prostheses were used and were press-fit implanted via Kaplan's lateral access and Kocher's anconeus approach to the humeroradial joint. At the follow-up, assessments were made of the pain, according to the visual analogic scale, range of motion (ROM), stability and functionality according to the Mayo Elbow Performance Score, presence of osteolysis and mobilization during radiography tests, personal satisfaction of the patients, Disabilities of the Arm, Shoulder and Hand and Patient-Rated Wrist Evaluation outcomes measurements. RESULTS: At the follow-up, we recorded an average level of pain of 1.8 in patients under acute treatments for radial head fractures and a marked reduction in the remaining cases from 6.7 to 2.1. ROM was found on average to be 107° of flexion-extension and 159° of pronosupination. Personal satisfaction was good-excellent in 23 cases. There was no case of infection; removal of the implant was necessary in three cases due to mobilization of the stem and oversized implants. In six cases, bone resorption was seen at the level of the prosthetic collar and it was in all cases asymptomatic. CONCLUSIONS: The results of this study suggest that the use of prostheses, if well positioned, is a valid solution in the treatment of secondary arthritis and fractures of the radial head with poor prognosis, with good results in the reduction of pain, recovery of movement and improved quality of life.

HydroCalc Proteome: a tool to identify distinct characteristics of effector proteins.

Bacterial pathogenicity is associated with secretion of effector proteins into intra- and extracellular spaces. These proteins interfere with cellular processes such as inhibition of phagosome-lysosome fusion, induction of apoptosis and autophagy, activation and suppression of kinases, regulation of receptor activity, and modulation of transcription factors. Knowledge regarding the characteristics of these proteins would assist in pathogenicity studies, and help to identify possible and novel targets for antibacterial drugs. Amino acid hydropathy is a property that can affect behavior patterns in effector proteins. The HydroCalc Proteome tool analyzes total hydropathy, average hydropathy, C-terminal hydropathy, C-terminal load, and basic polar amino acids at the C-terminus. These five properties could contribute to the identification of proteins with an effector potential. HydroCalc Proteome is a web tool that provides a simple interface for the analysis of hydropathy properties in proteins. This tool permits the analysis of a single protein or even the complete proteome, which cannot be achieved by using other hydropathy tools. The tool displays the result of five properties related to effector proteins in a single table. The HydroCalc Proteome (www.gmb.bio.br/hydrocalc) is a powerful tool for protein analysis, and can contribute to the study of effector proteins.

Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism.

Single nucleotide polymorphisms (SNPs) are valuable tools for ecological and evolutionary studies. In non-model species, the use of SNPs has been limited by the number of markers available. However, new technologies and decreasing technology costs have facilitated the discovery of a constantly increasing number of SNPs. With hundreds or thousands of SNPs potentially available, there is interest in comparing and developing methods for evaluating SNPs to create panels of high-throughput assays that are customized for performance, research questions, and resources. Here we use five different methods to rank 43 new SNPs and 71 previously published SNPs for sockeye salmon: F(ST), informativeness (I(n)), average contribution to principal components (LC), and the locus-ranking programs BELS and WHICHLOCI. We then tested the performance of these different ranking methods by creating 48- and 96-SNP panels of the top-ranked loci for each method and used empirical and simulated data to obtain the probability of assigning individuals to the correct population using each panel. All 96-SNP panels performed similarly and better than the 48-SNP panels except for the 96-SNP BELS panel. Among the 48-SNP panels, panels created from F(ST), I(n), and LC ranks performed better than panels formed using the top-ranked loci from the programs BELS and WHICHLOCI. The application of ranking methods to optimize panel performance will become more important as more high-throughput assays become available.

Multiplex preamplification PCR and microsatellite validation enables accurate single nucleotide polymorphism genotyping of historical fish scales.

Incorporating historical tissues into the study of ecological, conservation and management questions can broaden the scope of population genetic research by enhancing our understanding of evolutionary processes and anthropogenic influences on natural populations. Genotyping historical and low-quality samples has been plagued by challenges associated with low amounts of template DNA and the potential for pre-existing DNA contamination among samples. We describe a two-step process designed to (i) accurately genotype large numbers of historical low-quality scale samples in a high-throughput format and (ii) screen samples for pre-existing DNA contamination. First, we describe how an efficient multiplex preamplification PCR of 45 single nucleotide polymorphisms (SNPs) can generate highly accurate genotypes with low failure and error rates in subsequent SNP genotyping reactions of individual historical scales from sockeye salmon (Oncorhynchus nerka). Second, we demonstrate how the method can be modified for the amplification of microsatellite loci to detect pre-existing DNA contamination. A total of 760 individual historical scale and 182 contemporary fin clip samples were genotyped and screened for contamination. Genotyping failure and error rates were exceedingly low and similar for both historical and contemporary samples. Pre-existing contamination in 21% of the historical samples was successfully identified by screening the amplified microsatellite loci. The advantages of automation, low failure and error rates, and ability to multiplex both the preamplification and subsequent genotyping reactions combine to make the protocol ideally suited for efficiently genotyping large numbers of potentially contaminated low-quality sources of DNA.

SNP genotyping by the 5'-nuclease reaction: advances in high-throughput genotyping with nonmodel organisms.

Population genetics studies play an increasingly important role in the management and conservation of nonmodel organisms. Unlike studies with model organisms, a typical population genetics study of a nonmodel organism may be conducted by analyzing thousands or hundreds of thousands of individuals for several dozen single nucleotide polymorphisms (SNPs). The use of robust, robotically mediated TaqMan reactions provides substantial advantages in these types of studies. We describe the methods and laboratory setup for analyzing a sustained high throughput of SNP assays in routine university or natural resource agency laboratories with a handful of thermal cyclers. Agencies sustain rates of nearly 150,000 assays per week using uniplex reactions with the Applied Biosystems 7900HT Fast Real-Time PCR System (AB 7900HT). We further describe the medium-density array run on the BioMark from Fluidigm, which increases this rate to over 500,000 assays per week by multiplexing 96 samples for 96 SNPs.

Internal femoral osteosynthesis after external fixation in multiple-trauma patients.

In this study the authors evaluate the results of internal synthesis of femoral fractures in polytraumatised patients initially treated by external fixation (EF). From January 2002 to December 2005, 39 femurs in 37 polytraumatised patients (average age 34.2 years, range 18-44) with closed fractures and an ISS>20 were initially treated with EF. There were three groups: Group A, 13 cases when conversion to internal osteosynthesis occurred after 4-7 days (average 5.6 days); Group B, 11 cases with a 4-6-month interval before internal osteosynthesis, and after investigation using MRI and scintigraphy with labelled leucocytes; Group C, the remaining cases treated definitively with EF. Time of healing, lower limb function, time of return to previous activities and short and long-term complications were evaluated at the follow-up. The average time of follow-up was 23 months. In Group A the time of bone healing was 123 days; there were no events of embolism but one case of pseudoarthrosis and one case of instrument failure. In Group B the time of bone healing was 274 days, with one case of pseudoarthrosis and one case of deep infection. In Group C the average healing time was 193 days, with 3 cases of screw (half-pin) osteolysis. Functional recovery was delayed by the presence of other fractures. EF is a simple, quick and safe procedure to stabilise fractures in polytraumatised patients. According to damage control orthopaedic (DCO) concepts, it is possible to replace EF with internal synthesis after an interval as this reduces the risks of internal osteosynthesis when performed in the emergency period. EF can also be maintained as definitive treatment but should a change to internal synthesis be needed, it is possible to do it safely after excluding bone infection.

[Set-up, portals and normal exploration in wrist arthroscopy.] / Installation, voies d'abord et exploration normale en arthroscopie du poignet.

Arthroscopy is an accepted technique for evaluation of intra-articular pathology and treatment of a variety of disorders even in the wrist joint. Dedicated miniaturized instrumentation is needed along with a specific traction system. The external distraction alone (dry technique) allows for complete joint exploration and several type of arthroscopic surgery, avoiding annoying leaking in the subcutaneous tissues, though further distension of the articular pouches can be achieved by saline infusion (fluid distension or wet technique). Knowledge of surface anatomic landmarks and careful surgical technique are required for proper portal placement and in order to avoid injury to the numerous noble structures crossing nearby. Description of radio- and medio-carpal portals is provided along with the different bony, condral, synovial and ligamentous structures that can be visualised or treated through each portal. Surgeon can choose the most suitable portal for scope or instruments, according to specific needs for diagnostic or therapeutic purposes.

[Set-up, portals and normal exploration in wrist arthroscopy]. / Installation, voies d'abord et exploration normale en arthroscopie du poignet.

Arthroscopy is an accepted technique for evaluation of intra-articular pathology and treatment of a variety of disorders even in the wrist joint. Dedicated miniaturized instrumentation is needed along with a specific traction system. The external distraction alone (dry technique) allows for complete joint exploration and several type of arthroscopic surgery, avoiding annoying leaking in the subcutaneous tissues, though further distension of the articular pouches can be achieved by saline infusion (fluid distension or wet technique). Knowledge of surface anatomic landmarks and careful surgical technique are required for proper portal placement and in order to avoid injury to the numerous noble structures crossing nearby. Description of radio- and medio-carpal portals is provided along with the different bony, condral, synovial and ligamentous structures that can be visualised or treated through each portal. Surgeon can choose the most suitable portal for scope or instruments, according to specific needs for diagnostic or therapeutic purposes.