Biomechanics of the rabbit knee and ankle: muscle, ligament, and joint contact force predictions

Mathematical models of small animals that predict in vivo forces acting on the lower extremities are critical for studies of musculoskeletal biomechanics and diseases. Rabbits are advantageous in this regard because they remodel their cortical bone similar to humans. Here, we enhance a recent mathematical model of the rabbit knee joint to include the loading behavior of individual muscles, ligaments, and joint contact at the knee and ankle during the stance phase of hopping. Geometric data from the hindlimbs of three adult New Zealand white rabbits, combined with previously reported intersegmental forces and moments, were used as inputs to the model. Muscle, ligament, and joint contact forces were computed using optimization techniques assuming that muscle endurance is maximized and ligament strain energy resists tibial shear force along an inclined plateau. Peak forces developed by the quadriceps and gastrocnemius muscle groups and by compressive knee contact were within the range of theoretical and in vivo predictions. Although a minimal force was carried by the anterior cruciate and medial collateral ligaments, force patterns in the posterior cruciate ligament were consistent with in vivo tibial displacement patterns during hopping in rabbits. Overall, our predictions compare favorably with theoretical estimates and in vivo measurements in rabbits, and enhance previous models by providing individual muscle, ligament, and joint contact information to predict in vivo forces acting on the lower extremities in rabbits.     

Facile and efficient assembly of collagen-like triple helices on a TRIS scaffold

The TRIS scaffold, Boc-beta-Ala-TRIS-(OH)3, was utilized to assemble triple helices composed of the Gly-Nleu-Pro sequence (Nleu denotes N-isobutylglycine). The scaffold assembly can be achieved efficiently through direct coupling between long peptide chains and the TRIS scaffold using DEPBT, a recently developed peptide coupling reagent. CD spectroscopy and thermal denaturation studies demonstrated that Boc-beta-Ala-TRIS-[(Gly-Nleu-Pro)n-OMe]3 exhibits triple helicity in H2O when n equals 5, 6, and 8, while the shorter analogs (where n=1 and 4) do not. TRIS-assembled structures possess several advantages over the KTA- and TREN-assembled structures previously reported from our laboratory (where KTA and TREN denotes cis-1,3,5-trimethyl cyclohexane-1,3,5-tricarboxylic acid and tris(2-aminoethyl)amine, respectively). The protecting groups on the scaffold and at the C-terminus of the TRIS-assembled peptides can be readily removed to synthesize collagen mimetic dendrimers and metal-complexing collagen-like peptides respectively, both of which can lead to further enhanced thermal stability.     

THE QUICK AND THE DEAD? SPERM COMPETITION AND SEXUAL CONFLICT IN SEA

Our view of sperm competition is largely shaped by game-theoretic models based on external fertilizers. External fertilization is of particular interest as it is the ancestral mode of reproduction and as such, relevant to the evolution and maintenance of anisogamy (i.e., large eggs and tiny, numerous sperm). Current game-theoretic models have been invaluable in generating predictions of male responses to sperm competition in a range of internal fertilizers but these models are less relevant to marine broadcast spawners, the most common and archetypal external fertilizers. Broadcast spawners typically have incomplete fertilization due to sperm limitation and/or polyspermy (too many sperm), but the effects of incomplete (<100% fertilization rates) fertilization on game-theoretic predictions are unclear particular with regards to polyspermy. We show that incorporating the effects of sperm concentration on fertilization success changes the predictions of a classic game-theoretic model, dramatically reversing the relationship between sperm competition and the evolutionarily stable sperm release strategy. Furthermore, our results suggest that male and female broadcast spawners are likely to be in conflict at both ends of the sperm environment continuum rather than only in conditions of excess sperm as previously thought. Across the majority of the parameter space we explored, males release either too little to too much sperm for females to achieve complete fertilization. This conflict could result in a coevolutionary race that may have led to the evolution of internal fertilization in marine organisms.     

Chronic Inflammation Permanently Reshapes Tissue-Resident Immunity in Celiac Disease

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Molecular Classification and Comparative Taxonomics of Foveal and Peripheral Cells in Primate Retina

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TERAD: Extraction of transposable element composition from RADseq data

Transposable elements (TEs) – selfish DNA sequences that can move within the genome – comprise a large proportion of the genomes of many organisms. Although low‐coverage whole‐genome sequencing can be used to survey TE composition, it is noneconomical for species with large quantities of DNA. Here, we utilize restriction‐site associated DNA sequencing (RADSeq) as an alternative method to survey TE composition. First, we demonstrate in silico that double digest restriction‐site associated DNA sequencing (ddRADseq) markers contain the same TE compositions as whole genome assemblies across arthropods. Next, we show empirically using eight Synalpheus snapping shrimp species with large genomes that TE compositions from ddRADseq and low‐coverage whole‐genome sequencing are comparable within and across species. Finally, we develop a new bioinformatic pipeline, TERAD, to extract TE compositions from RADseq data. Our study expands the utility of RADseq to study the repeatome, making comparative studies of genome structure for species with large genomes more tractable and affordable.     

To burn or not to burn: Comparing reintroducing fire with cutting an encroaching conifer for conservation of an imperiled shrub‐steppe

Woody vegetation has increased on rangelands worldwide for the past 100–200 years, often because of reduced fire frequency. However, there is a general aversion to reintroducing fire, and therefore, fire surrogates are often used in its place to reverse woody plant encroachment. Determining the conservation effectiveness of reintroducing fire compared with fire surrogates over different time scales is needed to improve conservation efforts. We evaluated the conservation effectiveness of reintroducing fire with a fire surrogate (cutting) applied over the last ~30 years to control juniper (Juniperus occidentalis Hook.) encroachment on 77 sagebrush‐steppe sites. Critical to conservation of this imperiled ecosystem is to limit juniper, not encourage exotic annual grasses, and promote sagebrush dominance of the overstory. Reintroducing fire was more effective than cutting at reducing juniper abundance and extending the period of time that juniper was not dominating the plant community. Sagebrush was reduced more with burning than cutting. Sagebrush, however, was predicted to be a substantial component of the overstory longer in burned than cut areas because of more effective juniper control. Variation in exotic annual grass cover was explained by environmental variables and perennial grass abundance, but not treatment, with annual grasses being problematic on hotter and drier sites with less perennial grass. This suggests that ecological memory varies along an environmental gradient. Reintroducing fire was more effective than cutting at conserving sagebrush‐steppe encroached by juniper over extended time frames; however, cutting was more effective for short‐term conservation. This suggests fire and fire surrogates both have critical roles in conservation of imperiled ecosystems.     

Recent and rapid population growth and range expansion of the Lyme disease tick vector,Ixodes scapularis,in North America

Migration is a primary force of biological evolution that alters allele frequencies and introduces novel genetic variants into populations. Recent migration has been proposed as the cause of the emergence of many infectious diseases, including those carried by blacklegged ticks in North America. Populations of blacklegged ticks have established and flourished in areas of North America previously thought to be devoid of this species. The recent discovery of these populations of blacklegged ticks may have resulted from either in situ growth of long‐established populations that were maintained at very low densities or by migration and colonization from established populations. These alternative evolutionary hypotheses were investigated using Bayesian phylogeographic approaches to infer the origin and migratory history of recently detected blacklegged tick populations in the Northeastern United States. The data and results indicate that newly detected tick populations are not the product of in situ population growth from a previously established population but from recent colonization resulting in a geographic range expansion. This expansion in the geographic range proceeded primarily through progressive and local migration events from southern populations to proximate northern locations although long‐distance migration events were also detected.     

Convergent Evolution in the Assembly of Polyubiquitin Degradation Signals by the Shigella flexneri IpaH9.8 Ligase

The human pathogen Shigella flexneri subverts host function and defenses by deploying a cohort of effector proteins via a type III secretion system. The IpaH family of 10 such effectors mimics ubiquitin ligases but bears no sequence or structural homology to their eukaryotic counterpoints. Using rates of ¹²⁵I-polyubiquitin chain formation as a functional read out, IpaH9.8 displays V-type positive cooperativity with respect to varying concentrations of its Ubc5B∼¹²⁵I-ubiquitin thioester co-substrate in the nanomolar range ([S]_½ = 140 ± 32 nm; n = 1.8 ± 0.1) and cooperative substrate inhibition at micromolar concentrations ([S]_½ = 740 ± 240 nm; n = 1.7 ± 0.2), requiring ordered binding to two functionally distinct sites per subunit. The isosteric substrate analog Ubc5BC85S-ubiquitin oxyester acts as a competitive inhibitor of wild-type Ubc5B∼¹²⁵I-ubiquitin thioester (K_i = 117 ± 29 nm), whereas a Ubc5BC85A product analog shows noncompetitive inhibition (K_i = 2.2 ± 0.5 μm), consistent with the two-site model. Re-evaluation of a related IpaH3 crystal structure (PDB entry 3CVR) identifies a symmetric dimer consistent with the observed cooperativity. Genetic disruption of the predicted IpaH9.8 dimer interface reduces the solution molecular weight and significantly ablates the k_cat but not [S]_½ for polyubiquitin chain formation. Other studies demonstrate that cooperativity requires the N-terminal leucine-rich repeat-targeting domain and is transduced through Phe³⁹⁵. Additionally, these mechanistic features are conserved in a distantly related SspH2 Salmonella enterica ligase. Kinetic parallels between IpaH9.8 and the recently revised mechanism for E6AP/UBE3A (Ronchi, V. P., Klein, J. M., and Haas, A. L. (2013) E6AP/UBE3A ubiquitin ligase harbors two E2∼ubiquitin binding sites. J. Biol. Chem. 288, 10349–10360) suggest convergent evolution of the catalytic mechanisms for prokaryotic and eukaryotic ligases.