Effects of protein engineering and rational mutagenesis on crystal lattice of single chain antibody fragments

Protein crystallization is dependent upon, and sensitive to, the intermolecular contacts that assist in ordering proteins into a three‐dimensional lattice. Here we used protein engineering and mutagenesis to affect the crystallization of single chain antibody fragments (scFvs) that recognize the EE epitope (EYMPME) with high affinity. These hypercrystallizable scFvs are under development to assist difficult proteins, such as membrane proteins, in forming crystals, by acting as crystallization chaperones. Guided by analyses of intermolecular crystal lattice contacts, two second‐generation anti‐EE scFvs were produced, which bind to proteins with installed EE tags. Surprisingly, although noncomplementarity determining region (CDR) lattice residues from the parent scFv framework remained unchanged through the processes of protein engineering and rational design, crystal lattices of the derivative scFvs differ. Comparison of energy calculations and the experimentally‐determined lattice interactions for this basis set provides insight into the complexity of the forces driving crystal lattice choice and demonstrates the availability of multiple well‐ordered surface features in our scFvs capable of forming versatile crystal contacts. Proteins 2014; 82:1884–1895. © 2014 Wiley Periodicals, Inc.     

Frequency of MEFV gene mutations in Hatay province,Mediterranean region of Turkey and report of a novel missense mutation (I247V)

In the present study, 1000 patients with clinical suspicion of FMF were retrospectively reviewed to determine the spectrum of MEFV gene mutations by using DNA sequence analysis between September, 2008 and April, 2012. Sixteen different mutations and 55 different genotypes were detected in 618 of 1000 patients. Among 16 different mutations, R202Q (21.35%) was the most frequently observed mutation; followed by E148Q (8.85%), M694V (7.95%), M680I (2.40%), V726A (1.85%), M694I (0.95%), A744S (0.80%), R761H (0.55%), P283L (0.35%), K695R (0.20%), E230K (0.15%), L110P (0.10%), I247V (0.05%), G196W (0.05%) and G304R (0.05%). In the present study, a novel missense mutation (I247V) and a silent variant (G150G) were identified in the MEFV gene. On the other hand, P238L, G632A and G304R mutations are the first cases reported from Turkey. Our results indicated that MEFV mutations are highly heterogeneous in our study population as in other regions of Turkey and mutation screening techniques such as PCR-RFLP, amplification refractory mutation system or reverse hybridization do not adequately detect uncommon or novel mutations. Therefore, it was proven that sequence analysis of the MEFV gene could be useful for detection of rare or unknown mutations.     

Biosorption of Basic Blue 7 by fungal cells immobilized on the green-type biomatrix of Phragmites australis spongy tissue

Biosorption is an effective alternative method for the control of water pollution caused by different pollutants such as synthetic dyes and metals. A new and efficient biomass system was developed from the passively immobilized fungal cells. The spongy tissue of Phragmites australis was considered as the carrier for the immobilization of Neurospora sitophila cells employed for the biosorption of Basic Blue 7. This plant tissue was used for the first time as a carrier for fungal cells. The biosorption was examined through batch- and continuous-mode operations. The biosorption process conformed well to the Langmuir model. Maximum monolayer biosorption capacity of the biosorbent was recorded as 154.756 mg g^?1. Kinetic findings showed a very good compliance with the pseudo-second-order model. The negative values of ΔG° indicated a spontaneous nature of the biosorption process and a positive value of ΔH° (14.69 kJ mol^?1) concluded favorable decolorization at high temperature. The scanning electron microscopy analysis showed that a porous, rippled, and rough surface of biomass system was covered with BB7 molecular cloud. IR results revealed that functional groups like –OH, –NH, and C?O participated to the decolorization. Breakthrough and exhausted points were found as 360 and 570 minutes, respectively. The biomass system was successfully applied to the treatment of real wastewater.     

Development of stability indicating HPLC method for the separation and validation of enantiomers of miconazole

A selective and sensitive stability indicting HPLC method was developed for the analysis of enantiomers of miconazole. For this purpose, six different polysaccharide‐based chiral columns were evaluated. Optimization was performed using several polar organic and alcohol‐hydrocarbon mobile phases. As a result of optimization studies, the analysis was carried out using Lux Cellulose‐3, methanol as a mobile phase at a flow rate of 1 mL·min^?1, and the detection wavelength was arranged to 230 nm. Developed method has been fully validated according to International Council on Harmonization guidelines. Method was found linear in the concentration range of 1 to 200 μg·mL^?1. Coefficient of determination (R²) was calculated as 0.9996, intraday precision of the method was found with the RSD% of 0.56, and the recovery of the method was calculated close to 100%. Furthermore, some other validation parameters like specificity, selectivity, LOD, and LOQ were also investigated. Stability indicating capability of this method was shown by forced degradation studies, and the run time for each analysis was less than 6 minutes. As a result, simple, fast, reliable HPLC method was developed for the separation and determination of the enantiomers of miconazole. Applicability of the developed method was shown with the application of marketed pharmaceutical preparations.     

Thermoluminescence properties of annealed natural quartz after beta irradiation

Here we investigated the effects of annealing, heating rate and fading (after annealing at 800 °C) on the thermoluminescence (TL) glow curves of natural quartz (NQ). All of the samples were annealed at different temperatures between 100 °C and 800 °C and then irradiated with a beta dose of about 34 Gray (Gy), in order to determine the effects of annealing treatments on TL peaks of natural quartz. TL glow curves of the samples were recorded. It was observed that the intensities of TL peaks were strongly sensitive to annealing temperatures at 800 °C. The heating rate and fading effect of TL peaks of natural quartz were examined for the annealed samples at 800 °C for 30 min. It was observed that the intensities of the TL peaks were differently affected from heating rate and fading. Additionally, TL kinetic parameters (activation energy, frequency factor and order of kinetics) of all peaks were determined for annealed samples using a computerized glow curve deconvolution (CGCD) method and Mathematica software. Copyright © 2016 John Wiley & Sons, Ltd.     

Beh?et's: A Disease or a Syndrome? Answer from an Expression Profiling Study

Behçet’s disease (BD) is a chronic, relapsing, multisystemic inflammatory disorder with unanswered questions regarding its etiology/pathogenesis and classification. Distinct manifestation based subsets, pronounced geographical variations in expression, and discrepant immunological abnormalities raised the question whether Behçet’s is “a disease or a syndrome”. To answer the preceding question we aimed to display and compare the molecular mechanisms underlying distinct subsets of BD. For this purpose, the expression data of the gene expression profiling and association study on BD by Xavier et al (2013) was retrieved from GEO database and reanalysed by gene expression data analysis/visualization and bioinformatics enrichment tools. There were 15 BD patients (B) and 14 controls (C). Three subsets of BD patients were generated: MB (isolated mucocutaneous manifestations, n = 7), OB (ocular involvement, n = 4), and VB (large vein thrombosis, n = 4). Class comparison analyses yielded the following numbers of differentially expressed genes (DEGs); B vs C: 4, MB vs C: 5, OB vs C: 151, VB vs C: 274, MB vs OB: 215, MB vs VB: 760, OB vs VB: 984. Venn diagram analysis showed that there were no common DEGs in the intersection “MB vs C” ∩ “OB vs C” ∩ “VB vs C”. Cluster analyses successfully clustered distinct expressions of BD. During gene ontology term enrichment analyses, categories with relevance to IL-8 production (MB vs C) and immune response to microorganisms (OB vs C) were differentially enriched. Distinct subsets of BD display distinct expression profiles and different disease associated pathways. Based on these clear discrepancies, the designation as “Behçet’s syndrome” (BS) should be encouraged and future research should take into consideration the immunogenetic heterogeneity of BS subsets. Four gene groups, namely, negative regulators of inflammation (CD69, CLEC12A, CLEC12B, TNFAIP3), neutrophil granule proteins (LTF, OLFM4, AZU1, MMP8, DEFA4, CAMP), antigen processing and presentation proteins (CTSS, ERAP1), and regulators of immune response (LGALS2, BCL10, ITCH, CEACAM8, CD36, IL8, CCL4, EREG, NFKBIZ, CCR2, CD180, KLRC4, NFAT5) appear to be instrumental in BS immunopathogenesis.     

Rapid Quantitative Microbiological Assay of Antibiotics and Chemical Preservatives of a Nonantibiotic Nature

A rapid quantitative assay of 14 antibiotics and 6 chemical preservatives by the cylinder-plate diffusion method is described, in which Bacillus stearothermophilus ATCC 12980 was used as the test organism. After 4 hr of incubation at 65 C, the zones of inhibition can be read off easily with the naked eye. The 4-hr assay was compared under identical conditions with the conventional 16- to 18-hr agar diffusion assay, i.e., by using the test organisms and media proposed by the Code of Federal Regulations, and no difference in accuracy between the two methods was detected. In both cases, the coefficient of variation for replicate tests was less than 2%. The test strain is highly sensitive to penicillins, cephalosporins, and bacitracin and is consequently also particularly suitable for the determination of low-level concentrations of these substances in aqueous solutions and in urine.     

Toll-like receptor 8 and 9 polymorphisms in Crimean-Congo hemorrhagic fever

Crimean-Congo hemorrhagic fever (CCHF) is an acute viral hemorrhagic fever. The clinical course and outcome of the CCHF infection are different in humans. Toll-like receptors (TLRs) are a family of pathogen recognition receptors. TLR8 and TLR9 contribute to the recognition of viruses. We investigated frequency of TLR8 Met1Val, TLR8 -129C/G, TLR9 -1486T/C and TLR9 2458G/A polymorphisms in CCHF patients and healthy controls. Our study was conducted between June 1 and August 31, 2007 in Cumhuriyet University Hospital, Turkey. TLR genotypes were detected using the PCR-RFLP assay in 85 CCHF patients and 171 healthy controls. We found that heterozygous plus homozygous mutant genotypes frequency for TLR8 Met1Val and for TLR9 -1486T/C were significantly higher in CCHF patients than controls (p = 0.038 and p = 0.009, respectively). The frequency of TLR8 -129G/G genotype in the fatal CCHF patients was significantly higher than that of the non-fatal patients (p = 0.026). The frequency of TLR9 -1486C/C genotype was significantly higher in fatal CCHF patients than in healthy controls (p = 0.009) and in patients with severe disease compared to non-severe disease (p = 0.044). Our findings suggest that TLR8 Met1Val, TLR8 -129C/G, and TLR9 -1486T/C polymorphisms are important on clinical course of CCHF disease.