Genome sequencing in microfabricated high-density picolitre reactors

The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To achieve an approximately 100-fold increase in throughput over current Sanger sequencing technology, we have developed an emulsion method for DNA amplification and an instrument for sequencing by synthesis using a pyrosequencing protocol optimized for solid support and picolitre-scale volumes. Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine.     

基于免疫网络理论的TCSC与PSS协调控制

电力系统稳定器(PSS)和可控串联补偿器(TCSC)被广泛用于电力系统的稳定控制,多个控制器之间的交互作用会影响彼此的控制效果.本文介绍了生物免疫系统中不同类型的抗体协调合作,共同清除抗原的协调机理.提出了基于免疫网络理论的协调控制方法,用于在线协调控制多个阻尼控制器,抑制电力系统的功率振荡.以装有多个PSS和TCSC的系统为例,对多个控制器进行在线协调阻尼控制.仿真结果表明该方法能够缩短抑制振荡所需的时间,具有有效性和鲁棒性.     

Swimming and bipedal bottom-running in the pig-nosed turtle Carettochelys insculpta Ramsay, 1886

The pig-nosed freshwater turtle Carettochelys insculpta Ramsay, 1886 has paddle-shaped foreflippers that resemble those of sea turtles. These turtles exhibit a wide range of swimming capabilities. As well as swimming by the action of synchronized foreflippers alone, they sometimes used alternate hindlimb action at the same time. They could swim by ipsilaterally synchronized action of all four limbs, or by hindlimb action alone (combined with stabilizer/lift function of the foreflippers). The turtles also showed flexibility in bottom-walking. Besides the ipsilaterally synchronized quadrupedal action characteristic of other freshwater turtles, they exhibited a bipedal walking mechanism never previously described. Propelled by alternate action of the hindlimbs, the animals held the head and plastron above the substratum, with the large foreflippers acting to provide anterior lift and stability against roll and yaw. Because both hindlimbs were sometimes off the substratum simultaneously during bipedal locomotion, their duty factors were < 0.5, implying a bipedal run.     

A paleoecologic perspective on past plant invasions in Yellowstone

The role of climate and natural disturbance in the past provides a context for understanding present and future changes in biota. The vegetation history of the Yellowstone region, like that of North America as a whole, is largely one of plant invasions and extinctions in response to changes in climate and environment. When Holocene plant migrations are examined on multiple spatial and temporal scales, several generalities are apparent. First, at a continental and regional scale, plant migration patterns followed the direction of climate change, whereas at local scales plant colonization was governed by site-specific conditions and possibly by biotic interactions. Second, species were individualistic in their response to climate change, and, as their ranges shifted across the landscape, existing communities were dismantled and new ones were formed. Individual species met little resistance from existing communities. Third, rates of species invasion were astonishingly rapid, suggesting that rare long-distance dispersal events were critical. Fourth, fire during periods of climate change was an important catalyst in allowing the invasion of new species, but it is unlikely that a single fire event triggered irreversible vegetation change. Regional climate and biotic changes in response to projected increases in atmospheric CO 2 in the next century suggest an even more complex picture than in the past. Model simulations portray changes in temperature and precipitation in the Yellowstone region that have not occurred in the last 20,000 years. Likewise, projected changes in species ranges, including latitudinal, longitudinal, and elevational shifts, require faster rates than anything observed in the fossil record. Increased fire occurrence may help maintain some native taxa but promote the decline of others. Thus, future conditions are likely to create evermore opportunities for exotic species to invade and establish within the Yellowstone region.     

Roost sites used by Sandhill Crane staging along the Platte River, Nebraska

We assessed the influence of water depth, extent of unobstructed view, and human disturbance features on use of roost sites by Sandhill Cranes along the Platte River, Nebraska, during spring migratory stopover. Aerial photos taken near dawn were used to determine areas of flock use and habitat availability in four sample reaches, and measurements were made on the ground at flock roost areas. In general, depths of 1-13 cm were used by sandhill cranes in greater proportion than those available. Exposed sandbars and depths >20 cm were avoided, while depths of 14-19 cm were used in proportion to their availability. Sites 11-50 m from the nearest visual obstruction were used significantly greater than their availability, while sites 0-4 and >50 m from visual obstructions were avoided. Sandhill Cranes avoided sites near paved roads, gravel roads, single dwellings, and bridges when selecting roost sites; however, they did not appear to be disturbed by private roads, groups of residential buildings, gravel pits, railroads, or electrical transmission lines.     

Radio harness system for bobcat kittens

Eight bobcat kittens were fitted with a specially designed harness system supporting a radio transmitter. These kittens were the youngest known to be radio-instrumented. This system was used successfully through two seasons, from June 1989 to January 1991. Litters of kittens were located soon after birth for weighing, marking, and aging (by tooth eruption). During the first year when kittens were at least eight weeks old and six weeks old the second year, attempts were made to radio-instrument kittens in each litter. This harness system allowed litters to be located periodically until their death or dispersal. We were able to collect important data during the most crucial and least known weeks of the lives of bobcat kittens.     

Salvage logging and replanting reduce understory cover and richness compared to unsalvaged unplanted sites at Mount St. Helens, Washington

The 1980 eruption of Mount St. Helens killed trees in a broad 600-km2 swath north of the crater. Over most of the blast zone, dead trees were salvage logged and Abies procera was planted, except in areas within the Mount St. Helens National Volcanic Monument. We compared salvage-replanted sites and unsalvaged sites in 1 area of the blast zone where the sites were adjacent by using twenty-five 200-m 2 plots for each treatment. Salvaged-replanted plots had significantly lower herb and shrub cover, richness, diversity, litter depth, downed woody debris, nitrate, and phosphate. Salvaged-replanted sites also had significantly more stumps, bare area, and moss cover than unsalvaged plots. Soil organic matter and nonnative species cover did not differ. Nonnative species were not important components of any plots. Nitrate, total nitrogen, organic matter, and litter were correlated with the major patterns of species distribution in a canonical correspondence analysis of the salvaged-replanted plots. In the unsalvaged plots, slope, downed woody debris, and elevation were correlated with the major patterns of species distribution.     

Pilfering of stored seeds and the relative costs of scatter-hoarding versus larder-hoarding in yellow pine chipmunks

Yellow pine chipmunks ( Tamias amoenus ) scatter-hoard food during summer and autumn but must form a larder as a winter food source before winter begins. Yellow pine chipmunks do not larder-hoard large quantities of food during the summer, apparently because a summer larder could not be defended from pilferers. We tested the assumption that the rate of pilferage from an unguarded larder would be significantly greater than the rate of pilferage from surface caches (which are also unguarded by yellow pine chipmunks) during the summer and autumn. Buried plastic buckets were used as artificial nests containing larders of 1000 sunflower seeds or 200 Jeffrey pine ( Pinus jeffreyi ) seeds. The pilferage of larder contents was monitored daily and compared to pilferage of surface caches. Animals (yellow pine chipmunks and deer mice, Peromyscus maniculatus ) removed sunflower seeds from caches much faster than from larders, but caches of Jeffrey pine seeds disappeared much more slowly than pine seeds in larders. Further, animals removed pine seeds from larders more quickly than they did sunflower seeds from larders. The difference between seed species was probably because sunflower seeds have much stronger odors, which rodents readily detect, and because chipmunks prefer pine seeds over sunflower seeds. Yellow pine chipmunks must spend a considerable portion of their time foraging for seeds and may not be able to defend a large larder during summer.     

Varying prevalence of Taenia taeniaeformis strobilocerci in Microtus pennsylvanicus of Montana

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Correlates of burrow location in Beechey ground squirrels

Partial correlation analysis indicates that Beechey ground squirrels show a strong preference for digging burrows under and around large objects, may show a weaker tendency to locate their burrows under the cover of tree canopies, and avoid digging burrows in areas with both treecanopy and ground cover (stones, logs). These relationships hold for large but not small burrow systems. The need for unobstructed visual surveillance and an autumn food supply are proposed to be determinants of these preferences.