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Generating high-speed dynamic running gaits in a quadruped robot using an evolutionary search.

Over the past several decades, there has been a considerable interest in investigating high-speed dynamic gaits for legged robots. While much research has been published, both in the biomechanics and engineering fields regarding the analysis of these gaits, no single study has adequately characterized the dynamics of high-speed running as can be achieved in a realistic, yet simple, robotic system. The goal of this paper is to find the most energy-efficient, natural, and unconstrained gallop that can be achieved using a simulated quadrupedal robot with articulated legs, asymmetric mass distribution, and compliant legs. For comparison purposes, we also implement the bound and canter. The model used here is planar, although we will show that it captures much of the predominant dynamic characteristics observed in animals. While it is not our goal to prove anything about biological locomotion, the dynamic similarities between the gaits we produce and those found in animals does indicate a similar underlying dynamic mechanism. Thus, we will show that achieving natural, efficient high-speed locomotion is possible even with a fairly simple robotic system. To generate the high-speed gaits, we use an efficient evolutionary algorithm called set-based stochastic optimization. This algorithm finds open-loop control parameters to generate periodic trajectories for the body. Several alternative methods are tested to generate periodic trajectories for the legs. The combined solutions found by the evolutionary search and the periodic-leg methods, over a range of speeds up to 10.0 m/s, reveal "biological" characteristics that are emergent properties of the underlying gaits.

Algorithms↗

Two crystal structures of a potently sweet protein. Natural monellin at 2.75 A resolution and single-chain monellin at 1.7 A resolution.

Two refined structures of the sweet-tasting protein monellin are presented. The structure of natural monellin has been refined at 2.75 A resolution. The final model consists of four monellin molecules in the asymmetric unit, encompassing 3136 non-hydrogen atoms. The crystallographic R-factor is 0.193 for the 8853 reflections between 6.0 A and 2.75 A resolution, and the root-mean-square deviations from ideality are 0.017 A for bond lengths and 3.6 degrees for bond angles. The refined structure generally confirms, with some difference in detail, the initial backbone model of monellin that was based on 3.0 A resolution data. Single-chain monellin (scm) was genetically engineered by fusing the two chains of monellin into a single 94-residue polypeptide. Using the refined monellin coordinates as a search model, the crystal structure of scm has been solved with the techniques of molecular replacement, and has been refined against data to 1.7 A resolution. The final model consists of two scm molecules per asymmetric unit, and includes 137 bound water molecules. The crystallographic R-factor for this model is 0.174 for the 15,053 reflections (magnitude of FO magnitude of > 2 sigma (FO)) between 6.0 A and 1.7 A resolution. The root-mean-square deviations from ideal bond lengths and angles are 0.015 A and 2.86 degrees, respectively, and the average coordinate error is approximately 0.2 A, as estimated from a Luzzati plot. The error in the model was also estimated by comparing the two molecules in the asymmetric unit. The most significant differences between the two molecules occur in loop regions and at the C terminus of the protein, and are generally correlated to differences in crystal packing contacts. Linking the two chains of monellin has not substantially altered the structure beyond the region immediately surrounding the new peptide bond. Like natural monellin, the conformation of scm is dominated by a 17-residue alpha-helix folded into the concave side of a twisted, five-strand anti-parallel beta-sheet. We expect that the availability of a high-resolution structure of scm, along with the convenience of producing site-specific mutants of this protein, will make scm a good model with which to probe the structural basis of sweetness.

Amino Acid Sequence↗

Structural characterization of hellethionins from Helleborus purpurascens.

Thionins are relatively small-sized multiple-cystine peptides that are probably involved in the plant defense against pathogens. As such, these peptides constitute promising candidates for engineered plant resistance in the agricultural industry. More recently, thionins have been proposed as potential immunotoxins in tumor therapy. In the search for pharmacologically active natural products, a new family of thionins was recently discovered in the roots of Helleborus purpurascens that accordingly were termed hellethionins. The structural characterization by NMR of one representative member of this family, i.e., of hellethionin D, clearly reveals that thionins from different sources share a highly conserved overall fold. In fact, the well-defined 3D structure of hellethionin D is very similar to those reported so far for viscotoxins, purothionins, or crambin, although distinct differences could be detected in the C-terminal portion, especially for loop 36-39. These differences may derive from the unusual distribution of charged residues in the C-terminal half of the peptide sequence compared to other thionins and from the uncommon occurrence of four contiguous threonine residues in loop 36-39. As expected, reduction of the disulfide bonds in hellethionin D leads to complete unfolding, but upon oxidative refolding by air oxygen in the presence of glutathione the correct isomer is recovered in high yields, confirming the very robust fold of this class of bioactive cystine peptides.

Amino Acid Sequence↗

Analysis of a cross between green and red fluorescent trypanosomes.

Trypanosoma brucei undergoes genetic exchange in its insect vector, but the mechanism is unknown and no one has yet seen the process. By crossing genetically engineered red and green fluorescent trypanosomes, we have been able to pinpoint the location of genetic exchange in the fly and search for intermediate stages. In experimental crosses of red and green parental trypanosomes, yellow hybrid trypanosomes first appeared in the fly salivary glands as early as 13 days after infection and were observed only in flies with a mixture of red and green trypanosomes in one or both salivary glands. Despite high numbers of flies with mixed infections, yellow trypanosomes were not detected in the fly midgut or proventriculus. The hybrid nature of yellow trypanosomes was confirmed by analysis of molecular karyotypes and microsatellite alleles. As well as yellow hybrids, hybrid trypanosomes with red, green or no fluorescence were also recovered from fly salivary glands. Analysis of microsatellite alleles in parental and progeny clones showed Mendelian inheritance. Our findings are consistent with the hypothesis that mating takes place between trypanosomes in the salivary glands of the fly before they attach to the salivary gland epithelium.

Animals↗

Signalling substitutions in the periplasmic domain of chemoreceptor Trg induce or reduce helical sliding in the transmembrane domain.

We used in vivo oxidative cross-linking of engineered cysteine pairs to assess conformational changes in the four-helix transmembrane domain of chemoreceptor Trg. Extending previous work, we searched for and found a fourth cross-linking pair that spanned the intrasubunit interface between transmembrane helix 1 (TM1) and its partner TM2. We determined the effects of ligand occupancy on cross-linking rate constants for all four TM1-TM2 diagnostic pairs in conditions that allowed the formation of receptor-kinase complexes for the entire cellular complement of Trg. Occupancy altered all four rates in a pattern that implicated sliding of TM2 relative to TM1 towards the cytoplasm as the transmembrane signalling movement in receptor-kinase complexes. Transmembrane signalling can be reduced or induced by single amino acid substitutions in the ligand-binding region of the periplasmic domain of Trg. We determined the effects of these substitutions on conformation in the transmembrane domain and on ligand-induced changes using the diagnostic TM1-TM2 cysteine pairs. Effects on rates of in vivo cross-linking showed that induced signalling substitutions altered the relative positions of TM1 and TM2 in the same way as ligand binding, and reduced signalling substitutions blocked or attenuated the ligand-induced shift. These results provide strong support for the helical sliding model of transmembrane signalling.

Amino Acid Substitution↗

Human rights in the world of the genetic revolution.

The Biotechnological Revolution provides enormous possibilities to human development (nutrition, medicine, industry), while at the same time, creates social-ethical apprehensions due to the dangers to Human Rights that an improper use could generate. In this respect, Human Rights are presented as the "religion" of our time: accepted by all, although not equally practised. These rights, classified in the Universal Declaration of the United Nations, are the terms which society uses to ponder the ethical peformance of individuals and organizations. Harmonisation between Biotechnology and Human Rights should be based on a continuous social debate in which the principles that contribute to the respect of the human's essential nature should arise. As a starting point, considerations concerning the repercussions which the different genetic techniques have on each of the individually considered Human Rights, i.e. on dignity, equality, freedom, the right to health, to intimacy or to a worthy environment should be developed. Moreover, an international vision of the problem should be imposed since it should be remembered that initiatives that avoid attacks on Human Rights are either taken internationally or are condemned to failure. The following work was not written to give practical solutions to ethical conflicts but simply to consider some of the aspects which can create controversy in the search for a coherent future for human nature.

Biotechnology↗

[Tissue engineering: chances and challenges for application in rheumatic diseases].

Current technologies of tissue engineering offer new strategies for the treatment of cartilage and bone defects. Beyond implantation of cell suspensions, second generation products of biomaterial enforced with in vitro preformed tissues are clinically applied. Ongoing research and development focus on differentiation factors and tissue protection. In search for sources of autologous cells which are easier to collect and which may serve for more complex tissues like osteochondral implants, mesenchymal stem cells are investigated. The design of in vitro experiments, which are required for these investigations, has produced tissue engineering technologies, which may serve for pathophysiology research in inflammatory joint diseases and for exploration of treatment strategies. These together with the advances in biological therapies of rheumatic diseases are the basis of new concepts, which promise application of tissue engineering also in inflammatory joint diseases.

Animals↗

Conserved conformation of RecA protein after executing the DNA strand-exchange reaction. A site-specific linear dichroism structure study.

RecA protein and its eukaryotic homologue Rad51 protein catalyzes the DNA strand exchange, which is a key reaction of homologous recombination. At the initial step of the reaction, RecA proteins form a helical filament on a single-stranded DNA (ssDNA). Binding of double-stranded DNA (dsDNA) to the filament triggers the homology search; as homology is found, the exchange of strands occurs, and the displaced DNA is released. These are the principal steps of genetic recombination; however, despite many years of extensive study of RecA activities, the details of the mechanism are still obscure. A high-resolution structure of the active nucleoprotein filament could provide information to help understand this process. Using a linear dichroism polarized-light spectroscopy technique, in combination with protein engineering (the site-specific linear dichroism method), we have previously studied the arrangement of RecA in complex with ssDNA. In the present study, we have used this approach to search for structural variations of RecA at the atomic level as the DNA in the complex is changed from ssDNA to dsDNA. The structural data of the RecA-dsDNA filament are found to be very similar to the data previously obtained for the RecA-ssDNA complex, indicating that the overall orientation and also the internal structure of RecA in the active filament are not markedly altered when the bound DNA changes from single- to double-stranded. The implications of the structural similarities as well as the significance of some conformational variations observed for a few amino acid residues that may be involved in interactions with DNA are discussed.

DNA, Bacterial↗

Peptide engineering allows cytotoxic T-cell vaccination against human papilloma virus tumour antigen, E6.

Major histocompatibility complex (MHC) class I allele-specific binding motifs have proved useful in predicting cytotoxic T-cell epitopes from immunogenic proteins. In a search of the E6 protein from human papilloma virus type 16 utilizing the Kb binding motif, we discovered four potential binding peptides. One peptide, E6.1 (sequence 50-57, YDFAFRDL), was poor in its ability to stabilize empty Kb on RMA-S cells, with a t1/2 = 33 min versus 30 min for empty Kb. This peptide subsequently proved to be non-immunogenic upon mouse in vivo vaccination. It was hypothesized that an isoleucine for aspartate substitution at position 2 would improve Kb stabilization kinetics and therefore immunogenic potential. The engineered peptide E6.1 I2 increased the Kb t1/2 to 100 min and was immunogenic upon in vivo vaccination. Cytolytic T lymphocytes (CTL) raised with the E6.1 I2 peptide responded to cells pulsed with either the wild-type peptide or the engineered peptide, implying a blindness to the substitution. More striking, these CTL also lysed a syngeneic cell line transfected with the E6 gene, implying that the E6.1 peptide was processed and presented. These data demonstrate that subimmunogenic peptides can be engineered to improve binding kinetics, which in turn improves immunogenicity. Provided that poor binding peptides are processed, the induction threshold for CTL activation can be achieved with engineered peptides, thus allowing for the kill of wild-type target cells. This approach may prove relevant to the design of subunit vaccines to virally induced tumours.

Animals↗

Protease inhibitors and directed evolution: enhancing plant resistance to nematodes.

Plant nematodes are agricultural pests, the control of which relies on chemical nematicides and fumigants that are among the most toxic and environmentally damaging of all agrochemicals. New approaches to control, based on transgenic resistance, would provide important health and environmental benefits. In this chapter we consider briefly some targets for engineering nematode resistance and discuss the use of plant protease inhibitors as anti-feedants. This approach has provided plants that display good levels of resistance against a range of nematode species. To enhance this defence strategy further we are investigating the value of directed evolution to improve the characteristics of protease inhibitors. We describe the approaches of DNA shuffling and phage display that are being used to create and screen variant libraries in the search for inhibitors with improved features.

Animals↗

cDNA detection and analysis.

In the continuing search for a full-length cDNA cloning method, there is no clear winner. Perfecting these techniques may require the re-engineering of reverse transcriptase. There now exist two reasonably linear methods for deriving expression signatures from small amounts of biological material, but advances in serial analysis of gene expression provide a quantitative, if expensive, alternative to these methods.

Animals↗

WebProAnalyst: an interactive tool for analysis of quantitative structure-activity relationships in protein families.

WebProAnalyst is a web-accessible analysis tool (http://wwwmgs.bionet.nsc.ru/mgs/programs/panalyst/) designed for scanning quantitative structure-activity relationships in protein families. The tool allows users to search correlations between protein activity and physicochemical characteristics (i.e. hydrophobicity or alpha-helical amphipathicity) in queried sequences. WebProAnalyst uses aligned amino acid sequences and data on protein activity (pK, K(m), ED(50), among others). WebProAnalyst implements methods of the known ProAnalyst package, including the multiple linear regression analysis and the sequence-activity correlation coefficient. In addition, WebProAnalyst incorporates a method based on neural networks. The WebProAnalyst reports a list of sites in protein family, the regression analysis parameters (including correlation values) for the relationships between the amino acid physicochemical characteristics in the site and the protein activity values. WebProAnalyst is useful in search of the amino acid residues that are important for protein function/activity. Furthermore, WebProAnalyst may be helpful in designing the protein-engineering experiments.

Antimicrobial Cationic Peptides↗

Applied materials engineering for orthodontic wires.

In Australia, the history of materials engineering for orthodontic wires is generally related to the development of the Begg appliance. Therefore, until recently, it has helped in the search for light resilient forces produced by fine high-tensile stainless steel wires. Recently there has been added the desire to include wires of a low modulus of elasticity which also produce light forces but in larger diameter rectangular wires. There have been three periods of development, namely, up to and including the Second World War, up to Dr Begg's passing, and subsequently. A general metallurgical background for archwire selection and use is given including the following considerations: stiffness, flexibility, zero stress relaxation, formability, resiliency, high yield phenomena, and wire fracture and crack propagation; and how some of these may be evaluated by the fingers.

Materials Testing↗

[Oncogenes and oncogene products in urogenital cancer cells].

Recent development in microbiology and genetic engineering has provided the identification and characterization of so-called 'oncogenes'. The concept of oncogenes has much stimulated intense interest in searching the cause of uncontrolled cell growth and factors responsible for formation of tumors. Because of the fact that oncogenes were first discovered in an established cell line derived from patient with bladder tumor, the association between oncogenes and genitourinary cancer has much attention. Variety of pathways of tumor development in bladder cancer can be divided in two major forms, low grade papillary tumor and high grade infiltrating tumor. Activation and a sequence of oncogenes may be relevant to the ultimate expression of these separate pathways. Concept of initiation and promotion may also be factored into these consideration. The application of these principles to the different pathways of tumor development such as in bladder, kidney and prostate cancers, supports the concept that oncogenes may be required to production of malignant tumors. The purpose of this paper is to review recent evidence that has enhanced our understanding of the genetic basis of cancer development in the genitourinary tract cancer.

Aged↗

[Comparative hydrodynamic evaluation of variants of the cavopulmonary anastomosis].

An analysis of the range of postoperative complications following cavapulmonary anastomosis reveals a number of medical engineering problems in surgery techniques. The severity of the surgery due to the nonphysiological rearrangement of blood circulation makes it necessary to search for the most optimal types of anastomosis in terms of the hemo- and hydrodynamics of circulation. To optimize the performance of cavapulmonary anastomosis, namely to define the mutual localization and orientation of the implanted anastomoses against the axes of inflow and outflow, hemo- and hydrodynamic studies were made by Doppler laser anemometry. From the hydrodynamic point of view, the findings indicate the most optimal type of cavapulmonary anastomosis-cruciform anastomosis by displacing 0.5 d from the outflow axis at an angle of 60ë5 degrees.

Anastomosis, Surgical↗

MAGMA: a multiagent architecture for metaheuristics.

In this work, we introduce a multiagent architecture called the MultiAGent Metaheuristic Architecture (MAGMA) conceived as a conceptual and practical framework for metaheuristic algorithms. Metaheuristics can be seen as the result of the interaction among different kinds of agents: The basic architecture contains three levels, each hosting one or more agents. Level-0 agents build solutions, level-1 agents improve solutions, and level-2 agents provide the high level strategy. In this framework, classical metaheuristic algorithms can be smoothly accommodated and extended. The basic three level architecture can be enhanced with the introduction of a fourth level of agents (level-3 agents) coordinating lower level agents. With this additional level, MAGMA can also describe, in a uniform way, cooperative search and, in general, any combination of metaheuristics. We describe the entire architecture, the structure of agents in each level in terms of tuples, and the structure of their coordination as a labeled transition system. We propose this perspective with the aim to achieve a better and clearer understanding of metaheuristics, obtain hybrid algorithms, suggest guidelines for a software engineering-oriented implementation and for didactic purposes. Some specializations of the general architecture will be provided in order to show that existing metaheuristics [e.g., greedy randomized adaptive procedure (GRASP), ant colony optimization (ACO), iterated local search (ILS), memetic algorithms (MAs)] can be easily described in our framework. We describe cooperative search and large neighborhood search (LNS) in the proposed framework exploiting level-3 agents. We show also that a simple hybrid algorithm, called guided restart ILS, can be easily conceived as a combination of existing components in our framework.

Journal Article↗

Comparative analysis of genetically engineered immunodeficient mouse strains as recipients for human myoblast transplantation.

The development of an optimized animal model for the in vivo analysis of human muscle cells remains an important goal in the search of therapy for muscular dystrophy. Here we examined the efficiency of human myoblast xenografts in three distinct immunodeficient mouse models. We found that different conditioning regimes used to provoke host muscle regeneration (i.e., cardiotoxin versus cryodamage) had a marked impact on xenograft success. Tibialis anterior muscle of Rag2-, Rag-/gammac-, and Rag-/gammac-/C5- mice was treated by cardiotoxin or cryodamage, submitted to enzymatic digestion, and analyzed by cytofluorometry to quantitate inflammatory cells. Human myoblasts were injected into pretreated muscles from immunodeficient recipients and the cell engraftment evaluated by immunocytochemistry, 4-8 weeks after transplantation. Donor cell differentiation and dispersion within the host muscles was also investigated. Host regeneration in cardiotoxin-treated mice was accompanied by a higher inflammatory cell infiltration when compared to that induced by cryodamage. Accordingly, when compared to the cardiotoxin group, more human myogenic cells were found after cryodamage. When the distinct immunodeficient mice were compared, we found that the alymphoid strain lacking the complement component C5 (Rag-/gammac-/C5- mice) was the most efficient host for human muscle xenografts, when compared with C5(+)Rag-/gammac- mice or Rag- mice. Our results demonstrate that cryolesion-conditioned muscles of Rag-/gammac-/C5- mice provide the best environment for long-term in vivo human myoblast differentiation, opening the way for a novel approach to study the pathophysiology of human muscle disorders.

Animals↗