A brief history of vertebrate functional morphology

The discipline of functional morphology grew out of a comparativeanatomical tradition, its transformation into a modern experimentalscience facilitated largely by technological advances. Earlymorphologists, such as Cuvier, felt that function was predictablefrom organismal form, to the extent that animals and plantsrepresented perfect adaptations to their habits. However, anatomyalone could not reveal how organisms actually performed theiractivities. Recording techniques capable of capturing fast motionwere first required to begin to understand animal movement.Muybridge is most famous for his pioneering work in fast photographyin the late 19th century, enabling him to "freeze" images ofeven the fastest horse at a full gallop. In fact, contemporarykinematic analysis grew directly out of the techniques Muybridgedeveloped. Marey made perhaps an even greater contribution toexperimental science through his invention of automatic apparatifor recording events of animal motion. Over the first half ofthe 20th century, scientists developed practical methods torecord activity patterns from muscles of a living, behavinghuman or animal. The technique of electromyography, initiallyused in clinical applications, was co-opted as a tool of organismalbiologists in the late 1960s. Comparative anatomy, kinematicanalysis and electromyography have for many years been the mainstayof vertebrate functional morphology; however, those interestedin animal form and function have recently begun branching outto incorporate approaches from experimental biomechanics andother disciplines (see accompanying symposium papers), and functionalmorphology now stands at the threshold of becoming a truly integrative,central field in organismal biology.     

Terrestrial locomotion in sea snakes: the effects of sex and species on cliff-climbing ability in sea kraits (Serpentes, Elapidae, Laticauda)

Ecomorphological theory predicts a match between an organism's environment and its locomotor abilities, such that animals function most effectively under the conditions they experience in nature. However, amphibious species must simultaneously optimize performance in two different habitats posing incompatible demands on locomotor morphology and physiology. This situation may generate a mismatch between environment and locomotor function, with performance optimized only for the more important habitat type; alternatively, selection may fine-tune locomotor abilities for both types of challenges. Two species of sea kraits in New Caledonia offer an opportunity to examine this question: Laticauda laticaudata is more highly aquatic than L. colubrina , and males are more terrestrial than females within each taxon. We examined an aspect of locomotor performance that is critical to coming ashore on steep-walled rocky islets: the ability to climb steep cliffs. We also measured the muscular strength of these animals, a character that is likely critical to climbing performance. Laticauda colubrina was heavier-bodied and stronger (even relative to its body mass) than the more aquatic L. laticaudata ; and within each species, males were heavier-bodied and stronger than females. The same patterns were evident in cliff-climbing ability. Thus, the ability of different species and sexes of sea kraits to climb steep cliffs correlates with their body shape even though these primarily aquatic animals use terrestrial habitats only rarely.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 433–441.     

From the ground up: Integrative research in primate locomotion

Primate locomotor adaptation and evolution is a principal and thriving area of research by biological anthropologists. Research in this field generally targets hypotheses regarding locomotor kinetics and kinematics, form–function associations in both the soft and hard tissue components of the musculoskeletal system, and reconstructing locomotor behavior in fossil primates. A wide array of methodological approaches is used to address adaptive hypotheses in all of these realms. Recent advances in three-dimensional shape capture, musculoskeletal physiological measurements, and analytical processing technologies (e.g., laser and CT-scans, 3D motion analysis systems, finite element analysis) have facilitated the collection and analysis of larger and more complex locomotor datasets than previously possible. With these advances in technology, new methods of form–function analyses can be developed to produce a more thorough understanding of how form reflects an organism's mechanical requirements, how shape is influenced by external environmental factors, and how these investigations of living taxa can inform questions of primate paleobiology. The papers in this special section of the American Journal of Physical Anthropology present research that builds on that foundation, by combining new data on living primates and new methodologies and approaches to answer a range of questions on extant and extinct primates. Am J Phys Anthropol 156:495–497, 2015. © 2015 Wiley Periodicals, Inc.     

1998 ISEK Congress Keynote Lecture: The use of electromyography in applied physiology

Electromyogram (EMG) analyses (surface, intramuscular and evoked potentials) in studies of muscle function have attracted increasing attention during recent years and have been applied to assess muscle endurance capacity, anaerobic and lactate thresholds, muscle biomechanics, motor learning, neuromuscular relaxation, optimal walking and pedalling speeds, muscle soreness, neuromuscular diseases, motor unit (MU) activities (MU recruitment and rate coding), and skeletal muscle fatigue. This paper deals with the use of EMG analyses employed in the area of applied physiology and is divided into three sections: surface EMG analyses; intramuscular EMG analyses; and evoked potential analyses.     

Comparing methods for metabolic network analysis and an application to metabolic engineering

Bioinformatics tools have facilitated the reconstruction and analysis of cellular metabolism of various organisms based on information encoded in their genomes. Characterization of cellular metabolism is useful to understand the phenotypic capabilities of these organisms. It has been done quantitatively through the analysis of pathway operations. There are several in silico approaches for analyzing metabolic networks, including structural and stoichiometric analysis, metabolic flux analysis, metabolic control analysis, and several kinetic modeling based analyses. They can serve as a virtual laboratory to give insights into basic principles of cellular functions. This article summarizes the progress and advances in software and algorithm development for metabolic network analysis, along with their applications relevant to cellular physiology, and metabolic engineering with an emphasis on microbial strain optimization. Moreover, it provides a detailed comparative analysis of existing approaches under different categories.     

Engineered telomeres in transgenic Xenopus laevis

The expanding roles of telomeres in epigenetic gene regulation, nuclear organization, and human disease have necessitated the establishment of model organisms in which to study telomere function under normal developmental conditions. We present an efficient system for generating numerous vertebrate animals containing engineered telomeres using a Xenopus laevis transgenesis technique. Our results indicate Xenopus zygotes efficiently recognize telomeric repeats at chromosome break points and form telomeric complexes thus generating a new telomere. The resulting transgenic animals progress through normal development and successfully metamorphose into froglets despite the chromosome breakage. Overall, this presents an efficient mechanism for generating engineered telomeres in a vertebrate system and provides an opportunity to investigate epigenetic aspects of telomere function during normal vertebrate development.     

In vivo conditions to identify Prkci phosphorylation targets using the analog-sensitive kinase method in zebrafish

Protein kinase C iota is required for various cell biological processes including epithelial tissue polarity and organ morphogenesis. To gain mechanistic insight into different roles of this kinase, it is essential to identify specific substrate proteins in their cellular context. The analog-sensitive kinase method provides a powerful tool for the identification of kinase substrates under in vivo conditions. However, it has remained a major challenge to establish screens based on this method in multicellular model organisms. Here, we report the methodology for in vivo conditions using the analog-sensitive kinase method in a genetically-tractable vertebrate model organism, the zebrafish. With this approach, kinase substrates can uniquely be labeled in the developing zebrafish embryo using bulky ATPγS analogs which results in the thiophosphorylation of substrates. The labeling of kinase substrates with a thiophosphoester epitope differs from phosphoesters that are generated by all other kinases and allows for an enrichment of thiophosphopeptides by immunoaffinity purification. This study provides the foundation for using the analog-sensitive kinase method in the context of complex vertebrate development, physiology, or disease.     

Mechanical analysis of Drosophila indirect flight and jump muscles

The genetic advantages of Drosophila make it a very appealing choice for investigating muscle development, muscle physiology and muscle protein structure and function. To take full advantage of this model organism, it has been vital to develop isolated Drosophila muscle preparations that can be mechanically evaluated. We describe techniques to isolate, prepare and mechanically analyze skinned muscle fibers from two Drosophila muscle types, the indirect flight muscle and the jump muscle. The function of the indirect flight muscle is similar to vertebrate cardiac muscle, to generate power in an oscillatory manner. The indirect flight muscle is ideal for evaluating the influence of protein mutations on muscle and cross-bridge stiffness, oscillatory power, and deriving cross-bridge rate constants. Jump muscle physiology and structure are more similar to skeletal vertebrate muscle than indirect flight muscle, and it is ideal for measuring maximum shortening velocity, force-velocity characteristics and steady-state power generation.     

Genome engineering: unconventional biochemistry and food security

Unprecedented technological advances in biology provide the tools to enhance plant productivity to meet world hunger. The genome sequences of thousands of organisms and their analyses is the blue print of their genome architecture which can now be further improved. New Nucleases offer the opportunity of modifying plant genomes in a way that was not possible only a while ago. Synthetic DNA and methodology of gene assembly further expand Synthetic biology and allow construction of metabolic pathways to produce valuable molecules in Novel hosts. The knowledge of Quorum Sensing (QS), could add to the successful use of biocontrol agents. The technology has no limitations, and excitements in biology will be exploited to meet future energy needs.     

Computational tools for comparative phenomics: the role and promise of ontologies

A major aim of the biological sciences is to gain an understanding of human physiology and disease. One important step towards such a goal is the discovery of the function of genes that will lead to a better understanding of the physiology and pathophysiology of organisms, which will ultimately lead to better diagnosis and therapy. Our increasing ability to phenotypically characterise genetic variants of model organisms coupled with systematic and hypothesis-driven mutagenesis is resulting in a wealth of information that could potentially provide insight into the functions of all genes in an organism. The challenge we are now facing is to develop computational methods that can integrate and analyse such data. The introduction of formal ontologies that make their semantics explicit and accessible to automated reasoning provides the tantalizing possibility of standardizing biomedical knowledge allowing for novel, powerful queries that bridge multiple domains, disciplines, species, and levels of granularity. We review recent computational approaches that facilitate the integration of experimental data from model organisms with clinical observations in humans. These methods foster novel cross-species analysis approaches, thereby enabling comparative phenomics and leading to the potential of translating basic discoveries from the model systems into diagnostic and therapeutic advances at the clinical level.     

Targeted and proteome-wide analysis of metabolite–protein interactions

Understanding the molecular mechanisms of endogenous and environmental metabolites is crucial for basic biology and drug discovery. With the genome, proteome, and metabolome of many organisms being readily available, researchers now have the opportunity to dissect how key metabolites regulate complex cellular pathways in vivo. Nonetheless, characterizing the specific and functional protein targets of key metabolites associated with specific cellular phenotypes remains a major challenge. Innovations in chemical biology are now poised to address this fundamental limitation in physiology and disease. In this review, we highlight recent advances in chemoproteomics for targeted and proteome-wide analysis of metabolite–protein interactions that have enabled the discovery of unpredicted metabolite–protein interactions and facilitated the development of new small molecule therapeutics.     

Circuit neuroscience in zebrafish

A central goal of modern neuroscience is to obtain a mechanistic understanding of higher brain functions under healthy and diseased conditions. Addressing this challenge requires rigorous experimental and theoretical analysis of neuronal circuits. Recent advances in optogenetics, high-resolution in vivo imaging, and reconstructions of synaptic wiring diagrams have created new opportunities to achieve this goal. To fully harness these methods, model organisms should allow for a combination of genetic and neurophysiological approaches in vivo. Moreover, the brain should be small in terms of neuron numbers and physical size. A promising vertebrate organism is the zebrafish because it is small, it is transparent at larval stages and it offers a wide range of genetic tools and advantages for neurophysiological approaches. Recent studies have highlighted the potential of zebrafish for exhaustive measurements of neuronal activity patterns, for manipulations of defined cell types in vivo and for studies of causal relationships between circuit function and behavior. In this article, we summarize background information on the zebrafish as a model in modern systems neuroscience and discuss recent results.     

Cell-cell adhesion via the ECM: integrin genetics in fly and worm.

Integrins are essential for the development of the two genetically tractable invertebrate model organisms, the nematode worm Caenorhabditis elegans and the fruit fly Drosophila melanogaster. Just two integrins are present in C. elegans: one putative RGD binding integrin alphapat-2betapat-3, corresponding to Drosophila alphaPS2betaPS and vertebrate alpha5beta1, alphaVbeta1 and alpha8beta1, and one putative laminin binding integrin alphaina-1betapat-3, corresponding to Drosophila alphaPS1betaPS and vertebrate alpha3beta1, alpha6beta1 and alpha7beta1. In this review, the function of this minimal set of integrins during the development of these two invertebrates is compared. Despite the differences in bodyplan and developmental strategy, integrin adhesion to the extracellular matrix is required for similar processes: the formation of the link that translates muscle contraction into movement of the exoskeleton, cell migration, and morphogenetic interactions between epithelia. Other integrin functions, such as regulation of gene expression, have not yet been experimentally demonstrated in both organisms. Additional proteins have been characterised in each organism that are essential for integrin function, including extracellular matrix ligands and intracellular interacting proteins, but so far different proteins have been found in the two organisms. This in part represents the fact that the characterisation of the full set of interacting proteins is not complete in either system. However, in other cases different proteins appear to be used for similar functions in the two animals. The continued use of genetic approaches to identify proteins required for integrin function in these two model organisms should lead to the identification of the minimal set of conserved components that form integrin adhesive structures.     

Resolving Shifting Patterns of Muscle Energy Use in Swimming Fish

Muscle metabolism dominates the energy costs of locomotion. Although in vivo measures of muscle strain, activity and force can indicate mechanical function, similar muscle-level measures of energy use are challenging to obtain. Without this information locomotor systems are essentially a black box in terms of the distribution of metabolic energy. Although in situ measurements of muscle metabolism are not practical in multiple muscles, the rate of blood flow to skeletal muscle tissue can be used as a proxy for aerobic metabolism, allowing the cost of particular muscle functions to be estimated. Axial, undulatory swimming is one of the most common modes of vertebrate locomotion. In fish, segmented myotomal muscles are the primary power source, driving undulations of the body axis that transfer momentum to the water. Multiple fins and the associated fin muscles also contribute to thrust production, and stabilization and control of the swimming trajectory. We have used blood flow tracers in swimming rainbow trout (Oncorhynchus mykiss) to estimate the regional distribution of energy use across the myotomal and fin muscle groups to reveal the functional distribution of metabolic energy use within a swimming animal for the first time. Energy use by the myotomal muscle increased with speed to meet thrust requirements, particularly in posterior myotomes where muscle power outputs are greatest. At low speeds, there was high fin muscle energy use, consistent with active stability control. As speed increased, and fins were adducted, overall fin muscle energy use declined, except in the caudal fin muscles where active fin stiffening is required to maintain power transfer to the wake. The present data were obtained under steady-state conditions which rarely apply in natural, physical environments. This approach also has potential to reveal the mechanical factors that underlie changes in locomotor cost associated with movement through unsteady flow regimes.     

Chemical genetics: adding to the developmental biology toolbox

Recent advances in cell and molecular biology have generated important tools to probe developmental questions. In addition, new genetic model systems such as Danio rerio now make large-scale vertebrate early developmental mutant screens feasible. Nonetheless, some developmental questions remain difficult to study because of the need for finer temporal, spatial, or tuneable control of gene function within a developmental system. New uses for old teratogens as well as novel chemical modulators of development have begun to fill this void.     

Field swimming performance of bluegill sunfish,Lepomis macrochirus: implications for field activity cost estimates and laboratory measures of swimming performance

Mobility is essential to the fitness of many animals, and the costs of locomotion can dominate daily energy budgets. Locomotor costs are determined by the physiological demands of sustaining mechanical performance, yet performance is poorly understood for most animals in the field, particularly aquatic organisms. We have used 3‐D underwater videography to quantify the swimming trajectories and propulsive modes of bluegills sunfish (Lepomis macrochirus, Rafinesque) in the field with high spatial (1–3 mm per pixel) and temporal (60 Hz frame rate) resolution. Although field swimming trajectories were variable and nonlinear in comparison to quasi steady‐state swimming in recirculating flumes, they were much less unsteady than the volitional swimming behaviors that underlie existing predictive models of field swimming cost. Performance analyses suggested that speed and path curvature data could be used to derive reasonable estimates of locomotor cost that fit within measured capacities for sustainable activity. The distinct differences between field swimming behavior and performance measures obtained under steady‐state laboratory conditions suggest that field observations are essential for informing approaches to quantifying locomotor performance in the laboratory.