Trypsiligase-Catalyzed Labeling of Proteins on Living Cells

Fluorescent fusion proteins are powerful tools for studying biological processes in living cells, but universal application is limited due to the voluminous size of those tags, which might have an impact on the folding, localization or even the biological function of the target protein. The designed biocatalyst trypsiligase enables site-directed linkage of small-sized fluorescence dyes on the N terminus of integral target proteins located in the outer membrane of living cells through a stable native peptide bond. The function of the approach was tested by using the examples of covalent derivatization of the transmembrane proteins CD147 as well as the EGF receptor, both presented on human HeLa cells. Specific trypsiligase recognition of the site of linkage was mediated by the dipeptide sequence Arg-His added to the proteins’ native N termini, pointing outside the cell membrane. The labeling procedure takes only about 5 minutes, as demonstrated for couplings of the fluorescence dye tetramethyl rhodamine and the affinity label biotin as well.     

Deliberately Losing Control of C−H Activation Processes in the Design of Small-Molecule-Fragment Arrays Targeting Peroxisomal Metabolism

Combined photochemical arylation, “nuisance effect” (S_NAr) reaction sequences have been employed in the design of small arrays for immediate deployment in medium-throughput X-ray protein–ligand structure determination. Reactions were deliberately allowed to run “out of control” in terms of selectivity; for example the ortho-arylation of 2-phenylpyridine gave five products resulting from mono- and bisarylations combined with S_NAr processes. As a result, a number of crystallographic hits against NUDT7, a key peroxisomal CoA ester hydrolase, have been identified.     

Protecting local access telecommunications networks: Toward a minimum-cost solution

The problem of designing fibre-optic networks for local-access telecommunications generates (at least) three non-trivial subproblems. In the first of these subproblems one must determine how many fibre-optic cables (fibres) are required at either end of a street. In the next subproblem a minimum-cost network must be designed to support the fibres. The network must also provide distinct paths from either end of the street to the central exchange(s). Finally, the fibre-optic cables must be placed in protective covers. These covers are available in a number of different sizes, allowing some flexibility when covering each section of the network. In this paper we describe a dynamic programming (DP) formulation for finding a minimum-cost (protective) covering for the network (the third of the subproblems). This problem is a generalised set covering problem with side constraints and is further complicated by the introduction of fixed and variable welding costs. The DP formulation selects covers along each arc (in the network), but cannot exactly model the fixed costs and so does not guarantee optimality. We also describe an integer programming (IP) formulation for assessing the quality of the DP solutions. The cost of the networks constructed by the IP model is less than those designed using the DP model, but the saving is not significant for the problems examined (less than 0.1%). This indicates that the DP model will generally give very good solutions. Furthermore, as the problem dimensions grow, DP gives significantly better solution times than IP.     

Life is pleasant--and memory helps to keep it that way!

People's recollections of the past are often positively biased. This bias has 2 causes. The 1st cause lies in people's perceptions of events. The authors review the results of several studies and present several new comparative analyses of these studies, all of which indicate that people perceive events in their lives to more often be pleasant than unpleasant. A 2nd cause is the fading affect bias: The affect associated with unpleasant events fades faster than the affect associated with pleasant events. The authors review the results of several studies documenting this bias and present evidence indicating that dysphoria (mild depression) disrupts such bias. Taken together, this evidence suggests that autobiographical memory represents an important exception to the theoretical claim that bad is stronger than good. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Large deflection dynamics and control for planar continuum robots

This paper focuses on a class of robot manipulators termed "continuum" robots - robots that exhibit behavior similar to tentacles, trunks, and snakes. In previous work, we studied details of the mechanical design, kinematics, path-planning and small-deflection dynamics for continuum robots such as the Clemson "tentacle manipulator". In this paper, we discuss the dynamics of a planar continuum backbone section, incorporating a large-deflection dynamic model. Based on these dynamics, we formulate a vibration-damping setpoint controller, and include experimental results to illustrate the efficacy of the proposed controller.     

K-winner networks.

A special class of mutually inhibitory networks is analyzed, and parameters for reliable K-winner performance are presented. The network dynamics are modeled using interactive activation, and results are compared with the sigmoid model. For equal external inputs, network parameters that select the units with the larger initial activations (the network converges to the nearest stable state) are derived. Conversely, for equal initial activations, networks that select the units with larger external inputs (the network converges to the lowest energy stable state) are derived. When initial activations are mixed with external inputs, anomalous behavior results. These discrepancies are analyzed with several examples. Restrictions on initial states are derived which ensure accurate K-winner performance when unequal external inputs are used.     

Towards deterministic downscaling of SMOS soil moisture using MODIS derived soil evaporative efficiency

A deterministic approach for downscaling ～ 40 km resolution Soil Moisture and Ocean Salinity (SMOS) observations is developed from 1 km resolution MODerate resolution Imaging Spectroradiometer (MODIS) data. To account for the lower soil moisture sensitivity of MODIS surface temperature compared to that of L-band brightness temperature, the disaggregation scale is fixed to 10 times the spatial resolution of MODIS thermal data (10 km). Four different analytic downscaling relationships are derived from MODIS and physically-based model predictions of soil evaporative efficiency. The four downscaling algorithms differ with regards to i) the assumed relationship (linear or nonlinear) between soil evaporative efficiency and near-surface soil moisture, and ii) the scale at which soil parameters are available (40 km or 10 km). The 1 km resolution airborne L-band brightness temperature from the National Airborne Field Experiment 2006 (NAFE'06) are used to generate a time series of eleven clear sky 40 km by 60 km near-surface soil moisture observations to represent SMOS pixels across the three-week experiment. The overall root mean square difference between downscaled and observed soil moisture varies between 1.4% v/v and 1.8% v/v depending on the downscaling algorithm used, with soil moisture values ranging from 0 to 15% v/v. The accuracy and robustness of the downscaling algorithms are discussed in terms of their assumptions and applicability to SMOS.     

Oxygen content of the fixative is important in the interpretation of the ultrastructure of ischaemic myocardium

Isolated rat hearts were subjected to 15, 45, or 60 minutes of global ischaemia and then fixed by perfusion at 37°C with glutaraldehyde containing various amounts of oxygen. This either had been bubbled with 100% oxygen (PO₂ 620 mm Hg) or with 100% nitrogen (PO₂ 40 mm Hg) immediately before use, or it had been routinely prepared and stored exposed to atmospheric oxygen (PO₂ 245 mm Hg). The ultrastructure of myocytes and endothelial cells subjected to 15 minutes of ischaemia was not affected by the treatment of the fixative. However, when the tissue subjected to longer periods of ischaemia was fixed with routinely prepared or oxygen-bubbled glutaraldehyde, ultrastructural changes characteristic of reoxygenation damage were uniformly evident in both the microvasculature and myocytes. These qualitatively distinct changes included mitochondrial swelling, cell swelling, endothelial bleb formation, and narrowing of capillary lumina. These abnormalities were not observed in tissue fixed with nitrogen-bubbled glutaraldehyde. These findings indicate that deliberate steps should be taken to reduce or eliminate dissolved oxygen from the fixatives used to study ischaemic tissues. Otherwise artefactual reoxygenation damage in vitro may occur and make valid ultrastructural interpretation difficult or impossible.