Phylogeny of SARS-CoV based on high-dimensional information geometry

We proposed a novel methodology, which firstly, extracting features from species' complete genome data, using k-tuple, followed by studying the evolutionary relationship between SARS-CoV and other coronavirus species using the method, called "High-dimensional information geometry". We also used the mothod, namely "caculating of Minimum Spanning Tree", to construct the Phyligenetic tree of the coronavirus. From construction of the unrooted phylogenetic tree, we found out that the evolution distance between SARS-CoV and other coronavirus species is comparatively far. The tree accurately rebuilt the three groups of other coronavirus. We also validated the assertion from other literatures that SARS-CoV is similar to the coronavirus species in Group I.

Simple method for estimating minimum bend radii of SOI single mode curved rib waveguides

A simple method based on the effective index method was used to estimate the minimum bend radii of curved SOI waveguides. An analytical formula was obtained to estimate the minimum radius of curvature at which the mode becomes cut off due to the side radiative loss.

An algorithm of analysis tools on points distribution in high dimension space: The distance of a point and an infinite sub-space

This paper discusses the algorithm on the distance from a point and an infinite sub-space in high dimensional space With the development of Information Geometry([1]), the analysis tools of points distribution in high dimension space, as a measure of calculability, draw more attention of experts of pattern recognition. By the assistance of these tools, Geometrical properties of sets of samples in high-dimensional structures are studied, under guidance of the established properties and theorems in high-dimensional geometry.

An analysis and simulation about conditioned launch for very short reach (VSR-4)

VSR4 links use graded index multimode fibers (GIMMFs) as the transmission medium with operation wavelength 850nm. For cost reasons, VCSEL has been selected as the optical source to VSR4. The minimum bandwidth specification for 62.5um GIMMF in VSR4 is only 400 MHz(.)km for over-filled-launch (OFL) condition. The distance of 300 meters is limited over transmission rates of 1.25Gbit/s on the basis of this specification. In order to overcome the OFL bandwidth limit by selective excitation of a limited number of modes, conditioned launch technique is investigated. In this paper, based on a comprehensive dispersion theory of GIMMF, a model is built to simulate the transmission of optical signal in GIMMFs and a comparison between OFL and conditioned launch is analyzed. The result can be the guidelines for the best choice of techniques for various LAN and interconnect systems also.

Optimal distance from high power laser diode to cylindrical microlens in a coupling system

In a practical coupling system, a cylindrical microlens is used to collimate the emission of a high powerlaser diode (LD) in the dimension perpendicular to the junction plane. Using passive alignment, the LD isplaced in the focus of the cylindrical microlens generally, regardless of the performance of the multimodeoptical fiber and the LD. In this paper, a more complete analysis is arrived at by ray-tracing technique,by which the angle θ of the ray after refraction is computed as a function of the angle θo of the ray beforerefraction. The focus of the cylindrical microlens is not always the optimal position of the LD. In fact, inorder to achieve a higher coupling efficiency, the optimal distance from the LD to the cylindrical microlensis dependent on not only the radius R and the index of refraction n of the cylindrical microlens, but alsothe divergence angle of the LD in the dimension perpendicular to the junction plane and the numericalaperture (NA) of the multimode optical fiber. The results of this discussion are in good agreement withexperimental results.

Real-time far distance micro-vibration measurement using an external cavity semiconductor laser interferometer with a feedback control system

An external cavity semiconductor laser interferometer used to measure far distance micro-vibration in real time is proposed. In the interferometer, a single longitudinal mode and excellent coherent characteristic grating external cavity semiconductor laser is constructed and acted as a light source and a phase compensator. Its coherent length exceeds 200 meters. The angle between normal and incidence beam of the far object is allowed to change in definite range during the measurement with this interferometer, and this makes the far distance interference measurement easier and more convenient. Also, it is not required to keep the amplitudes of the first and second harmonic components equal, and then the dynamic range is increased. A feedback control system is used to compensate the phase disturbance between the two interference beams introduced by environmental vibration.

大熊猫“盛林1号”放归监测

大熊猫(Ailuropoda melanoleuca)是我国特有的珍稀濒危物种，国家Ⅰ级重点保护野生动物，被称为“国宝”。目前，大熊猫被局限在我国中西部的岷山、邛崃、大相岭、小相岭、凉山和秦岭6大山系中。对大熊猫的保护和研究，我国政府、保护生物学科研人员、社会各界及国际保护组织都做了大量的工作。根据全国三次大熊猫调查结果显示，大熊猫栖息地片段化现象依然存在，形成多个隔离的大熊猫小种群。尤其在小相岭、大相岭、岷山B和岷山C种群，大熊猫数量较少，且栖息地破碎，面临较大威胁。有的山系大熊猫种群数量些已低于最小可存活大熊猫种群的数量，如果不采取人工措施，这些种群的大熊猫存在灭绝的危险。 将圈养大熊猫放归野外，以补充野外大熊猫种群数量，增加其遗传多样性，复壮和扩大野生大熊猫种群，是大熊猫人工繁育的最终目标。为降低放归的风险性，在放归人工繁育大熊猫前，将救护存活的野生大熊猫先有计划放归野外，并对其进行跟踪监测，对积累大熊猫放归经验，进一步研究大熊猫野外生物学习性，丰富放归地大熊猫种群遗传多样性，为人工繁育大熊猫放归野外夯实基础，具有十分重要的意义。2005年8月8日，国家林业局和四川省人民政府联合将救护野生大熊猫“盛林1号”放归于龙溪－虹口国家级自然保护区内岷山B大熊猫种群栖息地，并进行系统监测研究。成功的积累了一些放归经验和放归大熊猫的生物学资料，为人工繁育大熊猫的放归奠定了一定基础。 2005年8月至2007年6月期间，我们采用GPS无线电项圈、粪便DNA检测和红外线自动触发相机陷阱的方法，对大熊猫“盛林１号”进行了追踪监测，获得了以下成果： 1.通过分析“盛林1号”放归后了活动趋势和采用两种贝叶斯方法，利用目前五大山系的已有微卫星遗传数据，检测“盛林１号”与五大山系的遗传关系的远近，推测其来源于邛崃山系的可能性较大。 2.收集了大量“盛林1号”野外生境选择数据。我们认为“盛林1号”放归后经历了应急期、初步稳定期、长途迁徙期三个阶段（这可能是今后放归大熊猫都必经的三个时期），并与当地大熊猫种群已发生交流。目前“盛林１号”仍在寻找适合的巢域。 3.结合过去监测数据分析，在放归区域大熊猫和羚牛尽管同域分布，但由于食性不同，对微生境选择还是有着很大差异，因此保护管理对策要有针对性。 4.“盛林1号”的放归是成功的。救护大熊猫异地放归工作应继续开展，但要改进放归后的监测技术。要改进现有对人工饲养大熊猫野化培训方法和放归方式，才能真正将人工繁殖个体放归野外。 Giant Panda (Ailuropoda melanoleuca) is an endangered species endemic to China. It was listed as National Protected I Class Species and is crowned as “National treasure” of China. The populations of Giant Panda are limited in 6 mountain system in Center-West of China, i.e. Mingshan, Mt. Qionglai, Mt. Daxiangling，Mt. Xiaoxiangling, Mt. Liangshan and Mt. Qinling. The results of the Third National Survey on Giant Panda showed that the habitats of Giant Panda is still fracted and Giant Panda population is divided into several isolated small populations. Population B from Mt. Daxiangling, Mt. Xiaoxiangling and Mt. Mingshan and Population C from Mt. Mingshan are very small with very fracted habitat and are more endangered. Several populations in those mountain systems are smaller than Minimum Viable Population of Giant Panda. It is very possible that those populations will be extinct without artificial help. The ultimate Goal of Reintroduction caged Giant Panda to wild is to increase wild population size and genetics diversity and rebuild and expand wild Giant Panda population. It is of significant to return rescued wild Giant Panda to wild and monitor their behavior before reintroduction artificial reproduced Giant Panda. It will increase our knowledge on reintroduction of Giant Panda. Aug 8th, 2005, “Shenglin 1”, a rescued wild Giant Panda was returned to Longxi-Hongkou National Nature Reservoir, which is habitat of Giant Panda Population B of Mt. Mingshan. A systematic monitor was carried out on “Shenglin 1”, and the successful return enriched our biological knowledge on Giant Panda reintroduction. It will be very help for future conservation work on reintroduce artificial reproduced Giant Panda. “Shenglin 1” was tracked with GPS collar, DNA in feces and infrared-trigged camera from Aug 2005 to Jun 2007. 1. Locomotion behavior and microsatellites comparison with Giant Panda from the 5 mountain systems indicated that “Shenglin 1” is possibly from Mt. Qionglai. 2. Habitat usage of “Shenglin 1” was studied. It was suggested that there were 3 phases after return, i.e. emergency response, preliminary stable phase and long distance locomotion, which could be a general process for other returned Giant Panda. It was indicated that there was some interaction between “Shenglin 1” and local population. “Shenglin 1” is seeking for suitable home range now. 3. Monitor data also indicated that microhabitat preference of Giant Panda and takin (Budorcas taxicolor) are different because of different diet, though they are sympatric. It was suggested that conservation management for the two species should be plan in particular. 4. The reintroduction of “Shenglin 1” is a successful case. The program of return rescued Giant Panda to other habitats is of value and should be continued. However, more improvement is needed for the monitor technique. More improvement is need for feralization and returning before we return artificial reproduced Giant Panda to wild.

同源四倍体与二倍体水稻的遗传差异及产量、品质性状研究

本文以中国科学院成都生物研究所培育的同源四倍体水稻和二倍体水稻为材料，进行遗传差异及产量、品质性状的研究：1、以二倍体水稻为对照，研究了同源四倍体水稻在2004 年和2005 年的结实情况。结果同源四倍体的花粉育性、结实率均不同程度下降，尤其低代材料更是大幅度下降。F 检验表明，同源四倍体不同个体间的各产量性状均差异显著，说明其具有很大的遗传改良潜力。从1996 年到2005 年对部分同源四倍体水稻进行了连续选择改良，T 检验表明经过9 年的选择改良，其结实率显著提高。本文还对同源四倍体水稻各产量性状间的相关性进行了分析,结果结实率与花粉育性、穗着粒数、穗实粒数极显著相关；理论产量与花粉育性、有效穗数、穗着粒数、穗实粒数、结实率及千粒重极显著相关。i2、用(CT)n 微卫星标记和PCR-Acc Ι分子标记对40 份同源四倍体和14 份二倍体水稻Wx 基因进行研究。结果，(CT)n 微卫星标记检测，Wx 基因呈Wx1、Wx2 和Wx3 3 种多态性；PCR-Acc Ι 检测，Wx 基因表现为G-型和T-型。测定稻米直链淀粉含量(AC)、胶稠度(GC)和糊化温度(GT)，并探讨其与Wx 基因的关系，结果，二倍体和同源四倍体水稻均存在：Wx 基因型相同，AC 差异较小，Wx 基因型不同时，AC 差异较大，Wx1 基因型品种AC 最高， Wx2 基因型品种AC 次之，Wx3 基因型品种AC 最低；基因型相同时，同源四倍体AC 低于二倍体；同源四倍体与对应二倍体间，Wx 基因型相同时，AC 差异很小；而Wx 基因型发生变异时，AC 差异很大。同时，进行相关性分析，结果二倍体和四倍体水稻均存在AC、GC 与Wx 基因密切相关；而GT 与Wx 基因相关不显著。综合分析，(CT)n微卫星标记与PCR-Acc Ι 分子标记检测的相关系数为0.842，呈极显著正相关，可以将其结合起来进行同源四倍体新品种的选育和改良。3、利用RAPD 技术，对同源四倍体和二倍体水稻的遗传差异进行分析。17条引物在同源四倍体中扩增出178 条带（PPB＝81.5%），在二倍体中扩增出173条带（PPB＝76.3%）；同源四倍体和二倍体的Shannon 遗传多样性指数分别为0.4848 和0.4679，多态信息量分别为0.3301 和0.3216，遗传距离分别为0.3572和0.3460；同源四倍体与其对应二倍体间遗传距离为0.1914-0.4633，平均为0.2914。表明同源四倍体的遗传多样性高于二倍体，且同源四倍体与其二倍体之间存在较大的遗传差异，这些将为水稻品种改良和新品种选育提供科学依据。上述产量、品质性状及遗传差异分析的结果，不仅有利于加快同源四倍体水稻的遗传改良进程，而且为进一步研究、利用同源四倍体水稻奠定了初步基础。 AbstractStudy on genetic diversity, yield characters and quality traitsof autotetraploid and diploid riceLiu Yuhua (Botany)Directed by Associate Prof. Tu ShengbinIn this study, diploid and autotetraploid rice, which were cultivated in ChengduInstitute of Biology were analyzed in genetic diversity, yield characters and qualitytraits.In the study, 2 diploid and 29 autotetraploid rice(2n=4x=48) materials, including4 preliminary and 25 advanced generation, were investigated for yield characters.Compared with diploid check, the pollen fertility and seed set of autotetraploiddeclined dramatically, especially in preliminary generation. F-test indicated that therewere remarkable differences among different varieties, showing that autotetraploidmaterials had strong potential for improvement. From 1996 to 2005, someautotetraploid rice had been selected and improved. T-test showed that seed setincreased obviously. The relationships among yield characters of autotetraploid ricewere analyzed. Seed set was strongly correlated with pollen fertility, total grainnumber per panicle and productive grain number per panicle; theoretical yield wasstrongly correlated with pollen fertility, productive panicle number per plant, totalgrain number per panicle, productive grain number, seed set and 1000-grain weight.Wx genotypes of 40 autotetraploid rice and 14 diploid rice were tested by usingthe (CT)n microsatellite marker and a cleaved amplified polymorphic sequence(CAPS) molecular marker named PCR-Acc Ι. Three microsatellite alleles wereproduced, i.e. Wx1, Wx2 and Wx3 both in autotetraploid and in diploid rice.Comparatively, PCR- Acc Ι molecular marker produced two genotypes, G-type andT-type for both autotetraploid and diploid rice. In this study, amylose content (AC), gel of consistency (GC) and gelatinization temperature (GT) of rice grain weremeasured and their relationships with Wx alleles were analyzed. The results showedthat variation of AC between autotetraploid and diploid rice was small when they hadthe same Wx genotype. However, variation of AC turned to be large when the Wxgenotypes were different. Actually, AC met the maximum value in Wx1 varieties andWx2 varieties the middle and Wx3 varieties the minimum. And AC was lower inautotetraploid than in diploid. Correlation analysis was done in this experiment. ACand GC of rice grain were probably controlled by Wx gene or other gene whoselocation was strictly linked to Wx gene, while GT of rice was not. The correlationcoefficient between Wx genotypes which revealed by (CT)n microsatellite marker andPCR-Acc Ι molecular marker was 0.842 with significant level. That revealed aconsistent result between the two types of markers. So it was possible to utilize boththe two types of markers to select and promote germplasm of autotetraploid rice.RAPD molecular markers were used to analyze the genetic diversity betweendiploid and autotetraploid rice. 178 repeatable bands were detected through 17 RAPDprimers with percentage of polymorphic bands was 81.5% in autotetraploid rice while173 repeatable bands were detected with percentage of polymorphic bands was 76.3%in diploid rice. According to the measurement of Shannon index, polymorphicinformation content and genetic distance, genetic diversity of autotetraploid was on ahigher level, genetic variation between autotetraploid and diploid rice was relativelyhigh. All these contributed to the genetic selection and improvement in rice breeding.As mentioned above, the results are not only helpful to promote the process ofrice improvement, but also to confirm the basic for further study of autotetraploid rice.