Ibrahim Baris

Microcantilever based disposable viscosity sensor for serum and blood plasma measurements

This paper proposes a novel method for measuring blood plasma and serum viscosity with a microcantilever-based MEMS sensor. MEMS cantilevers are made of electroplated nickel and actuated remotely with magnetic field using an electro-coil. Real-time monitoring of cantilever resonant frequency is performed remotely using diffraction gratings fabricated at the tip of the dynamic cantilevers. Only few nanometer cantilever deflection is sufficient due to interferometric sensitivity of the readout. The resonant frequency of the cantilever is tracked with a phase lock loop (PLL) control circuit. The viscosities of liquid samples are obtained through the measurement of the cantilevers frequency change with respect to a reference measurement taken within a liquid of known viscosity. We performed measurements with glycerol solutions at different temperatures and validated the repeatability of the system by comparing with a reference commercial viscometer. Experimental results are compared with the theoretical predictions based on Saders theory and agreed reasonably well. Afterwards viscosities of different Fetal Bovine Serum and Bovine Serum Albumin mixtures are measured both at 23°C and 37°C, body temperature. Finally the viscosities of human blood plasma samples taken from healthy donors are measured. The proposed method is capable of measuring viscosities from 0.86 cP to 3.02 cP, which covers human blood plasma viscosity range, with a resolution better than 0.04 cP. The sample volume requirement is less than 150 μl and can be reduced significantly with optimized cartridge design. Both the actuation and sensing are carried out remotely, which allows for disposable sensor cartridges.

Frequency of the 35delG mutation in the connexin 26 gene in Turkish hearing-impaired patients.

The 35delG mutation in the connexin 26 gene (GJB2) at the DFNB1 locus is the most common mutation in patients with autosomal‐recessive sensorineural deafness. Genetic diagnosis is crucial for genetic counseling. We have developed an easy and simple method and screened a total of 235 unrelated hearing‐impaired children. We found 48 of the subjects to be homozygous for the mutation, including 27 of 83 familial cases, 15 of 101 singletons, 4 of 9 subjects born to assortative marriages (deaf married to deaf), and 2 of 42 subjects for whom the parents claimed an environmental factor as the etiology of the condition. The high ratio of individuals homozygous for the mutation indicated that the 35delG mutation in the connexin gene accounts for more than 90% of the mutations at this locus.

Hereditary neuropathy with liability to pressure palsy (HNPP) in childhood: A case study emphasizing the relevance of detailed electrophysiological examination for suspected HNPP in the first decade

Hereditary neuropathy with liability to pressure palsy (HNPP) is an autosomal dominant disorder characterized by recurrent mono-neuropathies secondary to minor trauma or compression. Whilst typical episodes of palsy generally become apparent during the second and the third decades, HNPP is rarely diagnosed in the first decade. We present the case of a 6-year-old patient to draw attention to the possibility of HNPP attacks in the first decade and the importance of detailed electrophysiological examination.

Structure Based Discovery of Small Molecules to Regulate the Activity of Human Insulin Degrading Enzyme

Background Insulin-degrading enzyme (IDE) is an allosteric Zn+2 metalloprotease involved in the degradation of many peptides including amyloid-β, and insulin that play key roles in Alzheimers disease (AD) and type 2 diabetes mellitus (T2DM), respectively. Therefore, the use of therapeutic agents that regulate the activity of IDE would be a viable approach towards generating pharmaceutical treatments for these diseases. Crystal structure of IDE revealed that N-terminal has an exosite which is ∼30 Å away from the catalytic region and serves as a regulation site by orientation of the substrates of IDE to the catalytic site. It is possible to find small molecules that bind to the exosite of IDE and enhance its proteolytic activity towards different substrates. Methodology/Principal Findings In this study, we applied structure based drug design method combined with experimental methods to discover four novel molecules that enhance the activity of human IDE. The novel compounds, designated as D3, D4, D6, and D10 enhanced IDE mediated proteolysis of substrate V, insulin and amyloid-β, while enhanced degradation profiles were obtained towards substrate V and insulin in the presence of D10 only. Conclusion/Significance This paper describes the first examples of a computer-aided discovery of IDE regulators, showing that in vitro and in vivo activation of this important enzyme with small molecules is possible.

Development and validation of a cost-effective in-house method, tetra-primer ARMS PCR assay, in genotyping of seven clinically important point mutations

The single nucleotide polymorphism (SNP) genotyping is currently considered as a particularly valuable tool for the diagnosis of different pathologies. For this reason, over the past several years a great deal of effort has been devoted to developing accurate, rapid, and cost-effective technologies for SNP analysis. Although a large number of distinct approaches has been reported each laboratory use one of the published methods based on their technical and economical capacity. This article presents an application of an in-house assay, tetra-primer ARMS PCR assay, and its application in SNP genotyping. We have shown that this assay could be more advantageous when compared with PCR-RFLP, real time PCR, and DNA sequencing. We have shown that the assay is successful in genotyping using archived paraffin-embedded tissues, heparinated samples and amniotic fluids with meconium. These low-costed (3

Identification of two Amino Acids in the C-terminal Domain of Mouse CRY2 Essential for PER2 Interaction

/reaction) assays could be completed within 3-4 h after specimen receipt allowing for a reasonable turn-around time in the laboratory. Since tetra-primer ARMS PCR assay does not require any special equipment, the assay could be set up in most clinical diagnostic laboratories.

Investigation of the Interaction between the Large and Small Subunits of Potato ADP-Glucose Pyrophosphorylase

BackgroundCryptochromes (CRYs) are a class of flavoprotein blue-light signaling receptors found in plants and animals, and they control plant development and the entrainment of circadian rhythms. They also act as integral parts of the central circadian oscillator in humans and other animals. In mammals, the CLOCK-BMAL1 heterodimer activates transcription of the Per and Cry genes as well as clock-regulated genes. The PER2 proteins interact with CRY and CKIε, and the resulting ternary complexes translocate into the nucleus, where they negatively regulate the transcription of Per and Cry core clock genes and other clock-regulated output genes. Recent studies have indicated that the extended C-termini of the mammalian CRYs, as compared to photolyase proteins, interact with PER proteins.ResultsWe identified a region on mCRY2 (between residues 493 and 512) responsible for direct physical interaction with mPER2 by mammalian two-hybrid and co-immunoprecipitation assays. Moreover, using oligonucleotide-based degenerate PCR, we discovered that mutation of Arg-501 and Lys-503 of mCRY2 within this C-terminal region totally abolishes interaction with PER2.ConclusionsOur results identify mCRY2 amino acid residues that interact with the mPER2 binding region and suggest the potential for rational drug design to inhibit CRYs for specific therapeutic approaches.

SYBR green dye-based probe-free SNP genotyping: Introduction of T-Plex real-time PCR assay

ADP-glucose pyrophosphorylase (AGPase), a key allosteric enzyme involved in higher plant starch biosynthesis, is composed of pairs of large (LS) and small subunits (SS). Current evidence indicates that the two subunit types play distinct roles in enzyme function. Recently the heterotetrameric structure of potato AGPase has been modeled. In the current study, we have applied the molecular mechanics generalized born surface area (MM-GBSA) method and identified critical amino acids of the potato AGPase LS and SS subunits that interact with each other during the native heterotetrameric structure formation. We have further shown the role of the LS amino acids in subunit-subunit interaction by yeast two-hybrid, bacterial complementation assay and native gel. Comparison of the computational results with the experiments has indicated that the backbone energy contribution (rather than the side chain energies) of the interface residues is more important in identifying critical residues. We have found that lateral interaction of the LS-SS is much stronger than the longitudinal one, and it is mainly mediated by hydrophobic interactions. This study will not only enhance our understanding of the interaction between the SS and the LS of AGPase, but will also enable us to engineer proteins to obtain better assembled variants of AGPase which can be used for the improvement of plant yield.

A large family with Charcot-Marie-Tooth Type 1a and Type 2 diabetes mellitus.

Single-nucleotide polymorphism (SNP) genotyping is widely used in genetic association studies to characterize genetic factors underlying inherited traits. Despite many recent advances in high-throughput SNP genotyping, inexpensive and flexible methods with reasonable throughput levels are still needed. Real-time PCR methods for discovering and genotyping SNPs are becoming increasingly important in various fields of biology. In this study, we introduce a new, single-tube strategy that combines the tetra-primer ARMS PCR assay, SYBR Green I-based real-time PCR, and melting-point analysis with primer design strategies to detect the SNP of interest. This assay, T-Plex real-time PCR, is based on the T(m) discrimination of the amplified allele-specific amplicons in a single tube. The specificity, sensitivity, and robustness of the assay were evaluated for common mutations in the FV, PII, MTHFR, and FGFR3 genes. We believe that T-Plex real-time PCR would be a useful alternative for either individual genotyping requests or large epidemiological studies.

A Tetra-Primer Polymerase Chain Reaction Approach for the Detection of JAK2 V617F Mutation

Charcot-Marie-Tooth (CMT) disease is a hereditary demyelinating peripheral neuropathy, and CMT Type 1A is the most common form. In most cases, CMT1A is usually caused by duplication at chromosome 17p11.2–12. Type 2 diabetes mellitus (Type 2 DM) is a common metabolic disorder, characterized by chronic hyperglycemia that can be associated with micro- and/or macrovascular complications. Only a few studies reported CMT1A duplication in association with Type 2 DM. This article explores the characteristics of a large family of 69 members with respect to CMT1A and Type 2 DM. CMT1A was detected in 28 of them. Molecular genetic study was performed in 22, and duplication was detected in all of them. Six of the 22 members with CMT1A also had Type 2 DM based on the American Diabetes Association diagnostic criteria. Association of these two conditions may be coincidental; however, the occurence of these two diseases in this large family may also suggest a genetic basis. More extensive reports and further investigations of such families having this combination will certainly provide a better understanding of this link.