Microarray Analyses of Gene Expression during the Tetrahymena thermophila Life Cycle

Background: The model eukaryote, Tetrahymena thermophila, is the first ciliated protozoan whose genome has been sequenced, enabling genome-wide analysis of gene expression. Methodology/Principal Findings: A genome-wide microarray platform containing the predicted coding sequences (putative genes) for T. thermophila is described, validated and used to study gene expression during the three major stages of the organism's life cycle: growth, starvation and conjugation. Conclusions/Significance: Of the,27,000 predicted open reading frames, transcripts homologous to only,5900 are not detectable in any of these life cycle stages, indicating that this single-celled organism does indeed contain a large number of functional genes. Transcripts from over 5000 predicted genes are expressed at levels >5x corrected background and 95 genes are expressed at >250x corrected background in all stages. Transcripts homologous to 91 predicted genes are specifically expressed and 155 more are highly up-regulated in growing cells, while 90 are specifically expressed and 616 are up-regulated during starvation. Strikingly, transcripts homologous to 1068 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation. The patterns of gene expression during conjugation correlate well with the developmental stages of meiosis, nuclear differentiation and DNA elimination. The relationship between gene expression and chromosome fragmentation is analyzed. Genes encoding proteins known to interact or to function in complexes show similar expression patterns, indicating that co-ordinate expression with putative genes of known function can identify genes with related functions. New candidate genes associated with the RNAi-like process of DNA elimination and with meiosis are identified and the late stages of conjugation are shown to be characterized by specific expression of an unexpectedly large and diverse number of genes not involved in nuclear functions.

Investigation of high cycle and Very-High-Cycle Fatigue behaviors for a structural steel with smooth and notched specimens

The high cycle and Very-High-Cycle Fatigue (VHCF) properties of a structural steel with smooth and notched specimens were studied by employing a rotary bending machine with frequency of 52.5 Hz. For smooth specimens, VHCF failure did occur at fatigue cycles of 7.1 x 10(8) with the related S-N curve of stepwise tendency. Scanning Electron Microscopy (SEM) was used for the observations of the fracture surfaces It shows that for smooth specimens the crack origination is surface mode in the failure regime of less than 10(7) cycles While at VHCF regime, the material failed from the nonmetallic inclusion lies in the interior of material, leading to the formation of fisheye pattern. The dimensions of crack initiation region were measured and discussed with respect to the number of cycles to failure. The mechanism analysis by means of low temperature fracture technique shows that the nonmetallic inclusion in the interior of specimen tends to debond from surrounding matrix and form a crack. The crack propagates and results to the final failure. The stress intensity factor and fatigue strength were calculated to investigate the crack initiation properties. VHCF study on the notched specimens shows that the obtained S-N curve decreases continuously. SEM analysis reveals that multiple crack origins are dominant on specimen surface and that fatigue crack tends to initiate from the surface of the specimen. Based on the fatigue tests and observations, a model of crack initiation was used to describe the transition of fatigue initiation site from subsurface to surface for smooth and notched specimens. The model reveals the influences of load, grain size, inclusion size and surface notch on the crack initiation transition. (C) 2010 Elsevier Ltd. All rights reserved

Effects of oriented substrates on cell morphology, the cell cycle, and the cytoskeleton in Ros 17/2.8 cells

Absence of gravity or microgravity influences the cellular functions of bone forming osteoblasts. The underlying mechanism, however, of cellular sensing and responding to the gravity vector is poorly understood. This work quantified the impact of vector-directional gravity on the biological responses of Ros 17/2.8 cells grown on upward-, downward- or edge-on-oriented substrates. Cell morphology and nuclear translocation, cell proliferation and the cell cycle, and cytoskeletal reorganization were found to vary significantly in the three orientations. All of the responses were duration-dependent. These results provide a new insight into understanding how osteoblasts respond to static vector-directional gravity.

九寨沟湖泊湿地植物群落与植物地理研究

九寨沟湖泊湿地在维持九寨沟的生态平衡中起着重要的作用，在旅游产业的发展下，湿地生态系统及生物多样性面临着较大的威胁。尽管九寨沟湿地具有重要的生态价值，但目前对其研究尚比较薄弱。湿地植物群落和植物地理研究可以为湿地资源的可持续利用和监测保护提供科学依据。作者从2004年8月到2007年11月对九寨沟湿地的植物物种组成、地理分布、优势植物群落的结构、生长动态、湿地土壤种子库进行了调查研究。主要结果如下： 1. 九寨沟湿地物种组成、地理分布特点及湿地植物群落特点 九寨沟湿地共有苔藓植物8科13属16种，维管植物为48科107属199种。九寨沟湿地植物的地理成份较为丰富，维管植物在科级水平上有7种地理分布型（变型），在属级水平上有13种地理分布型（变型）， 在种级水平上共有29种地理分布型（变型）。九寨沟湿地植物以温带成份和我国特有成份为主，同时兼有热带、亚热带成份和环极—高山成份。九寨沟湿地植物的分布表现出明显的垂直地带性和水平地带性。湿地植物群落可划分21个群落类型，不同植物群落类型的物种多样性及物种组成存在较大的差异。九寨沟湿地植物的物种多样性和群落多样性以及较高的生产力特征，是维持其湿地生态景观多样性和稳定性的基础。 2. 土壤、水环境、海拔等对湿地植物的分布及生物多样性的影响 九寨沟湿地土壤、水等环境因子存在较大的差异。帕米尔苔草和宽叶香蒲等群落的凋落物较多，土壤有机碳、土壤总磷较高，可能是九寨沟湿地的重要土壤碳库。 九寨沟湿地植物沿水环境梯度的分布规律表现为：沉水植物（轮藻—篦齿眼子菜，水苦荬，杉叶藻）——挺水植物（水木贼，芦苇，宽叶香蒲）——湿生草本（苔草、节节草、披散木贼）——湿生灌木（柳灌丛，小檗灌丛）等。海拔也影响湿地植物的物种组成。 水深对物种多样性有影响，水深与物种丰富度负相关。随着水深的增加，水木贼、芦苇、杉叶藻、宽叶香蒲等群落的物种多样性下降；在长期淹水和季节性淹水的地方，水木贼群落物种多样性存在显著差异。土壤总氮与水木贼群落物种丰富度正相关。 3. 土壤营养元素、水环境对植物生长的影响 水深影响湿地植物生物量的分配。芦苇无性系分株在47 cm水深的环境中单株平均生物量最大；在干滩地中（地面水深0 cm），叶生物量百分比最大，而茎生物量百分比最小，茎的生物量百分比和生长速率随水深的增加而增加；在较干的滩地生境中，开花率、花序的生物量百分比明显大于水较深的生境。 水深与水木贼地上生物量负相关，但水木贼地上生物量在长期淹水和季节性淹水的地方没有显著的差异。在水浅的地方，杉叶藻、水木贼、芦苇等植物群落中，其他伴生物种的生物量占样方总生物量的百分比较大。 土壤有机碳、土壤总氮、土壤总磷等对湿地植物生物量的影响比较大：宽叶香蒲地上生物量与土壤总磷正相关；水木贼地上生物量与土壤总氮正相关；杉叶藻地上生物量与土壤有机碳正相关。 水深、土壤营养成分对湿地植物高度、密度等有影响。水木贼的平均高度在季节性淹水的地方比长期淹水的地方低，平均密度在长期淹水的地方比季节性淹水的地方低；除了5月份，其他观察月份水木贼的密度都与水深负相关，同时与土壤有机碳正相关。另外，芦苇密度与土壤有机碳含量正相关，宽叶香蒲密度与水深负相关，帕米尔苔草高度与土壤有机碳负相关。 4. 优势植物群落的动态变化 在优势植物群落中，优势种的高度、密度、盖度、生物量等在群落中占绝对优势。除五花海，水木贼群落的物种组成、高度、生物量在两年间没有显著的变化。芦苇群落的物种丰富度在近两年有所增加。 湿地植物生长表现为明显的季节动态，生长的峰值大多在7月－8月。优势植物群落的物候与水文周期有关。湿地植物群落的物种组成和密度，可以作为对湿地监测和保护的生物指示。 5. 九寨沟湿地土壤种子库特征及其在湿地生物多样性恢复中的作用 水深和现存植被物种丰富度可以解释湿地土壤种子库的变化。水深可以解释表层物种丰富度45%的变化。现存植被物种丰富度可以分别解释10 cm土层、2－5 cm土层及5－10 cm土层土壤种子库45%、48%和25%的变化。 湿地土壤种子库的密度为0－15945粒m-2, 种子库中共发现23个物种。现存植被优势物种和种子库优势物种不同。各层土壤种子库密度和物种丰富度并不存在显著的差异，但第二层土壤种子库密度最大。海拔、现存植被优势种盖度、土壤总磷、土壤总氮、土壤有机碳对湿地土壤种子库的密度和垂直结构没有影响。土壤种子库物种丰富度小于地上植被物种丰富度。湿地土壤种子库与地上植被的相关性不大。在浅水区域，湿地土壤种子库在湿地植被恢复中有一定作用。但在深水区域，保护现存植被更重要。 The lakeshore wetlands are valuable ecological units of the Jiuzhaigou lakes. Pressure for travel industry development pose a continuing and severe threat to the biodiversity-support function of the wetland system. Despite the ecological importance of wetlands in Jiuzhaigou, they are so far poorly studied. Both general plant communties and biogeographical studies are needed in order to attain basis for sustainable use the wetland resources and adequate protection of these areas. The present study was undertaken to examine aquatic plants distribution and the species compositon, structure and growth dynamics of their communities with variations of environmental factors along altitudes, water depth and soil properities gradients in Jiuzhaigou. Analysis of field survey data collected during August 2004 and November 2007 in lakeshore wetlands in Jiuzhaigou National Nature Reserve, Sichuan, China. The results were as following: (i) Species composition and biogeography in wetland vegetation 8 families, 13 genus, 16 species of moss and 48 families, 107 genus and 199 species of vascular plants in Jiuzhaigou wetlands were found. The floristic compositions were abundunt. Ten geographical distribution types at family level, 13 geographical distributions types at generic level and 29 geographical distribution types at specific level in vascular plants were found. Most species in Jiuzhaigou wetlands are temperate elements and Chinese endemic elements, with a few of tropical and subtropical and some circumarctic elements. And the plant distributions show clear vertical and horizontal patterns. There were 21 major wetland plant community types. Species composition and species richness in different plant communities are different. The species diversity and plant community diversity and their high biomass are the basis for the diversity and stability of wetland landscapes in Jiuzhaigou. (ii) Water depth, soil nutrients and altitudes influence on the species diversity and plant distribution. Total phosphorous and organic cabon in soil were higher in C. pamiernensis and T. latifolia communities, where are important cabon reservoirs in Jiuzhaigou wetlands. Along gradients of water depth, among populations of the dominant plant species present: submerged macrophytes (Chara vulgaris, Potagemonton pectinatus, Veronica anagalis-aquatica，Hippuris vulgaris), emergent macrophytes (Equisetum fluviatile, Phragamites australis, Typha latifolia), helophytes (Carex pamirensis )and shrubs (Salix sp., Berberis sp. ). Altitudes influence on the assemblage of plant communities. Water depth negatively correlated with species richness. Specie richness showed differences between permanently flooded sites and seasonally flooded sites in E. fluvatile communities. And total nitrogen in soil was negatively correlated with species richness in E. fluviatile communities. Altitudes show no significant influence on species richness, but in fact, through our analyses, they do have influence on the assemblage of wetland plants. (iii) Water depth, soil nutrients influence on the plant growth Water depth influences the biomass allocation in Phragmities australis. The average aboveground biomass of a single ramet (4.2 g) was the largest in the habitat with water level 47 cm above the soil surface. At the habitat with water level under soil surface 15 cm (－15 cm), the leaf biomass percentage (of the total ramet biomass) was the largest (46.1%), and the height and percentage of ramose ramets ( with branches on stem )(of the total ramets in a plot) were found obviously different. The deeper in water, the larger the biomass percentage and growth rate of stems were. The flowering rate and biomass of panicles were greater in shallow water than those in deep water. Water depth negatively correlated with aboveground biomass of E. fluviatile. However, above-ground biomass of E. fluviatile showed no significant difference between permanently flooded sites and seasonally flooded sites. But in shallow water, more biomasses of accompanying species were found in dominant plant communities such as H. vulgaris communities, E. fluviatile communities and P. australis communities. Water depth, soil nutrients influence on shoot density and shoot length of wetland plants. The shoot density of E. fluviatile was correlated to water depth in all growth months. Annual average density was significantly lower at permanently flooded sites than at seasonally flooded sites. But the annual average shoot length was significantly lower at seasonally flooded sites than at permanently flooded sites. (iv) Growth dynamics of dominant communities in Jiuzhaigou wetland The shoot length and shoot density, coverage and biomass of domiant species were dominated in plant communities. The species composition increased in P. australis communities in recent two years. The species richness in E. fluviatile communities showed no difference between 2005 and 2007. The above-ground biomass and shoot density in Five－flower Lake from July 2005 to July 2007 were significantly different, while in other sites, the differences were not significant. Shoot height, shoot density and above-ground biomass showed significant seasonal changes in all sites. Growth dynamics correlated with the cycle of water levels in lakes. Most plants growth parameters peaked at July or August. The biomass of T. latifolia peaked in August. But the shoot length of T. latifolia in deeper water peaked in July. The shoot length of E. fluviatile increased significantly from May to August except in seasonally flooded sites in Arrow-bamboo Lake. The species composition of communities and shoot density can be used as bioindicators in Jiuzhaigou wetland. (v) Soil seed bank in Jiuzhaigou wetland and its role in vegetation restoration Seed density in all soil layer samples was negatively correlated to water depth. Water depth can explain 45% variance of species richness in surface layer in sediment. Species richness in extant vegetation can explain 45%, 48%, 25% variance of species richness in total 10 cm and in 2－5 cm and 5－10 cm layer sediment respectively. Mean seed densities in wetlands ranged from 0 to 15945 m–2. A total of 23 species germinated in seed bank. The dominant species in seed bank and extant vegetation showed great difference. The total number of species and seedlings that germinated in different layers was not significantly different. But the second layer had the greatest seed density. In shallow water, seed bank can contribute to vegetation restoration, while in deeper water, protection of extant vegetation may be a better strategy.

川西北高寒草甸土壤呼吸研究：季节动态和放牧效应

除植被冠层的光合作用之外，土壤的呼吸作用是陆地生态系统碳收支中最大的通量。土壤呼吸即使发生较小的变化也能显著地减缓或加剧大气中CO2浓度的增加，从而明显影响到全球气候变化。土壤呼吸速率变化与否以及变化的方向可以反映生态系统对环境变化的敏感程度和响应模式。尽管如此，土壤呼吸仍是一个为人们了解不多的生态系统过程。 草地生态系统是陆地生态系统的一个重要组成部分。针对草地土壤呼吸进行野外实验研究和相应方法论的探讨将对区域乃至全球碳源汇性质的准确估算具有重要的科学意义。然而，近几年来关于草地土壤呼吸的主要研究工作都集中在温带草原和部分热带草原，而针对高寒草甸生态系统土壤呼吸的研究报道还很少。 2008年4月至2009年4月期间，我分别在2008年6、8、10、12月和2009年2月和4月分6次对川西北的典型高寒草甸群落的土壤呼吸进行观测，分析了不同类型高寒草甸群落土壤呼吸的季节变化特征以及环境因子和放牧模式对其影响。主要研究结果如下： 1）该地区高寒草甸生态系统在生长季（6月～8月）土壤呼吸速率较大（6.07～9.30μmolCO2¡m-2¡s-1 ） ， 在非生长季（ 12 月～ 2 月） 较小（ 0.16 ～0.49μmolCO2¡m-2¡s-1 ） 。土壤CO2 年累积最大释放量为3963 ～ 5730gCO2¡m-2¡yr-1，其中，生长季土壤CO2的释放量占年总释放量的85%～90%。非生长季占10%～15%。非生长季所占比例略小于冬季积雪覆盖地区的冬季土壤呼吸占年土壤呼吸量的比例（14%～30%）。温度，尤其地温，是影响该地区高寒草甸生态系统土壤呼吸速率的最主要环境因子。土壤呼吸速率与地上生物量和土壤水分之间没有显著相关性，但是土壤含水量过大会导致土壤呼吸速率下降。 2）在观测期内，草丘区的土壤呼吸显著高于对照区的土壤呼吸，其最大土壤呼吸速率为16.77μmolCO2¡m-2¡s-1，土壤CO2 年累积最大释放量为8145gCO2¡m-2¡yr-1，是对照区的近2 倍。由于草丘在高寒草甸中占有较大的面积比例（近30%），因此，它将对高寒草甸生态系统的碳循环起着重要的作用。 3）放牧模式不仅可以影响高寒草甸群落的土壤CO2 排放，而且还可以改变土壤呼吸的温度敏感性（Q10）。本研究表明，在生长季有长期放牧活动干扰时将会增加土壤向大气中释放二氧化碳的速度，促使土壤碳库中碳的流失。禁牧样地的土壤呼吸速率在刚禁牧时先迅速增大，随着禁牧时间的延长土壤呼吸速率将会下降。此外，与其它放牧模式相比，冬季放牧将高寒草甸群落土壤呼吸速率在生长季达到最大值的时间明显向后推迟。不同放牧模式下高寒草甸群落土壤呼吸的Q10 值大小顺序为：禁牧一年群落>冬季放牧群落>禁牧三年群落>夏季放牧群落>自由放牧群落。 4）基于呼吸室技术的观测方法中，测量前的剪草处理可以明显改变该地区高寒草甸群落的土壤温度和土壤呼吸速率。在生长季，剪草处理将使土壤呼吸速率的瞬时响应增加90%左右。由于剪草处理明显增加了剪草样方白天的土壤温度，而土壤温度与土壤呼吸之间存在着极显著的指数相关关系，因而剪草处理导致土壤呼吸速率迅速增加。因此，在高寒地区基于呼吸室技术观测的土壤呼吸应当进行校正。 综上所述，川西北高寒草甸生态系统土壤呼吸速率在生长季较高，而在非生长季较低。土壤温度是影响该地区土壤呼吸的最主要环境因子。在实验观测期，草丘区土壤呼吸速率显著高于对照区的，是对照区土壤呼吸速率的近2倍。由于测量前的剪草处理可以明显改变待测点的土壤呼吸速率，因此，应对在高寒地区基于呼吸室技术观测的土壤呼吸进行校正。 Soil respiration is the second largest component (less than plant phtotosynthesis) of carbon dioxide flux between terrestrial ecosystems and the atmosphere. A minor change in soil respiration rate can significantly slow down or accelerate the increase of atmospheric CO2 concentration that is closely related to global climatic change. In turn, the change in the flux direction and rate of soil respiration may indicate the elasticity and stability of ecosystems to global changes and human disturbance. However, soil respiration is still an ecosystem process that has been poorly understood. Grassland ecosystem is an important component of the terrestrial ecosystem. Accurately estimating the CO2 flux from soil to atmosphere in situ is the key to evaluating the carbon resource and sink regionally or globally. Despite of extensive studies on the temperate and tropic grasslands, the soil respiration of alpine meadows has not substantially been measured. In the current study, soil respiration was measured for an annual cycle from April, 2008 to April, 2009 for the alpine meadow in northwestern Sichuan Province of China to determine the seasonal variation of soil respiration for the typical plant communities. The results are shown as follows: 1) Large seasonal variation of soil respiration was observed in the alpine meadow. The rate of soil respiration was the greatest (6.07～9.30μmolCO2¡m-2¡s-1) in June and the smallest (0.16 ～ 0.49μmolCO2¡m-2¡s-1) occurred from December to February in the non-growing season. The total emission of soil CO2 was estimated as 3963～5730 gCO2¡m-2¡yr-1, 85%~90% of which was released during the growing season, and 10%~15% during the non-growing season which was slightly less than the ratio of winter and annual CO2 flux from soil. Temperature, particularly the soil temperature, was the major environmental factor regulating the soil respiration. Significant and positive relationships were not found between soil respiration and soil moisture and between soil respiration and plant above-ground biomass, but excessive soil water content would decrease in the rate of soil respiration. 2) The rate of soil respiration in grass hummock communities was up to 16.77μmolCO2¡m-2¡s-1, which was about twice as great as in the controls (communities located in low and even sites). Considering the large proportion (about 30% on average) of hummock area in the meadow, it can be concluded that the hummocks played an important role in the carbon cycling of the study ecosystem. 3) Grazing patterns affected the flux of CO2 emission and the temperature sensitivity of soil respiration (Q10) in the alpine meadow. Grazing during growing season increased the rate of soil respiration. The rate of soil respiration increased significantly immediately after the alpine meadow being fenced, but thereafter decreased. In addition, grazing in winter delayed the peak respiration rate relative to the non-grazing mode. The Q10 value was the largest in the non-grazed area for one year, and next came the area with grazing in winter, followed by the non-grazed area for three years, the area with grazing in summer, and the non-limited grazed area. 4) In the chamber-based techniques, clipping manipulation before each measurement increased the transient rate of soil respiration by about 90% in the summer of the alpine meadow. As increase in soil temperature at daytime in the clipped plots by clipping and the exponential relationship between soil respiration and temperature, clipping manipulation led to increase in the rate of soil respiration. This suggested that a correction should be done for the techniques if employed in alpine and cold regions. In summary, the rate of soil respiration in the alpine meadow was the greatest in June and the smallest occurred from ecember to February in the non-growing season. Soil temperature was the major environmental factor regulating the soil respiration. The rate of soil respiration in grass hummock communities was up to 16.77μmolCO2¡m-2¡s-1, which was about twice as great as in the controls. A correction should be done for the techniques if employed in alpine and cold regions, because of the effect of clipping manipulation on soil temperature and respiration.