Changes in the amino acid code.

The genetic code is characterized by a pattern arising from "wobble-pairing" between codons and anticodons, so that one nucleotide in the first anticodon position can pair with more than one nucleotide in the third position of a codon. Earlier codes may have existed in which there were fewer anticodons than at present, so that these earlier codes contained fewer amino acids. The universal code was formerly thought to be the only currently existing code used by terrestrial species. It is now known that differences exist from the universal code in mitochondrial coding systems, and also that mitochondrial systems differ from each other. These findings lend support to the proposal that archetypal codes preceded the present universal code. Such archetypal codes may have had some resemblances to mitochondrial codes.     

Possible complex organic compounds on Mars.

It is suggested that primitive Mars had somehow similar environments as primitive Earth. If life was born on the primitive earth using organic compounds which were produced from the early Earth environment, the same types of organic compounds were also formed on primitive Mars. Such organic compounds might have been preserved on Mars still now. We are studying possible organic formation on primitive and present Mars. A gaseous mixture of CO2, CO, N2 and H2O with various mixing ratios were irradiated with high energy protons (major components of cosmic rays). Hydrogen cyanide and formaldehyde were detected among volatile products, and yellow-brown-colored water-soluble non-volatile substances were produced, which gave amino acids after acid-hydrolysis. Major part of "amino acid precursors" were not simple molecules like aminonitriles, but complex compounds which eluted earlier than free amino acids in cation-exchange HPLC. These organic compounds should be major targets in the future Mars mission. Strategy for the detection of the complex organics on Mars will be discussed.     

Chemical evolution of primitive solar system bodies.

In this paper we summarize some of the most salient observations made recently on the organic molecules and other compounds of the biogenic elements present in the interstellar medium and in the primitive bodies of the solar system. They include the discovery of the first phosphorus molecular species in dense interstellar clouds, the presence of complex organic ions in the dust and gas phase of Halley's coma, the finding of unusual, probably presolar, deuterium-hydrogen ratios in the amino acids of carbonaceous chondrites, and new developments on the chemical evolution of Titan, the primitive Earth, and early Mars. Some of the outstanding problems concerning the synthesis of organic molecules on different cosmic bodies are also discussed from an exobiological perspective.     

A minimal living system and the origin of a protocell

Based on our current knowledge of molecular biology a living entity os a negentropic system, made of specific catalytic and informational macromolecules, which has the ability to reproduce itself, selectively interact with the environment, increase complexity, undergo mutation and evolve by natural selection. At the cellular level the essential molecular attributes of a minimal living system are considered to be the following: (a) Linear informational molecules, protoRNA (protoDNA) at least 10 mononucleotides long, capable to code for at least 2 amino acids; (b) Code-translating molecules, aminoacyl-proto tRNAs at least 5 mononucleotides long; (c) Protoenzymes, oligopeptides of at least 2 amino acids, with measurable catalytic activity for phosphodiester, pyrophosphate and peptide bond formation; (d) Protoribosomes, RNA-peptide complexes which facilitate the interaction of the above three types of molecules, and (e) Protomembranes, liposomes made of amphiphilic lipids and peptides which can provide the semipermeability and the proton gradient necessary for the synthesis of pyrophosphate, ATP and other biochemical compounds. The transition from subcellular Lamarckian evolution to cellular Darwinian evolution required the cooperative interaction, within an internal microenvironment, of the above five types of molecular species.     

Chemical evolution and the origin of life.

During the last three decades major advances have been made in our understanding of the formation of carbon compounds in the universe and of the occurence of processes of chemical evolution. 1) Carbon and other biogenic elements (C,H,N,O,S and P) are some of the most abundant in the universe. 2) The interstellar medium has been found to contain a diversity of molecules of these elements. 3) Some of these molecules have also been found in comets which are considered the most primordial bodies of the solar system. 4) The atmospheres of the outer planets and their satellites, for example, Titan, are actively involved in the formation of organic compounds which are the precursors of biochemical molecules. 5) Some of these biochemical molecules, such as amino acids, purines and pyrimidines, have been found in carbonaceous chondrites. 6) Laboratory experiments have shown that most of the monomers and oligomers necessary for life can be synthesized under hypothesized but plausible primitive Earth conditions from compounds found in the above cosmic bodies. 7) It appears that the primitive Earth had the necessary and sufficient conditions to allow the chemical synthesis of biomacromolecules and to permit the processes required for the emergence of life on our planet. 8) It is unlikely that the emergence of life occurred in any other body of the solar system, although the examination of the Jovian satellite Europa may provide important clues about the constraints of this evolutionary process. Some of the fundamental principles of chemical evolution are briefly discussed.     

Organics produced by ion irradiation of ices: some recent results.

Some results, recently obtained from laboratory experiments of ion irradiation of ice mixtures containing H, C, N, and O, are here summarized. They are relevant to the formation and evolution of complex organics on interstellar dust, comets and other small bodies in the external Solar System. In particular the formation of CN-bearing species is discussed. Interstellar dust incorporated into primitive Solar System bodies and subsequently delivered to the early Earth, may have contributed to the origin of life. The delivery of CN-bearing species seems to have been necessary because molecules containing the cyanogen bond are difficult to be produced in an environment that is not strongly reducing as that of the early Earth probably was. Moreover we report on an ongoing research program concerning the interaction between refractory materials produced by ion irradiation of simple ices and biological materials (amino acids, proteins, cells).     

Formation of bioorganic compounds in planetary atmospheres by cosmic radiation.

Simulated planetary atmospheres (mixtures of simple gases) were irradiated with high energy particles to simulate an action of cosmic rays. When a mixture of carbon monoxide, nitrogen and water was irradiated with 2.8-40 MeV protons, a wide variety of bioorganic compounds including amino acids, imidazole, and uracil were identified in the products. The amount of amino acids was proportional to the energy deposit to the system. Various kinds of simulated planetary atmospheres, such as "Titan type" and "Jovian type", were also irradiated with high energy protons, and gave amino acids in the hydrolyzed products. Since cosmic rays are a universal energy source in space, it was suggested that formation of bioorganic compounds in planetary atmospheres is inevitable in the course of cosmic evolution.     

Chemical evolution of RNA under hydrothermal conditions and the role of thermal copolymers of amino acids for the prebiotic degradation and formation of RNA.

The roles of thermal copolymers of amino acids (TCAA) were studied for the prebiotic degradation of RNA. A weak catalytic ability of TCAA consisted of Glu, L-Ala, L-Val, L-Glu, L-Asp, and optionally L-His was detected for the cleavage of the ribose phosphodiester bond of a tetranucleotide (5'-dCrCdGdG) in aqueous solution at 80 degees C. The rate constants of the disappearance of 5'-dCrCdGdG were determined in aqueous solutions using different pH buffer and TCAA. The degradation rates were enhanced 1.3-3.0 times in the presence of TCAA at pH 7.5 and 8.0 at 80 degrees C, while the hydrolysis of oligoguanylate (oligo(G)) was accelerated about 1.6 times at pH 8.0. A weak inhibitory activity for the cleavage of oligo(G) was detected in the presence of 0.055 M TCAA-Std. On the other hand, our recent study on the influences of TCAA for the template-directed reaction of oligo(G) on a polycytidylic acid template showed that TCAA has an acceleration activity for the degradation of the activated nucleotide monomer and an acceleration activity for the formation of G5' ppG capped oligo(G). This series of studies suggest that efficient and selective catalytic or inhibitory activities for either the degradation or formation of RNA under hydrothermal conditions could have hardly emerged from the simple thermal condensation products of amino acids. A scenario is going to be deduced on the chemical evolution of enzymatic activities and RNA molecules concerning hydrothermal earth conditions.     

两类DBL码的性能比较

设计出扩展的Large area Synchronization地址码(LS码)——Daoben Lab地址码(DBL码).DBL码由基本LS码与矩阵左、右直积生成,分别称为DBL左乘码和DBL右乘码,两类DBL码各有特点.DBL右乘码特点是把码字分组,码组间码字存在更大的零相关窗,增加了可用码字数,码组内码字非周期相关性与扩展矩阵行向量的相关性相同;DBL左乘码也是把码字分组,码组间的零相关窗长度不变,没有增加可用码字数,但当以正交矩阵扩展时,码组内有和原LS码同样长度的零相关窗.计算机仿真验证了两类DBL地址码的性质.      

The atmosphere of the primitive earth and the prebiotic synthesis of organic compounds.

The prebiotic synthesis of organic compounds using a spark discharge on various simulated prebiotic atmospheres at 25 degrees has been studied. Methane mixtures contained H2 + CH4 + H2O + N2 + NH3 with H2/CH4 molar ratios from 0 to 4 and pNH3 = 0.1 torr. A similar set of experiments without added NH3 was performed. The yields of amino acids (1.2 to 4.7% based on the carbon) are approximately independent of the H2/CH4 ratio and the presence of added NH3, and a wide variety of amino acids are obtained. Mixtures of H2 + CO + H2O + N2 and H2 + CO2 + H2O + N2, with and without added NH3, all give about 2% yields of amino acids at H2/CO and H2/CO2 ratios of 2 to 4. For the H2/CO and H2/CO2 ratios less than 1, the yields fall off drastically to as low as 10(-3)%. Glycine is almost the only amino acid produced from CO and CO2 atmospheres. These results show that the maximum yield is about the same for the three carbon sources at high H2/carbon ratios, but that CH4 is superior at low H2/carbon ratios. In addition, CH4 gives a much greater variety of amino acids than either CO or CO2. If it is assumed that amino acids more complex than glycine were required for the origin of life, then these results indicate the need for CH4 in the primitive atmosphere. The yields of cyanide and formaldehyde parallel the amino acid results, with yields of HCN and H2CO as high as 13% based on the carbon. Ammonia is also produced from N2 in experiments with no added NH3 in yields as high as 4.9%. These results show that large amounts of NH3 would have been synthesized on the primitive earth by electric discharges. The amount of ammonia formed by hydrolysis of HCN and various nitriles may have exceeded that formed directly in electric discharges.     

Three-dimensional global simulation of multiple ICMEs’ interaction and propagation from the Sun to the heliosphere following the 25–28 October 2003 solar events

This study performs simulations of interplanetary coronal mass ejection (ICME) propagation in a realistic three-dimensional (3D) solar wind structure from the Sun to the Earth by using the newly developed hybrid code, HAFv.2+3DMHD. This model combines two simulation codes, Hakamada–Akasofu–Fry code version 2 (HAFv.2) and a fully 3D, time-dependent MHD simulation code. The solar wind structure is simulated out to 0.08 AU (18 Rs) from source surface maps using the HAFv.2 code. The outputs at 0.08 AU are then used to provide inputs for the lower boundary, at that location, of the 3D MHD code to calculate solar wind and its evolution to 1 AU and beyond. A dynamic disturbance, mimicking a particular flare’s energy output, is delivered to this non-uniform structure to model the evolution and interplanetary propagation of ICMEs (including their shocks). We then show the interaction between two ICMEs and the dynamic process during the overtaking of one shock by the other. The results show that both CMEs and heliosphere current sheet/plasma sheet were deformed by interacting with each other.     

Characteristics and formation of amino acids and hydroxy acids of the Murchison meteorite.

Eight characteristics of the unique suite of amino acids and hydroxy acids found in the Murchison meteorite can be recognized on the basis of detailed molecular and isotopic analyses. The marked structural correspondence between the alpha-amino acids and alpha-hydroxy acids and the high deuterium/hydrogen ratio argue persuasively for their formation by aqueous phase Strecker reactions in the meteorite parent body from presolar, i.e., interstellar, aldehydes, ketones, ammonia, and hydrogen cyanide. The characteristics of the meteoritic suite of amino acids and hydroxy acids are briefly enumerated and discussed with regard to their consonance with this interstellar-parent body formation hypothesis. The hypothesis has interesting implications for the organic composition of both the primitive parent body and the presolar nebula.     

Emergence of adaptable systems and evolution of a translation device

An over-all organizational framework for the origin of life is outlined and attemps for realization are given. Evolution can be described as a process resulting in an increase of “knowledge” where knowledge is the number of carriers of genetic information discarded, on the average, until the evolutionary state under consideration is reached. A model for the evolution of a translation device, a crucial event in the origin of life, is described in detail. Aggregates of short polynucleotide strands in a hairpin conformation play a major role in this model. Experimental evidence for the selectivity of aggregation supports the idea of aggregates as error filters. Chromatographic separation as selection process during chemical evolution supports the model of the early translation device leading to the origin of the genetic code.     

Formation of amino acid precursors in cometary ice environments by cosmic radiation.

Cometary ices are believed to contain water, carbon monoxide, methane and ammonia, and are possible sites for the formation and preservation of organic compounds relating to the origin of life. Cosmic rays, together with ultraviolet light, are among the most effective energy sources for the formation of organic compounds in space. In order to study the possibility of the formation of amino acids in comets or their precursory bodies (interstellar dust grains), several types of ice mixtures made in a cryostat at 10 K ("simulated cometary ices") were irradiated with high energy protons. After irradiation, the volatile products were analyzed with a quadrupole mass spectrometer, while temperature of the cryostat was raised to room temperature. The non-volatile products remaining in the cryostat at room temperature were collected with water. They were acid-hydrolyzed, and analyzed by ion-exchange chromatography. When an ice mixture of carbon monoxide (or methane), ammonia and water was irradiated, some hydrocarbons were formed, and amino acids such as glycine and alanine were detected in the hydrolyzate. These results suggest the possible formation of "amino acid precursors" (compounds yielding amino acids after hydrolysis) in interstellar dust grains by cosmic radiation. We previously reported that amino acid precursors were formed when simulated primitive planetary atmospheres were irradiated with cosmic ray particles. It will be of great interest to compare the amount of bioorganic compounds that were formed in the primitive earth and that brought by comets to the earth.     

Detection of martian amino acids by chemical derivatization coupled to gas chromatography: in situ and laboratory analysis.

If there is, or ever was, life in our solar system beyond the Earth, Mars is the most likely place to search for. Future space missions will have then to take into account the detection of prebiotic molecules or molecules of biological significance such as amino acids. Techniques of analysis used for returned samples have to be very sensitive and avoid any chemical or biological contamination whereas in situ techniques have to be automated, fast and low energy consuming. Several possible methods could be used for in situ amino acid analyses on Mars, but gas chromatography would likely be the most suitable. Returned samples could be analyzed by any method in routine laboratory use such as gas chromatography, already successfully performed for analyses of organic matter including amino acids from martian meteorites. The derivatization step, which volatilizes amino acids to perform both in situ and laboratory analysis by gas chromatography, is discussed here.     

The evolution of nucleotides.

There has been much speculation about the types of molecules that were present in the first living forms. Recent discoveries show that RNA is a more versatile molecule than was previously believed, but whether it was ever able, for example, to synthesize its own monomers from available precursors is not yet known. If amino acids coexisted with nucleosides on the prebiotic Earth, then it seems likely that these two classes of molecules would have interacted with each other. We have been studying oligonucleotide-directed peptide bond formation, and during this work we discovered that aminoacylation of the internal 2'-hydroxyl groups of RNA occurred stereoselectively. Investigation of the mechanism of this reaction has been aided by the use of 3'-inosine methyl phosphate (as a simplified model for a dinucleoside monophosphate) and proton nmr spectroscopy of t-butoxycarbonyl-alanyl esters of nucleosides as models for the transition state of the aminoacylation reaction itself.     

Direct interaction between amino acids and nucleotides as a possible physicochemical basis for the origin of the genetic code.

A study of the association of homocodonic amino acids and selected heterocodonic amino acids with selected nucleotides in aqueous solution was undertaken to examine a possible physical basis for the origin of codon assignments. These interactions were studied using 1H nuclear magnetic resonance spectroscopy (NMR). Association constants for the various interactions were determined by fitting the changes in the chemical shifts of the anomeric and ring protons of the nucleoside moieties as a function of amino acid concentration to an isotherm which described the binding interaction. The strongest association of all homocodonic amino acids were with their respective anticodonic nucleotide sequences. The strength of association was seen to increase with increase in the chain length of the anticodonic nucleotide. The association of these amino acids with different phosphate esters of nucleotides suggests that a definite isomeric structure is required for association with a specified amino acid; the 5'-mononucleotides and (3'-5')-linked dinucleotides are the favored geometries for strong associations. Use of heterocodonic amino acids and nonprotein amino acids supports these findings. We conclude that there is at least a physicochemical, anticodonic contribution to the origin of the genetic code.     

采用LDPC码方案的战术数据链系统

战术数据链系统能够提高部队信息化作战能力,其中信道编码技术是保证消息传输可靠性的关键技术之一.构建了一种新的战术数据链系统,系统采用低密度奇偶校验(LDPC,Low-Density Parity-Check)码方案,LDPC码是适用于传输可靠性要求高的通信系统的新型码组.介绍了LDPC码方案中的和积算法,描述了系统的传输模型,分析了系统在固定频率和加性白色高斯噪声(AWGN,Additive White Gaussian Noise)信道条件下的链路性能.利用计算机进行蒙特卡罗仿真,结果表明:在AWGN信道和瑞利衰落信道下,LDPC编码方案可以有效地降低数据链系统的误比特率,取得比采用里德·所罗门编码的联合战术信息分发系统更好的误码性能.LDPC码作为信道编码技术的备选码组,为进一步提高战术数据链的可靠性提供了一种解决方案.      

Quantitative analysis of mutation and selection in self-replicating RNA.

Mutation and selection as principles of Darwinian evolution have contributed a wealth to qualitative insight and understanding of complex biological organizations. However, for quantitative measurements of Darwinian evolution, only model systems are sufficiently simple to allow calculation of values for the relevant evolution parameters. The model system used for our study comprises short-chained RNA species whose self-replication is catalyzed by Q beta replicase. In this system, phenotypic expression of a genotype is reduced to its efficiency in directing its own synthesis. The mechanism of single-stranded RNA reproduction is well understood: RNA synthesis profiles can be described by compact equations. The selection behaviour of competing RNA species can be precisely predicted, using these equations, from kinetic parameters of the species: at low concentrations, RNA species are selected for overall growth rate (fecundity), at higher concentrations, for rapid binding of replicase (selection for competition), and at still higher concentrations, for minimizing losses caused by formation of inactive double strands. Finally, an ecosystem may be established where the different species coexist, their relative concentrations being functions of their kinetic parameters. The analysis of competition and selection can be extended to mutants of a species. Experimental conditions can be found where quantitative measurement of mutation rates and selective values of mutants is possible. The interplay of mutation and selection results in establishing a quasispecies distribution where mutants are represented according to their rates of mutational formation and their selective values. Replicating RNA clones, when amplified, rapidly build up quasispecies distributions containing pronounced "hot spots", produced predominantly by error propagation of nearly neutral mutants. The primitive model system shows the same complex Darwinian behaviour as observed in evolution of biological systems. In the absence of extraneously added template, Q beta replicase synthesizes after long lag times self-replicating RNA de novo. In a first step, nucleoside triphosphates are condensed randomly; self-replicating templates produced by chance are amplified and optimized.     

低信噪比下分组交织器识别

针对现有的分组交织器识别算法计算复杂高且容错性差缺点,从分组交织后的同步码分布规律出发,提出了一种新的识别算法。首先,利用数据矩阵统计特性,给出了在任意矩阵列数下,同步码和随机业务数据位置上的概率密度分布函数,基于最小错误判决准则,设定了同步码检测门限,同时基于3倍标准差准则,求解出稳健的交织周期识别门限;其次,分析了数据矩阵中每一行与每一列累积量之间的对应关系,提出了一种快速交织周期遍历方法,使得数据矩阵的构建次数大大减少;最后,总结了4个分组交织后同步码分布规律,通过遍历同步码序列,利用同步码之间的位置关系,实现交织同步位置、分组交织列与交织行参数快速识别。仿真结果表明:所提算法具有较强的低信噪比容错性,在信噪比为-6 dB条件下,参数识别率能够达到98%以上,同时与现有的算法相比,其性能提升4~10 dB且计算效率明显提高。