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Results for “multiplex imaging”

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At least 415 records · Page 23Linked to original sources

PubMed1993

Genetic susceptibility in familial multiple sclerosis not linked to the myelin basic protein gene.

The myelin basic protein (MBP) gene is a candidate locus for disease susceptibility in familial multiple sclerosis. Amplification of a polymorphic tetranucleotide repeat region immediately 5' to MBP exon 1 demonstrated the presence of eight different alleles among members of 14 multiplex multiple sclerosis families (36 affected individuals). Linkage analysis was performed with autosomal dominant and autosomal recessive models, normal individuals with abnormal magnetic resonance scans being scored as either unknown or affected. Cumulative LOD scores were negative for both models of inheritance. The results do not demonstrate linkage between the MBP gene region and multiple sclerosis.

Alleles↗

PubMed1990

Imaging of DNA sequences with chemiluminescence.

We have coupled a chemiluminescent detection method that uses an alkaline phosphatase label to the genomic DNA sequencing protocol of Church and Gilbert [Church, G. M. & Gilbert, W. (1984) Proc. Natl. Acad. Sci. USA 81, 1991-1995]. Images of sequence ladders are obtained on x-ray film with exposure times of less than 30 min, as compared to 40 h required for a similar exposure with a 32P-labeled oligomer. Chemically cleaved DNA from a sequencing gel is transferred to a nylon membrane, and specific sequence ladders are selected by hybridization to DNA oligonucleotides labeled with alkaline phosphatase or with biotin, leading directly or indirectly to deposition of enzyme. If a biotinylated probe is used, an incubation with avidin-alkaline phosphatase conjugate follows. The membrane is soaked in the chemiluminescent substrate (AMPPD) and is exposed to film. Dephosphorylation of AMPPD leads in a two-step pathway to a highly localized emission of visible light. The demonstrated shorter exposure times may improve the efficiency of a serial reprobing strategy such as the multiplex sequencing approach of Church and Kieffer-Higgins [Church, G. M. & Kieffer-Higgins, S. (1988) Science 240, 185-188].

Adamantane↗

PubMed2000

Correction of odontoid dysplasia following bone-marrow transplantation and engraftment (in Hurler syndrome MPS 1H).

BACKGROUND: Odontoid dysplasia is recognized as a major component of the constellation of dysostosis multiplex lesions associated with Hurler's syndrome (MPS 1H). Because of this abnormality, there is an increased risk of atlantoaxial subluxation with potential cervical spinal cord injury. A significant alteration of the natural history of the disease with respect to the visceral, cardiac, and skeletal systems has resulted in an increased life span for MPS 1H patients associated with engraftment from normal donors. OBJECTIVE: The purpose of this study was to evaluate the longitudinal changes of odontoid dysplasia in MPS 1H following engraftment from bone-marrow transplantation (BMT). MATERIALS AND METHODS: A retrospective review of sequential plain film or cervical spine MR was performed in patients with MPS 1H. Odontoid morphology was graded as aplasia, severe dysplasia, moderate dysplasia, mild dysplasia, or normal. Odontoid morphology was plotted against the time interval. Fully engrafted, nontransplanted, and partially engrafted patients had careful imaging evaluation of the odontoid process. RESULTS: Ten patients were studied with a mean interval follow-up of 8.7 years post-BMT. Seven patients were totally engrafted. Two patients were nontransplanted, and one patient had only partial engraftment (20% enzyme activity). All totally engrafted patients had a progressive improvement in the grade of odontoid dysplasia following BMT. Patients with partial engraftment or without transplantation demonstrated static or increasing odontoid dysplasia. MR imaging showed abnormal dural soft-tissue masses at the level of C2 in all patients. Reduction in the grade of odontoid dysplasia was not associated with significant change in the appearance of the upper cervical soft-tissue masses. CONCLUSION: For the first time, this report documents that patients with MPS 1H show a decrease in the degree of odontoid dysplasia on imaging after successful engraftment following BMT.

Bone Diseases, Developmental↗

PubMed2005

[Non-Hodgkin's malignant lymphoma of the peripheral nervous system: clinicopathological correlations in ten patients].

INTRODUCTION: Identifying tumor infiltration or compression in patients with non-Hodgkin's malignant lymphoma presenting peripheral neuropathy can be a difficult task. METHODS: We collected a series of patients with peripheral neuropathy with demonstrated lymphomatous infiltration or compression managed between October 1977 and October 2001 to search for clinico-pathological correlations. RESULTS: Ten cases were reviewed. Neurological manifestations were the inaugural symptom of the disease in 7 patients. Clinical presentations included 5 focal (3 cranial nerve palsies, 2 brachial radiculopathies) and 5 diffuse neuropathies (3 polyradiculoneuropathies, 1 polyneuropathy and 1 mononeuritis multiplex). The mechanisms of peripheral nerve involvement were classified into lymphomatous meningoradiculitis (5 cases), involvement of cranial nerves or spinal roots in their extraneuraxial course (3 cases) and infiltration of distal peripheral nerves (2 cases). Four long lasting survivals after treatment were observed. CONCLUSIONS: Prognosis depends much more on the haematological disease than on the neurological symptoms or tumor location.

Adult↗

PubMed2003

Fast multi-dimensional Hadamard spectroscopy.

Multi-dimensional NMR spectroscopy can be speeded up by large factors by replacing the time-domain evolution dimensions by direct irradiation at signal-bearing sites with a frequency-domain multiplex scheme. There is no loss in sensitivity per unit time. The excitation and transfer operations are encoded according to Hadamard matrices and the detected NMR signals are decoded by reference to the same matrices. Most traditional multi-dimensional NMR pulse sequences can be readily converted into this new Hadamard mode. Three-dimensional TOCSY-HSQC experiments on strychnine at 700 MHz bear out these ideas, indicating that the measurement time can be reduced by as much as three orders of magnitude in favorable cases.

Algorithms↗

PubMed2003

Multiplexed computer-generated holograms with polygonal-aperture layouts optimized by genetic algorithm.

Using a novel genetic algorithm (GA) with a Lamarckian search we optimize the polygonal layout of a new type of multiplexed computer-generated hologram (MCGH) with polygonal apertures. A period ofthe MCGH is divided into cells, and the cell is further divided into polygonal apertures according to a polygonal layout, which is to be optimized. Among an ensemble of 1.21 x 10(24) possible polygonal layouts, we take a population of 102 solutions, which are coded as chromosomes of bits, and find the optimal solution with our GA. We introduce rank-based selection with cumulative normal distribution fitness, double crossover, exponentially decreasing mutation probability and Lamarckian downhill search with a small number of offspring chromosomes into our GA, which shows a rapid convergence to the global minimum of the cost function. In a second step of optimization the phase distributions over the subholograms in the MCGH are determined with our iterative subhologram design algorithm. Our MCGH designs show large-sie reconstructed images with high diffraction efficiency and low reconstruction error.

Journal Article↗

PubMed2006

Optical technologies for the read out and quality control of DNA and protein microarrays.

Microarray formats have become an important tool for parallel (or multiplexed) monitoring of biomolecular interactions. Surface-immobilized probes like oligonucleotides, cDNA, proteins, or antibodies can be used for the screening of their complementary targets, covering different applications like gene or protein expression profiling, analysis of point mutations, or immunodiagnostics. Numerous reviews have appeared on this topic in recent years, documenting the intriguing progress of these miniaturized assay formats. Most of them highlight all aspects of microarray preparation, surface chemistry, and patterning, and try to give a systematic survey of the different kinds of applications of this new technique. This review places the emphasis on optical technologies for microarray analysis. As the fluorescent read out of microarrays is dominating the field, this topic will be the focus of the review. Basic principles of labeling and signal amplification techniques will be introduced. Recent developments in total internal reflection fluorescence, resonance energy transfer assays, and time-resolved imaging are addressed, as well as non-fluorescent imaging methods. Finally, some label-free detection modes are discussed, such as surface plasmon microscopy or ellipsometry, since these are particularly interesting for microarray development and quality control purposes.

Animals↗

PubMed2005

Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labelling two-dimensional difference gel electrophoresis.

Differential protein expression analysis based on modification of selected amino acids with labelling reagents has become the major method of choice for quantitative proteomics. One such methodology, two-dimensional difference gel electrophoresis (2-D DIGE), uses a matched set of fluorescent N-hydroxysuccinimidyl (NHS) ester cyanine dyes to label lysine residues in different samples which can be run simultaneously on the same gels. Here we report the use of iodoacetylated cyanine (ICy) dyes (for labelling of cysteine thiols, for 2-D DIGE-based redox proteomics. Characterisation of ICy dye labelling in relation to its stoichiometry, sensitivity and specificity is described, as well as comparison of ICy dye with NHS-Cy dye labelling and several protein staining methods. We have optimised conditions for labelling of nonreduced, denatured samples and report increased sensitivity for a subset of thiol-containing proteins, allowing accurate monitoring of redox-dependent thiol modifications and expression changes. Cysteine labelling was then combined with lysine labelling in a multiplex 2-D DIGE proteomic study of redox-dependent and ErbB2-dependent changes in epithelial cells exposed to oxidative stress. This study identifies differentially modified proteins involved in cellular redox regulation, protein folding, proliferative suppression, glycolysis and cytoskeletal organisation, revealing the complexity of the response to oxidative stress and the impact that overexpression of ErbB2 has on this response.

Animals↗

PubMed2006

Highly sensitive biomolecular fluorescence detection using nanoscale ZnO platforms.

Fluorescence detection is currently one of the most widely used methods in the areas of basic biological research, biotechnology, cellular imaging, medical testing, and drug discovery. Using model protein and nucleic acid systems, we demonstrate that engineered nanoscale zinc oxide structures can significantly enhance the detection capability of biomolecular fluorescence. Without any chemical or biological amplification processes, nanoscale zinc oxide platforms enabled increased fluorescence detection of these biomolecules when compared to other commonly used substrates such as glass, quartz, polymer, and silicon. The use of zinc oxide nanorods as fluorescence enhancing substrates in our biomolecular detection permitted sub-picomolar and attomolar detection sensitivity of proteins and DNA, respectively, when using a conventional fluorescence microscope. This ultrasensitive detection was due to the presence of ZnO nanomaterials which contributed greatly to the increased signal-to-noise ratio of biomolecular fluorescence. We also demonstrate the easy integration potential of zinc oxide nanorods into periodically patterned nanoplatforms which, in turn, will promote the assembly and fabrication of these materials into multiplexed, high-throughput, optical sensor arrays. These zinc oxide nanoplatforms will be extremely beneficial in accomplishing highly sensitive and specific detection of biological samples involving nucleic acids, proteins and cells, particularly under detection environments involving extremely small sample volumes of ultratrace-level concentrations.

DNA↗

PubMed2001

Congenital cervical spinal atrophy: an intrauterine hypoxic insult.

We present two patients with congenital cervical spinal atrophy who were born at 37 and 33 weeks of gestation. Both patients were unrelated and had no family history of neuromuscular diseases. They presented at birth with arthrogryposis multiplex and symmetrical severe muscle weakness and wasting confined to the upper extremities. There was no sensory or bulbar symptom. Electromyography showed polyphasic and fast-firing units in the proximal muscles of the upper extremities. With the evidence of chronic denervation and re-innervation, we speculate that this static condition is most likely due to circulatory insufficiency causing anterior horn cell ischemia during the latter part of the first trimester.

Anterior Horn Cells↗

PubMed2006

High-spectral-resolution coherent anti-Stokes Raman scattering with interferometrically detected broadband chirped pulses.

To achieve high-spectral-resolution multiplex coherent anti-Stokes Raman scattering (CARS), one typically uses a narrowband pump pulse and a broadband Stokes pulse. This is to ensure a correspondence between anti-Stokes and vibrational frequencies. We obtain high-resolution CARS spectra of isopropanol, using a broadband chirped pump pulse and a broadband Stokes pulse, by detecting the anti-Stokes pulse with spectral interferometry. With the temporally resolved anti-Stokes signal, we can remove the chirp of the anti-Stokes pulse and restore high spectral resolution while also rejecting nonresonant scattering.

Equipment Design↗

PubMed2002

Automatic decoding of sensor types within randomly ordered, high-density optical sensor arrays.

In this paper automatic sensor identification of sensor classes within a high-density randomized array, without a priori knowledge of sensor locations, is demonstrated. Two different fluorescence-based sensor types, with hundreds of replicates each, were randomly distributed into an optical imaging fiber array platform. The sensor element types were vapor-sensitive microspheres with the environmentally-sensitive fluorescent dye Nile Red adsorbed on their surface. Nile Red undergoes spectral changes when exposed to different microenvironmental polarity conditions, e.g. microsphere surface polarity or odor exposure. These reproducible sensor spectral changes, or sensor-response profiles, enable sensors within a randomized array to be grouped into categories by optical decoding methods. Two computational decoding methods (supervised and unsupervised) are introduced; equal classification rates were achieved for both. By comparing sensor responses from a randomized array with those obtained from known (control) arrays, 587 sensors were correctly classified with 99.32% accuracy. Although both methods were equally effective, the unsupervised method, which uses sensor response changes to odor exposure, is a better decoding model for the vapor-sensitive arrays studied, because it relies only on the odor-response profiles. Another decoding technique employed the emission spectra of the sensors and is more applicable to other types of multiplexed fluorescence-based arrays and assays. The sensor-decoding techniques are compared to demonstrate that sensors within high-density optical chemosensor arrays can be positionally-registered, or decoded, with no additional overhead in time or expense other than collecting the sensor-response profiles.

Journal Article↗

PubMed2005

A true singles list-mode data acquisition system for a small animal PET scanner with independent crystal readout.

We present a unique data acquisition system designed to read out signals from the MADPET-II small animal LSO-APD PET tomograph. The scanner consists of 36 independent detector modules arranged in a dual-radial layer ring (phi 71 mm). Each module contains a 4 x 8 array of optically isolated, 2 x 2 mm LSO crystals, coupled one-to-one to a 32 channel APD. To take full advantage of the detector geometry, signals from each crystal are individually processed without any data reduction. This is realized using custom designed mixed-signal ASICs for analogue signal processing, and FPGAs to control the digitization of analogue signals and subsequent multiplexing. Analogue to digital converters (ADCs) digitize the signal peak height, time to digital converters (TDCs) time stamp each event relative to a system clock and two 32 bit words containing the energy, time and position information for each singles event are multiplexed through three FIFO stages before being written to disk via gigabit Ethernet. Every singles event is processed and stored in list-mode format, and coincidences are sorted post-acquisition in software. The 1152 channel data acquisition system was designed to be able to handle sustained data rates of up to 11 520 000 cps without loss (10 000 cps/channel). The timing resolution of the TDC was measured to be 1 ns FWHM. In addition to describing the data acquisition system, performance measurements made using a 128-channel detector prototype will be presented.

Animals↗

PubMed2006

Golli-MBP copy number analysis by FISH, QMPSF and MAPH in 195 patients with hypomyelinating leukodystrophies.

The inherited disorders of CNS myelin formation represent a heterogeneous group of leukodystrophies. The proteolipoprotein (PLP1) gene has been implicated in two X-linked forms, Pelizaeus-Merzbacher disease (PMD) and spastic paraplegia type 2, and the gap junction protein alpha12 (GJA12) gene in a recessive form of PMD. The myelin basic protein (MBP) gene, which encodes the second most abundant CNS myelin protein after PLP1, presents rearrangements in hypomyelinating murine mutants and is always included in the minimal region deleted in 18q- patients with an abnormal hypomyelination pattern on cerebral MRI. In this study, we looked at the genomic copy number at the Golli-MBP locus in 195 patients with cerebral MRI suggesting a myelin defect, who do not have PLP1 mutation. Although preliminary results obtained by FISH suggested the duplication of Golli-MBP in 3 out of 10 patients, no abnormal gene quantification was found using Quantitative Multiplex PCR of Short Fluorescent fragments (QMPSF), Multiplex Amplifiable Probe Hybridization (MAPH), or another FISH protocol using directly-labelled probes. Pitfalls and interest in these different techniques to detect duplication events are emphasised. Finally, the study of this large cohort of patients suggests that Golli-MBP deletion or duplication is rarely involved in inherited defects of myelin formation.

DNA Primers↗

PubMed2003

Potential for using a digital micromirror device as a signal multiplexer in visible spectroscopy.

A digital micromirror device (DMD) was tested to demonstrate its potential as a multiplexing device for the simultaneous detection of visible electromagnetic radiation. Using a Visual Basic program, four sections of the DMD were illuminated by a light source and each region of mirrors was modulated at different low frequencies (14.92, 20.00, 25.00, and 34.48 Hz). A time-domain, multiplexed signal was collected from the sectors and a Fourier transform was performed on these data. The resulting frequency-domain spectrum showed that signal intensities correlated well with what was expected. Three different times were used to establish the best frequency resolution. Using this calculated frequency resolution, a 16 s scan could allow simultaneous detection of up to 240 emission/absorption wavelengths. Data collected also shows the selectivity of micromirror regions and the ability to choose specific regions of the micromirror plane, which could be valuable for a number of spectroscopic techniques.

Equipment Design↗

PubMed2004

DNA microarrays for virus detection in cases of central nervous system infection.

A low-density, high-resolution diagnostic DNA microarray comprising 38 gene targets for 13 viral causes of meningitis and encephalitis was constructed. The array has been used for the detection of multiplex PCR-amplified viruses in cerebrospinal fluid (CSF) and non-CSF specimens. A total of 41 clinical specimens were positive for echoviruses (23 samples), herpes simplex virus type 2 (4 samples), varicella-zoster virus (4 samples), human herpesvirus 7 (1 sample), human herpesvirus 6A (1 sample) and 6B (2 samples), Epstein-Barr virus (three samples), polyomavirus JC (1 sample), and cytomegalovirus (2 samples). Probes for herpes simplex virus type 1, polyomavirus BK, and mumps and measles viruses were also included on the array. Three samples were false negative by the microarray assay due to discordant results between the multiplex PCR for all 13 viruses simultaneously and the virus-specific PCR alone. Fifteen CSF specimens were true negative. The clinical sensitivity, specificity, and negative and positive predictive values of the assay were 93, 100, 100, and 83%, respectively, when the results were compared to those of the single-virus PCR, which was used as the "gold standard." The microarray-based virus detection assay is qualitative and provides a single-format diagnostic tool for the detection of panviral CNS infections.

Central Nervous System Viral Diseases↗

PubMed2006

Experimental evaluation of the FluChip diagnostic microarray for influenza virus surveillance.

Global surveillance of influenza is critical for improvements in disease management and is especially important for early detection, rapid intervention, and a possible reduction of the impact of an influenza pandemic. Enhanced surveillance requires rapid, robust, and inexpensive analytical techniques capable of providing a detailed analysis of influenza virus strains. Low-density oligonucleotide microarrays with highly multiplexed "signatures" for influenza viruses offer many of the desired characteristics. However, the high mutability of the influenza virus represents a design challenge. In order for an influenza virus microarray to be of utility, it must provide information for a wide range of viral strains and lineages. The design and characterization of an influenza microarray, the FluChip-55 microarray, for the relatively rapid identification of influenza A virus subtypes H1N1, H3N2, and H5N1 are described here. In this work, a small set of sequences was carefully selected to exhibit broad coverage for the influenza A and B viruses currently circulating in the human population as well as the avian A/H5N1 virus that has become enzootic in poultry in Southeast Asia and that has recently spread to Europe. A complete assay involving extraction and amplification of the viral RNA was developed and tested. In a blind study of 72 influenza virus isolates, RNA from a wide range of influenza A and B viruses was amplified, hybridized, labeled with a fluorophore, and imaged. The entire analysis time was less than 12 h. The combined results for two assays provided the absolutely correct types and subtypes for an average of 72% of the isolates, the correct type and partially correct subtype information for 13% of the isolates, the correct type only for 10% of the isolates, false-negative signals for 4% of the isolates, and false-positive signals for 1% of the isolates. In the overwhelming majority of cases in which incomplete subtyping was observed, the failure was due to the nucleic acid amplification step rather than limitations in the microarray.

Animals↗

PubMed2006

Spastic paraplegia type 2 associated with axonal neuropathy and apparent PLP1 position effect.

OBJECTIVE: To report an association between spastic paraplegia type 2 with axonal peripheral neuropathy and apparent proteolipid protein gene (PLP1) silencing in a family. METHODS: Pulsed-field gel electrophoresis, custom array comparative genomic hybridization, and semi-quantitative multiplex polymerase chain reaction analyses were used to examine the PLP1 genomic region. RESULTS: Electrodiagnostic studies and a sural nerve biopsy showed features of a dystrophic axonal neuropathy. Molecular studies identified a small duplication downstream of PLP1. INTERPRETATION: We propose the duplication to result in PLP1 gene silencing by virtue of a position effect. Our observations suggest that genomic rearrangements that do not include PLP1 coding sequences should be considered as yet another potential mutational mechanism underlying PLP1-related dysmyelinating disorders.

DNA Mutational Analysis↗