Search

Coordinated spatiotemporal expression of large sets of genes is required for the development and homeostasis of organisms. To achieve this goal, organisms use myriad strategies where they form operons, utilize bidirectional promoters, cluster genes, share enhancers among genes by DNA looping, and form topologically associated domains and transcriptional condensates. Coexpression achieved by these different strategies is hypothesized to have functional importance in minimizing gene expression variability, establishing dosage balance to ensure stoichiometry of protein complexes, and minimizing accumulation of toxic intermediate metabolites. By combining gene-editing tools with computational modeling, recent studies tested the advantages of adjacent genes located in pairs and clusters. We propose that with the advancement of gene editing, single-cell sequencing, and imaging tools, one could readily test the functional importance of different coexpression strategies in a variety of biological processes.

This study aimed to analyze laboratory and radiological imaging results in the prediction of treatment strategy in patients with deep neck infections. Eighty-three patients (55 (66.3%) men, mean age: 38.2±14.5 years) were included in the study. Patients were divided into three groups according to the treatment strategy: group 1 received only antibiotic treatment, group 2 underwent abscess drainage with needle puncture in addition to antibiotic treatment, and group 3 underwent surgical drainage with antibiotic treatment. Laboratory outcomes, imaging methods, duration of hospital stay, treatment strategy, and clinical outcomes were analyzed.According to the laboratory results, complete blood count values did not vary among the three groups, but C reactive protein (CRP) and erythrocyte sedimentation rate (ESR) values were higher in group 3 (p

Gene expression is an inherently stochastic process1,2; however, organismal development and homeostasis require cells to coordinate the spatiotemporal expression of large sets of genes. In metazoans, pairs of co-expressed genes often reside in the same chromosomal neighbourhood, with gene pairs representing 10 to 50% of all genes, depending on the species3–6. Because shared upstream regulators can ensure correlated gene expression, the selective advantage of maintaining adjacent gene pairs remains unknown6. Here, using two linked zebrafish segmentation clock genes, her1 and her7, and combining single-cell transcript counting, genetic engineering, real-time imaging and computational modelling, we show that gene pairing boosts correlated transcription and provides phenotypic robustness for the formation of developmental patterns. Our results demonstrate that the prevention of gene pairing disrupts oscillations and segmentation, and the linkage of her1 and her7 is essential for the development of the body axis in zebrafish embryos. We predict that gene pairing may be similarly advantageous in other organisms, and our findings could lead to the engineering of precise synthetic clocks in embryos and organoids. The pairing of genes is essential for robust expression of segmentation clock genes during development in zebrafish embryos.

Background/aim We aimed to revealthe incidence and predictive role of insulin resistance and distorted oral glucose tolerance test in nondiabetic patients withBell’s Palsy (BP). Materials and methods Eighty-sixpatients with BP and 28 control subjects; all with normal blood glucose levels and no history of diabetes, were enrolled in the study. We investigated insulin resistance (IR) in all subjects, in terms of HOMA-IR greater than 2.7. Sixty-two of the patients also underwent an oral glucose tolerance test (OGTT). Results The mean HOMA-IR value was significantly increased in patients, compared to the control group (3.2 vs 1.6; P < 0.01). IR was detected more in BP patients than in controls (P < 0.05). The patients with higher HOMA-IR values had more severe facial dysfunction at the initial presentation and complete recovery time took longer than the patients with normal HOMA-IR value (75 days vs 42 days; P < 0.05). Following a 2h-OGTT, impaired glucose tolerance and newly diagnosed DM were found in 60% of the patients. Recovery time was significantly longer in prediabetics and newly diagnosed diabetic patients than in patients with normal glycemia (68 days, 52 days, and 32 days, respectively; P < 0.01). Conclusion There is a strong linkage between HOMA-IR value and BP prognosis so HOMA-IR value may have a significant role of predicting BP prognosis at presentation.

Amaç: Glomus karotikum, vagale ve jugulare tümörlerinde preoperatif yapılan endovasküler embolizasyon işlem sonuçlarının değerlendirilmesi amaçlandı.Gereç ve Yöntemler: 2012-2017 yılları arasında glomus tümörü nedeniyle 18 hastaya tanısal anjiyografi ve bazılarına da embolizasyon yapıldı. Hastaların demografik bilgileri, tümör tipleri, embolizasyon ve komplikasyon oranları analiz edildi. Tümör embolizasyonunun etkinliğine, girişim öncesi ve sonrası alınan anjiyografiler karşılaştırarak karar verildi. Hastalar girişim sonrası vital bulgular ve olası komplikasyonlar açısından en az 24-48 saat takip edildi.Bulgular: Tanısal anjiyografi yapılan 18 hastadan 10’una eş zamanlı embolizasyon da uygulandı. Altı hastada glomus jugulare, 1 hastada glomus vagale, 10 hastada glomus karotikum ve 1 hastada eş zamanlı glomus jugulare ve vagale mevcuttu. En sık embolize edilen arter %50 oranı ile asendan faringeal arterdi. Embolizasyon yapılan hastalarda tümör kan akımında en az %70 oranında bir azalma meydana geldiği saptandı. Yapılan işlemler ile ilgili herhangi bir komplikasyon oluşmadı. Sonuç: Endovasküler selektif arter embolizasyonu glomus tümörlerinin preoperatif tedavisinde güvenilir ve etkin bir yöntemdir.

Idiopathic subjective tinnitus has a complex pathophysiology in which not only cochlear and central classical auditory pathways but also nonclassical auditory pathways of different parts of the brain are involved. Vestibuloocular and vestibulocollic pathways are the central projections of utricle and saccule used in the vestibular evoked myogenic potential (VEMP) test. Aim of this study was to investigate the effects of idiopathic subjective tinnitus on vestibuloocular and vestibulocollic pathways via VEMP. We prospectively analyzed 30 unilateral idiopathic subjective tinnitus patient's cervical, ocular VEMP tests, tinnitus handicap index scores, symptom duration and compared with contralateral ear and 35 healthy volunteers. The latencies and amplitudes of P1 and N1 waves were recorded and pathologic wave criteria was calculated according to healthy volunteer's data. In cervical VEMP there were significant longer latencies of P1 and N1 waves with respect to contralateral ear and control group. In ocular VEMP test, N1 and P1 latencies and amplitudes were not significantly different. The percentages of pathologic wave of the tinnitus side were not significantly higher in both cervical VEMP and ocular VEMP tests with respect to contralateral side. Tinnitus handicap index scores and symptom duration had no relationship with latency and amplitude of VEMP tests. Although cervical VEMP P1 and N1 latencies were significantly longer, subjective tinnitus did not result in pathological alterations in the VEMP test. Presence of subjective tinnitus is not an influencing factor in the VEMP interpretation.

Surface-enhanced Raman scattering (SERS) is a technique capable of identifying each component in a mixture because of its intrinsically narrow spectral bands. In a clinical setting, the identification of bacteria from its initial culture by collecting the colonies on the culture plate significantly decreases the analysis time and the cost. The identification of bacteria from their mixtures is attempted using SERS. A simple mixing procedure of bacterial samples and concentrated colloidal suspension is proven to be mostly satisfactory for the generation of the reproducible SERS spectra that can be used for bacterial identification. The mixture of three different but related bacterial species Shigella sonnei, Proteus vulgaris, and Erwinia amylovara and three Escherichia coli strains (BFK13, BHK7, DH5 alpha) are used as model systems to test the feasibility of the approach. The results indicate that it is possible to identify the composition of a bacterial mixture. This approach can easily be utilized for the bacteria originating from the same source with similar growth profiles. Copyright (C) 2009 John Wiley & Sons, Ltd.

Conclusion: This method is an easy, non-expensive, and effective technique in bilateral vocal cord paralysis to improve glottic airway and clinical performance. Objective: To evaluate the effectiveness of ‘suture arytenoid laterofixation’ surgery in bilateral vocal cord paralysis. Materials and methods: A retrospective analysis of patients’ medical history undergoing ‘suture arytenoid laterofixation’ surgery for bilateral vocal cord paralysis. This technique was applied under general anesthesia with both microlaryngoscopy and video-monitoring. Two 16 g needles and one 1/0 nylon thread were used for the procedure with 1 cm skin incision; no tracheotomy or tissue excision was required. Pre–post-operative photographs of the glottic region were taken from the endoscopic records, and the areas of rima glottis openings were calculated with the Image-J programme. Results: Forty-seven patients were analyzed. The mean pre–post-operative rima glottis areas were 1.11 ± 0.56 and 2.24 ± 0.93 mm 2 , respectively (p < 0.001). Five patients with previous tracheotomy were decannulated within a few days after the operation. In three patients, mild complications developed in the early post-operative period (two laryngeal edemas, one submucosal hematoma). Tracheotomy was performed to only one pregnant patient in the post-operative first day. None of the patients had granulation formation or synechia.

The application of bio-active noble-metal-based nano-particles (NPs) with unique physico-chemical properties is multifaceted. Among other roles, they can be used as anti-viral agents, and at the same time might serve as matrix to facilitate the transport of various molecules for therapeutic purposes directly or via genetically modified microbes. For this reason, the influence of nano-materials on viral infection in living cells is described in this study utilizing pseudo-typed lenti-viral particles based on human immuno-deficiency virus 1 (HIV-1). Cells were exposed to various NPs and subsequently infected with lenti-virus. Transfection efficiency was quantified by flow-cytometry analysis. Gold-based NPs increased, silver-containing NPs decreased, while other NPs had little or no effect on viral infection rate. The opposing effect of NPs is determined by the size, chemical nature and surface chemistry of the nano-materials, which govern their interactions with molecular species present in their environment. These characteristics enable the distinct use of different NPs in various fields of bio-medicine. © 2013 Bentham Science Publishers. Russian Foundation for Basic Research: 11-04-00612-a

Self-assembly of 13 nm gold nanoparticles (AuNPs) engineered into 2D structures in solution using DNA tiles for their possible use for gene delivery and photothermal therapy is reported. The two different DNA tiles were constructed and the AuNPs coated with oligonucleotides possessing complementary sequence from the free ends were hybridized with the sticky ends of the tiles. The DNA tiles were bind to each other by mixing the tile structures without a heating and cooling step. The constructed nanostructures were 5 to 7 DNA tiles long since heat was not used to elongate them. When the DNA tiles were bound to the AuNPs, it was observed that AuNPs tend to stay in close proximity by filling the gaps between tiles. The stability of the constructed structures was tested against DNase, a DNA cleaving enzyme, for possible applications for gene delivery and photothermal therapy. It was found that the AuNP bound DNA tile structures resist the DNase cleavage up to eighty percent. Due to the presence of the AuNPs in the structure, the enzyme cannot bind to DNA sequences and this increases the DNA tile structures' stability. © 2012 AY, Sonay, et al.

The characterization, detection, and identification of bacteria using surface-enhanced Raman scattering (SERS) spectroscopy is drawing considerable attention due to its ability to provide rich intrinsic molecular information about molecules and molecular structures in close proximity to noble metal surfaces. However, sample preparation methods and experimental conditions must be carefully evaluated in order to obtain healthy, interpretable, and comparable results. In this study, several bacterial species including E. coli, B. megaterium, S. aureus, and S. cohnii were systematically evaluated to demonstrate the source of the spectral features of bacterial SERS spectra. It was found that the features observed in bacterial SERS spectra originate mostly from the bacteria surface with some contributions from metabolic activity or molecular species detached from the bacteria surface during sample preparation. © 2011 Society for Applied Spectroscopy.

The manipulation of colloidal nanoparticles (NPs) in a drying droplet has critical importance not only for several industrial applications but also their assembly into patterns on surfaces. The influence of a tip with hydrophilic or hydrophobic surfaces dipped into a drying droplet on hydrophilic or hydrophobic surfaces on the behavior of 98. nm latex NPs was investigated. The formation of concentric rings on hydrophilic glass surfaces regardless of the surface chemistry of the dipped tip was observed. On the other hand, no pattern formation on hydrophobic surfaces was observed with the insertion of the tip. With a hydrophilic tip, the concentric rings were formed due to stick-slip motion of the solvent contact line resulting from competition between pinning and capillary forces while the capillary effect was not effective until the surface of the tip was changed by adherent NPs making the tip surface available for water adherence with a hydrophobic tip, which results in the pulling of droplet towards the tip. It is also found that the tip thickness and suspension concentration significantly influences the formation of concentric rings on surfaces. This simple procedure can be used to influence the distribution or assembly of NPs in the droplet area. © 2011 Elsevier Inc. 108T605 The authors greatly acknowledge the financial support of TUBITAK (Grant No.: 108T605 ) and Yeditepe University . The authors also acknowledge the help of Assistant Prof. Dr. Andrew J. Harvey for his valuable criticisms during the writing of the manuscript.

The development of an assay for the detection of gene mutations has been attempted based on surface-enhanced Raman scattering (SERS). Using multiplexing property and high sensitivity of SERS technique, the detection of all mutation possibilities on one given spot is achievable. To test the feasibility of approach, SNPs and other types of mutations such as insertion and deletion are investigated. The PCR amplified and isolated genomic DNA without PCR amplification is immobilized on poly-L/D-lysine coated glass surface after denaturing with heating. The SERS probes are prepared by simultaneous attachment of oligonucleotides complementary to the target mutation regions and Raman active dyes to 13 nm gold nanoparticles (GNPs). After the hybridization of SERS probes on the poly-L/D-lysine surfaces, it was stained with silver colloidal nanoparticles for further enhancement of Raman scattering. In the second approach, Raman active dyes are chemically attached on gold nanoparticles and a thin layer of silver film is deposited on top of it to prepare core-shell nanoparticles. The complementary oligonucleotides to the target regions of the gene are chemically attached to silver surfaces of the nanoparticles. The promising results indicate that it is possible to detect certain mutation types without PCR amplification using the approach.

Objectives: This study aims to investigate the effect of acupuncture treatment on hearing and tinnitus in patients with sudden sensorineural hearing loss SNHL refractory to treatment. Patients and Methods: Between January 2013 and May 2015, a total of 25 patients 8 males, 17 females; median age: 43.3 years; range, 18 to 65 years resistant to medical treatment who underwent acupuncture as salvage therapy were retrospectively analyzed. The patients were evaluated with pure-tone audiometry, Speech Discrimination Score SDS , and Tinnitus Handicap Inventory THI at pre-treatment T0 , and after 10th T1 and 20th sessions T2 of acupuncture. Results: Hearing loss evaluated according to the four-frequency pure-tone average PTA; 500, 1,000, 2,000, and 4,000 kHz showed a statistically significant improvement at the end of the 10th session of acupuncture p=0.017 . There was also a significant improvement in the PTA values of the worst three consecutive frequencies at the end of the 20th session p=0.034 . A significant improvement in SDS p=0.022 and THI p