Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds

The presence of disulfide bonds is essential for maintaining the structure and function of many proteins. The disulfide bonds are usually formed dynamically during folding. This process is not accounted for in present algorithms for protein-structure prediction, which either deduce the possible positions of disulfide bonds only after the structure is formed or assume fixed disulfide bonds during the course of simulated folding. In this work, the conformational space annealing (CSA) method and the UNRES united-residue force field were extended to treat dynamic formation of disulfide bonds. A harmonic potential is imposed on the distance between disulfide-bonded cysteine side-chain centroids to describe the energetics of bond distortion and an energy gain of 5.5 kcal/mol is added for disulfide-bond formation. Formation, breaking and rearrangement of disulfide bonds are included in the CSA search by introducing appropriate operations; the search can also be carried out with a fixed disulfide-bond arrangement. The algorithm was applied to four proteins: 1EI0 (alpha), 1NKL (alpha), 1L1I (beta-helix) and 1ED0 (alpha + beta). For 1EI0, a low-energy structure with correct fold was obtained both in the runs without and with disulfide bonds; however, it was obtained as the lowest in energy only with the native disulfide-bond arrangement. For the other proteins studied, structures with the correct fold were obtained as the lowest (1NKL and 1L1I) or low-energy structures (1ED0) only in runs with disulfide bonds, although the final disulfide-bond arrangement was non-native. The results demonstrate that, by including the possibility of formation of disulfide bonds, the predictive power of the UNRES force field is enhanced, even though the disulfide-bond potential introduced here rarely produces disulfide bonds in native positions. To the best of our knowledge, this is the first algorithm for energy-based prediction of the structure of disulfide-bonded proteins without any assumption as to the positions of native disulfides or human intervention. Directions for improving the potentials and the search method are suggested.     

Recent changes in platinum group element concentrations and osmium isotopic composition in sediments from an urban lake

Automobile catalyst emissions have resulted in the occurrence of elevated Pt, Pd, and Rh concentration in the urban and roadside environment. We investigate the chronology of platinum group elements (PGE) accumulation in dated sediments from an urban lake near Boston, MA. Chronological profiles demonstrate that Pt, Pd, and Rh concentrations increased following the introduction in catalysts with accumulation rates 6-16 times larger in 1992-2002 than prior to the introduction of catalysts. Ratios of these elements closely match their ratios in catalysts, providing further evidence of an automobile source. Iridium and Ru accumulation in sediments also increased following the introduction of catalysts, and while past Os contamination is associated with leather tanning, recent changes in the isotopic composition of Os indicate another anthropogenic source for this element. The PGE have similar geochemical properties and are difficult to separate from one another, and therefore, we suggest that automobile catalyst emissions also result in increasing environmental concentrations of Ir, Ru, and Os, which occur as impurities in catalysts. An automobile catalyst source of Ir and Os is supported by elevated concentrations of these elements in a tunnel dust sample.     

Extracellular recordings from patterned neuronal networks using planar microelectrode arrays

Neuronal cell networks have been reconstructed on planar microelectrode arrays (MEAs) from dissociated hippocampal pyramidal neurons. Microcontact printing (microCP) and a photoresist-liftoff method were used to selectively localize poly-L-lysine (PLL) on the surface of MEAs. Haptotaxis led to the organization of the neurons into networks localized adjacent to microelectrodes. Various grids of PLL with 2-25-microm-wide lines spaced by 50-200 microm with 15-25-microm nodes at intersection points were used to guide cell body attachment and neurite outgrowth. Bursting activity with spike amplitude attenuation was observed, and multichannel recordings detected instances of coincident firing activity. Finally, we present here an extracellular recording from a approximately 2 microm bundle of guided neurites.     

Fabrication and measurement of low-stress membrane mirrors for adaptive optics

We have fabricated low-stress membranes from single-crystal silicon for use as deformable mirrors in adaptive optics. These membranes have lower stress than membranes made from silicon nitride or other materials and therefore are capable of greater deformation than previously used membrane mirrors. Membranes were assembled into devices by flip chip bonding to electrode chips with either 256 or 1024 electrodes. We have characterized devices with static and dynamic tests and compared their performance with an analytical model. We tracked the evolution of strain in the membrane during the device's fabrication and assembly and identified sources of stress and strain in this process. We identified boron dopant concentration as a critical determinant of intrinsic stress in the membrane.     

Multiple-dial check reading: Pointer symmetry compared with uniform alignment.

24 Ss participated in two experiments in which they were required to pick out, from printed panels containing 16 dials, the dial with a deviating pointer. Two versions of a uniformly-aligned configuration and one version of a symmetrically-aligned configuration were studied. S was required to identify both the "different" dial and the direction of the deviating pointer. It was found that (1) both configurations were equally effective for check reading after extended practice, (2) early in practice symmetrical alignment configurations appear to be more difficult, (3) transfer effects from pointer symmetry to uniform alignment are greater than transfer effects in the other direction. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Hierarchical control model for automated manufacturing systems

A mathematical model is presented to determine the hierarchical computer control requirements for a completely automated flexible manufacturing systems. This model can estimate the number and capacity of hierarchical computers needed to control a specified automated manufacturing system. The hierarchical control system is described by the major operating components common to all controlling computers and computer numerical controlled (CNC) machines: central processing unit, memory, input/output and communications. Each of these components is evaluated with respect to its operating speed and capacity. Costs are then determined as a function of the component's processing speed and capacity.A three-tier control system is examined. Starting with the CNC machines' speeds and capacities, each level of the computer hierarchical control system is modeled and related to the next tier by communication and data requirements. The physical machine layout required for a hierarchical control system is discussed. Part scheduling and process information requirements are also addressed. The model's utility is illustrated by an example using a typical manufacturing system.Optimization of this model is readily obtained using standard dynamic programming techniques. Being totally independent of any specific computer hardware technology, the model can be applied to present and future automated manufacturing systems.     

Visible light reflectance,transmittance, and absorptance of differently pigmented cotton leaves

Spectrophotometrically measured light reflectance and transmittance, and calculated absorptance over the 0.45–0.70 μm waveband (WB) of four differently pigmented cotton (Gossypium hirsutum L.) leaves are compared. Leaf color appearances were green (G), common red (CR), light red or bronze (B), and yellow-green (YG). The G and YG leaves (chlorophylls and carotenoid) had about the same reflectance and transmittance peaks at the 0.55-μm wavelength (WL), although YG leaves had much higher reflectance and transmittance than G leaves. Anthocyanin pigment manifestation in CR, B, and YG leaves occurred at about the 0.60-μm WL. The red light (0.65-μm) absorptances of leaves in decreasing magnitude were: CR, G, YG, and B. There was little effect on blue light (0.45-μm) absorptance. Spectral responses of cotton leaves were very sensitive to either their masked or predominant pigmentation over the 0.45–0.70-μm WBs. The possible importance of leaf pigmentation to LANDSAT-D's thematic mapper, visible light WBs is discussed.     

The potential uses of a computer animated film in the analysis of geographical patterns of traffic crashes

If one looks at research in progress regarding the phenomenon of traffic crashes, it can be seen that little of this work relates to the analysis of geographic patterns of traffic crashes. The geographic approach involves the analysis of patterns of data in a two dimensional spatial domain utilizing points and lines as primitives. Broadly speaking, the approaches which are applicable here are distributional, residual and cluster analyses in one and two dimensions.

The purpose of a computer animated film is to display the object(s) of analysis in a dynamic temporal setting. Scientific applications of this technique are beginning to see use in a large variety of areas since it is often far easier to display complicated spatiotemporal processes than to describe them either verbally or in mathematical terms. Uses of such a tool in a geographical setting are fundamentally twofold. Initially the film can be used as a cognitive device to aid the research person in perceiving the spatiotemporal dynamics of the process as represented by the patterns. Secondly, the film may be used as an heuristic device to aid in suggesting hypotheses which later may be tested in the data.

An example of this approach is a film which displays traffic crashes occurring in Washtenaw County, Michigan during the years of 1968–1970. Two scenes are displayed, collapsed real time and a composite week each representing different temporal frequencies as defined by the sampling theorem. Both scenes prove useful as a cognitive and hypothesis formulating device. The film is in color and of seven minutes duration.     

Suprathreshold intrinsic dynamics of the human visual system

Intrinsic high-frequency neural activities have been observed in the visual system of several species, but their functional significance for visual perception remains a fundamental puzzle in cognitive neuroscience. Spatiotemporal integration in the human visual system acts as a low-pass filter and makes the psychophysical observation of high-frequency activities very difficult. A computational model of retino-cortical dynamics (RECOD) is used to derive experimental paradigms that allow psychophysical studies of high-frequency neural activities. A reduced-parameter version of the model is used to quantitatively relate psychophysical data collected in two of these experimental paradigms. Statistical analysis shows that the model's account of the variance in the data is, in general, highly significant. We suggest that psychophysically measured oscillations reflect intrinsic neuronal oscillations observed in the visual cortex.     

Concentration of DNA in a flowing stream for high-sensitivity capillary electrophoresis

A novel sample pretreatment device is described, and its application to the concentration and purification of crude DNA samples in a flowing stream for subsequent capillary electrophoresis is demonstrated. The device consists of two gap junctions, each covered with a conductive membrane material and built upon a flow channel made of PEEK tubing. Upon the application of an electric field between the junctions, the negatively charged DNA fragments can resist the hydrodynamic flow stream and are trapped between the junctions. DNA fragments dissolved in microliter volumes are captured in a nanoliter-sized band by simply pushing the sample solution through the device. Depending on their electrophoretic mobility, other interfering materials in a crude sample can be removed from the trapped DNA fragments by washing. The selective permeability of the membrane to small ions allows efficient desalting. The concentrated and purified DNA fragments are released by simply turning off or reversing the electric field. Recovery is up to 95%. Performance of the device was evaluated using crude products of fluorescent dye-primer cycle-sequencing reactions. Compared to these crude reaction products, samples purified in the capture device and subsequently collected showed dramatically enhanced signal and resolution when run on a conventional capillary-electrophoresis instrument. Furthermore, the device could be connected in-line to a capillary system for direct injection. The device has great potential for enabling lab-on-a-chip systems to be used with real-world samples.