3D Modelling of Biological Systems for Biomimetics

1　IntroductionBasedonthereviewofthepreviousworkof 3Dgeometricalmodellingtechniquesandsystemsdevelopedforindustrial,medicalandanimationapplications,thispaperdiscussestheproblemsassociatedwiththeexist ingtechniquesandsystems ,especiallywhenappliedto3Dmodellingof plants ,insectsandanimalsforbiomimeticsresearchanddevelopment .Then ,paperproposessomeareasofresearchinterestsin 3Dmod ellingofplants ,insectsandanimalsforBiomimetics .Toavoidtherepeating ,inthispaper ,biologicalobjectswillbeusedtorep…     

Biomimetic modelling

Biomimetics is seen as a path from biology to engineering. The only path from engineering to biology in current use is the application of engineering concepts and models to biological systems. However, there is another pathway: the verification of biological mechanisms by manufacture, leading to an iterative process between biology and engineering in which the new understanding that the engineering implementation of a biological system can bring is fed back into biology, allowing a more complete and certain understanding and the possibility of further revelations for application in engineering. This is a pathway as yet unformalized, and one that offers the possibility that engineers can also be scientists.     

Biomimetic engineering of cellulose-based materials

Biomimetics is a field of science that investigates biological structures and processes for their use as models for the development of artificial systems. Biomimetic approaches have considerable potential in the development of new high-performance materials with low environmental impact. The cell walls of different plant species represent complex and highly sophisticated composite materials that can provide inspiration on how to design and fabricate lightweight materials with unique properties. Such materials can provide environmentally compatible solutions in advanced packaging, electronic devices, vehicles and sports equipment. This review gives an overview of the structures and interactions in natural plant cell walls and describes the first attempts towards mimicking them to develop novel biomaterials.     

Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria

Background

Currently a huge amount of protein-protein interaction data is available therefore extracting meaningful ones are a challenging task. In a protein-protein interaction network, hubs are considered as key proteins maintaining function and stability of the network. Therefore, studying protein-protein complexes from a structural perspective provides valuable information for predicted interactions.

Results

In this study, we have predicted by comparative modelling and docking methods protein-protein complexes of hubs of human NR-RTK network inferred from our earlier study. We found that some interactions are mutually excluded while others could occur simultaneously. This study revealed by structural analysis the key role played by Estrogen receptor (ESR1) in mediating the signal transduction between human Receptor Tyrosine kinases (RTKs) and nuclear receptors (NRs).

Conclusions

Although the methods require human intervention and judgment, they can identify the interactions that could occur together or ones that are mutually exclusive. This adds a fourth dimension to interaction network, that of time, and can assist in obtaining concrete predictions consistent with experiments.

Open peer review

This article was reviewed by Dr. Anthony Almudevar, Prof. James Faeder and Prof. Eugene Koonin. For the full reviews, please go to the Reviewers' comments.     

Correlation between soil characters and forest types: a study in multiple discriminant analysis

Multiple discriminant analysis is a useful multivariate technique in vegetation studies that can be employed for several purposes, even if the underlying statistical assumptions are not satisfied. An example of application of this method is discussed: multiple discriminant analysis was successfully used for evaluating the predictivity of forest types defined by numerical classification of vegetation data with respect to soil variables.Species nomenclature follows Pignatti (1982) for vascular plants and Augier (1966) for mosses.The research has been supported by the IDROSER (Bologna, Italy) and by the Italian C. N. R. (Grant no. 83.02548.04, resp. Prof. A. Pirola). We wish to thank Prof. E. Feoli, Prof. E. van der Maarel, Prof. L. Orlóci and Prof. A. Pirola for suggestions. We are also indebted to Dr N. Filippi who analyzed the soil samples.     

A “Living” Machine

Biomimetics (or bionics) is the engineering discipline that constructs artificial systems using biological principles. The ideal final result in biomimetics is to create a living machine. But what are the desirable and non-desirable properties of biomimetic product7 Where can natural prototypes be found7 How can technical solutions be transferred from nature to technology? Can we use living nature like LEC, O bricks for oonstmction our machines? How can biology help us? What is a living machine? In biomimetic practice only some “part“ (organ, part of organ, tissue) of the observed whole organism is utilized. A possible template for future super-organism extension for biornimetic methods might be drawn from experiments in holistic ecological agriculture (ecological design, permacuhure, ecological engineering, etc. ). The necessary translation of these roles to practical action can be achieved with the Russian Theory of Inventive Problem Solving (TRIZ), specifically adjusted to biology. Thus, permaculture, reinforced by a TRIZ conceptual framework, might provide the basis for Super-Organismic Bionics, which is hypothesized as necessary for effective ecological engineering. This hypothesis is supported by a case study-the design of a sustainable artificial nature reserve for wild pollinators as a living machine.     

An electron microscopic observation on the cross-striated fibrils occurring in the human spermatocyte

Summary Cross-striated fibrils associated with the centriole were found in a presumed young spermatocyte of the human biopsy material. This resembles the structure in the ciliary rootlets already reported in some ciliated epithelia. Probable nature of this structure is briefly discussed.The author wishes to express his sincere thanks to Prof. T. Nonaka and Prof. K. Kurosumi The author wishes to express his sincere thanks to Prof. T. Nonaka and Prof. K. Kurosumi     

Effect of anabolic steroids on rat heart muscle cells

Summary Long-term treatment of female rats with the anabolic steroid hormone Methandrostenolone results in a conspicuous increase of intermediate sized, nonmyofibrillar filaments in muscle cells of the left cardiac ventricle, as revealed by electron microscopy. These filaments, measuring 70–110 Å in diameter, form a characteristic network at the Z-level of the sarcomere, either encircling or penetrating the Z-bands, and appear to insert into the nuclear membrane. The T-system is accompanied by the filaments adjacent to the site of the couplings. Here they are attached to subsarcolemmal electron-dense patches, which may be Z-line precursor material. The filaments may function as a cytoskeleton, to provide passive support in the mechanism of contraction and to mediate nucleo-sarcolemmal and nucleomyofibrillar exchange.The author wishes to thank Prof. Dr. C. Stang-Voss for advice and discussion     

Editorial: "crossing boundaries: stem cells, materials, and mesoscopic sciences"

"Crossing Boundaries: Stem Cells, Materials, and Mesoscopic Sciences". This Special Issue, edited by Prof. Anthony Ho and Prof. Norio Nakatsuji, comprises review articles on the interdisciplinary study of stem cells and material science and is a celebration of the friendship and collaboration between Heidelberg University and Kyoto University in Germany and Japan, respectively.     

Informationsverarbeitung in homogenen Netzen von Neuronenmodellen

Summary The interconnection structures of the peripheral part of the nervous system, which are considered here, are two-dimensional homogeneous networks with time and space dependent inputs and outputs. The principles of connection under consideration comprise lateral inhibition and facilitation. The transfer functions of those linear networks as well as the stability problem are investigated on a digital computer using different system parameters. A closed form solution is given for an infinitely large element density which describes the network properties. In this case an inhibition system acts as high pass filter on the spatial frequencies of the input, whereas a facilitation network acts as low pass filter. The properties of the networks and the transformations in case of moving patterns are analysed using the methods of systems theory.

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Auszug aus einer Dissertation an der Fakultät für Maschinenwesen der Technischen Universität Hannover, Institut für Theoretische Elektrotechnik (Prof. Dr.-Ing. habil. H. Tischner).

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Herrn Prof. Dr.-Ing. habil. H. Tischner danke ich für die Anregung zu dieser Arbeit und seine ständige Unterstützung. Mein Dank gilt ferner der Firma Brown, Boveri & Cie. AG, Mannheim, für die finanzielle Förderung. Den Mitarbeitern im Institut für Schwingungsforschung, insbesondere Herrn Direktor Dr.-Ing. A. Schief bin ich für wertvolle Diskussionen verpflichtet.     

Water near lipid membranes as seen by infrared spectroscopy

The ordering and H-bonding characteristics of the hydration water of the lipid 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) were studied using polarized infrared spectroscopy by varying either the temperature or the relative humidity of the ambient atmosphere of multibilayer samples. The OH-stretching band of lipid-bound water was interpreted by a simplified two-state model of well-structured, low density “network” water and of less-structured dense “multimer” water. The IR-spectroscopic data reflect a rather continuous change of the water properties with increasing distance from the membrane and with changing temperature. Network and multimer water distribute across the whole polar interphase with changing composition and orientation. Upon dehydration the fraction of network water increases from about 30 to 60%, a value which is similar to that in supercooled water at −25°C. The highly ordered gel phase gives rise to an increased fraction of structured network water compared with the liquid crystalline phase. The IR order parameter shows that the water dipoles rearrange from a more parallel towards a more perpendicular orientation with respect to the membrane normal with progressive hydration. Dedicated to Prof. K. Arnold on the occasion of his 65th birthday.     

Heteropolarity in unicellular cyanobacteria: structure and development ofCyanocystis violacea

Cyanocystis violacea isolated from a marine rock sample conforms with the diagnosis ofDermocarpa violacea Crouan in all significant characteristics. The distinct heteropolarity of the cells and simultaneous cell divisions, are stable characters in culture. Development and growth of cells, simultaneous cell division and nanocyte formation have been documented by single-cell slide cultures and fine structural studies. The reddish violet color of the cytoplasm is due to the abundance of phycoerythrin.This paper is dedicated to Prof. DrLothar Geitler, whose monumental contribution to the knowledge of blue-green algae will remain the basis for future studies on these organisms for many years to come. One of us (EIF) was fortunate enough to have had Prof.Geitler as his major professor. All of us consider Prof.Geitler our teacher.     

On the harderian gland of the domestic duck (Anas platyrhynchus)

Summary The parenchyma of the Harderian gland of the domestic duck consists of numerous tubular terminal portions, lined by a simple columnar epithelium. Its secretory surface is increased by intratubular folds. Within the cytoplasm of the epithelial cells secretory granules are observed. Polysaccharides of different nature are demonstrated. Strikingly, all centrally located cells contain a periodate reactive mucin. The successive administration of the PAS reaction and of Alcian Blue reveals the coexistence of acid and neutral mucins in the same cells. A metachromatic reaction of the mucosubstances at pH 1.0 was observed and the presence of acid sulfated groups in the Harderian gland, as demonstrated byAlcian Blue at pH 0.5, thereby confirmed. There was no glycogen reaction.The author wishes to thank Prof. Dr. W. Kühnel for his assistance and introduction to the topic for his dissertation. His thanks also go to Prof. Dr. G. Petry, and Prof. Dr. E. Roosen-Runge of the University of Washington, Seattle, USA, for their interest and suggestions.     

Protein Design and Evolution for Biocatalysis

Cover illustration: Soon designing proteins on demand? This is the vision expressed by the designer pencils pointing at the logo of the meeting held in September 2006 in Greifswald, Germany. This special issue was edited by Prof. Uwe Bornscheuer from Greifswald, who selected papers from keynote speakers at this meeting. With special thanks to Prof. Romas Kazlauskas, University of Minnesota, for the design of the conference logo. Pencils © FOTOLIA.     

实验室大纪事

本实验室学术委员会第一次会议于一九八五年十一月二十七一二十九日在北京举行.除了艾棣教授(赫尔辛基大学)、柯夫教授(康乃尔大学)及朱澄教授(北京大学)因故缺席以外,其余委员都出席了会议.中国科学院微生物研究所所长宋大康教授致辞并代表研究所向各委员颁发了聘书.研究所业务处处长杨菊菊同志出席了会议.学术委员会主任魏江春同志向委员们传达了中国科学院院长卢嘉锡及副院长周光召关于开放实验室的讲话内容;介绍了该实验室的筹建过程;提出了本实验室的研究方向及课题申请指南草案交会议审议.经会议讨论修改后一致通过了本实验室的研究方向及课题申请指南.会议还审议了十二件课题申请书;通过了其中九项.此外,经会议讨论决定,本实验室将编辑出版年报,以发表本实验室的研究成果.年报将以英文版公开发行.本实验室学术委员会同时也是年报编辑委员会.     

Chromosome breakage and blastic transformation of lymphocytes in ataxia-telangiectasia

Cytogenetic studies in two homozygous siblings with ataxia-telangiectasia show a high degree of endogenous chromosomal breakage in lymphocyte cultures. The responsiveness of the lymphocytes to phytohemagglutinin is impaired.Direktor: Prof. Dr. H. Hamperl Direktor: Prof. Dr. H. Hungerland     

Biomimetics: From Bioinformatics to Rational Design of Dendrimers as Gene Carriers

Biomimetics, or the use of principles of Nature for developing new materials, is a paradigm that could help Nanomedicine tremendously. One of the current challenges in Nanomedicine is the rational design of new efficient and safer gene carriers. Poly(amidoamine) (PAMAM) dendrimers are a well-known class of nanoparticles, extensively used as non-viral nucleic acid carriers, due to their positively charged end-groups. Yet, there are still several aspects that can be improved for their successful application in in vitro and in vivo systems, including their affinity for nucleic acids as well as lowering their cytotoxicity. In the search of new functional groups that could be used as new dendrimer-reactive groups, we followed a biomimetic approach to determine the amino acids with highest prevalence in protein-DNA interactions. Then we introduced them individually as terminal groups of dendrimers, generating a new class of nanoparticles. Molecular dynamics studies of two systems: PAMAM-Arg and PAMAM-Lys were also performed in order to describe the formation of complexes with DNA. Results confirmed that the introduction of amino acids as terminal groups in a dendrimer increases their affinity for DNA and the interactions in the complexes were characterized at atomic level. We end up by briefly discussing additional modifications that can be made to PAMAM dendrimers to turned them into promising new gene carriers.     

Eulogy to the Quartet and The Gleaning Platform (Trend and End)

The following two poems are a tribute to honor the four prominent Igbo Scholars who have passed away, and whose works touch most directly on the area of Igbo culture and identity: Prof Don Ohadike, convener of the first Igbo Studies Association conference at Ithaca, Prof Ikenna Nzimiro, member of Dialectical Anthropology’s international editorial board, Prof Victor Uchendu, author of the classic ethnography, The Igbo of Southeastern Nigeria, and most recently, Prof Michael Mbabuike, executive board member of Dialectical Anthropology.