Doping of carbon nanotubes with nitrogen improves protein coverage whilst retaining correct conformation.

Relevant parameters for non-covalent protein functionalization of carbon nanotubes are explored. Multiwalled carbon nanotubes are carboxylated and functionalized with metalloproteins. Using atomic force microscopy (AFM) we quantitatively determine that coverage with nitrogen-doped multiwalled carbon nanotubes is superior compared to coverage with un-doped multiwalled carbon nanotubes, due to enhanced carboxylation. Conformational analysis using a combination of AFM, antibody binding assays, circular dichroism and UV-visible spectroscopy demonstrates that the metalloproteins retain their native structure when adsorbed to nitrogen-doped multiwalled carbon nanotubes irrespective of their size, charge or folding motif.

Electrostatic and steric interactions determine bacteriorhodopsin single-molecule biomechanics.

Bacteriorhodopsin (bR) is a haloarchaeal membrane protein that converts the energy of single photons into large structural changes to directionally pump protons across purple membrane. This is achieved by a complex combination of local dynamic interactions controlling bR biomechanics at the submolecular level, producing efficient amplification of the retinal photoisomerization. Using single molecule force spectroscopy at different salt concentrations, we show that tryptophan (Trp) residues use steric specific interactions to create a rigid scaffold in bR extracellular region and are responsible for the main unfolding barriers. This scaffold, which encloses the retinal, controls bR local mechanical properties and anchors the protein into the membrane. Furthermore, the stable Trp-based network allows ion binding to two specific sites on the extracellular loops (BC and FG), which are involved in proton release and lateral transport. In contrast, the cytoplasmic side of bR is mainly governed by relatively weak nonspecific electrostatic interactions that provide the flexibility necessary for large cytoplasmic structural rearrangements during the photocycle. The presence of an extracellular Trp-based network tightly enclosing the retinal seems common to most haloarchaeal rhodopsins, and could be relevant to their exceptional efficiency.

Differential stiffness and lipid mobility in the leaflets of purple membranes.

Purple membranes (PM) are two-dimensional crystals formed by bacteriorhodopsin and a variety of lipids. The lipid composition and density in the cytoplasmic (CP) leaflet differ from those of the extracellular (EC) leaflet. A new way of differentiating the two sides of such asymmetric membranes using the phase signal in alternate contact atomic force microscopy is presented. This method does not require molecular resolution and is applied to study the stiffness and intertrimer lipid mobility in both leaflets of the PM independently over a broad range of pH and salt concentrations. PM stiffens with increasing salt concentration according to two different regimes. At low salt concentration, the membrane Young's normal modulus grows quickly but differentially for the EC and CP leaflets. At higher salt concentration, both leaflets behave similarly and their stiffness converges toward the native environment value. Changes in pH do not affect PM stiffness; however, the crystal assembly is less pronounced at pH > or = 10. Lipid mobility is high in the CP leaflet, especially at low salt concentration, but negligible in the EC leaflet regardless of pH or salt concentration. An independent lipid mobility study by solid-state NMR confirms and quantifies the atomic force microscopy qualitative observations.

Nonequilibrium quasiparticle relaxation in the vortex state of La2-xSrxCuO4.

We have measured the charge dynamics in the vortex state of La(2-x)Sr(x)CuO(4) by femtosecond time-resolved reflectance, which we demonstrate to be a direct probe of low-energy quasiparticle states. Application of a c-axis magnetic field induces regions surrounding vortex cores that display pseudogap charge dynamics. We determine the characteristic width approximately 130 A in optimally doped material and we show that it increases with decreasing doping. These results confirm a new experimental method of probing the microscopic properties of vortices in the cuprates.

Longitudinal photocurrent spectroscopy of a single GaAs/AlGaAs v-groove quantum wire.

Modulation-doped GaAs v-groove quantum wires (QWRs) have been fabricated with novel electrical contacts made to two-dimensional electron-gas (2DEG) reservoirs. Here, we present longitudinal photocurrent (photoconductivity/PC) spectroscopy measurements of a single QWR. We clearly observe conductance in the ground-state one-dimensional subbands; in addition, a highly temperature-dependent response is seen from other structures within the v-groove. The latter phenomenon is attributed to the effects of structural topography and localization on carrier relaxation. The results of power-dependent PC measurements suggest that the QWR behaves as a series of weakly interacting localized states, at low temperatures.

GeneMachine: gene prediction and sequence annotation.

MOTIVATION: A number of free-standing programs have been developed in order to help researchers find potential coding regions and deduce gene structure for long stretches of what is essentially 'anonymous DNA'. As these programs apply inherently different criteria to the question of what is and is not a coding region, multiple algorithms should be used in the course of positional cloning and positional candidate projects to assure that all potential coding regions within a previously-identified critical region are identified. RESULTS: We have developed a gene identification tool called GeneMachine which allows users to query multiple exon and gene prediction programs in an automated fashion. BLAST searches are also performed in order to see whether a previously-characterized coding region corresponds to a region in the query sequence. A suite of Perl programs and modules are used to run MZEF, GENSCAN, GRAIL 2, FGENES, RepeatMasker, Sputnik, and BLAST. The results of these runs are then parsed and written into ASN.1 format. Output files can be opened using NCBI Sequin, in essence using Sequin as both a workbench and as a graphical viewer. The main feature of GeneMachine is that the process is fully automated; the user is only required to launch GeneMachine and then open the resulting file with Sequin. Annotations can then be made to these results prior to submission to GenBank, thereby increasing the intrinsic value of these data. AVAILABILITY: GeneMachine is freely-available for download at http://genome.nhgri.nih.gov/genemachine. A public Web interface to the GeneMachine server for academic and not-for-profit users is available at http://genemachine.nhgri.nih.gov. The Web supplement to this paper may be found at http://genome.nhgri.nih.gov/genemachine/supplement/.

The breast cancer information core: database design, structure, and scope.

The Breast Cancer Information Core (BIC) is an open access, on-line mutation database for breast cancer susceptibility genes. In addition to creating a catalogue of all mutations and polymorphisms in breast cancer susceptibility genes, a principle aim of the BIC is to facilitate the detection and characterization of these genes by providing technical support in the form of mutation detection protocols, primer sequences, and reagent access. Additional information at the site includes a literature review compiled from published studies, links to other internet-based, breast cancer information and research resources, and an interactive discussion forum which enables investigators to post or respond to questions and/or comments on a bulletin board. Hum Mutat 16:123-131, 2000. Published 2000 Wiley-Liss, Inc.

Comparative genome mapping in the sequence-based era: early experience with human chromosome 7.

The success of the ongoing Human Genome Project has resulted in accelerated plans for completing the human genome sequence and the earlier-than-anticipated initiation of efforts to sequence the mouse genome. As a complement to these efforts, we are utilizing the available human sequence to refine human-mouse comparative maps and to assemble sequence-ready mouse physical maps. Here we describe how the first glimpses of genomic sequence from human chromosome 7 are directly facilitating these activities. Specifically, we are actively enhancing the available human-mouse comparative map by analyzing human chromosome 7 sequence for the presence of orthologs of mapped mouse genes. Such orthologs can then be precisely positioned relative to mapped human STSs and other genes. The chromosome 7 sequence generated to date has allowed us to more than double the number of genes that can be placed on the comparative map. The latter effort reveals that human chromosome 7 is represented by at least 20 orthologous segments of DNA in the mouse genome. A second component of our program involves systematically analyzing the evolving human chromosome 7 sequence for the presence of matching mouse genes and expressed-sequence tags (ESTs). Mouse-specific hybridization probes are designed from such sequences and used to screen a mouse bacterial artificial chromosome (BAC) library, with the resulting data used to assemble BAC contigs based on probe-content data. Nascent contigs are then expanded using probes derived from newly generated BAC-end sequences. This approach produces BAC-based sequence-ready maps that are known to contain a gene(s) and are homologous to segments of the human genome for which sequence is already available. Our ongoing efforts have thus far resulted in the isolation and mapping of >3,800 mouse BACs, which have been assembled into >100 contigs. These contigs include >250 genes and represent approximately 40% of the mouse genome that is homologous to human chromosome 7. Together, these approaches illustrate how the availability of genomic sequence directly facilitates studies in comparative genomics and genome evolution.

The homeodomain resource: a prototype database for a large protein family.

The Homeodomain Resource is an annotated collection of non-redundant protein sequences, three-dimensional structures and genomic information for the homeodomain protein family. Release 2.0 contains 765 full-length homeodomain-containing sequences, 29 experimentally derived structures and 116 homeobox loci implicated in human genetic disorders. Entries are fully hyperlinked to facilitate easy retrieval of the original records from source databases. A simple search engine with a graphical user interface is provided to query the component databases and assemble customized data sets. A new feature for this release is the addition of more automated methods for database searching, maintenance and implementation of efficient data management. The Homeodomain Resource is freely available through the WWW at http://genome.nhgri.nih.gov/homeodomain

Informatic selection of a neural crest-melanocyte cDNA set for microarray analysis.

With cDNA microarrays, it is now possible to compare the expression of many genes simultaneously. To maximize the likelihood of finding genes whose expression is altered under the experimental conditions, it would be advantageous to be able to select clones for tissue-appropriate cDNA sets. We have taken advantage of the extensive sequence information in the dbEST expressed sequence tag (EST) database to identify a neural crest-derived melanocyte cDNA set for microarray analysis. Analysis of characterized genes with dbEST identified one library that contained ESTs representing 21 neural crest-expressed genes (library 198). The distribution of the ESTs corresponding to these genes was biased toward being derived from library 198. This is in contrast to the EST distribution profile for a set of control genes, characterized to be more ubiquitously expressed in multiple tissues (P < 1 x 10(-9)). From library 198, a subset of 852 clustered ESTs were selected that have a library distribution profile similar to that of the 21 neural crest-expressed genes. Microarray analysis demonstrated the majority of the neural crest-selected 852 ESTs (Mel1 array) were differentially expressed in melanoma cell lines compared with a non-neural crest kidney epithelial cell line (P < 1 x 10(-8)). This was not observed with an array of 1,238 ESTs that was selected without library origin bias (P = 0.204). This study presents an approach for selecting tissue-appropriate cDNAs that can be used to examine the expression profiles of developmental processes and diseases.

WebBLAST 2.0: an integrated solution for organizing and analyzing sequence data.

SUMMARY: WebBLAST is a suite of programs intended to assist in organizing sequencing data and to provide first-pass sequence analysis in an automated fashion. Data processing is fully automated, with end-users being presented both graphical and tabular summaries of data that can be viewed using any Web browser. AVAILABILITY: The program is free and available at http://genome.nhgri.nih. gov/webblast.

Spatio-temporal contrast sensitivity, coherent motion, and visible persistence in developmental dyslexia.

Three experiments measured spatio-temporal contrast sensitivity, coherent motion, and visible persistence in a single group of children with developmental dyslexia and a matched control group. The findings were consistent with a transient channel disorder in the dyslexic group which showed a reduction in contrast sensitivity at low spatial frequencies, a significant reduction in sensitivity for coherent motion, and a significantly longer duration of visible persistence. The results were also examined by classifying the dyslexic group into dyseidetic, dysphonetic, and mixed (dysphoneidetic) subgroups. There were no differences between the control and dyseidetic groups in contrast sensitivity, in coherent motion and in visible persistence. In comparison to the control group, the mixed (dysphoneidetic) dyslexic subgroup was found to have a significant reduction in contrast sensitivity at low spatial frequencies, a significant reduction in sensitivity for coherent motion, and a significantly longer duration of visible persistence. In comparison to the control group, the dysphonetic group only showed a reduction in contrast sensitivity at low spatial frequencies. Comparisons between the dyseidetic, dysphonetic and mixed dyslexic subgroups showed that there were no substantive differences in contrast sensitivity, coherent motion, and visible persistence. The results support the proposal and findings by Borsting et al. (Borsting E, Ridder WH, Dudeck K, Kelley C, Matsui L, Motoyama J. Vis Res 1996;36:1047-1053) that a transient channel disorder may only be present in a dysphoneidetic dyslexic subgroup. Psychometric assessment revealed that all the children with dyslexia appear to have a concurrent disorder in phonological coding, temporal order processing, and short-term memory.

The Homeodomain Resource: sequences, structures and genomic information.

The Homeodomain Resource is a comprehensive collection of sequence, structure and genomic information on the homeodomain protein family. Available through the Resource are both full-length and domain-only sequence data, as well as X-ray and NMR structural data for proteins and protein-DNA complexes. Also available is information on human genetic diseases and disorders in which proteins from the homeodomain family play an important role; genomic information includes relevant gene symbols, cytogenetic map locations, and specific mutation data. Search engines are provided to allow users to easily query the component databases and assemble specialized data sets. The Homeodomain Resource is available through the World Wide Web at http://genome.nhgri.nih.gov/homeodomain

Femtosecond quadrature-squeezed light generation in CdSe at 1.55 mum.

We generated pulsed quadrature-squeezed light by cross-phase modulation in single-crystal hexagonal CdSe at wavelengths of 1.4 to 1.55mum . We measured 0.4-dB squeezing (0.7 dB is inferred at the crystal) with 100-fs laser pulses. The wavelength and the intensity dependence, as well as variations in the local oscillator configuration, are examined. At higher intensities squeezing is shown to deteriorate owing to competing nonlinear processes.

Sudden unexplained death in a patient with a family history of malignant hyperthermia.

A 23-year-old healthy white male in excellent physical condition developed cardiac arrest and rigidity during moderate exercise. He had a strong family history of malignant hyperthermia (MH). Two hours postmortem, his temperature was noted to be markedly elevated [41 degrees C (106 degrees F)]. A review of the possible differential diagnoses point to MH as a reasonable etiology.

Myoplasmic calcium changes precede metabolic and clinical signs of porcine malignant hyperthermia.

This study examines the chronologic relationship of the biochemical and clinical development of malignant hyperthermia (MH) in susceptible swine. Four pigs previously established by challenge to be susceptible to MH were studied. Monitors included end-tidal CO2 (ETCO2), transcutaneous oxygen saturation (Spo2), intraarterial blood pressure, rectal temperature, electrocardiogram (ECG), and train-of-four twitch measurements. Calcium-selective microelectrodes were used to monitor changes in the concentration of free myoplasmic calcium ([Ca2+]i). The animals were studied in the resting state, during the development of the syndrome, and after treatment with dantrolene sodium. The increase in [Ca2+]i preceded the increase in ETCO2 that preceded a decrease in Spo2 that preceded the classic first sign, tachycardia, and all preceded the increase in rectal temperature. Dantrolene reversed all of these physiologic changes in the same order of precedence as the increase.