DIRECT OBSERVATION OF NATIVE AND UNFOLDED GLUCOSE-OXIDASE STRUCTURES BY SCANNING-TUNNELING-MICROSCOPY

Native and unfolded glucose oxidase (GOD) structures have been directly observed with scanning tunnelling microscopy (STM) for the first time. STM images show an opening butterfly-shaped pattern for the native GOD. When GOD molecules are extended on anodi

Consensus scoring for enriching near-native structures from protein-protein docking decoys

The identification of near native protein-protein complexes among a set of decoys remains highly challenging. A stategy for improving the success rate of near native detection is to enrich near native docking decoys in a small number of top ranked decoys. Recently, we found that a combination of three scoring functions (energy, conservation, and interface propensity) can predict the location of binding interface regions with reasonable accuracy. Here, these three scoring functions are modified and combined into a consensus scoring function called ENDES for enriching near native docking decoys. We found that all individual scores result in enrichment for the majority of 28 targets in ZDOCK2.3 decoy set and the 22 targets in Benchmark 2.0. Among the three scores, the interface propensity score yields the highest enrichment in both sets of protein complexes. When these scores are combined into the ENDES consensus score, a significant increase in enrichment of near-native structures is found. For example, when 2000 dock decoys are reduced to 200 decoys by ENDES, the fraction of near-native structures in docking decoys increases by a factor of about six in average. ENDES was implemented into a computer program that is available for download at http://sparks.informatics.iupui.edu.

Refining near-native protein-protein docking decoys by local resampling and energy minimization

How to refine a near-native structure to make it closer to its native conformation is an unsolved problem in protein-structure and protein-protein complex-structure prediction. In this article, we first test several scoring functions for selecting locally resampled near-native protein-protein docking conformations and then propose a computationally efficient protocol for structure refinement via local resampling and energy minimization. The proposed method employs a statistical energy function based on a Distance-scaled Ideal-gas REference state (DFIRE) as an initial filter and an empirical energy function EMPIRE (EMpirical Protein-InteRaction Energy) for optimization and re-ranking. Significant improvement of final top-1 ranked structures over initial near-native structures is observed in the ZDOCK 2.3 decoy set for Benchmark 1.0 (74% whose global rmsd reduced by 0.5 angstrom or more and only 7% increased by 0.5 angstrom or more). Less significant improvement is observed for Benchmark 2.0 (38% versus 33%). Possible reasons are discussed.

The contribution of trace elements from seawater to chimneys: a case study of the native sulfur chimneys in the sea area off Kueishantao, northeast of Taiwan Island

Hydrothermal fluid containing abundant matter erupts from seafloor, meets ambient cold seawater and forms chimneys. So the main matter origins of chimneys are seawater and matter which are taken by hydrothermal fluid from deep reservoir. However, because of seawater's little contribution to the forming of chimneys, it is usually covered by the abundant matter which is taken by hydrothermal fluid. Therefore, chimneys formed in ordinary deep seawater hydrothermal activity, containing complex elements, cannot be used to study the seawater's contribution to their formation. While the native sulfur chimneys, formed by hydrothermal activity near the sea area off Kueishantao, are single sulfur composition (over 99%), and within chimneys distinct layers are seen. Different layers were sampled for trace element determination, with Inductively Coupled Plasma Mass Spectrometry (ICP-MS). By analyzing the data, we consider C-layer (secondary inner-layer) as the framework layer of the chimney which formed early (Fig. 4), and its trace elements derive from hydrothermal fluid. While the trace elements within A, B, D layers have undergone later alteration. A, B layers are affected by seawater and D layer by hydrothermal fluid. The increase of trace elements of A and B layers was calculated using C layer as background. Based on the known typical volume of chimneys of the near sea area off Kueishantao, we calculated the volume of seawater that contributed trace element to chimneys formation to be about 6.37 x 10(4) L. This simple quantified estimate may help us better understand the seafloor hydrothermal activity and chimneys.

Origin of a native sulfur chimney in the Kueishantao hydrothermal field, offshore northeast Taiwan

Analyses of rare earth and trace element concentrations of native sulfur samples from the Kueishantao hydrothermal field were performed at the Seafloor Hydrothermal Activity Laboratory of the Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences. Using an Elan DRC II ICP-MS, and combining the sulfur isotopic compositions of native sulfur samples, we studied the sources and formation of a native sulfur chimney. The results show, when comparing them with native sulfur from crater lakes and other volcanic areas, that the native sulfur content of this chimney is very high (99.96%), the rare earth element (REE) and trace element constituents of the chimney are very low (Sigma REE < 21x10(-9)), and the chondrite-normalized REE patterns of the native sulfur samples are similar to those of the Kueishantao andesite, implying that the interaction of subseafloor fluid-andesite at the Kueishantao hydrothermal field was of short duration. The sulfur isotopic compositions of the native sulfur samples reveal that the sulfur of the chimney, from H2S and SO2, originated by magmatic degassing and that the REEs and trace elements are mostly from the Kueishantao andesite and partly from seawater. Combining these results with an analysis of the thermodynamics, it is clear that from the relatively low temperature (< 116 degrees C), the oxygenated and acidic environment is favorable for formation of this native sulfur chimney in the Kueishantao hydrothermal field.

Effect of plateau zokors on vegetation characteristics and productivity of alpine meadow

This research was conducted on alpine meadow site at Menyuan county, Qinghai Province, People's Republic of China to determine the effects of native, subterranean rodent of Qinghai-Tibet grasslands, the plateau zokors (Myospalax baileyi), on seasonal above-and below-ground plant biomass, plant species diversity and productivity. Both total peaks of above-and below-ground biomass were the greatest (413.600 g/m~2 and 2297.502 g/m~2) in the patch no any plateau zokors colonized by plateau zokors over 10 years in August and October, respectively. Both above-and below-ground biomass were significantly increased in the patches where plateau zokors were removed or the burrow systems were abandoned for five years compared to the patches plateau zokors colonized over 10 years. However, both above-and below-ground biomass in abandoned patches were significantly lower than that in uncolonized patches. Monocotyledonous biomass was reduced greatly, but the non-palatable dicots were significantly increased in colonized patches. The palatable biomass of monocots and dicots were increased in abandoned patches. Total plant species diversity was the greatest in uncolonized patchesand least in abandoned patch. The total net primary production in colonized patches was reduced by 68.98% compared with uncolonized patches. Although the patches were without any plateau zokors disturbance for fives years, the total net primary production just reached 58.69% of the uncolonized patches. The above-ground net primary production in abandoned patches increased 28.74% and the below-ground increased 54.91% compared with the colonized patches. We suggest that plateau zokor-induced changes in plant above- and below-ground biomass and species diversity may lead to further alterations of nutrient cycling and trophic dynamics in this alpine meadow ecosystem.

Genetic variation within and among populations of Rhodiola alsia (Crassulaceae) native to the Tibetan Plateau as detected by ISSR markers

Genetic variation of 10 Rhodiola alsia ( Crassulaceae) populations from the Qinghai - Tibet Plateau of China was investigated using intersimple sequence repeat (ISSR) markers. R. alsia is an endemic species of the Qinghai - Tibet Plateau. Of the 100 primers screened, 13 were highly polymorphic. Using these primers, 140 discernible DNA fragments were generated with 112 (80%) being polymorphic, indicating pronounced genetic variation at the species level. Also there were high levels of polymorphism at the population level with the percentage of polymorphic bands (PPB) ranging from 63.4 to 88.6%. Analysis of molecular variance (AMOVA) showed that the genetic variation was mainly found among populations (70.3%) and variance within populations was 29.7%. The main factors responsible for the high level of differentiation among populations are probably the isolation from other populations and clonal propagation of this species. Occasional sexual reproduction might occur in order to maintain high levels of variation within populations. Environmental conditions could also influence population genetic structure as they occur in severe habitats. The strong genetic differentiation among populations in our study indicates that the conservation of genetic variability in R. alsia requires maintenance of as many populations as possible.

学前儿童朴素生物学“理论”的发展——对“生长”认知的实验研究

There is a debate in cognitive development theory on whether cognitive development is general or specific. More and more researchers think that cognitive development is domain specific. People start to investigate preschoolers' native theory of human being's basic knowledge systems. Naive biology is one of the core domains. But there is argument whether there is separate native biological concepts among preschoolers. The research examined preschoolers' cognitive development of naive biological theory on two levels which is "growth" and "aliveness", and it also examined individual difference and factors that lead to the difference. Three studies were designed. Study 1 was to study preschoolers' cognition on growth, which is a basic trait of living things, and whether children can distinguish living and non-living things with the trait and understanding the causality. Study 2 was to investigate preschoolers' distinction between living things and non-living things from an integrated level. Study 3 was to investigate how children make inferences to unfamiliar things with their domain specific knowledge. The results showed the following: 1. Preschoolers gradually developed naive theory of biology on growth level, but their naive theory on integrated level has not developed. 2 Preschoolers' naive theory of biology is not "all or none", 4- and 5-year-old children showed some distinction between living and non-living things to some extent, they use non-intentional reason to explain the cause of growth and their explanation showed coherence. But growth has not been a criteria of ontological distinction of living and non-living things for 4- and 5-year-old children, most 6-year-old children can distinguish between living and non-living things, and these show the developing process of biological cognition. 3. Preschoolers' biological inference is influenced by their domain-specific knowledge, whether they can make inference to new trait of living things depends on whether they have specific knowledge. In the deductive task, children use their knowledge to make inference to unfamiliar things. 4-year-olds use concrete knowledge more often while the 6-year-old use generalized knowledge more frequency. 4. Preschoolers' knowledge grow with age, but individuals' cognitive development speed at different period. Urban and rural educational background affect cognitive performance. As time goes by, the urban-rural knowledge difference to distinguish living and nonliving things reduces. And preschoolers' are at the same developmental stage because the three age groups have similar causal explanation both in quantity and quality. 5. There is intra-individual difference on preschoolers' naive biological cognition. They show different performance on different tasks and domains, and their cognitive development is sequential, they understand growth earlier than they understand "alive", which is an integrated concept. The intra-individual differences decrease with age.

Surviving the Information Explosion: How People Find Their Electronic Information

We report on a study of how people look for information within email, files, and the Web. When locating a document or searching for a specific answer, people relied on their contextual knowledge of their information target to help them find it, often associating the target with a specific document. They appeared to prefer to use this contextual information as a guide in navigating locally in small steps to the desired document rather than directly jumping to their target. We found this behavior was especially true for people with unstructured information organization. We discuss the implications of our findings for the design of personal information management tools.

How People Re-find Information When the Web Changes

This paper investigates how people return to information in a dynamic information environment. For example, a person might want to return to Web content via a link encountered earlier on a Web page, only to learn that the link has since been removed. Changes can benefit users by providing new information, but they hinder returning to previously viewed information. The observational study presented here analyzed instances, collected via a Web search, where people expressed difficulty re-finding information because of changes to the information or its environment. A number of interesting observations arose from this analysis, including that the path originally taken to get to the information target appeared important in its re-retrieval, whereas, surprisingly, the temporal aspects of when the information was seen before were not. While people expressed frustration when problems arose, an explanation of why the change had occurred was often sufficient to allay that frustration, even in the absence of a solution. The implications of these observations for systems that support re-finding in dynamic environments are discussed.

Aplicação da JNI - Java Native Interface - na construção da ferramenta ServCLIPS.

Linguagem de programação Java. Java native interface (JNI). Ferramenta ServCLIPS:um exemplo de uso da JNI.

A review of the effectiveness and meaningfulness of education interventions to enable children, young people and their families to self-care for their gastrostomy tubes in the community.

A systematic review of qualitative and quantitative evidence of the effectiveness and meaningfulness of education interventions to enable children, young people and their families to self-care for their gastrostomy tubes in the community