Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria

Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e. g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.

Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria

Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e. g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.

Phylogenetic relationships of five pika species (genus Ochotona) based on mitochondrial DNA restriction maps

Restriction site mapping of mitochondrial DNA (mtDNA) with 16 restriction endonucleases was used to examine the phylogenetic relationships of Ochotona cansus, O. huangensis, O. thibetana, O. curzoniae and O. erythrotis. A 1-kb length variation between O. erythrotis of subgenus Pika and other four species of subgenus Ochotona was observed, which may be a useful genetic marker for identifying the two subgenera. The phylogenetic tree constructed using PAUP based on 61 phylogenetically informative sites suggests that O. erythrotis diverged first, followed by O. cansus, while O. curzoniae and O. huangensis are sister taxa related to O. thibetana, The results indicate that both O. cansus and O. huangensis should be treated as independent species. If the base substitution rate of pikas mtDNA was 2% per million years, then the divergence time of the two subgenera, Pika and Ochotana, is about 8.8 Ma ago of late Miocence, middle Bao-dian of Chinese mammalian age, and the divergence of the four species in subgenus Ochotona would have occurred about 2.5 - 4.2 Ma ago, Yushean of Chinese mammalian age. This calculation appears to be substantiated by the fossil record.

Resonant mode analysis in toroidal cavities with elliptic cross-sections

Resonant cavity modes in a torus with elliptical cross section are studied by means of a direct variational method. The nonlinear effects of toroidicity and ellipticity on the frequency of the basic mode are analyzed simply and systematically without the restriction of linear theory. It is shown that the toroidicity effect on the m = 0 transverse magnetic mode is less-than-or-equal-to 11%. The frequency of the mode shifts approximately 11-29% when the elongation of the cross section changes from 1 to 2. The effects of toroidicity and ellipticity differ for each resonant mode.

Development of a Cell Size Relaxed Scheme for the Direct Simulation Monte Carlo Method

The conventional direct simulation Monte Carlo (DSMC) method has a strong restriction on the cell size because simulated particles are selected randomly within the cell for collisions. Cells with size larger than the molecular mean free path are generally not allowed in correct DSMC simulations. However, the cell-size induced numerical error can be controlled if the gradients of flow properties are properly involved during collisions. In this study, a large cell DSMC scheme is proposed to relax the cell size restriction. The scheme is applied to simulate several test problems and promising results are obtained even when the cell size is greater than 10 mean free paths of gas molecules. However, it is still necessary, of course, that the cell size be small with respect to the flow field structures that must be resolved.

High-performance 4H-SiC based metal-semiconductor-metal ultraviolet photodetectors with Al2O3 SiO2 films

4H-silicon carbide (SiC) metal-semiconductor-metal (MSM) ultraviolet (UV) photodetectors with Al2O3/SiO2 (A/S) films employed as antireflection/passivation layers have been demonstrated. The devices showed a peak responsivity of 0.12 A/W at 290 nm and maximum external quantum efficiency of 50% at 280 nm under 20 V electrical bias, which were much larger than conventional MSM detectors. The redshift of peak responsivity and response restriction effect were found and analyzed. The A/S/4H-SiC MSM photodetectors were also shown to possess outstanding features including high UV to visible rejection ratio, large photocurrent, etc. These results demonstrate A/S/4H-SiC photodetectors as a promising candidate for OEIC applications. (C) 2008 American Institute of Physics.

内蒙古锡林河流域草原植物和群落热值的时空变异研究

第一部分：内蒙古锡林河流域草原植物种群和群落热值的时空变异研究 热值的研究是评价生态系统能量固定、传输和转化的基础，也是评价植物光合作用效率和植物营养值的有用参数。同种植物热值会随着植物部位、光照、养分条件、季节、土壤类型和气候条件的不同而发生变化。不同的种类和类群之间热值也存在差异。本项研究以内蒙古锡林河流域中段草原植物群落为对象，研究了植物种群和群落热值的时空变异规律。 对内蒙古羊草草原群落不同植物种群热值的时问动态研究结果表明，42种植物地上部分的热值在13.16土1.14 kJ.g-l和18.14土0.53 kJ.g-1之间变动，所有物种的平均热值为16.90土0,84 kJ.g-1，种间变异系数4.9%。小叶锦鸡儿(Caraganamicrophylla)具有最高的热值。禾草的平均热值高于杂草。根据生活型和生长型，草本物种被进一步分组，热值从高到低的排列顺序为：高禾草>豆科植物>矮禾草>其余杂草>半灌木>一二年生植物。 主要植物种群地下部分热值的分布范围为15.05-16.41 kJ.g-1。其中根茎型草地下部分热值较高。不同种类植物地下部分热值差异并不与地上部分一致。根茎型禾草地上、地下部分热值差异较小，而须根型植物差异较大。不同种群的植物地上部分热值随植物物候期的不同而波动，其变化规律是与植物种群本身的生物学特性相联系的。不同植物种群热值的年际波动规律有所不同，羊草(Leymuschinensis)、大针茅(Stipa grandis)和洽草(Koeloria cristata)的年际热值波动相关显著，但与生长季降水量和生长季累积日照时数之间无明显相关性。在某种程度上，植物热值的种内变化反映了植物生长状况的差异。 42种植物的热值和它们在群落中的相对生物量存在显著正相关关系。表现为优势种(17.74 kJ.g-1)>伴生种(17.24 kJ．g-l)>偶见种(16.65 kJ.g-1)。高热值的植物更具竞争力，在群落中通常占据优势地位，而低热值的植物竞争力通常较弱，构成草原群落的伴生种或偶见种。 以内蒙古锡林河流域3个草原群落类型（羊草典型草原，大针茅典型草原，羊草草甸草原）的放牧退化梯度系列（包括未退化，轻度退化，中度退化和重度退化4个强度）为研究对象，对主要植物种群和群落热值随草原类型和退化梯度的空间变异规律及热值与其他群落和土壤性质的相关性进行了研究。 结果表明，研究区出现的60个植物种平均热值为17.25土0.92 kJ.g-1，变异系数5.4%．热值大于18.00 kJ.g-1的高能植物包括3种优势高禾草(羊草、大针茅和羽茅(A. sibiricum))和一些有毒植物，热值小于17.00 kJ.g-1的低能值植物包括多数一年生杂草;热值在17.00-18.00 kJ.g-1之间的中能值植物包括大多数多年生杂草和矮禾草。 按照生活型分类，灌木的热值最高，多年生禾草显著高于一二年生植物，半灌木和多年生杂草介于二者之间。按照水分生态类型分类，旱生植物、中旱生、旱中生和中生植物之间在热值上没有明显差异。不同科之间热值存在显著差异，禾本科、豆科、菊科植物热值较高，藜科植物平均热值最低。 二因素方差分析结果表明，主要优势物种热值在不同草原类型之间存在显著差异，表现为羊草草甸草原>羊草典型草原>大针茅典型草原。对于大多数优势禾草，热值没有随退化梯度发生明显变化，洽草(K. cristata)、冰草(A．ctistatum)和所有优势杂草随退化程度的增强热值趋于下降。对于大多数优势物种，热值随不同草原类型的空间变异大于放牧退化所导致的空间变异。 不同草原类型的群落热值为羊草草甸草原>羊草典型草原>大针茅典型草原，群落平均热值表现出随退化强度的增加而下降的趋势，这主要归因于沿退化梯度不同物种构成比例的变化，即随退化程度的加剧，高能值植物在群落中的比例下降。其次是特定物种热值随退化梯度的变化。在同一草原区，放牧对群落热值的影响大于立地条件之间的差异。 群落和主要物种热值均表现出与某些群落特征和土壤性质的相关性。 关键词：内蒙古，锡林河流域，羊草草原;物种和群落热值，时空变异，退化梯度，草原类型，土壤性质 第二部分内蒙古羊草草原17年刈割演替过程中功能群组成动态及其对群落净初级生产力稳定性的影响 基于17年的野外实验数据，研究了内蒙古羊草草原群落刈割演替过程中的功能群组成动态，探索功能群组成变化与群落净初级生产力(ANPP)之间的关系，分析结构参数怎样影响功能参数。结果显示：在17年的割草演替过程中，群落的结构与功能均发生了变化。随着羊草群落刈割演替的进行，群落的功能群组成发生了显著变化，根茎禾草在群落中的优势地位相继被一二年生植物，高丛生禾草，矮丛生禾草所取代。到17年末，群落变成根茎禾草，矮丛生禾草，高丛生禾草共同建群的群落。在对照群落中ANPP与年降水量显著相关，但在刈割群落中二者则不相关。年降水量解释对照群落ANPP变异的62%，而连年的刈割干扰则是刈割群落中ANPP动态的主要驱动因子。群落净初级生产则显出对刈割干扰的抵抗能力，在刈割干扰的前几年，依靠群落内功能群组成的不断调节，保持相对稳定的水平，当刈割进行5年之后，群落结构的变化积累到一定程度，净初级生产迅速下降到一个较低的水平，此后依靠群落结构的不断调节来维持这一功能水平。因此，群落结构是以渐变的方式改变的，而群落功能的下降则是以跃变的形式完成的。群落依赖于结构的不断调整来保持功能的相对稳定，但结构变化到一定程度也会导致功能的衰退。 关键词：内蒙古，羊草草原;刈割演替;功能群组成;净初级生产;群落;稳定性

神农架巴山冷杉天然林凋落物特性的研究

神农架地区的巴山冷杉（Abies fargesii）林是秦巴山地重要的森林生态系统类型，长期以来其在水土保持、水源涵养、林产品供给等方面的生态服务功能受到了广泛的重视，近年来该类森林的生物地球化学循环正成为关注的热点。本文以神农架巴山冷杉天然林为研究对象，从其凋落物的数量、养分、能量3个方面入手，着重研究1)凋落物组成及其凋落量的月变化模式;2)凋落物养分含量及养分年归还量的特征;3）凋落物的能流量及其月变化模式。研究表明： 巴山冷杉天然林的年凋落量为5702.99kg.hm-2，处于亚热带森林年凋落量的范围内;巴山冷杉林的凋落物组成比较丰富，主要有落叶、落枝、球花、球果和其它五部分，其中以落叶为多，占总凋落量的46.00%;凋落量的月变化模式呈双峰型，分别在2006年10-11月和2007年4-5月达到峰值。 巴山冷杉林凋落物养分含量的大小顺序为：N＞K＞Ca＞P＞Mg;N、P、K、Ca、Mg的年归还量分别为：39.1063 kg.hm-2、4.5346 kg.hm-2、13.4367 kg.hm-2、5.4965 kg.hm-2、0.0911 kg.hm-2，以N的年归还量最多;就凋落物各组分的养分年归还量而言，落叶的养分归还量远远大于其余组分的养分归还量，占总归还量的52.65%。因此，不论凋落量还是养分归还量，巴山冷杉林凋落物中的落叶都占有绝对的优势。 在巴山冷杉林凋落物各组分中，干重热值介于20.60 KJ/g 至22.70 KJ/g之间，灰分浓度介于1.38%至5.94%之间，去灰分热值介于21.34 KJ/g至23.55KJ/g之间，充分表明了灰分对热值的影响。在各组分中，无论是干重热值还是去灰分热值，均以落叶的热值最高。从整年来看，落叶的热值在2006年10－11月和2007年6－7月较高。巴山冷杉林通过凋落物的年能流量为 12500.96 KJ.m-2，以落叶能流量最大，占总能流量的47.72%。通过计算凋落物的能流量占太阳有效辐射的百分数可以得出太阳辐射进入凋落物的转化效率，巴山冷杉林凋落物的能量转化效率为0.61%，这在亚热带和热带森林类型中属于中等水平。

MULTIPLE GENOTYPES OF MITOCHONDRIAL-DNA WITHIN A HORSE POPULATION FROM A SMALL REGION IN YUNNAN PROVINCE OF CHINA

mtDNA genotypes of six domestic horses (three adult short horses whose heights are under 1 m and three common domestic horses) from a small region of 15 km(2) in Malipo county of Yunnan province of China were investigated by the technique of restriction fragment length polymorphism (RFLP) with restriction endonucleases which recognize 6-bp sequences. An average of fragments for an individual was obtained. Unlike other domestic animals, this population of horses exhibits high mtDNA genetic diversity. Each of the six horses has a specific mtDNA genotype showing a pattern of multiple maternal origins, as suggested by fossil and literature records. We think the population of horses is an amazing seed-resource pool of horses and hence deserves to be paid more attention from the view of conservation genetics. However it is also remarkable that we did not find any typical mtDNA genetic markers which would discriminate between short horses and common domestic horses.

Phylogenetic relationships among two species of golden monkey and three species of leaf monkey inferred from rDNA variation

Restriction maps of rDNA repeats of five species of Colobinae and three outgroup taxa, Hylobates leucogenys, Macaca mulatta, and Macaca irus, were constructed using 15 restriction endonucleases and cloned 18S and 28S rRNA gene probes. The site variation between Rhinopithecus roxellana and Rhinopithecus bieti is comparable to that between Presbytis francoisi and Presbytis phayrei, implying that R. bieti is a valid species rather than a subspecies of R. roxellana. Phylogenetic analysis on the 47 informative sites supports the case for Rhinopithecus being an independent genus and closely related to Presbytis. Furthermore, branch lengths of the tree seem to support the hypothesis that the leaf monkeys share some ancestral traits as well as some automorphic characters.

Genetic diversity in crucian carp (Carassius auratus)

A survey of restriction fragment polymorphism in mitochondrial DNA of three subspecies of Carassius auratus throughout four provinces in China was undertaken using 17 restriction enzymes. Two carp, Cyprinus carpio rubbrofuscus and Cyprinus carpio carpio, were included as the outgroup. A total of 16 haplotypes was observed: 5 in tetraploids of C. auratus auratus; 8 in hexaploids of C. auratus auratus; and 2 in C. auratus gibelio and C. auratus cuvieri, respectively. The tetraploids and hexaploids share three common haplotypes as I, V, and VI. C. a. Cuvieri may have diverged first among the three subspecies. Interestingly, C. a. auratus and C. a. cuvieri did not form monophyletic clades, which indicated that the classification of carassius auratus required further studies. The current hypothesis, that hexaploids originated from tetraploids by a polyploidy event, is less favorable, based on the distribution of haplotypes and the lower diversity in tetraploids than in hexaploids. Our data also indicate that divergence of hexaploids and tetraploids might be recent and mtDNA polymorphism existed before the divergence. Meanwhile, genetic isolation exists between the hexaploids and the tetraploids.

Mitochondrial DNA variation in cattle of South China: origin and introgression

Ten restriction endonucleases were used to investigate the mitochondrial DNA restriction fragment length polymorphism (mtDNA RFLP) of 11 native cattle breeds and one cultivated cattle breed in South China. Twenty-three restriction morphs were detected, which can be sorted into five haplotypes, A phylogenetic tree of the haplotypes was constructed by using the 'upgma' method. Our study showed that haplotype I and II are identical to the zebu (Bos indicus) and taurine (Bos taurus) haplotypes, respectively. Zebu and taurine were the two major origins of cattle populations in South China, and the zebu probably had more influence on the native cattle population than taurine did. Haplotype III is identical to haplotype I of yak (Bos grunniens), which was only detected in the Diqing cattle breed. Haplotype IV was detected for the first time. This haplotype, found only in Dehong cattle, might be from an independent domestication event, probably from another Bos indicus population. Divergence of haplotypes I and IV occurred about 268,000-535 000 years ago, much earlier than the 10,000-year history of cattle husbandry. Our results also suggest a secondary introgression of mtDNA from yak to Diqing cattle.

Characterization of Sarcocystis species in domestic animals using a PCR-RFLP analysis of variation in the 18S rRNA gene: a cost-effective and simple technique for routine species identification

Thirteen restriction endonucleases were used to investigate nucleotide sequence variation in the 18S rRNA DNA of 88 individuals from ten Sarcocystis taxa collected as cysts from their intermediate hosts, swine, cattle and water buffalo. A DNA sequence of

A PCR-based RFLP analysis of Sarcocystis cruzi (Protozoa : Sarcocystidae) in Yunnan province, PR china, reveals the water buffalo (Bubalus bubalis) as a natural intermediate host

A polymerase chain reaction-based restriction fragment length polymorphism (RFLP) approach is used to examine Sarcocystis cruzi-like taxa from the atypical intermediate host, water buffalo, in Yunnan, People's Republic of China. The loci examined lie with