Does a crouched leg posture enhance running stability and robustness?

Humans and birds both walk and run bipedally on compliant legs. However, differences in leg architecture may result in species-specific leg control strategies as indicated by the observed gait patterns. In this work, control strategies for stable running are derived based on a conceptual model and compared with experimental data on running humans and pheasants (Phasianus colchicus). From a model perspective, running with compliant legs can be represented by the planar spring mass model and stabilized by applying swing leg control. Here, linear adaptations of the three leg parameters, leg angle, leg length and leg stiffness during late swing phase are assumed. Experimentally observed kinematic control parameters (leg rotation and leg length change) of human and avian running are compared, and interpreted within the context of this model, with specific focus on stability and robustness characteristics. The results suggest differences in stability characteristics and applied control strategies of human and avian running, which may relate to differences in leg posture (straight leg posture in humans, and crouched leg posture in birds). It has been suggested that crouched leg postures may improve stability. However, as the system of control strategies is overdetermined, our model findings suggest that a crouched leg posture does not necessarily enhance running stability. The model also predicts different leg stiffness adaptation rates for human and avian running, and suggests that a crouched avian leg posture, which is capable of both leg shortening and lengthening, allows for stable running without adjusting leg stiffness. In contrast, in straight-legged human running, the preparation of the ground contact seems to be more critical, requiring leg stiffness adjustment to remain stable. Finally, analysis of a simple robustness measure, the normalized maximum drop, suggests that the crouched leg posture may provide greater robustness to changes in terrain height.     

Task-Level Strategies for Human Sagittal-Plane Running Maneuvers Are Consistent with Robotic Control Policies

The strategies that humans use to control unsteady locomotion are not well understood. A “spring-mass” template comprised of a point mass bouncing on a sprung leg can approximate both center of mass movements and ground reaction forces during running in humans and other animals. Legged robots that operate as bouncing, “spring-mass” systems can maintain stable motion using relatively simple, distributed feedback rules. We tested whether the changes to sagittal-plane movements during five running tasks involving active changes to running height, speed, and orientation were consistent with the rules used by bouncing robots to maintain stability. Changes to running height were associated with changes to leg force but not stance duration. To change speed, humans primarily used a “pogo stick” strategy, where speed changes were associated with adjustments to fore-aft foot placement, and not a “unicycle” strategy involving systematic changes to stance leg hip moment. However, hip moments were related to changes to body orientation and angular speed. Hip moments could be described with first order proportional-derivative relationship to trunk pitch. Overall, the task-level strategies used for body control in humans were consistent with the strategies employed by bouncing robots. Identification of these behavioral strategies could lead to a better understanding of the sensorimotor mechanisms that allow for effective unsteady locomotion.     

Inhibition of nonsense-mediated decay rescues p53β/γ isoform expression and activates the p53 pathway in MDM2-overexpressing and select p53-mutant cancers

Inactivation of p53 is present in almost every tumor, and hence, p53-reactivation strategies are an important aspect of cancer therapy. Common mechanisms for p53 loss in cancer include expression of p53-negative regulators such as MDM2, which mediate the degradation of wildtype p53 (p53α), and inactivating mutations in the TP53 gene. Currently, approaches to overcome p53 deficiency in these cancers are limited. Here, using non–small cell lung cancer and glioblastoma multiforme cell line models, we show that two alternatively spliced, functional truncated isoforms of p53 (p53β and p53γ, comprising exons 1 to 9β or 9γ, respectively) and that lack the C-terminal MDM2-binding domain have markedly reduced susceptibility to MDM2-mediated degradation but are highly susceptible to nonsense-mediated decay (NMD), a regulator of aberrant mRNA stability. In cancer cells harboring MDM2 overexpression or TP53 mutations downstream of exon 9, NMD inhibition markedly upregulates p53β and p53γ and restores activation of the p53 pathway. Consistent with p53 pathway activation, NMD inhibition induces tumor suppressive activities such as apoptosis, reduced cell viability, and enhanced tumor radiosensitivity, in a relatively p53-dependent manner. In addition, NMD inhibition also inhibits tumor growth in a MDM2-overexpressing xenograft tumor model. These results identify NMD inhibition as a novel therapeutic strategy for restoration of p53 function in p53-deficient tumors bearing MDM2 overexpression or p53 mutations downstream of exon 9, subgroups that comprise approximately 6% of all cancers.     

An Experimental Study on the Gait Patterns and Kinematics of Chinese Mitten Crabs

Despite the many studies on eight-legged animals and the importance of their mechanics of terrestrial locomotion, the mechanical energy of crabs in voluntary locomotion on uneven, unpredictable terrain surfaces has received little attention thus far. In this paper, motion video images of Chinese mitten crab (Eriocheir sinensis Milne-Edwards) locomotion on five types of terrains were recorded using a high-speed three-dimensional (3D) recording video system. The typical variables of locomotion such as gait patterns, duty factor, mechanical energy of the mass center, mass-specific rate of the total mechanical power of the mass center, and percentage recovery, were analyzed. Results show that the Chinese mitten crab uses random gaits instead of the alternating tetrapod gait with the increasing terrain roughness. The duty factors of the rows of the leading legs are greater for all terrains than those of the rows of the trailing legs. On smooth terrain, the duty factors of the rows of the trailing legs are greater than that on rough terrains. Kinematic measurements and calculations reveal that similar to mammals, birds, and arthropods, the Chinese mitten crab uses two fundamental gaits to save mechanical energy: the inverted pendulum gait and the bouncing gait. The bouncing gait is the main pattern of mechanical energy conservation. The low probability of injury and energy expenditure due to adaptations to various terrains induce the Chinese mitten crab to modify the mass-specific rate of the total mechanical power of the mass center. The statistical results of percentage recovery also reveal that the Chinese mitten crab has lower energy recovery efficiency over rough terrains compared with smooth terrains.     

People Bouncing on Trampolines: Dramatic Energy Transfer,a Table-Top Demonstration,Complex Dynamics and a Zero Sum Game

Jumping on trampolines is a popular backyard recreation. In some trampoline games (e.g., “seat drop war”), when two people land on the trampoline with only a small time-lag, one person bounces much higher than the other, as if energy has been transferred from one to the other. First, we illustrate this energy-transfer in a table-top demonstration, consisting of two balls dropped onto a mini-trampoline, landing almost simultaneously, sometimes resulting in one ball bouncing much higher than the other. Next, using a simple mathematical model of two masses bouncing passively on a massless trampoline with no dissipation, we show that with specific landing conditions, it is possible to transfer all the kinetic energy of one mass to the other through the trampoline – in a single bounce. For human-like parameters, starting with equal energy, the energy transfer is maximal when one person lands approximately when the other is at the bottom of her bounce. The energy transfer persists even for very stiff surfaces. The energy-conservative mathematical model exhibits complex non-periodic long-term motions. To complement this passive bouncing model, we also performed a game-theoretic analysis, appropriate when both players are acting strategically to steal the other player''s energy. We consider a zero-sum game in which each player''s goal is to gain the other player''s kinetic energy during a single bounce, by extending her leg during flight. For high initial energy and a symmetric situation, the best strategy for both subjects (minimax strategy and Nash equilibrium) is to use the shortest available leg length and not extend their legs. On the other hand, an asymmetry in initial heights allows the player with more energy to gain even more energy in the next bounce. Thus synchronous bouncing unstable is unstable both for passive bouncing and when leg lengths are controlled as in game-theoretic equilibria.     

Why Do More Divergent Sequences Produce Smaller Nonsynonymous/Synonymous Rate Ratios in Pairwise Sequence Comparisons?

Several studies have reported a negative correlation between estimates of the nonsynonymous to synonymous rate ratio (ω = d_N/d_S) and the sequence distance d in pairwise comparisons of the same gene from different species. That is, more divergent sequences produce smaller estimates of ω. Explanations for this negative correlation have included segregating nonsynonymous polymorphisms in closely related species and nonlinear dynamics of the ratio of two random variables. Here we study the statistical properties of the maximum-likelihood estimates of ω and d in pairwise alignments and explore the possibility that the negative correlation can be entirely explained by those properties. We show that the ω estimate is positively biased for small d and that the bias decreases with the increase of d. We also show that the estimates of ω and d are negatively correlated when ω < 1 and positively correlated when ω > 1. However, the bias in estimates of ω and the correlation between estimates of ω and d are not enough to explain the much stronger correlation observed in real data sets. We then explore the behavior of the estimates when the model is misspecified and suggest that the observed correlation may be due to protein-level selection that causes very different amino acids to be favored in different domains of the protein. Widely used models fail to account for such among-site heterogeneity and cause underestimation of the nonsynonymous rate and ω, with the bias being much stronger for distant sequences. We point out that tests of positive selection based on the ω ratio are invariant to the parameterization of the model and thus unaffected by bias in the ω estimates or the correlation between estimates of ω and d.     

NADPH–Cytochrome P450 Reductase Mediates the Fatty Acid Desaturation of ω3 and ω6 Desaturases from Mortierella alpina

Fatty acid desaturases play an important role in maintaining the appropriate structure and function of biological membranes. The biochemical characterization of integral membrane desaturases, particularly ω3 and ω6 desaturases, has been limited by technical difficulties relating to the acquisition of large quantities of purified proteins, and by the fact that functional activities of these proteins were only tested in an NADH-initiated reaction system. The main aim of this study was to reconstitute an NADPH-dependent reaction system in vitro and investigate the kinetic properties of Mortierella alpina ω3 and ω6 desaturases in this system. After expression and purification of the soluble catalytic domain of NADPH–cytochrome P450 reductase, the NADPH-dependent fatty acid desaturation was reconstituted for the first time in a system containing NADPH, NADPH–cytochrome P450 reductase, cytochrome b5, M. alpina ω3 and ω6 desaturase and detergent. In this system, the maximum activity of ω3 and ω6 desaturase was 213.4 ± 9.0 nmol min⁻¹ mg⁻¹ and 10.0 ± 0.5 nmol min⁻¹ mg⁻¹, respectively. The highest k_cat/K_m value of ω3 and ω6 desaturase was 0.41 µM⁻¹ min⁻¹ and 0.09 µM⁻¹ min⁻¹ when using linoleoyl CoA (18:2 ω6) and oleoyl CoA (18:1 ω9) as substrates, respectively. M. alpina ω3 and ω6 desaturases were capable of using NADPH as reductant when mediated by NADPH–cytochrome P450 reductase; although, their efficiency is distinguishable from NADH-dependent desaturation. These results provide insights into the mechanisms underlying ω3 and ω6 fatty acid desaturation and may facilitate the production of important fatty acids in M. alpina.     

Leg Regrowth in Blaberus discoidalis (Discoid Cockroach) following Limb Autotomy versus Limb Severance and Relevance to Neurophysiology Experiments

Background

Many insects can regenerate limbs, but less is known about the regrowth process with regard to limb injury type. As part of our neurophysiology education experiments involving the removal of a cockroach leg, 1) the ability of Blaberus discoidalis cockroaches to regenerate a metathoracic leg was examined following autotomy at the femur/trochanter joint versus severance via a transverse coxa-cut, and 2) the neurophysiology of the detached legs with regard to leg removal type was studied by measuring spike firing rate and microstimulation movement thresholds.

Leg Regrowth Results

First appearance of leg regrowth was after 5 weeks in the autotomy group and 12 weeks in the coxa-cut group. Moreover, regenerated legs in the autotomy group were 72% of full size on first appearance, significantly larger (p<0.05) than coxa-cut legs (29% of full size at first appearance). Regenerated legs in both groups grew in size with each subsequent molt; the autotomy-removed legs grew to full size within 18 weeks, whereas coxa-cut legs took longer than 28 weeks to regrow. Removal of the metathoracic leg in both conditions did not have an effect on mortality compared to matched controls with unmolested legs.

Neurophysiology Results

Autotomy-removed legs had lower spontaneous firing rates, similar marked increased firing rates upon tactile manipulation of tibial barbs, and a 10% higher electrical microstimulation threshold for movement.

Summary

It is recommended that neurophysiology experiments on cockroach legs remove the limb at autotomy joints instead of coxa cuts, as the leg regenerates significantly faster when autotomized and does not detract from the neurophysiology educational content.     

Beyond arbitrium: identification of a second communication system in Bacillus phage phi3T that may regulate host defense mechanisms

The evolutionary stability of temperate bacteriophages at low abundance of susceptible bacterial hosts lies in the trade-off between the maximization of phage replication, performed by the host-destructive lytic cycle, and the protection of the phage-host collective, enacted by lysogeny. Upon Bacillus infection, Bacillus phages phi3T rely on the “arbitrium” quorum sensing (QS) system to communicate on their population density in order to orchestrate the lysis-to-lysogeny transition. At high phage densities, where there may be limited host cells to infect, lysogeny is induced to preserve chances of phage survival. Here, we report the presence of an additional, host-derived QS system in the phi3T genome, making it the first known virus with two communication systems. Specifically, this additional system, coined “Rapφ-Phrφ”, is predicted to downregulate host defense mechanisms during the viral infection, but only upon stress or high abundance of Bacillus cells and at low density of population of the phi3T phages. Post-lysogenization, Rapφ-Phrφ is also predicted to provide the lysogenized bacteria with an immediate fitness advantage: delaying the costly production of public goods while nonetheless benefiting from the public goods produced by other non-lysogenized Bacillus bacteria. The discovered “Rapφ-Phrφ” QS system hence provides novel mechanistic insights into how phage communication systems could contribute to the phage-host evolutionary stability.Subject terms: Bacteriophages, Viral genetics     

GEOTROPIC ORIENTATION IN ARTHROPODS : II. TETRAOPES.

The creeping of the beetle Tetraopes tetraopthalmus during negatively geotropic orientation shows the angles of orientation (θ) on a surface inclined at α° to the horizontal to be proportional to sin α. The direction of orientation easily suffers temporary reversal to positive as result of handling. Mechanical stability during upward progression should be just possible when K ₁ cot α = K ₂ sin θ + K ₃ cos θ, the weight of the body being supported on the tripod formed by the legs on either side and by the posterior tip of the abdomen. Lack of this stability produces tensions on the legs through (1) the bilaterally distributed pull of the body mass on the legs, and (2) the torque on the legs due to the weight of the abdomen. The downward gravitational displacement of the tip of the abdomen causes K ₂ and K ₃ in the preceding formula to be functions of α. These relations have been tested in detail by shifting the location of the center of gravity, by attaching additional masses anteriorly and posteriorly, and by decreasing the total load through amputation of the abdomen; the latter operation changes the conditions for stability. Different formulæ are thus obtained (cf. earlier papers) for the orientation of animals in which the mechanics of progression and the method of support of the body weight on an inclined surface are not the same. This demonstrates in a direct way that the respective empirical equations cannot be regarded as accidents. The results are in essence the same as that already obtained with young mammals. The diversity of equations required for the physically unlike cases merely strengthens the conception of geotropic orientation as limited by the tensions applied to the musculature of the body (caterpillars, slugs) or of appendages (beetles, and certain other forms) when the body is supported upon an inclined surface, since equations respectively pertaining to the several instances, and satisfactorily describing the observations, are deduced on this basis.     

Human hopping on damped surfaces: strategies for adjusting leg mechanics

Fast-moving legged animals bounce along the ground with spring-like legs and agilely traverse variable terrain. Previous research has shown that hopping and running humans maintain the same bouncing movement of the body's centre of mass on a range of elastic surfaces by adjusting their spring-like legs to exactly offset changes in surface stiffness. This study investigated human hopping on damped surfaces that dissipated up to 72% of the hopper's mechanical energy. On these surfaces, the legs did not act like pure springs. Leg muscles performed up to 24-fold more net work to replace the energy lost by the damped surface. However, considering the leg and surface together, the combination appeared to behave like a constant stiffness spring on all damped surfaces. By conserving the mechanics of the leg-surface combination regardless of surface damping, hoppers also conserved centre-of-mass motions. Thus, the normal bouncing movements of the centre of mass in hopping are not always a direct result of spring-like leg behaviour. Conserving the trajectory of the centre of mass by maintaining spring-like mechanics of the leg-surface combination may be an important control strategy for fast-legged locomotion on variable terrain.     

Fish Oil Attenuates Omega-6 Polyunsaturated Fatty Acid-Induced Dysbiosis and Infectious Colitis but Impairs LPS Dephosphorylation Activity Causing Sepsis

Clinically, excessive ω-6 polyunsaturated fatty acid (PUFA) and inadequate ω-3 PUFA have been associated with enhanced risks for developing ulcerative colitis. In rodent models, ω-3 PUFAs have been shown to either attenuate or exacerbate colitis in different studies. We hypothesized that a high ω-6: ω-3 PUFA ratio would increase colitis susceptibility through the microbe-immunity nexus. To address this, we fed post-weaned mice diets rich in ω-6 PUFA (corn oil) and diets supplemented with ω-3 PUFA (corn oil+fish oil) for 5 weeks. We evaluated the intestinal microbiota, induced colitis with Citrobacter rodentium and followed disease progression. We found that ω-6 PUFA enriched the microbiota with Enterobacteriaceae, Segmented Filamentous Bacteria and Clostridia spp., all known to induce inflammation. During infection-induced colitis, ω-6 PUFA fed mice had exacerbated intestinal damage, immune cell infiltration, prostaglandin E2 expression and C. rodentium translocation across the intestinal mucosae. Addition of ω-3 PUFA on a high ω-6 PUFA diet, reversed inflammatory-inducing microbial blooms and enriched beneficial microbes like Lactobacillus and Bifidobacteria, reduced immune cell infiltration and impaired cytokine/chemokine induction during infection. While, ω-3 PUFA supplementation protected against severe colitis, these mice suffered greater mortality associated with sepsis-related serum factors such as LPS binding protein, IL-15 and TNF-α. These mice also demonstrated decreased expression of intestinal alkaline phosphatase and an inability to dephosphorylate LPS. Thus, the colonic microbiota is altered differentially through varying PUFA composition, conferring altered susceptibility to colitis. Overall, ω-6 PUFA enriches pro-inflammatory microbes and augments colitis; but prevents infection-induced systemic inflammation. In contrast, ω-3 PUFA supplementation reverses the effects of the ω-6 PUFA diet but impairs infection-induced responses resulting in sepsis. We conclude that as an anti-inflammatory agent, ω-3 PUFA supplementation during infection may prove detrimental when host inflammatory responses are critical for survival.     

Molecular Anatomy of ParA-ParA and ParA-ParB Interactions during Plasmid Partitioning

Firmicutes multidrug resistance inc18 plasmids encode parS sites and two small homodimeric ParA-like (δ₂) and ParB-like (ω₂) proteins to ensure faithful segregation. Protein ω₂ binds to parS DNA, forming a short left-handed helix wrapped around the full parS, and interacts with δ₂. Protein δ₂ interacts with ω₂ and, in the ATP-bound form, binds to nonspecific DNA (nsDNA), forming small clusters. Here, we have mapped the ω₂·δ₂ and δ₂·δ₂ interacting domains in the δ₂ that are adjacent to but distinct from each other. The δ₂ nsDNA binding domain is essential for stimulation of ω₂·parS-mediated ATP hydrolysis. From the data presented here, we propose that δ₂ interacts with ATP, nsDNA, and with ω₂ bound to parS at near equimolar concentrations, facilitating a δ₂ structural transition. This δ₂ “activated” state overcomes its impediment in ATP hydrolysis, with the subsequent release of both of the proteins from nsDNA (plasmid unpairing).     

Selective Enrichment of Omega-3 Fatty Acids in Oils by Phospholipase A1

Omega fatty acids are recognized as key nutrients for healthier ageing. Lipases are used to release ω-3 fatty acids from oils for preparing enriched ω-3 fatty acid supplements. However, use of lipases in enrichment of ω-3 fatty acids is limited due to their insufficient specificity for ω-3 fatty acids. In this study use of phospholipase A1 (PLA1), which possesses both sn-1 specific activity on phospholipids and lipase activity, was explored for hydrolysis of ω-3 fatty acids from anchovy oil. Substrate specificity of PLA1 from Thermomyces lenuginosus was initially tested with synthetic p-nitrophenyl esters along with a lipase from Bacillus subtilis (BSL), as a lipase control. Gas chromatographic characterization of the hydrolysate obtained upon treatment of anchovy oil with these enzymes indicated a selective retention of ω-3 fatty acids in the triglyceride fraction by PLA1 and not by BSL. ¹³C NMR spectroscopy based position analysis of fatty acids in enzyme treated and untreated samples indicated that PLA1 preferably retained ω-3 fatty acids in oil, while saturated fatty acids were hydrolysed irrespective of their position. Hydrolysis of structured triglyceride,1,3-dioleoyl-2-palmitoylglycerol, suggested that both the enzymes hydrolyse the fatty acids at both the positions. The observed discrimination against ω-3 fatty acids by PLA1 appears to be due to its fatty acid selectivity rather than positional specificity. These studies suggest that PLA1 could be used as a potential enzyme for selective concentrationof ω-3 fatty acids.     

Significance of Population Size on the Fixation of Nonsynonymous Mutations in Genes Under Varying Levels of Selection Pressure

Previous studies observed a higher ratio of divergences at nonsynonymous and synonymous sites (ω = d_N/d_S) in species with a small population size compared to that estimated for those with a large population size. Here we examined the theoretical relationship between ω, effective population size (N_e), and selection coefficient (s). Our analysis revealed that when purifying selection is high, ω of species with small N_e is much higher than that of species with large N_e. However the difference between the two ω reduces with the decline in selection pressure (s → 0). We examined this relationship using primate and rodent genes and found that the ω estimated for highly constrained genes of primates was up to 2.9 times higher than that obtained for their orthologous rodent genes. Conversely, for genes under weak purifying selection the ω of primates was only 17% higher than that of rodents. When tissue specificity was used as a proxy for selection pressure we found that the ω of broadly expressed genes of primates was up to 2.1-fold higher than that of their rodent counterparts and this difference was only 27% for tissue specific genes. Since most of the nonsynonymous mutations in constrained or broadly expressed genes are deleterious, fixation of these mutations is influenced by N_e. This results in a higher ω of these genes in primates compared to those from rodents. Conversely, the majority of nonsynonymous mutations in less-constrained or tissue-specific genes are neutral or nearly neutral and therefore fixation of them is largely independent of N_e, which leads to the similarity of ω in primates and rodents.     

A nonsense exon in the Tpm1 gene is silenced by hnRNP H and F

As well as generating protein isoform diversity, in some cases alternative splicing generates RNAs that harbor premature termination codons and that are subject to nonsense-mediated decay (NMD). We previously identified an apparent pseudo-exon in the rat α-tropomyosin (Tpm1) gene as a probable genuine alternatively spliced exon that causes NMD when spliced into Tpm1 RNA. Here, we report the analysis of cis-acting splicing regulatory elements within this “nonsense exon.” Guided by the data set of predicted splicing enhancer and silencer elements compiled by Zhang and Chasin, we made a series of mutations through the nonsense exon and found that like authentic exons it is densely packed with enhancer and silencer elements. Strikingly, 11 of 13 tested mutations behaved as predicted computationally. In particular, we found that a G-rich silencer at the 5′ end, which is crucial for skipping of the nonsense exon, functions by binding hnRNP-H and F.     

siRNA screening identifies METTL9 as a histidine Nπ-methyltransferase that targets the proinflammatory protein S100A9

Protein methylation is one of the most common post-translational modifications observed in basic amino acid residues, including lysine, arginine, and histidine. Histidine methylation occurs on the distal or proximal nitrogen atom of its imidazole ring, producing two isomers: Nτ-methylhistidine or Nπ-methylhistidine. However, the biological significance of protein histidine methylation remains largely unclear owing in part to the very limited knowledge about its contributing enzymes. Here, we identified mammalian seven-β-strand methyltransferase METTL9 as a histidine Nπ-methyltransferase by siRNA screening coupled with methylhistidine analysis using LC–tandem MS. We demonstrated that METTL9 catalyzes Nπ-methylhistidine formation in the proinflammatory protein S100A9, but not that of myosin light chain kinase MYLK2, in vivo and in vitro. METTL9 does not affect the heterodimer formation of S100A9 and S100A8, although Nπ-methylation of S100A9 at His-107 overlaps with a zinc-binding site, attenuating its affinity for zinc. Given that S100A9 exerts an antimicrobial activity, probably by chelation of zinc essential for the growth of bacteria and fungi, METTL9-mediated S100A9 methylation might be involved in the innate immune response to bacterial and fungal infection. Thus, our findings suggest a functional consequence for protein histidine Nπ-methylation and may add a new layer of complexity to the regulatory mechanisms of post-translational methylation.