Predicting sumoylation sites using support vector machines based on various sequence features, conformational flexibility and disorder

Background Sumoylation, which is a reversible and dynamic post-translational modification, is one of the vital processes in a cell. Before a protein matures to perform its function, sumoylation may alter its localization, interactions, and possibly structural conformation. Abberations in protein sumoylation has been linked with a variety of disorders and developmental anomalies. Experimental approaches to identification of sumoylation sites may not be effective due to the dynamic nature of sumoylation, laborsome experiments and their cost. Therefore, computational approaches may guide experimental identification of sumoylation sites and provide insights for further understanding sumoylation mechanism. Results In this paper, the effectiveness of using various sequence properties in predicting sumoylation sites was investigated with statistical analyses and machine learning approach employing support vector machines. These sequence properties were derived from windows of size 7 including position-specific amino acid composition, hydrophobicity, estimated sub-window volumes, predicted disorder, and conformational flexibility. 5-fold cross-validation results on experimentally identified sumoylation sites revealed that our method successfully predicts sumoylation sites with a Matthew's correlation coefficient, sensitivity, specificity, and accuracy equal to 0.66, 73%, 98%, and 97%, respectively. Additionally, we have showed that our method compares favorably to the existing prediction methods and basic regular expressions scanner. Conclusions By using support vector machines, a new, robust method for sumoylation site prediction was introduced. Besides, the possible effects of predicted conformational flexibility and disorder on sumoylation site recognition were explored computationally for the first time to our knowledge as an additional parameter that could aid in sumoylation site prediction

Prediction of neddylation sites from protein sequences and sequence-derived properties

Background Neddylation is a reversible post-translational modification that plays a vital role in maintaining cellular machinery. It is shown to affect localization, binding partners and structure of target proteins. Disruption of protein neddylation was observed in various diseases such as Alzheimer's and cancer. Therefore, understanding the neddylation mechanism and determining neddylation targets possibly bears a huge importance in further understanding the cellular processes. This study is the first attempt to predict neddylated sites from protein sequences by using several sequence and sequence-based structural features. Results We have developed a neddylation site prediction method using a support vector machine based on various sequence properties, position-specific scoring matrices, and disorder. Using 21 amino acid long lysine-centred windows, our model was able to predict neddylation sites successfully, with an average 5-fold stratified cross validation performance of 0.91, 0.91, 0.75, 0.44, 0.95 for accuracy, specificity, sensitivity, Matthew's correlation coefficient and area under curve, respectively. Independent test set results validated the robustness of reported new method. Additionally, we observed that neddylation sites are commonly flexible and there is a significant positively charged amino acid presence in neddylation sites. Conclusions In this study, a neddylation site prediction method was developed for the first time in literature. Common characteristics of neddylation sites and their discriminative properties were explored for further in silico studies on neddylation. Lastly, up-to-date neddylation dataset was provided for researchers working on post-translational modifications in the accompanying supplementary material of this article

Open heart surgery in dialysis-dependent patients with end stage renal failure

Objective: Patients with chronic renal insufficiency remaina risky subgroup in open heart surgery becauseof various reasons. The incidence of cardiovascular diseasein hemodialysis dependent renal failure is found tobe higher when compared with the normal population.Chronic dialysis is still a very important independent riskfactor for mortality and morbidity despite of many studies.In this study, we retrospectively evaluated the outcome ofpatients with chronic renal failure who had undergone toopen cardiac surgery.Methods: The medical charts of 36 patients on maintenancedialysis who underwent cardiovascular surgerywere retrospectively analyzed. Peroperative findings ofthese patients were analyzed from patients’ hospital records.Results: Twenty-seven men (75%) and nine women(25%) totally 36 patients were included to study. Themean age was 58.3±8.5 (range, 44-76) years. 12 patientsunderwent coronary artery bypass surgery, 10 hadconcomitant coronary artery bypass surgery and valvereplacements, five had valve replacements, three hadconcomitant coronary artery bypass surgery and left ventriculectomy,four had valve replacement with other valverepair, two had aortic surgery due to ascending aortic aneurysms.The mean cross clamp time was 78.1±31.3 minand the mean perfusion time was 158.8±92.2 min. Themean intensive care unit stay was 60±41 hours, and themean hospital stay was 12±5 days. Hospital mortality ratewas %38.8.Conclusions: Cardiac and renal functions are closely associatedwith each other. Cardiac surgery operations canbe applied to patients with end-stage renal failure underacceptable risks. Appropriate preoperative preparationwith good postoperative patient follow-up is necessary tohave acceptable levels of morbidity and mortality rates. JClin Exp Invest 2013; 4 (3): 335-338Key words: Cardiac surgery, chronic renal failure, mortalit

Diagnosis, treatment and prevention of infective endocarditis: Turkish consensus report-2019 [İnfektif endokarditin tanısı, tedavisi ve önlenmesi: Ulusal uzlaşı raporu-2019]

Infective endocarditis (IE) is a rare but still important as an infectious disease due to high rate of morbidity and substantial mortality. Although IE is not a notifiable disease in Turkey, and an incidence study has not been performed, the incidence may be higher than that in the developed countries due to frequent predisposing cardiac conditions and higher rates of nosocomial bacteremia, which may lead to IE in risk groups. IE generally affects the elderly in developed countries but it is frequently encountered among young individuals in Turkey. In order to reduce mortality and morbidity, it is critical to diagnose IE, to determine the causative agent, and to start treatment rapidly. Most patients cannot be diagnosed at the first visit, about half can be diagnosed after 3 months, and the disease often goes unnoticed. In patients diagnosed with IE, the rate of the identification of a causative organism is significantly lower in Turkey than that in developed countries. Some important microbiological diagnostic tests are not performed in most centers and several antimicrobials that are recommended as the first option for the treatment particularly antistaphylococcal penicillins, are unavailable in Turkey. These problems necessitate reviewing the epidemiological, laboratory, and clinical characteristics of IE in our country, as well as the current information about its diagnosis, treatment, and prevention together with local data. The diagnosis and treatment processes of IE should be standardized at every stage so that the management can be conducted in a setting in which physicians of various specialties are involved and is consistent with the current recommendations. The Study Group for Infective Endocarditis and Other Cardiovascular Infections of the Turkish Society of Clinical Microbiology and Infectious Diseases called for the collaboration of the relevant specialist organizations to establish a consensus report on the diagnosis, treatment, and prevention of IE in the context of current information and local data in Turkey. © 2020 Turkish Society of Cardiology

Amino acid preferences at neddylation sites

Neddylation is a dynamic post-translational modification in which NEDD8 proteins are covalently attached to the target site lysine residue. Neddylation may affect a target protein’s localization, binding partners and structure. Targets of this modification have commonly found in nucleus and the most well characterized target family is cullins, which is modulating ubiquitination and proteosomal degradation system in a cell. Disruptions in neddylation pathway implicated in various diseases such as Alzheimer’s, Parkinson’s and cancer. Therefore, understanding neddylation site recognition bears a huge importance in understanding the complete functional mechanism of this post-translational modification and revealing the mechanisms of associated diseases towards a cure. However, there is no study in literature investigating whether a common neddylation site motif exists or not. In this work, we have identified various amino acid preferences and hydrophobicity patterns seen in neddylation sites, differing from not neddylated lysine residues

The evaluation of root fracture with cone beam computed tomography (CBCT) : an epidemiological study

The aim of this study was evaluation of the cone-beam computed tomography (CBCT) image of 50 patients at the ages of 8-15 suspecting root fracture and root fracture occurred, exposed to dental traumatic. In additionally, this study was showed effect of crown fracture on root fracture healing. All of the individuals included in the study were obtained images with the cone-beam computed tomography range of 0,3 voxel and 8.9 seconds.(i-CAT®, Model 17-19, Imaging SciencesInternational, Hatfield, Pa USA).The information obtained from the history and CBCT images of patients were evaluated using chi-square test statistical method the mean and the distribution of the independent variables. 50 children, have been exposed to trauma, was detected root fracture injury in 97 teeth. Horizontal root fracture 63.9% of the 97 tooth, the oblique in 31.9%, both the horizontal and oblique in 1.03%, partial fracture in 2.06% ,and both horizontally and vertical in 1.03% was observed.The most affected teeth, respectively of, are the maxillary central incisor (41.23% left, right, 37.11%), maxillary left lateral incisor (9.27%), maxillary right lateral incisor (11.34%), and mandibular central incisor (1.03%). Crown fractures have negative effects on spontaneous healing of root fractures. CBCT are used selected as an alternative to with conventional radiography for diagnosis of root fractures. In particular, ?t?s cross-sectional image is quite useful and has been provided more conveniences seeing the results of diagnosis and treatment for clinician

An evaluation of clinical, radiological and three-dimensional dental tomography findings in ectodermal dysplasia cases

Background:This study aimed to review the results related to head and jaw disorders in cases of ectodermal dysplasia. The evaluation of ectodermal dysplasia cases was made by clincal examination and examination of the jaw and facial areas radiologically and on cone-beam 3-dimensional dental tomography (CBCT) images. Material and Methods: In the 36 cases evaluated in the study, typical clinical findings of pure hypohidrotic ectodermal displasia (HED) were seen, such as missing teeth, dry skin, hair and nail disorders. CBCT images were obtained from 12 of the 36 cases, aged 1.5- 45 years, and orthodontic analyses were made on these images. Results: The clinical and radiological evaluations determined, hypodontia or oligodontia, breathing problems, sweating problems, a history of fever, sparse hair, saddle nose, skin peeling, hypopigmentation, hyperpigmentation, finger and nail deformities, conical teeth anomalies, abnormal tooth root formation, tooth resorption in the root, gingivitis, history of epilepsy, absent lachrymal canals and vision problems in the cases which included to the study. Conclusions: Ectodermal dysplasia cases have a particular place in dentistry and require a professional, multi- disciplinary approach in respect of the chewing function, orthognathic problems, growth, oral and dental health. It has been understood that with data obtained from modern technologies such as three-dimensional dental tomography and the treatments applied, the quality of life of these cases can be improved

A Novel Label-Free Optical Biosensor Using Synthetic Oligonucleotides from E. coli O157:H7: Elementary Sensitivity Tests

SiO2-TiO2 thin films for use as fiber optic guiding layers of optical DNA biosensors were fabricated by the sol-gel dip coating technique. The chemical structure and the surface morphology of the films were characterized before immobilization. Single probe DNA strands were immobilized on the surface and the porosity of the films before the hybridization process was measured. Refractive index values of the films were measured using a Metricon 2010 prism coupler. On the surface of each film, 12 different spots were taken for measurement and calculation of the mean refractive index values with their standard deviations. The increased refractive index values after the immobilization of single DNA strands indicated that immobilization was successfully achieved. A further refractive index increase after the hybridization with target single DNA strands showed the possibility of detection of the E. coli O157:H7 EDL933 species using strands of 20-mers (5′-TAATATCGGTTGCGGAGGTG -3′) sequence

Multiplex-PCR-based screening and computational modeling of virulence factors and t-cell mediated immunity in helicobacter pylori infections for accurate clinical diagnosis

The outcome of H. pylori infection is closely related with bacteria's virulence factors and host immune response. The association between T cells and H. pylori infection has been identified, but the effects of the nine major H. pylori specific virulence factors; cagA, vacA, oipA, babA, hpaA, napA, dupA, ureA, ureB on T cell response in H. pylori infected patients have not been fully elucidated. We developed a multiplex- PCR assay to detect nine H. pylori virulence genes with in a three PCR reactions. Also, the expression levels of Th1, Th17 and Treg cell specific cytokines and transcription factors were detected by using qRT-PCR assays. Furthermore, a novel expert derived model is developed to identify set of factors and rules that can distinguish the ulcer patients from gastritis patients. Within all virulence factors that we tested, we identified a correlation between the presence of napA virulence gene and ulcer disease as a first data. Additionally, a positive correlation between the H. pylori dupA virulence factor and IFN-γ, and H. pylori babA virulence factor and IL-17 was detected in gastritis and ulcer patients respectively. By using computer-based models, clinical outcomes of a patients infected with H. pylori can be predicted by screening the patient's H. pylori vacA m1/m2, ureA and cagA status and IFN-γ (Th1), IL-17 (Th17), and FOXP3 (Treg) expression levels. Herein, we report, for the first time, the relationship between H. pylori virulence factors and host immune responses for diagnostic prediction of gastric diseases using computer—based models

Living Bacterial Sacrificial Porogens to Engineer Decellularized Porous Scaffolds

Decellularization and cellularization of organs have emerged as disruptive methods in tissue engineering and regenerative medicine. Porous hydrogel scaffolds have widespread applications in tissue engineering, regenerative medicine and drug discovery as viable tissue mimics. However, the existing hydrogel fabrication techniques suffer from limited control over pore interconnectivity, density and size, which leads to inefficient nutrient and oxygen transport to cells embedded in the scaffolds. Here, we demonstrated an innovative approach to develop a new platform for tissue engineered constructs using live bacteria as sacrificial porogens. E.coli were patterned and cultured in an interconnected three-dimensional (3D) hydrogel network. The growing bacteria created interconnected micropores and microchannels. Then, the scafold was decellularized, and bacteria were eliminated from the scaffold through lysing and washing steps. This 3D porous network method combined with bioprinting has the potential to be broadly applicable and compatible with tissue specific applications allowing seeding of stem cells and other cell types