Lightweight Design of Mechanical Structures based on Structural Bionic Methodology

With increasing concern over the excessive energy consumption and environment pollution, structural bionics is a viable new tool of lightweight design by mechanical engineers. The structural solutions derived from nature can be successfully transferred into technical construction for maximum structural efficiency from minimal resources. The goal of the study is to develop a standard methodology for bionic mechanical structures with dead-load reduction and performance improvement. Similarity theory and fuzzy assessment method are deployed for selection of analogical samples and analysis based on structure, loading and function similarities. The type spectrum of lightweight design is established for selection convenience and principle extraction, vital to concept designs. Finite element method is used as an effective tool for mechanical performance simulation and comparison. The rapid prototyping, investment casting and Numerical Control (NC) machining are discussed for model fabrication. The static and dynamic test results indicate that the bionic models are lighter but stiffer than the original ones. So by mimicking biological structural principles, the structural bionic design offers a new solution for updating traditional design concepts and achieving maximum structural efficiency.     

壳聚糖衍生物及其胶束：特性、功能化修饰和在药物传递系统中的应用

壳聚糖是一种天然多糖,具有无毒、可生物降解、生物相容性等诸多优点,但水溶性差的自身特点限制了其在药剂学中的应用,而其经合理的结构设计、修饰和优化,可获得性能良好的两亲性壳聚糖衍生物,这些衍生物在水溶液中能自组装成具有良好药物传输性能（如载药量、稳定性、刺激敏感性、靶向性等）的胶束,并被广泛应用于构建药物传递系统,以改善药物的溶解性、靶向性、生物利用度及耐药性,降低药物的毒副作用。综述壳聚糖衍生物结构对其胶束药物传输性能的影响以及壳聚糖衍生物及其胶束的功能化修饰和在药物传递系统中的应用。     

Synthetic Spider Silk Production on a Laboratory Scale

As society progresses and resources become scarcer, it is becoming increasingly important to cultivate new technologies that engineer next generation biomaterials with high performance properties. The development of these new structural materials must be rapid, cost-efficient and involve processing methodologies and products that are environmentally friendly and sustainable. Spiders spin a multitude of different fiber types with diverse mechanical properties, offering a rich source of next generation engineering materials for biomimicry that rival the best manmade and natural materials. Since the collection of large quantities of natural spider silk is impractical, synthetic silk production has the ability to provide scientists with access to an unlimited supply of threads. Therefore, if the spinning process can be streamlined and perfected, artificial spider fibers have the potential use for a broad range of applications ranging from body armor, surgical sutures, ropes and cables, tires, strings for musical instruments, and composites for aviation and aerospace technology. In order to advance the synthetic silk production process and to yield fibers that display low variance in their material properties from spin to spin, we developed a wet-spinning protocol that integrates expression of recombinant spider silk proteins in bacteria, purification and concentration of the proteins, followed by fiber extrusion and a mechanical post-spin treatment. This is the first visual representation that reveals a step-by-step process to spin and analyze artificial silk fibers on a laboratory scale. It also provides details to minimize the introduction of variability among fibers spun from the same spinning dope. Collectively, these methods will propel the process of artificial silk production, leading to higher quality fibers that surpass natural spider silks.     

Pathway analysis of genomic data: concepts, methods, and prospects for future development

Genome-wide data sets are increasingly being used to identify biological pathways and networks underlying complex diseases. In particular, analyzing genomic data through sets defined by functional pathways offers the potential of greater power for discovery and natural connections to biological mechanisms. With the burgeoning availability of next-generation sequencing, this is an opportune moment to revisit strategies for pathway-based analysis of genomic data. Here, we synthesize relevant concepts and extant methodologies to guide investigators in study design and execution. We also highlight ongoing challenges and proposed solutions. As relevant analytical strategies mature, pathways and networks will be ideally placed to integrate data from diverse -omics sources to harness the extensive, rich information related to disease and treatment mechanisms.     

Contributions to the Biomechanics of Plants. I. Stabilities of Plant Stems with Strengthening Elements of Different Cross-Sections Against Weight and Wind Forces*

Biophysical considerations allow estimates of the mechanical stresses on self-bearing vertical stems of plants. Even at moderate wind velocities the stresses induced by aerodynamic forces dominate over those induced by the own weight. Using polar coordinates, analytical expressions of cross-sectional area and axial second moment of area for centrisymmetric structures with symmetries threefold or higher are derived. Calculating the relative section modulus for various (centrisymmetric) arrangements of stabilizing structures leads to an estimate of the “mechanical effectivity” of these structures. If for plant stems, seen as composite materials, the second moments of area and the elastic moduli are known, the contribution of the different tissues to mechanical stability can be determined quantitatively. The mechanical design of early “vascular” land plants and of stems of (fossil) trees and lianas in different ontogenetic stages can be assessed.     

Structural trees for proteins containing φ-motifs

In the present study, a novel structural motif of proteins referred to as the phi-motif is considered, and two novel structural trees in which the phi-motif is taken as the root structure have been constructed. The simplest phi-motif is formed by three adjacent beta-strands connected by loops and packed in one beta-sheet so that its overall fold resembles the Greek letter phi. Construction of the structural trees and modeling of folding pathways have shown that all structures of the protein superfamilies can be obtained by stepwise addition of alpha-helices and/or beta-strands to the root phi-motif taking into account a restricted set of rules inferred from known principles of protein structure. The structural trees are a good tool for structure comparison, structural classification of proteins, as well as for searching for all possible protein folds and folding pathways.     

The autoreactivity of anti-phosphorylcholine antibodies for atherosclerosis-associated neo-antigens and apoptotic cells

Abs specific for phosphorylcholine (PC) are known to contribute to the immune defense against a variety of microbial infections. To assess for other types of binding interactions, we performed surveys of anti-PC Abs of diverse biologic origins and structural diversity and demonstrated a common autoreactivity for oxidatively modified low density lipoprotein and other oxidation-specific structures containing PC-Ags. We also found that cells undergoing apoptosis sequentially express a range of oxidation-specific neo-self PC determinants. Whereas natural Abs to PC recognized cells at early stages of apoptosis, by contrast, an IgG anti-PC Ab, representative of a T cell-dependent response, recognized PC determinants primarily associated with late stages of apoptosis. Cumulatively, these results demonstrate a fundamental paradigm in which Abs from both the innate and the T cell-dependent tiers of the B cell compartment recognize a minimal molecular motif arrayed both on microbes and as neo-self Ags linked to atherosclerosis and autoimmune disease.     

Measurement of prestrain in trees: implications for the determination of safety factors

1. It has long been known that wood in trees is under internally generated tensile or compressive forces, known as 'prestrains'. These prestrains are thought to limit compressive loading at points of high strain within the tree to counteract the mechanical anisotropy of wood. Prestrains can be relieved by making cuts in wood, allowing it to recover to an unstrained state.
2. Recently, electrical resistance strain gauges have been used to measure surface strains on the trunk, roots and branches of trees. We have found that, by making a shallow cut above and below gauges, the prestrain can be measured as an apparent residual negative strain. This negative strain, after prestrain relief, is indicative of a tensile prestrain having been present in the wood before cutting.
3. It is a simple procedure to determine prestrain magnitude at the site of gauge attachment. By knowing the prestrain state of wood at the measurement site of strain determination, a more reliable estimate of surface stress and safety factors in tree design can be made.     

Structural trees for protein superfamilies

Structural trees for large protein superfamilies, such as β proteins with the aligned β sheet packing, β proteins with the orthogonal packing of α helices, two-layer and three-layer α/β proteins, have been constructed. The structural motifs having unique overall folds and a unique handedness are taken as root structures of the trees. The larger protein structures of each superfamily are obtained by a stepwise addition of α helices and/or β strands to the corresponding root motif, taking into account a restricted set of rules inferred from known principles of the protein structure. Among these rules, prohibition of crossing connections, attention to handedness and compactness, and a requirement for α helices to be packed in α-helical layers and β strands in β layers are the most important. Proteins and domains whose structures can be obtained by stepwise addition of α helices and/or β strands to the same root motif can be grouped into one structural class or a superfamily. Proteins and domains found within branches of a structural tree can be grouped into subclasses or subfamilies. Levels of structural similarity between different proteins can easily be observed by visual inspection. Within one branch, protein structures having a higher position in the tree include the structures located lower. Proteins and domains of different branches have the structure located in the branching point as the common fold. Proteins 28:241–260, 1997. © 1997 Wiley-Liss Inc.     

Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design

Understanding the structural repertoire of RNA is crucial for RNA genomics research. Yet current methods for finding novel RNAs are limited to small or known RNA families. To expand known RNA structural motifs, we develop a two-dimensional graphical representation approach for describing and estimating the size of RNA’s secondary structural repertoire, including naturally occurring and other possible RNA motifs. We employ tree graphs to describe RNA tree motifs and more general (dual) graphs to describe both RNA tree and pseudoknot motifs. Our estimates of RNA’s structural space are vastly smaller than the nucleotide sequence space, suggesting a new avenue for finding novel RNAs. Specifically our survey shows that known RNA trees and pseudoknots represent only a small subset of all possible motifs, implying that some of the ‘missing’ motifs may represent novel RNAs. To help pinpoint RNA-like motifs, we show that the motifs of existing functional RNAs are clustered in a narrow range of topological characteristics. We also illustrate the applications of our approach to the design of novel RNAs and automated comparison of RNA structures; we report several occurrences of RNA motifs within larger RNAs. Thus, our graph theory approach to RNA structures has implications for RNA genomics, structure analysis and design.     

Home Range,Body Condition,and Survival of Rehabilitated Raccoons (Procyon lotor) During Their First Winter

The effects of raccoon (Procyon lotor) rehabilitation on postrelease survivorship are unknown. Raccoon rehabilitation success was measured as differences in prewinter body condition, home range size, distance to manmade structures, and during-winter survival between raccoons in the wild and those who have been rehabilitated. Prewinter body condition did not differ between wild and rehabilitated raccoons, but there was a trend for rehabilitated raccoons to have better body conditions. There was no difference between wild and rehabilitated raccoon adaptive kernel (AK) home range for 95% and 90% AK home ranges, or for core (50% AK) use areas. There was no sex difference in distance traveled from the release site within rehabilitated raccoons. However, rehabilitated raccoons were found significantly closer (49.4 ± 4.7 m) to manmade structures than wild raccoons (92.2 ± 14.4 m), and female raccoons were found significantly closer (64.8 ± 4.5 m) to manmade structures than male raccoons (72.3 ± 17.6 m). The results of this study indicate that raccoons can be successfully rehabilitated, but they may occupy habitat closer to manmade structures than wild raccoons.     

Pure moment testing for spinal biomechanics applications: Fixed versus sliding ring cable-driven test designs

In vitro multi-axial bending testing using pure moment loading conditions has become the standard in evaluating the effects of different types of surgical intervention on spinal kinematics. Simple, cable-driven experimental set-ups have been widely adopted because they require little infrastructure. Traditionally, “fixed ring” cable-driven experimental designs have been used; however, there have been concerns with the validity of this set-up in applying pure moment loading. This study involved directly comparing the loading state induced by a traditional “fixed ring” apparatus versus a novel “sliding ring” approach. Flexion-extension bending was performed on an artificial spine model and a single cadaveric test specimen, and the applied loading conditions to the specimen were measured with an in-line multiaxial load cell. The results showed that the fixed ring system applies flexion-extension moments that are 50–60% less than the intended values. This design also imposes non-trivial anterior–posterior shear forces, and non-uniform loading conditions were induced along the length of the specimen. The results of this study indicate that fixed ring systems have the potential to deviate from a pure moment loading state and that our novel sliding ring modification corrects this error in the original test design. This suggests that the proposed sliding ring design should be used for future in vitro spine biomechanics studies involving a cable-driven pure moment apparatus.     

18S rRNA gene sequence-structure phylogeny of the Trypanosomatida (Kinetoplastea,Euglenozoa) with special reference to Trypanosoma

Parasites of the order Trypanosomatida are known due to their medical relevance. Despite the progress made in the past decades on understanding the evolution of this group of organisms, there are still many open questions that require robust phylogenetic markers to increase the resolution of trees. Using two known 18S rRNA gene template structures (from Trypanosoma cruzi Chagas, 1909 and Trypanosoma brucei Plimmer and Bradford, 1899), individual 18S rRNA gene secondary structures were predicted by homology modeling. Sequences and their secondary structures, automatically encoded by a 12-letter alphabet (each nucleotide with its three structural states, paired left, paired right, unpaired), were simultaneously aligned. Sequence-structure trees were generated by neighbor joining and/or maximum likelihood. The reconstructed trees allowed us to discuss not only the big picture of trypanosomatid phylogeny but also a comprehensive sampling of trypanosomes evaluated in the context of trypanosomatid diversity. The robust support (bootstrap > 75) for well-known clades and critical branches suggests that the simultaneous use of 18S rRNA sequence and secondary structure data can reconstruct robust phylogenetic trees and can be used by the trypanosomatid research community for future analysis.     

Measuring fractional forest canopy element cover and openness – definitions and methodologies revisited

Canopy structural parameters are often used to give adequate representation of vegetated ecosystems for various purposes including primary productivity, climate system, water and carbon gas exchanges, and radiation extinction. Canopy structural parameters are usually described using several pseudo‐synonymous terms, often measuring different components of vegetation canopies. Standardization in the definitions has fallen short, leading to confusion of terms even in standard text books making the comparison of historic measures futile. Here we clarify concepts that have been used for fractional canopy element cover and openness measures. The fractional canopy element cover and openness concepts considered are canopy closure, canopy cover, canopy openness, crown closure, crown completeness, crown cover, crown porosity, site openness and tilt openness. New methodologies are presented to obtain large scale fractional canopy element cover and openness measures using hemispherical photography. The new methodologies and variations in definitions of fractional canopy element cover and openness concepts are demonstrated using photographic measurements in complex topography. The results indicate that both fractional canopy element cover and openness parameters can be estimated with a few point‐based measurements using hemispherical photography. Hemispherical photography is therefore less time, labour and resource intensive, as compared to point based measuring techniques of canopy element cover and openness. Most of the commonly and interchangeably used concepts of fractional canopy element cover and openness measures represent physically different structural properties of a vegetated ecosystem.     

A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction

Background  

Predicting which molecules can bind to a given binding site of a protein with known 3D structure is important to decipher the protein function, and useful in drug design. A classical assumption in structural biology is that proteins with similar 3D structures have related molecular functions, and therefore may bind similar ligands. However, proteins that do not display any overall sequence or structure similarity may also bind similar ligands if they contain similar binding sites. Quantitatively assessing the similarity between binding sites may therefore be useful to propose new ligands for a given pocket, based on those known for similar pockets.     

Kinetic and structural characterization of triacylglycerol lipases possessing phospholipase A1 activity

The pancreatic lipase gene family displays various substrate selectivities for triglycerides and phospholipids. The structural basis for this difference in substrate specificity has not been definitively established. Based on a kinetic comparative study between various pancreatic lipase family members, we showed here that porcine pancreatic lipase (PPL), which was so far classified as “classical lipase”, was able to hydrolyze phosphatidylcholine (PC). Amino acid sequence alignments revealed that Val260 residue in PPL lid could be critical for the interaction with lipid substrate. Molecular dynamics was applied to investigate PC binding modes within the catalytic cavity of PPL and human pancreatic lipase (HPL), aiming to explain the difference of specificity of these enzymes towards phospholipids. Results showed that with HPL, the oxyanion hole was not able to accommodate the PC molecule, suggesting that no activity could be obtained. With PPL, the formation of a large pocket involving Val260 allowed the PC molecule to come near the catalytic residues, suggesting that it could be hydrolyzed. One more interesting finding is that human pancreatic lipase related protein 2 could hydrolyze phospholipids through its PLA₁ and PLA₂ activities. Overall, our study shed the light on new structural features of the phospholipase activity of pancreatic lipase family members.     

Protein-Protein Docking: From Interaction to Interactome

The protein-protein docking problem is one of the focal points of activity in computational biophysics and structural biology. The three-dimensional structure of a protein-protein complex, generally, is more difficult to determine experimentally than the structure of an individual protein. Adequate computational techniques to model protein interactions are important because of the growing number of known protein structures, particularly in the context of structural genomics. Docking offers tools for fundamental studies of protein interactions and provides a structural basis for drug design. Protein-protein docking is the prediction of the structure of the complex, given the structures of the individual proteins. In the heart of the docking methodology is the notion of steric and physicochemical complementarity at the protein-protein interface. Originally, mostly high-resolution, experimentally determined (primarily by x-ray crystallography) protein structures were considered for docking. However, more recently, the focus has been shifting toward lower-resolution modeled structures. Docking approaches have to deal with the conformational changes between unbound and bound structures, as well as the inaccuracies of the interacting modeled structures, often in a high-throughput mode needed for modeling of large networks of protein interactions. The growing number of docking developers is engaged in the community-wide assessments of predictive methodologies. The development of more powerful and adequate docking approaches is facilitated by rapidly expanding information and data resources, growing computational capabilities, and a deeper understanding of the fundamental principles of protein interactions.     

Protein-Protein Docking: From Interaction to Interactome

The protein-protein docking problem is one of the focal points of activity in computational biophysics and structural biology. The three-dimensional structure of a protein-protein complex, generally, is more difficult to determine experimentally than the structure of an individual protein. Adequate computational techniques to model protein interactions are important because of the growing number of known protein structures, particularly in the context of structural genomics. Docking offers tools for fundamental studies of protein interactions and provides a structural basis for drug design. Protein-protein docking is the prediction of the structure of the complex, given the structures of the individual proteins. In the heart of the docking methodology is the notion of steric and physicochemical complementarity at the protein-protein interface. Originally, mostly high-resolution, experimentally determined (primarily by x-ray crystallography) protein structures were considered for docking. However, more recently, the focus has been shifting toward lower-resolution modeled structures. Docking approaches have to deal with the conformational changes between unbound and bound structures, as well as the inaccuracies of the interacting modeled structures, often in a high-throughput mode needed for modeling of large networks of protein interactions. The growing number of docking developers is engaged in the community-wide assessments of predictive methodologies. The development of more powerful and adequate docking approaches is facilitated by rapidly expanding information and data resources, growing computational capabilities, and a deeper understanding of the fundamental principles of protein interactions.     

A new method of survey and data analysis in phenology

Abstract. A new, computerized method is presented for the survey and analysis of phenological data on the vegetative cycle of tree species in complex forest structures. It is based on the principles of classical phenology, phytosociological sampling techniques and the main concepts of growth analysis. The method considers the development of phenological phases as a stochastic process, and allows a quantitative and mathematical-statistical comparisonbetweenphenorhythms of trees and crown sections, and correlations with environmental variables.