Orthographic Structure Versus Morphological Structure: Principles of Lexical Organization in a Given Language.

Most models of visual word recognition in alphabetic orthographies assume that words are lexically organized according to orthographic similarity. Support for this is provided by form-priming experiments that demonstrate robust facilitation when primes and targets share similar sequences of letters. The authors examined form-orthographic priming effects in Hebrew, Arabic, and English. Hebrew and Arabic have an alphabetic writing system but a Semitic morphological structure. Hebrew morphemic units are composed of noncontiguous phonemic (and letter) sequences in a given word. Results demonstrate that form-priming effects in Hebrew or Arabic are unreliable, whereas morphological priming effects with minimal letter overlap are robust. Hebrew bilingual subjects, by contrast, showed robust form-priming effects with English material, suggesting that Semitic words are lexically organized by morphological rather than orthographic principles. The authors conclude that morphology can constrain lexical organization even in alphabetic orthographies and that visual processing of words is first determined by morphological characteristics. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

A Demonstration of High-Throughput Electrophoresis

Automating electrophoresis significantly reduces the time required for loading a large number of samples, increases the speed of electrophoresis analysis, and maximizes the resolution power (clear separation of fragments) of this technique. In addition, automation increases the precision of electrophoresis analysis. Here we demonstrate an automated, high-throughput method of loading 96 samples simultaneously onto an electrophoresis gel, using the Apogent Discoveries Tango™ system and the Invitrogen™ E-Gel® 96 system.     

Bioorthogonal Chemical Reporters for Monitoring Unsaturated Fatty‐Acylated Proteins

Dietary unsaturated fatty acids, such as oleic acid, have been shown to be covalently incorporated into a small subset of proteins, but the generality and diversity of this protein modification has not been studied. We synthesized unsaturated fatty‐acid chemical reporters and determined their protein targets in mammalian cells. The reporters can induce the formation of lipid droplets and be incorporated site‐specifically onto known fatty‐acylated proteins and label many proteins in mammalian cells. Quantitative proteomics analysis revealed that unsaturated fatty acids modify similar protein targets to saturated fatty acids, including several immunity‐associated proteins. This demonstrates that unsaturated fatty acids can directly modify many proteins to exert their unique and often beneficial physiological effects in vivo.     

Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites

Inspection of the amino acid-base interactions in protein-DNA complexes is essential to the understanding of specific recognition of DNA target sites by regulatory proteins. The accumulation of information on protein-DNA co-crystals challenges the derivation of quantitative parameters for amino acid-base interaction based on these data. Here we use the coordinates of 53 solved protein-DNA complexes to extract all non-homologous pairs of amino acid-base that are in close contact, including hydrogen bonds and hydrophobic interactions. By comparing the frequency distribution of the different pairs to a theoretical distribution and calculating the log odds, a quantitative measure that expresses the likelihood of interaction for each pair of amino acid-base could be extracted. A score that reflects the compatibility between a protein and its DNA target can be calculated by summing up the individual measures of the pairs of amino acid-base involved in the complex, assuming additivity in their contributions to binding. This score enables ranking of different DNA binding sites given a protein binding site and vice versa and can be used in molecular design protocols. We demonstrate its validity by comparing the predictions using this score with experimental binding results of sequence variants of zif268 zinc fingers and their DNA binding sites.     

"What can we learn from the morphology of Hebrew? A masked-priming investigation of morphological representation": Correction to Frost et al. 1997.

Reports an error in "What can we learn from the morphology of Hebrew? A masked-priming investigation of morphological representation" by Ram Frost, Kenneth I. Forster and Avital Deutsch (Journal of Experimental Psychology: Learning, Memory, and Cognition, 1997[Jul], Vol 23[4], 829-856). On page 854, two Hebrew words are missing from Appendix F. The corrected Appendix appears with the erratum. (The following abstract of the original article appeared in record 1997-05320-003.) All Hebrew words are composed of 2 interwoven morphemes: a triconsonantal root and a phonological word pattern. The lexical representations of these morphemic units were examined using masked priming. When primes and targets shared an identical word pattern, neither lexical decision nor naming of targets was facilitated. In contrast, root primes facilitated both lexical decisions and naming of target words that were derived from these roots. This priming effect proved to be independent of meaning similarity because no priming effects were found when primes and targets were semantically but not morphologically related. These results suggest that Hebrew roots are lexical units whereas word patterns are not. A working model of lexical organization in Hebrew is offered on the basis of these results. (A correction concerning this article appears in Journal of Experimental Psychology: Learning, Memory, and Cognition, 1997, Vol 23(5), 1189-1191. On page 854 of the current issue, two Hebrew words are missing from Appendix F. The corrected Appendix appears in this correction.) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Tunneling in field induced diode in indium antimonide

Tunneling in the forward bias polarity of a field induced diode in indium antimonide is treated theoretically and experimentally. The theory leads to tunneling current-voltage characteristics with a region of negative resistance which are dependent upon the various parameters of the device, such as the gate voltage, substrate acceptor concentration and oxide thickness. A three-terminal device in which the gate voltage controls the tunneling I–V characteristics can thus be realized.Measurements were performed on an experimental device obtained by diffusion of cadmium into N-type InSb semiconductor. A chemically deposited SiO₂ layer was used to isolate the evaporated CrAu gate electrode from the substrate. Deviations from theory are shown to result from the two-dimensional character of the device.     

In vivo quantitative three-dimensional localization of tumor labeled with exogenous specific fluorescence markers

We introduce a diffused optical detection system based on the administration of a fluorophore-antibody conjugate to diseased tissue. The conjugate interacts with the antigens expressed by the diseased tissue, resulting in fluorescent labeling of the antigen. By combining an optical detection system with a reconstruction algorithm developed on the basis of the random-walk model, we were able to determine the position of the fluorophore (and, thus, of the diseased cells) in the tissue. We present three-dimensional reconstructions of the location of a fluorophore (FITC-fluorescein isothiocyanate) in the tongues of mice. Measurements were performed with the fluorophore embedded at various simulated depths. The simulations were performed with agarose-based gel slabs applied to the tongue as tissuelike phantoms. Reconstructed fluorophore locations agree well with the actual values.     

GemCell: A generic platform for modeling multi-cellular biological systems

The mass and complexity of biological information requires computer-aided simulation and analysis to help scientists achieve understanding and guide experimentation. Although living organisms are composed of cells, actual genomic and proteomic data have not yet led to a satisfactory model of working cell in silico. We have set out to devise a user-friendly generic platform, GemCell, for Generic Executable Modeling of Cells, based on whole, functioning cells. Starting with the cell simplifies life, because all cells expresses essentially five generic types of behavior: replication, death, movement (including change of shape and adherence), export (secretion, signaling, etc.) and import (receiving signals, metabolites, phagocytosis, etc.). The details of these behaviors are specified in GemCell for particular kinds of cells as part of a database of biological specifics (the DBS), which specifies the cell properties and functions that depend on the cell’s history, state, environment, etc. The DBS is designed in an intuitive fashion, so users are able to easily insert their data of interest. The generic part of GemCell, built using Statecharts, is a fully dynamic model of a cell, its interactions with the environment and its resulting behavior, individually and collectively. Model specificity emerges from the DBS, so that model execution is carried out by the statecharts executing with the aid of specific data extracted from the DBS dynamically. Our long term goal is for GemCell to serve as a broadly applicable platform for biological modeling and analysis, supporting user-friendly in silico experimentation, animation, discovery of emergent properties, and hypothesis testing, for a wide variety of biological systems.     

Synergistic activity between a spinach-derived natural antioxidant (NAO) and commercial antioxidants in a variety of oxidation systems

Recently, there has been great interest in the potential health benefits of foods containing polyphenols, especially from plants, due to their antioxidant content. Natural antioxidant (NAO) is a unique, powerful antioxidant which was isolated in our lab from spinach leaves. The main goal of this study was to examine potential synergistic activity in combinations of NAO and commercial antioxidants. The antioxidant activity was tested in several in vitro systems including fatty acid and fat oxidation and also in cancer cell lines. We used the unique optical live cell array (LCA) technology to monitor the generation of reactive oxygen species (ROS) in single cells over time. NAO was combined with selected commercial antioxidants, and synergistic activity that reduced ROS generation was found with three polyphenols – ferulic acid, caffeic acid, and epigallocatechin-3-gallate (EGCG). These findings demonstrate the importance of using antioxidant ‘cocktails’ which may enhance medical effects in many kinds of diseases, including cardiovascular diseases and cancer.