Open-Ended Study of Our Changing Earth

“At Washington School, Evanston, Illinois, the children themselves are proving that the ‘underachiever’ and the ‘slow learner’ may become obsolete as a classroom problem.”     

All Aboard! The Polar Express Is Traveling to Science—Understanding the States of Matter while Differentiating Instruction for Young Learners

This standards-based science lesson introduces young learners to scientific inquiry and critical thinking by using activities to demonstrate three phases of matter (solid, liquid, and gas). By learning about the states of matter through a 5E instructional approach, students are encouraged to observe changes in the states of matter and to discuss their understanding in both small and large group forums. Student participants will be involved in hands-on activities along with small and large group discourse while actively learning about the states of matter and enjoying a hot chocolate demonstration with sampling. Developmentally appropriate instructional approaches are emphasized throughout this lesson.     

Leaf detective: using evidence of damage on mangrove leaves to measure the effects of different herbivores

Abstract

Herbivores are important to ecosystems because they transfer energy stored in plant matter to other organisms. However, when herbivores occur in high abundances, they can become pests and harm the plants that form the basis of food webs. Mangroves are saltwater tolerant trees found along most tropical and subtropical shorelines. Because mangroves live between land and sea, a wide range of herbivores and other organisms, such as pathogens and parasites, affect them. Many of these organisms leave distinctive marks on the leaves that they eat or infect; scientists can use those marks to help identify the organisms that caused the damage. In this activity, students will take on the role of “Leaf Detectives” and examine patterns of leaf damage on red mangrove leaves (Rhizophora mangle) to infer which organism(s) are harming the mangroves on fictional Lobster Island. Students will collect data from their sample leaves, summarize the results with a graph, and then make a conclusion based on the scientific evidence. By classifying and measuring different damage patterns on leaves, students will learn how different organisms affect plants and food webs, develop pattern recognition skills, and practice using the scientific method to make evidence-based conclusions.     

Seasonal Variability of Particulate Organic Matter in a Mountain Stream in Central Spain

The aim of this paper was to study the influence of environmental characteristics of the Mediterranean climate on seasonal variability of particulate organic matter abundance in a mountain stream. Coarse and fine fractions of both suspended and benthic particulate organic matter were determined on 14 occasions between February 1998 and November 1999 in a second‐order Mediterranean stream in Central Spain (Arroyo Mediano). Temporal variability of suspended organic matter followed a seasonal pattern, attributed to litter‐fall inputs, instream processing, and the hydrological regime. Suspended organic matter (SOM) and its seasonal variability fall well within the range reported for streams in temperate non‐Mediterranean deciduous forest. However, we found no seasonal trend in benthic organic matter (BOM) storage, and it seems that the amount of BOM remained fairly constant throughout the year. Reach retention (evaluated as the ratio between BOM and SOM per m²) was higher in summer during reduced stream flow, mainly due to coarse particulate organic matter storage. These observations do not differ from those reported for other headwater streams in temperate forested biomes, from which we conclude that there was no evidence of a Mediterranean influence on particulate organic matter dynamics in the Mediano stream, nor probably in other headwater Mediterranean streams. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

On the Emergence of Biological Complexity: Life as a Kinetic State of Matter

A kinetic model that attempts to further clarify the nature of biological complexification is presented. Its essence: reactions of replicating systems and those of regular chemical systems follow different selection rules leading to different patterns of chemical behavior. For regular chemical systems selection is fundamentally thermodynamic, whereas for replicating chemical systems selection is effectively kinetic. Building on an extension of the kinetic stability concept it is shown that complex replicators tend to be kinetically more stable than simple ones, leading to an on-going process of kinetically-directed complexification. The high kinetic stability of simple replicating assemblies such as phages, compared to the low kinetic stability of the assembly components, illustrates the complexification principle. The analysis suggests that living systems constitute a kinetic state of matter, as opposed to the traditional thermodynamic states that dominate the inanimate world, and reaffirms our view that life is a particular manifestation of replicative chemistry.     

Using Amphibians and Reptiles to learn the Process of Science

The National Research Council's document, Inquiry and the National Science Education Standards (2000) describes an elementary science classroom as one that is composed of learners who are engaged in scientific processes. In such a setting, children ask real-world questions and seek real-world solutions. As students pursue their inquiries, they often move away from science textbooks, and they implement mathematical skills, read literature, conduct research in electronic databases, write stories, and so forth in a larger context. What was originally a regular science lesson becomes an opportunity for integration across the curriculum. This article describes an integrated unit on bats and specifically addresses the National Science Education Standards.     

Modeling changes in soil organic matter in Amazon forest to pasture conversion with the Century model

Land use and land cover changes in the Brazilian Amazon region have major implications for regional and even global carbon cycling. We analyzed the effects of the predominant land use change, conversion of tropical forest to pasture, on total soil C and N, using the Century ecosystem model and data collected from the Nova Vida ranch, Western Brazilian Amazon. We estimated equilibrium organic matter levels, plant productivity and residue carbon inputs under native forest conditions, then simulated deforestation following the slash and burn procedure. Soil organic matter dynamics were simulated for pastures established in 1989, 1987, 1983, 1979, 1972, 1951, and 1911. Using input data from the Nova Vida ranch, the Century model predicted that forest clearance and conversion to pasture would cause an initial decline in soil C and N stocks, followed by a slow rise to levels exceeding those under native forest. Simulated soil total C and N levels (2500 g C m^?2 and 245 g N m^?2 in the 0–20 cm layer) prior to conversion to pasture were close to those measured in the native forest. Simulated above‐ and below‐ground biomass for the forest and pasture were comparable with literature values from this region. The model predicted the long‐term changes in soil C and N under pasture inferred from the pasture chronosequence, but there was considerable variation in soil C stocks for pastures <20 years in age. Differences in soil texture between pastures were relatively small and could not account for much of the variability between different pastures of similar ages, in either the measured or simulated data. It is likely that much of the variability in C stocks between pastures of similar ages is related to initial C stocks immediately following deforestation and that this was the largest source of variability in the chronosequence. Internal C cycling processes in Century were evaluated using measurements of microbial biomass and soil δ¹³C. The relative magnitude and long‐term trend in microbial biomass simulated by the model were consistent with measurements. The close fit of simulated to measured values of δ¹³C over time suggests that the relative loss of forest‐derived C and its replacement by pasture‐derived C was accurately predicted by the model. After 80 years, almost 90% of the organic matter in the top 20 cm was pasture derived. While our analysis represents a single ‘case study’ of pasture conversion, our results suggest that modeling studies in these pasture systems can help to evaluate the magnitude of impacts on C and N cycling, and determine the effect of management strategies on pasture sustainability.     

Gaming as a Platform for Developing Science Practices

Gaming, an integral part of many students’ lives outside school, can provide an engaging platform for focusing students on important disciplinary core concepts as an entry into developing students’ understanding of these concepts through science practices. This article highlights how S’cape can be used to support student learning aligned with the most recent standards documents. Through combining students’ initial engagement in a motivating gaming experience with a two-experiment scaffolded inquiry sequence enhanced with information literacy-targeted homework, this article reveals how support can be offered for asking questions, planning and carrying out investigations, analyzing and interpreting data, constructing explanations, and engaging in argument from evidence to refine understandings of core concepts. We believe that as science teachers strive to explore important concepts with students through allowing them to actually practice science, games such as S’cape strategically leveraged and sequenced with scaffolded inquiry experiences can support these efforts.     

Molecular Modeling of the Full-length Human TRPV1 Channel in Closed and Desensitized States

The transient receptor potential vanilloid subtype 1 (TRPV1) is a member of the TRP family gated by vanilloids, heat, and protons. Structurally, TRPV1 subunits have a modular architecture underlying different functionalities, namely stimuli recognition, channel gating, ion selectivity, subunit oligomerization, and regulation by intracellular signaling molecules. Considering modular organization and recent structural information in the ion channel field, we have modeled a full-length TRPV1 by assembly of its major modules: the cytosolic N-terminal, C-terminal, and membrane-spanning region. For N-terminal, we used the ankyrin repeat structure fused with the N-end segment. The membrane domain was modeled with the structure of the eukaryotic, voltage-gated Kv1.2 K⁺ channel. The C-terminus was cast using the coordinates of HCN channels. The extensive structure–function data available for TRPV1 was used to validate the models in terms of the location of molecular determinants of function in the structure. Additionally, the current information allowed the modeling of the vanilloid receptor in the closed and desensitized states. The closed state shows the N-terminal module highly exposed and accessible to adenosine triphosphate and the C-terminal accessible to phosphoinositides. In contrast, the desensitized state depicts the N-terminal and C-terminal modules close together, compatible with an interaction mediated by Ca²⁺–calmodulin complex. These models identify potential previously unrecognized intra- and interdomain interactions that may play an important functional role. Although the molecular models should be taken with caution, they provide a helpful tool that yields testable hypothesis that further our understanding on ion channels work in terms of underlying protein structure.     

气候条件与高粱干物质积累动态特征分析

气候条件和栽培管理技术直接影响着高梁的干物质积累状况和最终产量。在栽培技术基本相同条件下,干物质的积累主要受气候条件所制约。因此,通过分析不同产量年型下气候     

On the Relationship between Intramolecular Dynamics and the Density of States

The relationship between the intramolecular dynamics and the spectra has been analyzed by means of the molecular dynamics technique. Time autocorrelation functions of bond lengths, bending angles and torsional angles have been evaluated in a crystalline trans-polyacetylene system. The Fourier transforms of such functions have been compared with the densities of states obtained both for carbon and hydrogen atoms. This comparison is aimed at investigating the microscopic origin of the peaks which appear in the densities of states. This approach can be used in the analysis of the spectroscopic data of any molecular or polymeric system.     

A method for the determination of flux in elementary modes, and its application to Lactobacillus rhamnosus

In this article we address the question of how, given information about the reaction fluxes of a system, flux values can be assigned to the elementary modes of that system. Having described a method by which this may be accomplished, we first illustrate its application to a hypothetical, in silico system, and then apply it to fermentation data from Lactobacillus rhamnosus. This reveals substantial changes in the flux values assigned to elementary modes, and thus to the internal metabolism, as the fermentation progresses. This is information that could not, to our knowledge, be obtained by existing methods. The relationship between our technique and the well-known method of Metabolic Flux Analysis is also discussed.     

Orientation and Mobility of Actin in Different Intermediate States of the ATP Hydrolysis Cycle

Using polarization fluorimetry, we have investigated conformational changes of FITC-phalloidin-labeled F-actin in ghost muscle fibers. These changes were induced by myosin subfragment-1 (S1) in the absence and presence of MgADP, MgAMP-PNP, MgATPgammaS, or MgATP. Modeling of various intermediate states was accompanied by discrete changes in actomyosin orientation and mobility of fluorescent dye dipoles. This suggests multistep changes of orientation and mobility of actin monomers during the ATPase cycle. The most pronounced differences in orientation (~4 degrees ) and in mobility (~43%) of actin were found between the actomyosin states induced by MgADP and MgATP.     

长白落叶松幼苗在受控条件下干物质积累的模拟

本文通过建立长白落叶松（Ｌａｒｉｘ ｏｌｇｅｎｓｉｓ）幼苗在受控环境条件下的净光合速率与温度和ＣＯ２等因子之间的关系,模拟了在受控条件下开白落叶松幼苗的日净光合速率进程与生长季中日干物质积累过程,并预测了在温度与ＣＯ２浓度改变后干物质积累的变化。     

Coarse Particulate Organic Matter Distribution in the Pools and Riffles of a Second-order Stream

Coarse particulate organic matter distribution was investigated in a 270-m interval of a 2nd-order forest stream, the Yanase River. The dominant tree type was Keyaki (Zelkova serrata). CPOM sampling was conducted, and the sampled CPOM was sorted into leaves and branches, and water depth and current velocity were measured along with stone width, stone height and distance between the stones in the riffles. The collected CPOM was categorized by their accumulation type: LSS, SLP, SLPi, SLPo and DD. LSS was leaf packs at the leading edge of the stones, SLP was the sinking leaf packs in the pools, SLPi was the sinking leaf packs at the inner side of the stream bend in the pools, while SLPo was the sinking leaf packs at the outer side of the stream bend, and finally, DD was the leaf packs in the debris dams. The accumulated CPOM amounts at each leaf pack type were correlated with the measured physical stream variables. From the results, CPOM accumulation in riffles is controlled by stones projecting above the water surface and by their arrangements. In pools, CPOM accumulation occurs at high stream flow where the pools provide low velocities and a thick boundary layer of relatively quiescent flow. At stream meandering points, CPOM accumulation occurs by production of a secondary flow. Finally, CPOM accumulation in debris dams is important where they occur frequently. LSS was the largest in CPOM amount, and the stones in the riffles were the most retentive structures. On the other hand, SLP and SLPo were the least CPOM amounts, and the pools in the mainstream and at the outer side of the stream bend were the least retentive stream morphologies.     

Identification of Plasmolipin as a Major Constituent of White Matter Clathrin-Coated Vesicles

We have isolated and characterized coated vesicles from bovine white matter and compared them to those isolated from gray matter. The virtual absence of synaptic vesicle antigens in the white matter coated vesicles indicates they are distinct from those found in gray matter and from vesicles derived from synaptic membranes. The white matter coated vesicles also lack compact myelin components, e.g., the myelin proteolipid, galactocerebroside, and sulfatides, as well as the periaxolemmal myelin marker myelin-associated glycoprotein. On the other hand, these vesicles contain 2',3'-cyclic nucleotide phosphohydrolase. The vesicles also contain high levels of plasmolipin, a protein present in myelin and oligodendrocytes. Plasmolipin was found to be four to five times higher in white matter coated vesicles than in gray matter coated vesicles. Based on western blot quantitation, the concentration of plasmolipin in white matter coated vesicles is 3-4% of the vesicle bilayer protein. These studies indicate that a significant proportion of coated vesicles from white matter may be derived from unique membrane domains of the myelin complex or oligodendroglial membrane, which are enriched in plasmolipin.     

Modeling the Dynamics of Disease States in Depression

Major depressive disorder (MDD) is a common and costly disorder associated with considerable morbidity, disability, and risk for suicide. The disorder is clinically and etiologically heterogeneous. Despite intense research efforts, the response rates of antidepressant treatments are relatively low and the etiology and progression of MDD remain poorly understood. Here we use computational modeling to advance our understanding of MDD. First, we propose a systematic and comprehensive definition of disease states, which is based on a type of mathematical model called a finite-state machine. Second, we propose a dynamical systems model for the progression, or dynamics, of MDD. The model is abstract and combines several major factors (mechanisms) that influence the dynamics of MDD. We study under what conditions the model can account for the occurrence and recurrence of depressive episodes and how we can model the effects of antidepressant treatments and cognitive behavioral therapy within the same dynamical systems model through changing a small subset of parameters. Our computational modeling suggests several predictions about MDD. Patients who suffer from depression can be divided into two sub-populations: a high-risk sub-population that has a high risk of developing chronic depression and a low-risk sub-population, in which patients develop depression stochastically with low probability. The success of antidepressant treatment is stochastic, leading to widely different times-to-remission in otherwise identical patients. While the specific details of our model might be subjected to criticism and revisions, our approach shows the potential power of computationally modeling depression and the need for different type of quantitative data for understanding depression.     

人工湿地运行过程中有机物质的积累

研究了杭州西湖边人工湿地污水净化生态工程经一年多运行后有机质的积累情况,同时测定了基质的孔隙度和水力传导性,结果表明,人工湿地在运行一年后总有机质积累达到0.658kg/m^2,60%有机质积累主要在0-100mm。湿地上,下池有机质积累有明显差异。且随着基质中的深度和离入水口的距离都呈下降趋势。两池中下层孔隙度均高于上层,并存在显著差异。有机质积累对水力传导性和净化效果均有一定影响,可通过定期收割植物和清除枯落物来维持湿地的长期运作能力。     

Modeling of loops in protein structures

Comparative protein structure prediction is limited mostly by the errors in alignment and loop modeling. We describe here a new automated modeling technique that significantly improves the accuracy of loop predictions in protein structures. The positions of all nonhydrogen atoms of the loop are optimized in a fixed environment with respect to a pseudo energy function. The energy is a sum of many spatial restraints that include the bond length, bond angle, and improper dihedral angle terms from the CHARMM-22 force field, statistical preferences for the main-chain and side-chain dihedral angles, and statistical preferences for nonbonded atomic contacts that depend on the two atom types, their distance through space, and separation in sequence. The energy function is optimized with the method of conjugate gradients combined with molecular dynamics and simulated annealing. Typically, the predicted loop conformation corresponds to the lowest energy conformation among 500 independent optimizations. Predictions were made for 40 loops of known structure at each length from 1 to 14 residues. The accuracy of loop predictions is evaluated as a function of thoroughness of conformational sampling, loop length, and structural properties of native loops. When accuracy is measured by local superposition of the model on the native loop, 100, 90, and 30% of 4-, 8-, and 12-residue loop predictions, respectively, had <2 A RMSD error for the mainchain N, C(alpha), C, and O atoms; the average accuracies were 0.59 +/- 0.05, 1.16 +/- 0.10, and 2.61 +/- 0.16 A, respectively. To simulate real comparative modeling problems, the method was also evaluated by predicting loops of known structure in only approximately correct environments with errors typical of comparative modeling without misalignment. When the RMSD distortion of the main-chain stem atoms is 2.5 A, the average loop prediction error increased by 180, 25, and 3% for 4-, 8-, and 12-residue loops, respectively. The accuracy of the lowest energy prediction for a given loop can be estimated from the structural variability among a number of low energy predictions. The relative value of the present method is gauged by (1) comparing it with one of the most successful previously described methods, and (2) describing its accuracy in recent blind predictions of protein structure. Finally, it is shown that the average accuracy of prediction is limited primarily by the accuracy of the energy function rather than by the extent of conformational sampling.     

The Effect of Mineral Particulate Matter on the Productive Characteristics of Bacterioplankton and the Degradation of Labile Organic Material

The effect of mineral particulate matter on the population of bacterioplankton, its aggregation, and productive characteristics was studied in model experiments with different concentrations of particulate kaolin and the same concentration of organic substance (sodium humate). It was found that the presence of mineral particulate matter stimulated the aggregation of bacterioplankton, improved bacterial production, and extended the productive period of bacterioplankton. The integral specific production of aggregated bacterioplankton was higher than that of free-swimming bacterioplankton. The energy metabolic coefficient K ₂ of bacterioplankton in the presence of mineral particulate matter was higher than in its absence.