In Vivo Measurement of Hindlimb Dorsiflexor Isometric Torque from Pig.

Reliable assessment of skeletal muscle strength is arguably the most important outcome measure in neuromuscular and musculoskeletal disease and injury studies, particularly when evaluating regenerative therapies' efficacy. Additionally, a critical aspect of translating many regenerative therapies is the demonstration of scalability and effectiveness in a large animal model. Various physiological preparations have been established to evaluate intrinsic muscle function properties in basic science studies, primarily in small animal models. The practices may be categorized as: in vitro (isolated fibers, fiber bundles, or whole muscle), in situ (muscle with intact vascularization and innervation but distal tendon attached to a force transducer), and in vivo (structures of the muscle or muscle unit remain intact). There are strengths and weaknesses to each of these preparations; however, a clear advantage of in vivo strength testing is the ability to perform repeated measurements in the same animal. Herein, the materials and methods to reliably assess isometric torque produced by the hindlimb dorsiflexor muscles in vivo in response to standard peroneal electrical stimulation in anesthetized pigs are presented.

In vivo Measurement of Knee Extensor Muscle Function in Mice.

Skeletal muscle plasticity in response to countless conditions and stimuli mediates concurrent functional adaptation, both negative and positive. In the clinic and the research laboratory, maximal muscular strength is widely measured longitudinally in humans, with knee extensor musculature the most reported functional outcome. Pathology of the knee extensor muscle complex is well documented in aging, orthopedic injury, disease, and disuse; knee extensor strength is closely related to functional capacity and injury risk, underscoring the importance of reliable measurement of knee extensor strength. Repeatable, in vivo assessment of knee extensor strength in pre-clinical rodent studies offers valuable functional endpoints for studies exploring osteoarthritis or knee injury. We report an in vivo and non-invasive protocol to repeatedly measure isometric peak tetanic torque of the knee extensors in mice across time. We demonstrate consistency using this novel method to measure knee extensor strength with repeated assessment in multiple mice producing similar results.

A novel ex vivo protocol to mimic human walking gait: implications for Duchenne muscular dystrophy.

We developed a novel ex vivo mouse protocol to mimic in vivo human soleus muscle function predicted by musculoskeletal simulations to better understand eccentric contractions during gait and ultimately to better understand their effects in Duchenne muscular dystrophy (DMD) muscles. DMD muscles are susceptible to eccentric injury because the protein dystrophin is absent. The mdx mouse, a DMD model that also lacks dystrophin, is often subjected to ex vivo acute but nonphysiological eccentric injury protocols. It is possible these acute protocols either over- or underestimate eccentric stresses and strains compared with those from humans during gait. To explore this possibility, healthy human soleus excitation, force, and length change profiles during a single walking stride (gait cycle) were simulated using OpenSim and then scaled to an ex vivo mouse soleus preparation based on muscle architectural measurements. Aurora Scientific, Inc., software and a 701C electrical stimulator were modified to discretely modulate muscle stimulation voltage at constant frequency and finely control muscle length changes to produce a force pattern that correctly mimicked the gait cycle from simulations. In a proof-of-principle study, wild-type and mdx mice soleus muscles were subjected to 25 gait cycles. Modest fatigue was evident in the muscles at the 25th versus first gait cycle for both genotypes, but both rapidly recovered isometric force within 1 min of the last cycle. These data indicate that the ex vivo gait protocol was well tolerated. More important, this protocol provides a novel assessment tool to determine the effects of physiological eccentric contractions on dystrophic muscle.NEW & NOTEWORTHY A novel ex vivo mouse soleus protocol that mimics scaled length change and excitation profiles predicted by a mathematical model of human soleus during gait is presented. A custom stimulator was developed that enabled an innovative muscle stimulation technique to modulate voltage to closely match the excitation pattern of human soleus during gait. This ex vivo protocol provides assessment of simulated human movement in mouse muscle, including components of eccentric contractions.

Assembling draft genomes using contiBAIT.

SUMMARY: Massively parallel sequencing is now widely used, but data interpretation is only as good as the reference assembly to which it is aligned. While the number of reference assemblies has rapidly expanded, most of these remain at intermediate stages of completion, either as scaffold builds, or as chromosome builds (consisting of correctly ordered, but not necessarily correctly oriented scaffolds separated by gaps). Completion of de novo assemblies remains difficult, as regions that are repetitive or hard to sequence prevent the accumulation of larger scaffolds, and create errors such as misorientations and mislocalizations. Thus, complementary methods for determining the orientation and positioning of fragments are important for finishing assemblies. Strand-seq is a method for determining template strand inheritance in single cells, information that can be used to determine relative genomic distance and orientation between scaffolds, and find errors within them. We present contiBAIT, an R/Bioconductor package which uses Strand-seq data to repair and improve existing assemblies. AVAILABILITY AND IMPLEMENTATION: contiBAIT is available on Bioconductor. Source files available from GitHub. CONTACT: koneill@bcgsc.ca or mark.hills@stemcell.com. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Auxin gradients are associated with polarity changes in trees.

Models of plant growth and development propose that changes in cell polarity are mediated by gradients of the plant hormone auxin. With use of gas chromatography-mass spectrometry, we measured the redistribution of endogenous auxin in stems of quaking aspen trees (Populus tremuloides) after wounding. Persistent (lasting at least 24 hours) auxin gradients were observed in the region of the cambium where cell polarity was changing. A computer model of the auxin redistribution shows agreement with measured concentrations.