JLIN: A java based linkage disequilibrium plotter

BACKGROUND: A great deal of effort and expense are being expended internationally in attempts to detect genetic polymorphisms contributing to susceptibility to complex human disease. Techniques such as Linkage Disequilibrium mapping are being increasingly used to examine and compare markers across increasingly large datasets. Visualisation techniques are becoming essential to analyse the ever-growing volume of data and results available with any given analysis. RESULTS: JLIN (Java LINkage disequilibrium plotter) is a software package designed for customisable, intuitive visualisation of Linkage Disequilibrium (LD) across all common computing platforms. Customisation allows the user to choose particular visualisations, statistical measures and measurement ranges. JLIN also allows the user to export images of the LD visualisation in several common document formats. CONCLUSION: JLIN allows the user to visually compare and contrast the results of a range of statistical measures on the input dataset(s). These measures include the commonly used D' and r(2 )statistics and empirical p-values. JLIN has a number of unique and novel features that improve on existing LD visualisation tools

Genome-wide linkage and association mapping of disease genes with the GAW14 simulated datasets

We combined the results of whole-genome linkage and association analyses to determine which markers were most strongly associated with Kofendrerd Personality Disorder. Using replicate 1 from the Genetic Analysis Workshop 14 Aipotu, Karangar, Danacaa, and New York City simulated populations, we determined that several markers showed significant linkage and association with disease status. We used both SNP and microsatellite markers to determine patterns and chromosomal regions of markers. Three consistently associated markers were C01R0050, C03R0280, and C10R0882. Using generalized linear mixed models, we modelled the effect of the three predefined phenotypic categories on disease status and concluded that the phenotypes defining the "anxiety-related" category best predicted the outcome

The effect of missing data on linkage disequilibrium mapping and haplotype association analysis in the GAW14 simulated datasets

We used our newly developed linkage disequilibrium (LD) plotting software, JLIN, to plot linkage disequilibrium between pairs of single-nucleotide polymorphisms (SNPs) for three chromosomes of the Genetic Analysis Workshop 14 Aipotu simulated population to assess the effect of missing data on LD calculations. Our haplotype analysis program, SIMHAP, was used to assess the effect of missing data on haplotype-phenotype association. Genotype data was removed at random, at levels of 1%, 5%, and 10%, and the LD calculations and haplotype association results for these levels of missingness were compared to those for the complete dataset. It was concluded that ignoring individuals with missing data substantially affects the number of regions of LD detected which, in turn, could affect tagging SNPs chosen to generate haplotypes

SimHap GUI: An intuitive graphical user interface for genetic association analysis

<p>Abstract</p> <p>Background</p> <p>Researchers wishing to conduct genetic association analysis involving single nucleotide polymorphisms (SNPs) or haplotypes are often confronted with the lack of user-friendly graphical analysis tools, requiring sophisticated statistical and informatics expertise to perform relatively straightforward tasks. Tools, such as the <it>SimHap </it>package for the R statistics language, provide the necessary statistical operations to conduct sophisticated genetic analysis, but lacks a graphical user interface that allows anyone but a professional statistician to effectively utilise the tool.</p> <p>Results</p> <p>We have developed SimHap GUI, a cross-platform integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. SimHap GUI features a novel workflow interface that guides the user through each logical step of the analysis process, making it accessible to both novice and advanced users. This tool provides a seamless interface to the <it>SimHap </it>R package, while providing enhanced functionality such as sophisticated data checking, automated data conversion, and real-time estimations of haplotype simulation progress.</p> <p>Conclusion</p> <p>SimHap GUI provides a novel, easy-to-use, cross-platform solution for conducting a range of genetic and non-genetic association analyses. This provides a free alternative to commercial statistics packages that is specifically designed for genetic association analysis.</p

Controlled spatial and conformational display of immobilised bone morphogenetic protein-2 and osteopontin signalling motifs regulates osteoblast adhesion and differentiation in vitro

<p>Abstract</p> <p>Background</p> <p>The interfacial molecular mechanisms that regulate mammalian cell growth and differentiation have important implications for biotechnology (production of cells and cell products) and medicine (tissue engineering, prosthetic implants, cancer and developmental biology). We demonstrate here that engineered protein motifs can be robustly displayed to mammalian cells <it>in vitro </it>in a highly controlled manner using a soluble protein scaffold designed to self assemble on a gold surface.</p> <p>Results</p> <p>A protein was engineered to contain a C-terminal cysteine that would allow chemisorption to gold, followed by 12 amino acids that form a water soluble coil that could switch to a hydrophobic helix in the presence of alkane thiols. Bioactive motifs from either bone morphogenetic protein-2 or osteopontin were added to this scaffold protein and when assembled on a gold surface assessed for their ability to influence cell function. Data demonstrate that osteoblast adhesion and short-term responsiveness to bone morphogenetic protein-2 is dependent on the surface density of a cell adhesive motif derived from osteopontin. Furthermore an immobilised cell interaction motif from bone morphogenetic protein supported bone formation <it>in vitro </it>over 28 days (in the complete absence of other osteogenic supplements). In addition, two-dimensional patterning of this ligand using a soft lithography approach resulted in the spatial control of osteogenesis.</p> <p>Conclusion</p> <p>These data describe an approach that allows the influence of immobilised protein ligands on cell behaviour to be dissected at the molecular level. This approach presents a durable surface that allows both short (hours or days) and long term (weeks) effects on cell activity to be assessed. This widely applicable approach can provide mechanistic insight into the contribution of immobilised ligands in the control of cell activity.</p

Human osteoblasts obtained from distinct periarticular sites demonstrate differences in biological function in vitro.

AIMS: Accumulated evidence indicates that local cell origins may ingrain differences in the phenotypic activity of human osteoblasts. We hypothesized that these differences may also exist in osteoblasts harvested from the same bone type at periarticular sites, including those adjacent to the fixation sites for total joint implant components. METHODS: Human osteoblasts were obtained from the acetabulum and femoral neck of seven patients undergoing total hip arthroplasty (THA) and from the femoral and tibial cuts of six patients undergoing total knee arthroplasty (TKA). Osteoblasts were extracted from the usually discarded bone via enzyme digestion, characterized by flow cytometry, and cultured to passage three before measurement of metabolic activity, collagen production, alkaline phosphatase (ALP) expression, and mineralization. RESULTS: Osteoblasts from the acetabulum showed lower proliferation (p = 0.034), cumulative collagen release (p < 0.001), and ALP expression (p = 0.009), and produced less mineral (p = 0.006) than those from the femoral neck. Osteoblasts from the tibia produced significantly less collagen (p = 0.021) and showed lower ALP expression than those from the distal femur. CONCLUSION: We have demonstrated for the first time an anatomical regional variation in the biological behaviours of osteoblasts on either side of the hip and knee joint. The lower osteoblast proliferation, matrix production, and mineralization from the acetabulum compared to those from the proximal femur may be reflected in differences in bone formation and implant fixation at these sites. Cite this article: Bone Joint Res 2021;10(9):611-618

Preliminary fish survey of Lac Tseny in northwestern Madagascar

We surveyed the fish fauna of Lac Tseny, in the Sofia Region of northwestern Madagascar, during October 2010 by observing commercial catches and targeted netting of areas used by endemic species. We recorded seven native fish species at the lake, including three endemic cichlids, a herring and a catfish. We confirmed the continued survival of the Critically Endangered Paretroplus menarambo, as well as the presence of a Paretroplus taxon that may be new to science. The commercial fishery in the lake is sustained by introduced tilapiines and the native Savagella robusta. The three endemic cichlids (Paretroplus spp.) were not targeted by commercial fishermen, but when caught in small numbers were retained for domestic consumption. Submerged trees in the west of the lake restrict fishing with nets and probably provide important habitat for P. menarambo. Priority next steps at the lake include (i) additional surveys and biological studies of the endemic fish species and the Critically Endangered Madagascar big-headed turtle, Erymnochelys madagascariensis, (ii) clarification of the taxonomic status of Paretroplus cf. kieneri and, should it prove a new taxon, its formal scientific description, and (iii) continued engagement with fishing communities and authorities to promote practices that benefit livelihoods and the survival of threatened fish species.   RÉSUMÉ La composition spécifique de l'ichtyofaune du lac Tseny, dans l'ouest de Madagascar (région de Sofia) a été inventoriée au cours du mois d’octobre 2010, en observant les prises des pêcheurs et des pêches ciblées sur les espèces endémiques. Sept espèces de poissons indigènes ont été observés, dont trois cichlidés endémiques (Paretroplus menarambo, Paretroplus lamenabe et Paretroplus cf. kieneri), un hareng indigène (Sauvagella robusta) et un poisson-chat (Arius madagascariensis). Deux de ces espèces sont classées comme Menacées dans la Liste Rouge de l'UICN : P. menarambo est une espèce en Danger Critique d’Extinction qui n’est connue que du lac Tseny et A. madagascariensis est une espèce en Danger d’Extinction et endémique de la région de Sofia. Un des poissons que nous avons inventorié dans le genre Paretroplus semble être une forme non décrite. Les pêcheurs ont indiqué que P. menarambo est associé à des arbres immergés le long de la rive occidentale du lac qui offrent un habitat propice à la reproduction et à l'alimentation. Ces arbres immergés empêchent l'utilisation des filets pour la pêche et limitent ainsi la pression de pêche qui s’exerce sur cette espèce. Les trois espèces endémiques de Paretroplus sont prisées par les pêcheurs qui les gardent pour leur consommation personnelle plutôt que de les vendre. La pêche commerciale pratiquée dans le lac semble pérenne grâce à la présence de tilapias allogènes et du hareng indigène (Sauvagella robusta) qui approvisionnent les marchés de poisson local (Tsaratanana), régionaux (Boriziny et Mandritsara) et national (Antananarivo). Les populations locales ont rapporté que la surpêche, l'immigration, l’utilisation illégale de filets à petit maillage et le non respect de la saison de fermeture de la pêche étaient les principales menaces pesant sur l’ichtyofaune du lac Tseny. Une baisse de la pêche commerciale pourrait entraîner une ruée vers les espèces endémiques et l'ouverture des zones d’arbres immergés pour la pêche. Le lac Tseny abrite un assemblage unique de poissons qui doivent être protégés dans leur habitat qui est essentiel aux cichlidés endémiques par le maintien d'une pêche commerciale pérenne. Les prochaines étapes à mener en priorité pour le lac incluent : (i) des études supplémentaires sur la biologie des poissons endémiques et de la Podocnémide de Madagascar (Erymnochelys madagascariensis), une tortue en Danger Critique d’Extinction, (ii) la clarification du statut taxinomique de Paretroplus cf. kieneri qui pourrait être une nouvelle espèce et sa description, le cas échéant, et (iii) l’engagement continu avec les communautés de pêcheurs et les autorités locales pour promouvoir des pratiques équitables en faveur des populations riveraines et pour la survie des espèces de poissons menacées

Dynamic contrast-enhanced MRI of synovitis in knee osteoarthritis: repeatability, discrimination and sensitivity to change in a prospective experimental study

OBJECTIVES: Evaluate test-retest repeatability, ability to discriminate between osteoarthritic and healthy participants, and sensitivity to change over 6 months, of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) biomarkers in knee OA. METHODS: Fourteen individuals aged 40-60 with mild-moderate knee OA and 6 age-matched healthy volunteers (HV) underwent DCE-MRI at 3 T at baseline, 1 month and 6 months. Voxelwise pharmacokinetic modelling of dynamic data was used to calculate DCE-MRI biomarkers including Ktrans and IAUC60. Median DCE-MRI biomarker values were extracted for each participant at each study visit. Synovial segmentation was performed using both manual and semiautomatic methods with calculation of an additional biomarker, the volume of enhancing pannus (VEP). Test-retest repeatability was assessed using intraclass correlation coefficients (ICC). Smallest detectable differences (SDDs) were calculated from test-retest data. Discrimination between OA and HV was assessed via calculation of between-group standardised mean differences (SMD). Responsiveness was assessed via the number of OA participants with changes greater than the SDD at 6 months. RESULTS: Ktrans demonstrated the best test-retest repeatability (Ktrans/IAUC60/VEP ICCs 0.90/0.84/0.40, SDDs as % of OA mean 33/71/76%), discrimination between OA and HV (SMDs 0.94/0.54/0.50) and responsiveness (5/1/1 out of 12 OA participants with 6-month change > SDD) when compared to IAUC60 and VEP. Biomarkers derived from semiautomatic segmentation outperformed those derived from manual segmentation across all domains. CONCLUSIONS: Ktrans demonstrated the best repeatability, discrimination and sensitivity to change suggesting that it is the optimal DCE-MRI biomarker for use in experimental medicine studies. KEY POINTS: • Dynamic contrast-enhanced MRI (DCE-MRI) provides quantitative measures of synovitis in knee osteoarthritis which may permit early assessment of efficacy in experimental medicine studies. • This prospective observational study compared DCE-MRI biomarkers across domains relevant to experimental medicine: test-retest repeatability, discriminative validity and sensitivity to change. • The DCE-MRI biomarker Ktrans demonstrated the best performance across all three domains, suggesting that it is the optimal biomarker for use in future interventional studies

Insights into patient preferences for elective surgery during the COVID-19 pandemic.

AIMS: To investigate factors that contribute to patient decisions regarding attendance for arthroplasty during the COVID-19 pandemic. METHODS: A postal questionnaire was distributed to patients on the waiting list for hip or knee arthroplasty in a single tertiary centre within the UK. Patient factors that may have influenced the decision to attend for arthroplasty, global quality of life (QoL) (EuroQol five-dimension three-level (EQ-5D-3L)), and joint-specific QoL (Oxford Hip or Knee Score) were assessed. Patients were asked at which 'COVID-alert' level they would be willing to attend an NHS and a "COVID-light" hospital for arthroplasty. Independent predictors were assessed using multivariate logistic regression. RESULTS: Of 540 distributed questionnaires, 400 (74.1%; 236 awaiting hip arthroplasty, 164 awaiting knee arthroplasty) complete responses were received and included. Less than half (48.2%) were willing to attend for hip or knee arthroplasty while a UK COVID-19 epidemic was in circulation (COVID-alert levels 3 to 5). Patients with worse joint-specific QoL had a preference to proceed with surgery at COVID-alert levels 3 to 5 compared to levels 1 and 2 (hip arthroplasty odds ratio (OR) 1.54 (95% confidence interval (CI) 1.45 to 1.63); knee arthroplasty OR 1.16 (1.07 to 1.26)). The odds of patients with worse joint-specific QoL being willing to attend for surgery at COVID-alert levels 3 to 5 increased further if surgery in a private, "COVID-light" hospital was available (hip arthroplasty OR 3.50 (95% CI 3.26 to 3.71); knee arthroplasty OR 1.41 (95% CI 1.29 to 1.53). CONCLUSION: Patient decisions surrounding elective surgery have been influenced by the global COVID-19 pandemic, highlighting the importance of patient involvement in ensuring optimized provision of elective surgery during these challenging times. Cite this article: Bone Jt Open 2021;2(4):261-270