ABSTRACT
In computational methods, position weight matrices (PWMs) are commonly applied for transcription factor binding site (TFBS) prediction. Although these matrices are more accurate than simple consensus sequences to predict actual binding sites, they usually produce a large number of false positive (FP) predictions and so are impoverished sources of information. Several studies have employed additional sources of information such as sequence conservation or the vicinity to transcription start sites to distinguish true binding regions from random ones. Recently, the spatial distribution of modified nucleosomes has been shown to be associated with different promoter architectures. These aligned patterns can facilitate DNA accessibility for transcription factors. We hypothesize that using data from these aligned and periodic patterns can improve the performance of binding region prediction. In this study, we propose two effective features, "modified nucleosomes neighboring" and "modified nucleosomes occupancy", to decrease FP in binding site discovery. Based on these features, we designed a logistic regression classifier which estimates the probability of a region as a TFBS. Our model learned each feature based on Sp1 binding sites on Chromosome 1 and was tested on the other chromosomes in human CD4+T cells. In this work, we investigated 21 histone modifications and found that only 8 out of 21 marks are strongly correlated with transcription factor binding regions. To prove that these features are not specific to Sp1, we combined the logistic regression classifier with the PWM, and created a new model to search TFBSs on the genome. We tested the model using transcription factors MAZ, PU.1 and ELF1 and compared the results to those using only the PWM. The results show that our model can predict Transcription factor binding regions more successfully. The relative simplicity of the model and capability of integrating other features make it a superior method for TFBS prediction.
Subject(s)
Binding Sites/physiology , Nucleosomes/metabolism , Protein Binding/physiology , Transcription Factors/metabolism , Computational Biology , Humans , Promoter Regions, Genetic , Transcription Initiation SiteABSTRACT
BACKGROUND: Toxoplasmosis is a worldwide-distributed infection which is mostly asymptomatic but can cause serious health problems in congenitally-infected newborns and immunecompromised individuals. Research is undergoing both to improve Toxoplasma serological tests, which play the main role in laboratory diagnosis of the infection, and develop an effective vaccine to prevent the infection. Some studies showed usefulness of rhoptry protein 1 (ROP1) antigen of Toxoplasma gondii (T. gondii) in serodiagnosis of the infection and induction of protective immunity. The purpose of this study was to produce recombinant ROP1 and evaluate its antigenicity against human infected sera. METHODS: DNA encoding ROP1, amino acids 171 to 574, was obtained from T. gondii RH strain by polymerase chain reaction amplification and cloned in prokaryotic expression plasmid pET-15b. rROP1 was expressed in Escherichia coli (E. coli) and purified in a single step by immobilized metal ion affinity chromatography. RESULTS: DNA sequencing showed 99% similarity between the cloned sequence and the corresponding sequence in Gene bank. Results indicated the proper antigenicity of rROP1. Sera from Toxoplasma infected individuals specifically recognized rROP1 in Western blotting. CONCLUSION: rROP1 is antigenic toward human infected sera and can be used in studies for development of both a Toxoplasma serological test and a protective vaccine.
ABSTRACT
PURPOSE: Achieving the desired outcome in rhinoplasty depends on many factors. Osteotomy and adjustment of the lateral nasal wall are important steps that necessitate careful planning and execution. A cadaver study was performed to evaluate the osteotomy result obtained with a newly designed piezoelectric-based scalpel. MATERIALS AND METHODS: Twenty lateral osteotomies of the nasal wall were performed in 10 human cadaver noses. The osteotomies were conducted in 6 female and 4 male cadavers (age range, 65 to 83 yr; mean age, 74.8 yr). A specially designed Piezosurgery-based scalpel was used endonasally to perform the lateral osteotomy. Cutting of the bony nasal wall was performed subperiostally along the planned osteotomy route under tactile control. Digital infracturing was accomplished by applying gentle pressure. After completing the osteotomy, the osteotomy line and nasal mucosa were examined endoscopically. The skin cover was removed to examine the lateral bony nasal wall for the shape and amount of bone fragments, the osteotomy path, and mucosa involvement. RESULTS: Using the Piezosurgery-based scalpel required a learning curve, but the handling was easy. It allowed an exact performance of the osteotomy and caused no mucosal tearing. If excessive force was used, the piezo tip stopped working. There was no comminuted fracture pattern and the lateral nasal wall remained in 1 piece. The duration of the osteotomy was 5 to 10 minutes on each side. CONCLUSION: The piezoelectric-based scalpel is a useful tool, which can be used to perform osteotomy of the nasal wall. In addition, this specifically designed tool tip allows an endonasal approach, is easy to handle, and allows effective irrigation of the osteotomy region.
Subject(s)
Nasal Bone/surgery , Osteotomy/instrumentation , Piezosurgery/instrumentation , Rhinoplasty/instrumentation , Aged , Aged, 80 and over , Cadaver , Female , Humans , MaleABSTRACT
PURPOSE: Auricular reconstruction is a challenging surgical intervention that requires perfect surgical skills, exact planning, and esthetic knowledge. It is necessary to use a suitable method of reconstruction for each patient. From 10 years of experience, the authors have developed a general concept for auricular reconstruction. PATIENTS AND METHODS: Seventy-five patients (62 male, 13 female; age range, 8 to 92 yr; mean age, 65.9 yr) underwent partial to total auricular reconstruction. Tissue loss occurred from different causes: 19 cases of squamous cell carcinoma (25.3%), 18 cases of basal cell carcinoma (24%), 14 cases of Bowen disease (18.7), 11 cases of malignant melanoma (14.7%), 7 cases of trauma (9.3%), 3 different malignant tumors (4%), and 3 cases of congenital deformity (4%). RESULTS: Defects smaller than one fourth the vertical auricular size (15 to 20 mm) could be treated by primary closure. A larger defect closed by this method caused visible deformity. In defects larger than one to three fourths the vertical auricular size (40 to 55 mm), a reversed retroauricular flap was used successfully if there was no contraindication or rejection. This flap can be combined with other flaps, depending on the flap location, size, and tissue involved. In defects exceeding three fourths the vertical auricular size, an implant-retained prosthesis was preferred. CONCLUSION: The location and size of a defect, the medical condition of the patient, and the desired esthetic outcome play an important role in choosing the appropriate method. According to the authors' experience, the only contraindications for the reversed retroauricular flap are medical condition, poor prognosis, and patient refusal.
Subject(s)
Ear Auricle/surgery , Adolescent , Adult , Aged , Aged, 80 and over , Child , Ear Auricle/pathology , Ear Neoplasms/rehabilitation , Female , Humans , Male , Middle Aged , Young AdultABSTRACT
PURPOSE: Large defects in the face resulting from the excision of malignant tumors, trauma, and congenital malformation pose a significant challenge to reconstructive surgeons. Achieving good esthetic and functional outcomes is often very demanding. PATIENTS AND METHODS: A facelift technique was used in 47 patients (25 female, 22 male; age range, 17.5 to 82.3 years; mean age, 49.3 years) to replace lost tissue of the face from 2009 through 2012. The minimum defect size was 2 cm in diameter and the maximum was 8 cm. To achieve tension-free coverage with a reliable blood supply, a deep-plane dissection, including the skin and superficial musculoaponeurotic system (SMAS), was performed. The deep sub-SMAS dissection was extended into the neck and the contralateral part, as needed. A thick flap was created and composite lifting was performed. RESULTS: No significant deformity concerning the lower eyelids, nose, and lip was registered. Most scars could be placed in hidden regions and became undetectable after a year. The facial nerve function remained intact in all patients. CONCLUSION: Using these facelift techniques, including the incision, sub-SMAS dissection for volumetric positioning of the skin, and the SMAS flap, the closure of extensive facial defects with excellent functional and esthetic results is conceivable.