Detection of mitochondrial single nucleotide polymorphisms using a primer elongation reaction on oligonucleotide microarrays

We have developed a novel allele-specific primer elongation protocol using a DNA polymerase on oligonucleotide chips. Oligonucleotide primers carrying polymorphic sites at their free 3'end were covalently bound to glass slides. The generation of single-stranded targets of genomic DNA containing single nuclotide polymorphisms (SNPs) to be typed was achieved by an asymmetric PCR reaction or exonuclease treatment of phosphothioate (PTO)-modified PCR products. In the presence of DNA polymerase and all four dNTPs, with Cy3-dUTP replacing dTTP, allele-specific extension of the immobilized primers took place along a stretch of target DNA sequence. The yield of elongated products was increased by repeated reaction cycles. We performed multiplexed assays with many small DNA targets, or used single targets of up to 4.4 kb mitochondrial DNA (mtDNA) sequence to detect multiple SNPs in one reaction. The latter approach greatly simplifies preamplification of SNP-containing regions, thereby providing a framework for typing hundreds of mtDNA polymorphisms.     

Thiocyanate overload and thyroid disease

Thiocyanate [SCN-] is a complex anion which is a potent inhibitor of iodide transport. It is the detoxification product of cyanide and can easily be measured in body fluids. Consumption of naturally occurring goitrogens, certain environmental toxins and cigarette smoke can significantly increase SCN- concentrations to levels potentially capable of affecting the thyroid gland. Goiter endemics were reported to develop when the critical urinary iodine/ SCN- ratio decreases below 3 microg iodine per mg SCN-. Iodine supplementation completely reverses the goitrogenic influence of SCN-. SCN- is also generated from cigarette smoking as a detoxifying product of cyanide. During the past two decades many reports dealt with the possible effects of cigarette smoking on thyroid hormone synthesis, thyroid gland size and thyroid autoimmunity including infiltrative ophtalmopathy of Graves' disease. In this mini-review, issues regarding thiocyanate overload and thyroid disease will be summarized.     

Light directed massively parallel on-chip synthesis of peptide arrays with t-Boc chemistry

Peptide and peptidomimetic molecule arrays are emerging powerful tools for parallel screening of binding in proteomics and pharmaceutical discovery research. Up to now the common method of preparing peptide arrays was based on spotting on glass using a library of presynthesized peptides. However, due to the large number of monomers (amino acids) it is not possible to have combinatorial libraries which include all combinations of natural and synthetic amino acids. We describe a very flexible on-chip oligopeptide synthesis method which uses the well developed t-Boc based solid state synthesis chemistry. A very high degree of flexibility is achieved by using light photo generated acids and maskless projection lithography for spatially directed deprotection. Use of microfluidic chips enables moderately high densities, short reaction times and off-the-shelf chemicals. Examples are given from synthesis of metal ion binding peptides and epitope binding assays.     

Discrimination of Arcobacter butzleri isolates by polymerase chain reaction-mediated DNA fingerprinting

AIMS: The objective of this study was to subtype Arcobacter butzleri isolates using RAPD-PCR. METHODS AND RESULTS: Thirty-five A. butzleri isolates obtained from chicken carcasses were examined. PCR-mediated DNA fingerprinting technique with primers of the variable sequence motifs was used to detect polymorphism within the isolates. Eleven distinct DNA profiles were obtained as follows: Of the 35 strains, 10 as profile 4; seven as profile 1; five as profile 3; three as profiles 2 and 9; two as profile 10; one as profiles 5, 6, 7, 8 and 11. CONCLUSIONS: Chicken carcasses sold in markets were found to be contaminated with several different strains of A. butzleri. RAPD-PCR technique was found to be a useful technique for distinguishing A. butzleri isolates. SIGNIFICANCE AND IMPACT OF THE STUDY: The presence of several different A. butzleri strains on chicken carcasses may indicate multiple sources of contamination. The epidemiological role of A. butzleri in human and animal diseases should be investigated further.     

Electromagnetic interference on pacemakers

External sources, either within or outside the hospital environment, may interfere with the appropriate function of pacemakers which are being implanted all around the world in current medical practice. The patient and the physician who is responsible for follow-up of the pacing systems may be confronted with some specific problems regarding the various types of electromagnetic interference (EMI). To avoid these unwanted EMI effects one must be aware of this potential problem and need to take some precautions. The effects of EMI on pacemaker function and precautions to overcome some specific problems were discussed in this review article. There are many sources of EMI interacting with pacemakers. Magnetic resonance imaging creates real problem and should be avoided in pacemaker patients. Cellular phones might be responsible for EMI when they were held on the same side with the pacemaker. Otherwise they don't cause any specific type of interaction with pacemakers. Sale security systems are not a problem if one walks through it without lingering in or near it. Patients having unipolar pacemaker systems are prone to develop EMI because of pectoral muscle artifacts during vigorous active physical exercise.     

Cytophobic surface modification of microfluidic arrays for in situ parallel peptide synthesis and cell adhesion assays

A combination of PEG-based surface passivation techniques and spatially addressable SPPS (solid-phase peptide synthesis) was used to demonstrate a highly specific cell-peptide adhesion assay on a microfluidic platform. The surface of a silicon-glass microchip was modified to form a mixed self-assembled monolayer that presented PEG moieties interspersed with reactive amino terminals. The PEG provided biomolecular inertness and the reactive amino groups were used for consequent peptide synthesis. The cytophobicity of the surface was characterized by on-chip fluorescent binding assays and was found to be resistant to nonspecific attachment of cells and proteins. An integrated system for parallel peptide synthesis on this reactive amino surface was developed using photogenerated acid chemistry and digital microlithography. A constant synthesis efficiency of >98% was observed for up to 7mer peptides. To demonstrate specific cell adhesion on these synthetic peptide arrays, variations of a 7mer cell binding peptide that binds to murine B lymphoma cells were synthesized. Sequence-specific binding was observed on incubation with fluorescently labeled, intact murine B lymphoma cells, and key residues for binding were identified by deletional analysis.     

Simulation and visualization of flow pattern in microarrays for liquid phase oligonucleotide and peptide synthesis

Microfluidic microarrays have been developed for economical and rapid parallel synthesis of oligonucleotide and peptide libraries. For a synthesis system to be reproducible and uniform, it is crucial to have a uniform reagent delivery throughout the system. Computational fluid dynamics (CFD) is used to model and simulate the microfluidic microarrays to study geometrical effects on flow patterns. By proper design geometry, flow uniformity could be obtained in every microreactor in the microarrays.     

The effect of moderate hypothermia in acute ischemic stroke on pericyte migration: an ultrastructural study

Pericytes are essential components of the blood–brain barrier together with endothelial cells and astrocytes. Any disturbance of brain perfusion may result in blood–brain barrier dysfunction due to pericyte migration from the microvascular wall. The neuroprotective influence of hypothermia on ischemic brain injury has been clearly shown in models of both global and focal ischemia. Leakage of plasma proteins contributes to the extension of neuronal injury and hypothermia has a neuroprotective influence during the ischemic insult. This line of thinking impelled us to investigate the possible role of the pericytes in the occurrence of hypothermic protection during cerebral ischemia.In this study, we examined at the ultrastructural level the effect of moderate hypothermia on microvascular pericyte responses using a rat model of permanent middle cerebral artery occlusion. Twenty rats were divided into four groups. Middle cerebral artery occlusion was performed in all rats except the control group (first group), which was used to determine the pericyte morphology under normal conditions. In the second group, pericyte response to irreversible ischemia under normothermic conditions was examined at the end of the first hour. In the third group, pericyte response to hypoxia was examined under normothermic conditions three hours after ischemia. In the fourth group, temporalis muscle temperature was maintained at 27–29 °C for 1 h after middle cerebral artery occlusion and pericyte response was then examined at the ultrastructural level. In ischemic normothermic conditions at the end of the first hour (Group 2), a separation was observed between pericytes and the basement membrane and this was interpreted as pericyte migration from the microvascular wall. In ischemic normothermic conditions at the end of the third hour (Group 3), basement membrane disorganization and increased space between the basement membranes were seen in addition to the differentiation of second group. In ischemic hypothermic conditions at the end of the first hour (Group 4), pericyte separation or migration from basement membrane were not seen and the blood–brain barrier remained firm. These findings were interpreted by the authors as a possible relationship between pericyte behavior and neural protection during hypothermia. We suggest that hypothermia may delay the pericyte response but not necessarily attenuate it, and should be associated with hypothermic protection.