The Complete Genome of Teredinibacter turnerae T7901: An Intracellular Endosymbiont of Marine Wood-Boring Bivalves (Shipworms)

Here we report the complete genome sequence of Teredinibacter turnerae T7901. T. turnerae is a marine gamma proteobacterium that occurs as an intracellular endosymbiont in the gills of wood-boring marine bivalves of the family Teredinidae (shipworms). This species is the sole cultivated member of an endosymbiotic consortium thought to provide the host with enzymes, including cellulases and nitrogenase, critical for digestion of wood and supplementation of the host's nitrogen-deficient diet. T. turnerae is closely related to the free-living marine polysaccharide degrading bacterium Saccharophagus degradans str. 2–40 and to as yet uncultivated endosymbionts with which it coexists in shipworm cells. Like S. degradans, the T. turnerae genome encodes a large number of enzymes predicted to be involved in complex polysaccharide degradation (>100). However, unlike S. degradans, which degrades a broad spectrum (>10 classes) of complex plant, fungal and algal polysaccharides, T. turnerae primarily encodes enzymes associated with deconstruction of terrestrial woody plant material. Also unlike S. degradans and many other eubacteria, T. turnerae dedicates a large proportion of its genome to genes predicted to function in secondary metabolism. Despite its intracellular niche, the T. turnerae genome lacks many features associated with obligate intracellular existence (e.g. reduced genome size, reduced %G+C, loss of genes of core metabolism) and displays evidence of adaptations common to free-living bacteria (e.g. defense against bacteriophage infection). These results suggest that T. turnerae is likely a facultative intracellular ensosymbiont whose niche presently includes, or recently included, free-living existence. As such, the T. turnerae genome provides insights into the range of genomic adaptations associated with intracellular endosymbiosis as well as enzymatic mechanisms relevant to the recycling of plant materials in marine environments and the production of cellulose-derived biofuels

The Complete Genome of \u3cem\u3eTeredinibacter turnerae\u3c/em\u3e T7901: An Intracellular Endosymbiont of Marine Wood-Boring Bivalves (Shipworms)

Here we report the complete genome sequence of Teredinibacter turnerae T7901. T. turnerae is a marine gamma proteobacterium that occurs as an intracellular endosymbiont in the gills of wood-boring marine bivalves of the family Teredinidae (shipworms). This species is the sole cultivated member of an endosymbiotic consortium thought to provide the host with enzymes, including cellulases and nitrogenase, critical for digestion of wood and supplementation of the host\u27s nitrogen-deficient diet. T. turnerae is closely related to the free-living marine polysaccharide degrading bacterium Saccharophagus degradans str. 2–40 and to as yet uncultivated endosymbionts with which it coexists in shipworm cells. Like S. degradans, the T. turnerae genome encodes a large number of enzymes predicted to be involved in complex polysaccharide degradation (\u3e100). However, unlike S. degradans, which degrades a broad spectrum (\u3e10 classes) of complex plant, fungal and algal polysaccharides, T. turnerae primarily encodes enzymes associated with deconstruction of terrestrial woody plant material. Also unlike S. degradans and many other eubacteria, T. turnerae dedicates a large proportion of its genome to genes predicted to function in secondary metabolism. Despite its intracellular niche, the T. turnerae genome lacks many features associated with obligate intracellular existence (e.g. reduced genome size, reduced %G+C, loss of genes of core metabolism) and displays evidence of adaptations common to free-living bacteria (e.g. defense against bacteriophage infection). These results suggest that T. turnerae is likely a facultative intracellular ensosymbiont whose niche presently includes, or recently included, free-living existence. As such, the T. turnerae genome provides insights into the range of genomic adaptations associated with intracellular endosymbiosis as well as enzymatic mechanisms relevant to the recycling of plant materials in marine environments and the production of cellulose-derived biofuels

A framework for evolutionary systems biology

<p>Abstract</p> <p>Background</p> <p>Many difficult problems in evolutionary genomics are related to mutations that have weak effects on fitness, as the consequences of mutations with large effects are often simple to predict. Current systems biology has accumulated much data on mutations with large effects and can predict the properties of knockout mutants in some systems. However experimental methods are too insensitive to observe small effects.</p> <p>Results</p> <p>Here I propose a novel framework that brings together evolutionary theory and current systems biology approaches in order to quantify small effects of mutations and their epistatic interactions <it>in silico</it>. Central to this approach is the definition of fitness correlates that can be computed in some current systems biology models employing the rigorous algorithms that are at the core of much work in computational systems biology. The framework exploits synergies between the realism of such models and the need to understand real systems in evolutionary theory. This framework can address many longstanding topics in evolutionary biology by defining various 'levels' of the adaptive landscape. Addressed topics include the distribution of mutational effects on fitness, as well as the nature of advantageous mutations, epistasis and robustness. Combining corresponding parameter estimates with population genetics models raises the possibility of testing evolutionary hypotheses at a new level of realism.</p> <p>Conclusion</p> <p>EvoSysBio is expected to lead to a more detailed understanding of the fundamental principles of life by combining knowledge about well-known biological systems from several disciplines. This will benefit both evolutionary theory and current systems biology. Understanding robustness by analysing distributions of mutational effects and epistasis is pivotal for drug design, cancer research, responsible genetic engineering in synthetic biology and many other practical applications.</p

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

How do dislocation rates differ between different approaches to total hip arthroplasty? A systematic review and meta-analysis

Background: Different surgical approaches for total hip arthroplasty (THA) exist, without predisposition when it comes to dislocation risk. The direct anterior approach (DAA) is thought to have reduced risk since soft tissue trauma is minimalized. Therefore, we assessed the dislocation risk for different surgical approaches, and the relative dislocation risk of DAA compared to other approaches. Methods: Six electronic databases were systematically searched for prospective studies reporting dislocation following THA. Proportion meta-analyses were performed to assess the dislocation rate for subgroups of the surgical approach. Meta-analysis for binary outcomes was performed to determine the relative risk of dislocation for the DAA compared to other approaches. Results: Eleven studies with 2025 patients were included (mean age 64.6 years, 44% male, mean follow-up 10.5 months), of which four studies were also used in the risk ratio meta-analysis. Overall dislocation rate was 0.79% (95% CI 0.37–1.69). Subgroup analyses showed that most dislocations occurred in the posterior approaches group (1.38%), however non-significant. Furthermore, the DAA emerged with a non-significant lower risk of dislocation (RR 0.37, 95% CI 0.05–2.46) compared to other surgical approaches. Conclusion: Current literature shows non-significant predisposition for a surgical approach to THA regarding dislocation risk. To what extent patient characteristics influence the risk of dislocation could not be determined. Future research should focus on this, as well as on the influence of a surgeon's experience with a specific approach

System identification: a feasible, reliable and valid way to quantify upper limb motor impairments

Abstract Background Upper limb impairments in a hemiparetic arm are clinically quantified by well-established clinical scales, known to suffer poor validity, reliability, and sensitivity. Alternatively, robotics can assess motor impairments by characterizing joint dynamics through system identification. In this study, we establish the merits of quantifying abnormal synergy, spasticity, and changes in joint viscoelasticity using system identification, evaluating (1) feasibility and quality of parametric estimates, (2) test–retest reliability, (3) differences between healthy controls and patients with upper limb impairments, and (4) construct validity. Methods Forty-five healthy controls, twenty-nine stroke patients, and twenty cerebral palsy patients participated. Participants were seated with the affected arm immobilized in the Shoulder-Elbow-Perturbator (SEP). The SEP is a one-degree-of-freedom perturbator that enables applying torque perturbations to the elbow while providing varying amounts of weight support to the human arm. Participants performed either a ‘do not intervene’ or a resist task. Elbow joint admittance was quantified and used to extract elbow viscosity and stiffness. Fifty-four of the participants performed two sessions to establish the test–retest reliability of the parameters. Construct validity was assessed by correlating system identification parameters to parameters extracted using a SEP protocol that objectifies current clinical scales (Re-Arm protocol). Results Feasibility was confirmed by all participants successfully completing the study protocol within ~ 25 min without reporting pain or burden. The parametric estimates were good with a variance-accounted-for of ~ 80%. A fair to excellent test–retest reliability was found ( $$ICC = 0.46-0.98$$ I C C = 0.46 - 0.98 ) for patients, except for elbow stiffness with full weight support ( $$ICC = 0.35$$ I C C = 0.35 ). Compared to healthy controls, patients had a higher elbow viscosity and stiffness during the ‘do not intervene’ task and lower viscosity and stiffness during the resist task. Construct validity was confirmed by a significant (all $$p<0.03$$ p < 0.03 ) but weak to moderate ( $$r = 0.36-0.50$$ r = 0.36 - 0.50 ) correlation with parameters from the Re-Arm protocol. Conclusions This work demonstrates that system identification is feasible and reliable for quantifying upper limb motor impairments. Validity was confirmed by differences between patients and controls and correlations with other measurements, but further work is required to optimize the experimental protocol and establish clinical value

Wheelchair Shuttle Test for Assessing Aerobic Fitness in Youth With Spina Bifida : Validity and Reliability

Background: Testing aerobic fitness in youth is important because of expected relationships with health. Objective: The purpose of the study was to estimate the validity and reliability of the Shuttle Ride Test in youth who have spina bifida and use a wheelchair for mobility and sport. Design: Ths study is a validity and reliability study. Methods: The Shuttle Ride Test, Graded Wheelchair Propulsion Test, and skill-related fitness tests were administered to 33 participants for the validity study (age = 14.5 ± 3.1 y) and to 28 participants for the reliability study (age = 14.7 ± 3.3 y). Results: No significant differences were found between the Graded Wheelchair Propulsion Test and the Shuttle Ride Test for most cardiorespiratory responses. Correlations between the Graded Wheelchair Propulsion Test and the Shuttle Ride Test were moderate to high (r = .55-.97). The variance in peak oxygen uptake (VO2peak) could be predicted for 77% of the participants by height, number of shuttles completed, and weight, with large prediction intervals. High correlations were found between number of shuttles completed and skill-related fitness tests (CI = .73 to -.92). Intraclass correlation coefficients were high (.77-.98), with a smallest detectable change of 1.5 for number of shuttles completed and with coefficients of variation of 6.2% and 6.4% for absolute VO2peak and relative VO2peak, respectively. Conclusions: When measuring VO2peak directly by using a mobile gas analysis system, the Shuttle Ride Test is highly valid for testing VO2peak in youth who have spina bifida and use a wheelchair for mobility and sport. The outcome measure of number of shuttles represents aerobic fitness and is also highly correlated with both anaerobic performance and agility. It is not possible to predict VO2peak accurately by using the number of shuttles completed. Moreover, the Shuttle Ride Test is highly reliable in youth with spina bifida, with a good smallest detectable change for the number of shuttles completed

Wheelchair Shuttle Test for Assessing Aerobic Fitness in Youth With Spina Bifida : Validity and Reliability

Background: Testing aerobic fitness in youth is important because of expected relationships with health. Objective: The purpose of the study was to estimate the validity and reliability of the Shuttle Ride Test in youth who have spina bifida and use a wheelchair for mobility and sport. Design: Ths study is a validity and reliability study. Methods: The Shuttle Ride Test, Graded Wheelchair Propulsion Test, and skill-related fitness tests were administered to 33 participants for the validity study (age = 14.5 ± 3.1 y) and to 28 participants for the reliability study (age = 14.7 ± 3.3 y). Results: No significant differences were found between the Graded Wheelchair Propulsion Test and the Shuttle Ride Test for most cardiorespiratory responses. Correlations between the Graded Wheelchair Propulsion Test and the Shuttle Ride Test were moderate to high (r = .55-.97). The variance in peak oxygen uptake (VO2peak) could be predicted for 77% of the participants by height, number of shuttles completed, and weight, with large prediction intervals. High correlations were found between number of shuttles completed and skill-related fitness tests (CI = .73 to -.92). Intraclass correlation coefficients were high (.77-.98), with a smallest detectable change of 1.5 for number of shuttles completed and with coefficients of variation of 6.2% and 6.4% for absolute VO2peak and relative VO2peak, respectively. Conclusions: When measuring VO2peak directly by using a mobile gas analysis system, the Shuttle Ride Test is highly valid for testing VO2peak in youth who have spina bifida and use a wheelchair for mobility and sport. The outcome measure of number of shuttles represents aerobic fitness and is also highly correlated with both anaerobic performance and agility. It is not possible to predict VO2peak accurately by using the number of shuttles completed. Moreover, the Shuttle Ride Test is highly reliable in youth with spina bifida, with a good smallest detectable change for the number of shuttles completed