Toward a human-like biped robot with compliant legs

Conventional models of bipedal walking generally assume rigid body structures, while elastic material properties seem to play an essential role in nature. On the basis of a novel theoretical model of bipedal walking, this paper investigates a model of biped robot which makes use of minimum control and elastic passive joints inspired from the structures of biological systems. The model is evaluated in simulation and a physical robotic platform with respect to the kinematics and the ground reaction force. The experimental results show that the behavior of this simple locomotion model shows a considerable similarity to that of human walking. © 2006 The authors.

Finding resonance: Adaptive frequency oscillators for dynamic legged locomotion

There is much to gain from providing walking machines with passive dynamics, e.g. by including compliant elements in the structure. These elements can offer interesting properties such as self-stabilization, energy efficiency and simplified control. However, there is still no general design strategy for such robots and their controllers. In particular, the calibration of control parameters is often complicated because of the highly nonlinear behavior of the interactions between passive components and the environment. In this article, we propose an approach in which the calibration of a key parameter of a walking controller, namely its intrinsic frequency, is done automatically. The approach uses adaptive frequency oscillators to automatically tune the intrinsic frequency of the oscillators to the resonant frequency of a compliant quadruped robot The tuning goes beyond simple synchronization and the learned frequency stays in the controller when the robot is put to halt. The controller is model free, robust and simple. Results are presented illustrating how the controller can robustly tune itself to the robot, as well as readapt when the mass of the robot is changed. We also provide an analysis of the convergence of the frequency adaptation for a linearized plant, and show how that analysis is useful for determining which type of sensory feedback must be used for stable convergence. This approach is expected to explain some aspects of developmental processes in biological and artificial adaptive systems that "develop" through the embodied system-environment interactions. © 2006 IEEE.

Embodied artificial intelligence: Trends and challenges

The field of Artificial Intelligence, which started roughly half a century ago, has a turbulent history. In the 1980s there has been a major paradigm shift towards embodiment. While embodied artificial intelligence is still highly diverse, changing, and far from "theoretically stable", a certain consensus about the important issues and methods has been achieved or is rapidly emerging. In this non-technical paper we briefly characterize the field, summarize its achievements, and identify important issues for future research. One of the fundamental unresolved problems has been and still is how thinking emerges from an embodied system. Provocatively speaking, the central issue could be captured by the question "How does walking relate to thinking?" © Springer-Verlag Berlin Heidelberg 2004.

Design and control of a pendulum driven hopping robot

In this paper a new kind of hopping robot has been designed which uses inverse pendulum dynamics to induce bipedal hopping gaits. Its mechanical structure consists of a rigid inverted T-shape mounted on four compliant feet. An upright "T" structure is connected to this by a rotary joint. The horizontal beam of the upright "T" is connected to the vertical beam by a second rotary joint. Using this two degree of freedom mechanical structure, with simple reactive control, the robot is able to perform hopping, walking and running gaits. During walking, it is experimentally shown that the robot can move in a straight line, reverse direction and control its turning radius. The results show that such a simple but versatile robot displays stable locomotion and can be viable for practical applications on uneven terrain.

结合飞行的快速步行导航技术

在对现有虚拟环境导航技术进行分析的基础上,针对单一导航方式难以同时胜任多种导航任务的问题,提出并实现了一种结合飞行的快速步行导航技术。该导航技术通过对用户交互意图和场景上下文的感知自动调整导航模式以适应不同类型导航任务的需求,从总体上提高了复杂虚拟环境下的导航效率。

几种PCR方法在克隆鸭肠炎病毒未知基因中的应用

以DEV基因组DNA为模板,用简并PCR、改良Targeted gene walking PCR、改良的热不对称交错PCR和Long-PCR,获得了5350bp、11083bp和2905bp3段DEV未知基因片段,DNA序列分析发现包含9个开放阅读框,将这些序列提交GenBank分别获得的登录号为:EF554396~EF554403。结果表明,多种PCR方法联合使用可以高效的实现对鸭肠炎病毒未知基因的克隆。

Genomic organization, nucleotide sequence analysis of the core histone genes cluster in Chlamys farreri and molecular evolution assessment of the H2A and H2B

This work represents the nucleotide sequence of the core histone gene cluster from scallop Chlamys farreri. The tandemly repeated unit of 5671 bp containing a copy of the four core histone genes H4, H2B, H2A and H3 was amplified and identified by the techniques of homology cloning and genomic DNA walking. All the histone genes in the cluster had the structures in their 3' flanking region which related to the evolution of histone gene expression patterns throughout the cell cycle, including two different termination signals, the hairpin structure and at least one AATAAA polyadenylation signal. In their 5' region, the transcription initiation sites with a conserved sequence of 5'-PyATTCPu-3' known as the CAP site were present in all genes except to H2B, generally 37-45 bp upstream of the start code. Canonical TATA and CAAT boxes were identified only in certain histone genes. In the case of the promoters of H2B and H2A genes, there was a 5'-GATCC-3' element, which had been found to be essential to start transcription at the appropriate site. After this element, in the promoter of H2B, there was another sequence, 5'-GGATCGAAACGTTC-3', which was similar to the consensus sequence of 5'-GGAATAAACGTATTC-3' corresponding to the H2B-specific promoter element. The presence of enhancer sequences (5'-TGATATATG-3') was identified from the H4 and H3 genes, matching perfectly with the consensus sequence defined for histone genes. There were several slightly more complex repetitive DNA in the intergene regions. The presence of the series of conserved sequences and reiterated sequences was consistent with the view that mollusc histone gene cluster arose by duplicating of an ancestral precursor histone gene, the birth-and-death evolution model with strong purifying selection enabled the histone cluster less variation and more conserved function. Meanwhile, the H2A and the H2B were demonstrated to be potential good marks for phylogenetic analysis. All the results will be contributed to the characterization of repeating histone gene families in molluscs.

stochastic process algebra based software process simulation modeling

Chinese Acad Sci, ISCAS Lab Internet Software Technologies

Expression pattern of dmrt4 from olive flounder (Paralichthys olivaceus) in adult gonads and during embryogenesis

The dmrt (doublesex and mab-3 related transcription factor) gene family comprises several transcription factors that share a conserved DM domain. Dmrt1 is considered to be involved in sexual development, but the precise function of other family members is unclear. In this study, we isolated genomic DNA and cDNA sequences of dmrt4, a member of the dmrt gene family, from olive flounder, Paralichthys olivaceus, through genome walking and real-time reverse transcriptase (RT)-PCR. Sequence analysis indicated that its genomic DNA contains two exons and one intron. A transcriptional factor binding sites prediction program identified a sexual development-related protein, Sox9 (Sry-like HMG box containing 9) in its 5' promoter. Protein alignment and phylogenetic analysis suggested that flounder Dmrt4 is closely related to tilapia Dmo (DM domain gene in ovary). The expression of dmrt4 in adult flounder was sexually dimorphic, as shown by real-time RT-PCR analysis, with strong expression in the testis but very weak expression in the ovary. Its expression was also strong in the brain and gill, but there was only weak or no expression at all in some of the other tissues tested of both sexes. During embryogenesis, its expression was detected in most developmental stages, although the level of expression was distinctive of the various stages. Whole mount in situ hybridization revealed that the dmrt4 was expressed in the otic placodes, forebrain, telencephalon and olfactory placodes of embryos at different developmental stages. These results will improve our understanding of the possible role of flounder dmrt4 in the development of the gonads, nervous system and sense organs.

Cloning and characterization of beta-carotene ketolase gene promoter in Haematococcus pluvialis

The unicellular green alga Haematococcus pluvialis accumulates a highly valuable ketocarotenoid, astaxanthin, under various environmental stresses. beta-carotene ketolase (BKT) plays a key role in astaxanthin biosynthesis in H. pluvialis. In this paper, an approximate 700 bp 5'-flanking region of the bkt gene containing a putative promoter was cloned through walking upstream. The results of the sequence analysis showed that this bkt 5'-flanking region might have cis-acting elements such as sterol regulatory element (SRE-1)-like motifs, the C-repeat/dehydration responsive element (DRE) and al-3 proximal element (APE)-like motifs, except for typical TATA and CCAAT boxes. The results of the P-galactosidase assay and the transient expression of lacZ driven by a series of sequential deletions revealed that a minimal promoter-like region might exist from -630 to -408 bp, and the highest promoter activity was observed to span the positions from -630 to -308 bp. The results of the site-directed mutagenesis of a C-repeat/DRE and two APE-like motifs in a promoter-like region (-630 to -308 bp) suggested that two APE-like motifs might be essential for transcriptional control of the bkt gene.

Preliminary study on a potential antibacterial peptide derived from histone H2A in hemocytes of scallop Chlamys farreri

Histone H2A is reported to participate in host defense response through producing novel antimicrobial peptides (AMPs) from its N-terminus in vertebrates and invertebrates, while the AMPs derived from H2A have not to our knowledge been reported in mollusca. In the present study, gene cloning, mRNA expression of H2A from scallop Chlamys farreri, and the recombinant expression of its N-terminus were conducted to investigate whether a similar mechanism exists in mollusca. The full-length DNA of H2A was identified by the techniques of homology cloning and genomic DNA walking, The full-length DNA of the scallop H2A was 696 bp long, including a 5'-terminal untranslated region (UTR) of 90 bp, a 3'-terminal UTR of 228 bp with a stem-loop structure and a canonical polyadenylation signal sequence AATAAA, and an open reading frame of 375 bp encoding a polypeptide of 125 amino acids. The mRNA expression of H2A in the hemocytes of scallop challenged by microbe was measured by semi-quantitative RT-PCR. The expression of H2A was not upregulated after stimulation, suggesting that H2A did not participate in immunity response directly. The DNA fragment of 117 bp encoding 39 amino acids corresponding to the N-terminus of scallop H2A, which was homologous to buforin I in vertebrates, was cloned into Pichia pastoris GS115. The transformants (His(+) Mut(+)) containing multi-copy gene insertion were selected with increasing concentration of antibiotic G418. The peptide of 39 amino acids was expressed by induction of 0.5% methanol. The recombinant product exerted antibacterial activity against both Gram-positive (G(+)) and Gram-negative (G(-)) bacteria. The antibacterial activity toward G(+) bacteria was 2.5 times more than that against G(-) bacteria. The results elucidated that N-terminus of H2A was a potential AMP and provided a promising candidate for a new antibiotic screening. However, whether H2A is really involved in scallop immune response mechanisms needs to be further investigated. (C) 2006 Elsevier Ltd. All rights reserved.

Complete mitochondrial genome of the Asian paddle crab Charybdis japonica (Crustacea: Decapoda: Portunidae): gene rearrangement of the marine brachyurans and phylogenetic considerations of the decapods

Given the commercial and ecological importance of the Asian paddle crab, Charybdis japonica, there is a clearly need for genetic and molecular research on this species. Here, we present the complete mitochondrial genome sequence of C. japonica, determined by the long-polymerase chain reaction and primer walking sequencing method. The entire genome is 15,738 bp in length, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes, plus the putative control region, which is typical for metazoans. The total A+T content of the genome is 69.2%, lower than the other brachyuran crabs except for Callinectes sapidus. The gene order is identical to the published marine brachyurans and differs from the ancestral pancrustacean order by only the position of the tRNA (His) gene. Phylogenetic analyses using the concatenated nucleotide and amino acid sequences of 13 protein-coding genes strongly support the monophyly of Dendrobranchiata and Pleocyemata, which is consistent with the previous taxonomic classification. However, the systematic status of Charybdis within subfamily Thalamitinae of family Portunidae is not supported. C. japonica, as the first species of Charybdis with complete mitochondrial genome available, will provide important information on both genomics and molecular ecology of the group.

Molecular cloning, characterization and evolutionary analysis of phytoene desaturase (PDS) gene from Haematococcus pluvialis

Phytoene desaturase is one of the most important enzymes necessary for the biosynthesis of carotenoids in some cyanobacteria, green algae and plants. In this study, genomic DNA and cDNA of pds were cloned from unicellular green alga Haematococcus pluvialis strain323 using PCR and RT-PCR methods. The cDNA was cloned into plasmid pET-28a and efficiently expressed in Escherichia coli BL21. The complete genomic PDS gene of H. pluvialis, 3.3 kb in size, included eight exons and seven introns. To locate transcriptional regulation elements, an approximate 1 kb of 5'-flanking region was isolated by genome-walking method. Results of bioinformatic analysis showed several putative cis-elements e.g. the ABRE motif (abscisic acid responsive element), the C-repeat/DRE (dehydration responsive element) motif and the GCN4 motif were located in 5'-flanking region of pds. Results of phylogenetic analyses reveal that different sources of PDS genes form a separate clade, respectively, with 100% bootstrap support. Moreover, a maximum likelihood approach was employed to detect evidence of positive selection in the evolution of PDS genes. Results of branch-site model analysis suggest that 7.9% of sites along the green algal branch are under positive selection, and the PDS gene in green algae exhibits a different evolutionary pattern from its counterparts in cyanobacteria and plants.

扇贝大防御素和G型溶菌酶的基因克隆与重组表达

扇贝养殖是我国传统的海水养殖产业，但自1997 年以来，养殖扇贝陆续爆发的大规模死亡，不但造成了巨大的经济损失，而且严重影响了该产业的健康发展。扇贝病害的不断爆发以及病因的多样性迫切要求制定新的疾病防治措施和开发新型的抗菌物质。 从扇贝自身的免疫防御因子入手，筛选和克隆参与免疫防御的功能基因，一方面可以研究抗病功能基因在病原感染或环境胁迫条件下的表达规律，深入探讨扇贝的免疫防御机制，并可作为抗病良种选育的分子标记，指导扇贝的遗传改良和抗病品系的培育；另一方面，可对抗菌效应物实现重组表达，开发新型的病害预防治疗制剂，取代目前普遍使用的抗生素和化学药物。抗菌效应物是机体在免疫应答过程中产生的多肽类物质，对侵入生物体内的细菌、病毒具有很强的免疫杀灭作用，对抗菌效应物的研究有助于深入了解机体先天性免疫防御的机制。 本研究采用大规模EST测序方法，结合cDNA末端快速扩增（RACE）技术，从海湾扇贝血淋巴中克隆到了大防御素基因（big defensin, AiBD）的全长cDNA序列，该cDNA全长为531 bp，其中5' 非编码区（UTR）为24 bp，开放阅读框（Open Reading Frame, ORF）含有369 bp，编码122 个氨基酸残基；随后为138-bp 的3' UTR，包括一个多聚腺苷酸信号序列（AATAAA）和ploy A尾巴。分析表明，海湾扇贝大防御素是以前体的形式合成，前体分子包括信号肽、前域和成熟肽三部分。采用Northern blot方法，以DIG标记的DNA探针检测了 AiBD mRNA在不同组织中的表达。结果发现，AiBD 基因的转录本主要在血淋巴中表达，在鳃中也有微量的表达，而在外套膜、闭壳肌、性腺及肝胰腺中检测不到杂交信号。采用QRT-PCR（quantitative real time PCR）对鳗弧菌感染后海湾扇贝血淋巴中AiBD mRNA 的表达量进行了检测，结果发现在感染后8 h 内， AiBD mRNA 的相对表达量平缓升高；随着刺激时间的增长，AiBD基因的mRNA表达量急剧增加，在刺激后16 h 和32 h 分别达到了空白组的72.3 倍和131.1 倍。为了研究海湾扇贝大防御素的抗菌活性，将其成熟肽编码区克隆到毕赤酵母表达载体pPIC9K并实现了重组表达。抑菌实验表明，重组AiBD具有广谱的抗菌活性，其对供试的三株革兰氏阳性菌（藤黄微球菌、溶壁微球菌、金黄色葡萄球菌）都表现出显著的抗菌活性，而对革兰氏阴性菌（鳗弧菌、亮弧菌）的抑菌活性则相对较弱；此外，重组AiBD对表达宿主也表现出杀菌活性，证明其具有抗真菌活性。 根据栉孔扇贝G 型溶菌酶基因的cDNA序列，利用构建的Genome Walking 文库获得了栉孔扇贝G 型溶菌酶基因的全长序列，该基因序列全长为8131 bp，由六个外显子和五个内含子组成。六个外显子长度分别为55 bp，60 bp，90 bp，113 bp，145 bp 和140 bp；五个内含子的长度分别为1126 bp，2161 bp，2744 bp，750 bp和592 bp；内含子的两侧都具有RNA正确剪接所必需的识别位点（GT/AG）。利用TRANSFAC 软件对栉孔扇贝G 型溶菌酶基因的5' 侧翼序列分析发现，该基因的5' 侧翼具有 TATA box 和 CAAT box 的共有序列；此外，在该基因的5' 侧翼发现了C/EBP、NF-κB、OCT-1 和 NF-IL6 等参与免疫基因激活的转录因子潜在结合位点。采用Northern blot方法，以生物素标记的RNA 探针检测了栉孔扇贝G 型溶菌酶基因在不同组织中的表达。结果发现，该基因的转录本主要在鳃、性腺及肝胰腺中表达，在血细胞和外套膜中也有微量的的表达，而在闭壳肌中检测不到杂交信号，这表明栉孔扇贝G 型溶菌酶可能兼备参与机体免疫防御和消化的功能。为了研究栉孔扇贝G 型溶菌酶的抗菌活性，将其成熟肽编码区克隆到毕赤酵母表达载体pPIC9K并实现了重组表达。抑菌实验表明，重组产物具有显著的抗阳性菌活性，其对供试的藤黄微球菌、溶壁微球菌表现出明显的抑制作用，对金黄色葡萄球菌未检测到抑制活性；而对革兰氏阴性菌仅表现出微弱的抑菌活性（亮弧菌和鳗弧菌），对大肠杆菌则基本无抑制活性。

栉孔扇贝核心组蛋白的基因结构及H2A抗菌活性的研究

栉孔扇贝是我国传统的海水养殖品种，但自1997 年以来，养殖扇贝陆续爆发的大规模死亡，不但造成了巨大的经济损失，而且严重影响了该产业的健康发展。目前，虽然针对扇贝养殖环境、病原以及养殖技术等方面开展了大量的研究工作，提出了许多防病治病的措施，并取得了一定的成效。但由于引起养殖扇贝病害的病原和发病原因的多样性，大量使用抗菌素和农药后造成病原微生物抗药性的提高以及对环境造成的严重破坏，贝类养殖业要摆脱病害的困扰，必须开辟新的疾病防治途径。 从扇贝自身的免疫防御因子入手，筛选和克隆参与免疫防御的功能基因，尤其是一些新颖的具有抗菌活性的分子，对于深入探讨扇贝的免疫防御机制，指导扇贝的遗传改良和抗病品系的培育具有重要的意义；另一方面，可对抗菌效应物实现重组表达，开发新型的病害预防治疗制剂，取代目前普遍使用的抗生素和化学药物。抗菌效应物是机体在免疫应答过程中产生的多肽类物质，对侵入生物体内的细菌、病毒具有很强的免疫杀灭作用，对抗菌效应物的研究有助于深入了解机体先天性免疫防御的机制。 本研究在同源克隆策略的基础上，从利用构建的Genome Walking 文库中克隆到了栉孔扇贝核心组蛋白群的全长序列，该串联重复序列全长5671bp，包括各一个拷贝的组蛋白H4, H2B, H2A 和 H3。所有的核心组蛋白在3’侧翼序列均具有与其在细胞周期进化模式相关的特征结构，即两个不同的终止信号：发卡结构和至少一个多聚腺苷酸信号序列（AATAAA）。在5’区域的起始密码子上游37–45 bp处的保守的CAP位点（5’-PyCATTCPu-3’）存在于除H2B外的每一个基因中；规则的TATA 和CAAT元件也在核心组蛋白群中的个别的基因中找到。在H2B 和H2A基因的启动子区域，对于定位转录起始位点非常重要的元件（5’-GATCC-3’）也相对保守； 在H2B启动子区域存在着与其特征序列（5’-GGAATAAACGTATTC-3’）相似性很高的序列结构5’-GGATCGAAACGTTC-3’。增强子序列只发现存在于H4 和 H3基因中，其序列结构与组蛋白增强子序列(5’-TGATATATG-3’)基本匹配。在组蛋白基因群中存在着一些保守的序列和重复结构表明组蛋白基因的进化是采取“生与死的进化模 式”并伴随着强的纯化选择压力，使得该基因群变异较少以保持其基本功能。同时，利用18S rRNA做参照，探讨了H2A 和H2B作为分子系统进化分析的潜在分子标记，表明组蛋白H2A 和H2B可以作为分子系统进化分析得候选分子，它们在区分近缘种的分辨率上表现出了更高的灵敏度。该研究结果为进一步定性软体动物组蛋白重复单位提供了基础。 在脊椎动物中，组蛋白H2A通过特异性剪切其N末端产生新颖的抗菌肽的形式来参与宿主的免疫应答反应，在软体动物中是否存在同样的机制还未有研究报道。本研究利用上述克隆的H2A基因研究了其在病原胁迫下的表达变化规律并对其N末端39aa进行了重组表达和抗菌活性分析，以期为开发和利用软体动物的新颖的抗菌肽提供理论依据。半定量RT-PCR发现血细胞中H2A 的mRNA 在微生物感染前后的表达量没有任何显著的变化，表明H2A本身并不直接参与对病原的清除过程或者说病原微生物并不能诱导H2A的表达。因此，我们推测该基因可能象脊椎动物一样以前体形式存在，经剪切后参与宿主的免疫应答过程，为此我们研究了H2A的N末端的抗菌活性。通过将与脊椎动物buforin I同源的H2A的N末端39aa克隆到毕赤酵母表达载体pPIC9K实现了该基因N末端的重组表达。抑菌实验表明，重组产物具有广谱的抗菌活性，其对供试的革兰氏阳性菌藤黄微球菌表现出显著的抗菌活性，而对革兰氏阴性菌（鳗弧菌、亮弧菌）的抑菌活性则相对较弱；此外，重组产物对毕赤酵母GS115也表现出一定的杀菌活性，证明其具有抗真菌活性。上述研究结果证明组蛋白H2A的N末端是一种潜在的抗菌肽，但该抗菌肽是否参与机体的免疫应答过程需要进一步的深入研究。