Direction biasing by brief apparent motion stimuli

The perceived direction of a motion step (probe stimulus) can be influenced by an earlier motion step or a brief motion sweep containing a series of steps (biasing stimulus). Depending upon experimental conditions, the biasing of the direction of the probe step (a phase shift of 180 degrees +/- Phi) by a biasing stimulus which precedes it by approximately 250 ms can either increase (positive filter biasing) or decrease (negative filter biasing) the tendency to see the probe move: in the biasing direction as computed with a motion filter with a biphasic temporal impulse response. In a series of experiments it was found that biasing motions traversing 90 degrees of phase angle in fewer than six steps in less than 100 ms produced positive filter biasing. Also, biasing of the probe direction could be dissociated from the consciously reported direction of the biasing stimulus, and it did not occur when the probe preceded rather than followed the biasing stimulus. A biasing sweep containing more than six steps traversing 90 degrees or a sweep traversing 270 degrees produced negative filter biasing. Perceptual fusion of the steps of the sweep was not a necessary condition for obtaining negative filter biasing. In general, the negative filter biasing effects were found to be the: most pervasive for the conditions investigated, and they are suggestive of a direction-specific, adaptation-like (gain-control) process in first-order motion filters. The exception to the negative biasing rule was found only with biasing stimuli which were short in duration or distance spanned. (C) 2000 Elsevier Science Ltd. All rights reserved

Integrated optical Mach-Zehnder interferometer as simazine immunoprobe

Immunoassay has become a versatile tool in several fields of analytical chemistry. We describe the characterization and the application of different integrated optical channel waveguide Mach-Zehnder interferometers (MZIs) as label-free immunoprobes. The performance of the classical MZI is compared with that of a modified structure which incorporates a 3x3 coupler. Characterization of the devices demonstrates a dramatic improvement gained by using the 3x3 coupler. Two main advantages are achieved by the modified device. First, the possibility of referencing the output signal allows the elimination of signal fluctuations due to coupling and light-source instabilities. An increase of the signal-to-noise ratio by a factor of up to 10 is achieved. Secondly, the phase shift between the three outputs allows unambiguous detection with optimum sensitivity. For the detection of the herbicide simazine, the functional properties of the transducer surface are optimized by an appropriate chemical modification. Using this improved device, a simazine immunoassay has been carried out with a test midpoint of 0.3 ppb and a detection limit of approximately 0.1 ppb. The excellent performance, established manufacturing techniques and the potential for simplification and parallelization make the device attractive for further development

The human ABC transporter pseudogene family: Evidence for transcription and gene-pseudogene interference

<p>Abstract</p> <p>Background</p> <p>Pseudogenes are an integral component of the human genome. Little attention, however, has so far been paid to the phenomenon that some pseudogenes are transcriptionally active. Recently, we demonstrated that the human ortholog of the rodent testis-specific ATP-binding cassette (ABC) transporter Abca17 is a ubiquitously transcribed pseudogene (<it>ABCA17P</it>). The aim of the present study was to establish a complete inventory of all ABC transporter pseudogenes in the human genome and to identify transcriptionally active ABC transporter pseudogenes. Moreover, we tested the hypothesis that a regulatory interdependency exists between ABC transporter pseudogenes and their parental protein coding equivalents.</p> <p>Results</p> <p>Systematic bioinformatic analysis revealed the existence of 22 ABC transporter pseudogenes within the human genome. We identified two clusters on chromosomes 15 and 16, respectively, which harbor almost half of all pseudogenes (n = 10). Available information from EST and mRNA databases and RT-PCR expression profiling indicate that a large portion of the ABC transporter pseudogenes (45%, n = 10) are transcriptionally active and some of them are expressed as alternative splice variants. We demonstrate that both pseudogenes of the pseudoxanthoma elasticum gene <it>ABCC6</it>, <it>ABCC6P1 </it>and <it>ABCC6P2</it>, are transcribed. <it>ABCC6P1 </it>and <it>ABCC6 </it>possess near-identical promoter sequences and their tissue-specific expression profiles are strikingly similar raising the possibility that they form a gene-pseudogene dual transcription unit. Intriguingly, targeted knockdown of the transcribed pseudogene <it>ABCC6P1 </it>resulted in a significant reduction of <it>ABCC6 </it>mRNA expression levels.</p> <p>Conclusion</p> <p>The human genome contains a surprisingly small number of ABC transporter pseudogenes relative to other known gene families. They are unevenly distributed across the chromosomes. Importantly, a significant portion of the ABC transporter pseudogenes is transcriptionally active. The downregulation of <it>ABCC6 </it>mRNA levels by targeted suppression of the expression of its pseudogene <it>ABCC6P1 </it>provides evidence, for the first time, for a regulatory interdependence of a transcribed pseudogene and its protein coding counterpart in the human genome.</p

Ultrathin nucleoporin phenylalanine-glycine repeat films and their interaction with nuclear transport receptors

Nuclear pore complexes (NPCs) are highly selective gates that mediate the exchange of all proteins and nucleic acids between the cytoplasm and the nucleus. Their selectivity relies on a supramolecular assembly of natively unfolded nucleoporin domains containing phenylalanine–glycine (FG)‐rich repeats (FG repeat domains), in a way that is at present poorly understood. We have developed ultrathin FG domain films that reproduce the mode of attachment and the density of FG repeats in NPCs, and that exhibit a thickness that corresponds to the nanoscopic dimensions of the native permeability barrier. By using a combination of biophysical characterization techniques, we quantified the binding of nuclear transport receptors (NTRs) to such FG domain films and analysed how this binding affects the swelling behaviour and mechanical properties of the films. The results extend our understanding of the interaction of FG domain assemblies with NTRs and contribute important information to refine the model of transport across the permeability barrier

Molecular structure of a novel cholesterol-responsive A subclass ABC transporter, ABCA9

We recently identified a novel ABC A subclass transporter, ABCA6, in human macrophages. Here, we report the molecular cloning of an additional ABC A subfamily transporter from macrophages denoted ABCA9. The identified coding sequence is 4.9 kb in size and codes for a 1624 amino acid protein product. In accordance with the proposed nomenclature, the novel transporter was designated ABCA9. The putative full-length ABC transporter polypeptide consists of two transmembrane domains and two nucleotide binding folds and thus conforms to the group of full-size ABC transporters. We identified alternative ABCA9 mRNA variants in human macrophages that predict the existence of three truncated forms of the novel transporter. Among the human ABC A subfamily transporters, ABCA9 exhibits the highest amino acid sequence homology with ABCA8 (72%) and ABCA6 (60%), respectively. The striking amino acid sequence similarity between these transporter molecules supports the notion that they represent an evolutionary more recently emerged subgroup within the family of ABC A transporters, which we refer to as “ABCA6-like transporters.” ABCA9 mRNA is ubiquitously expressed with the highest mRNA levels in heart, brain, and fetal tissues. Analysis of the genomic structure revealed that the ABCA9 gene consists of 39 exons that are located within a genomic region of ∼85 kb size on chromosome 17q24.2. In human macrophages, ABCA9 mRNA is induced during monocyte differentiation into macrophages and suppressed by cholesterol import indicating that ABCA9, like other known ABC A subfamily transporters, is a cholesterol-responsive gene. Based on this information, ABCA9 is likely involved in monocyte differentiation and macrophage lipid homeostasis

Parallelized Manipulation of Adherent Living Cells by Magnetic Nanoparticles-Mediated Forces

The remote actuation of cellular processes such as migration or neuronal outgrowth is a challenge for future therapeutic applications in regenerative medicine. Among the different methods that have been proposed, the use of magnetic nanoparticles appears to be promising, since magnetic fields can act at a distance without interactions with the surrounding biological system. To control biological processes at a subcellular spatial resolution, magnetic nanoparticles can be used either to induce biochemical reactions locally or to apply forces on different elements of the cell. Here, we show that cell migration and neurite outgrowth can be directed by the forces produced by a switchable parallelized array of micro-magnetic pillars, following the passive uptake of nanoparticles. Using live cell imaging, we first demonstrate that adherent cell migration can be biased toward magnetic pillars and that cells can be reversibly trapped onto these pillars. Second, using differentiated neuronal cells we were able to induce events of neurite outgrowth in the direction of the pillars without impending cell viability. Our results show that the range of forces applied needs to be adapted precisely to the cellular process under consideration. We propose that cellular actuation is the result of the force on the plasma membrane caused by magnetically filled endo-compartments, which exert a pulling force on the cell periphery

Integrated optical directional coupler sensor for pesticide analysis

Integrated optical transducers for the measurement of interactions between biological molecules and the specific detection of chemical and biochemical species are the subject of growing interest. Targeted applications include environmental monitoring, industrial process control and medical diagnostics. Integrated optical devices are capable of delivering the high detection sensitivity achievable through optical techniques in a compact format, and offer the potential for the detection of several analytes simultaneously through the fabrication of multiple transducers on a single chip. Here we describe the use of a new type of integrated optical sensor applied to the detection of low concentrations of the pesticide atrazine in aqueous solution. The transducer is based on a planar waveguide directional coupler structure fabricated by Ag+-Na+ ion-exchange in a low-index glass substrate. This sensor has the advantage of differential outputs, which gives improved signal-to-noise characteristics and offers the potential for the simultaneous measurement of the real and imaginary parts of the refractive indices of bulk or thin-film analytes

Ligand-induced type II interleukin-4 receptor dimers are sustained by rapid re-association within plasma membrane microcompartments

Biological and Soft Matter Physic