Objectives To develop a multi-stage and multi-epitope vaccine, which consists of epitopes from the early secretory and latency-associated antigens of Mycobacterium tuberculosis (MTB). Methods The B-cell, cytotoxic T-lymphocyte (CTL) and helper T-lymphocyte (HTL) epitopes of 12 proteins were predicted using an immunoinformatics. The epitopes with antigenicity, without cytotoxicity and sensitization, were further screened to construct the multi-epitope vaccine. Furthermore, the proposed vaccine underwent physicochemical properties analysis and secondary structure prediction as well as 3D structure modeling, refinement and validation. Then the refined model was docked with TLR4. Finally, an immune simulation of the vaccine was carried out. Results The proposed vaccine, which consists of 12 B-cell, 11 CTL and 12 HTL epitopes, had a flexible and stable globular conformation as well as a thermostable and hydrophilic structure. A stable interaction of the vaccine with TLR4 was confirmed by molecular docking. The efficiency of the candidate vaccine to trigger effective cellular and humoral immune responses was assessed by immune simulation. Conclusion A multi-stage multi-epitope MTB vaccine construction strategy based on immunoinformatics is proposed, which is expected to prevent both active and latent MTB infection.
Mycobacterium tuberculosis/metabolism* ; Molecular Docking Simulation ; Toll-Like Receptor 4 ; Epitopes, T-Lymphocyte/chemistry* ; Epitopes, B-Lymphocyte/chemistry* ; Vaccines, Subunit/chemistry* ; Computational Biology/methods*

As an important anthropometric characteristic, human height not only contributes to the recognition of other anthropological characteristics and genetic risk factors, but also is an important part of forensic DNA phenotyping studies. Accurate estimation of height can provide more complete information about the phenotype of suspects and provide help to solve cases. In recent years, having benefited from the rapid development of molecular biological techniques and bioinformatics, height-related genetics research has made some progress. This paper describes the research progress of human height estimation from the genetic variation and the epigenetic inheritance perspectives and looks into the future research direction.
Humans ; Phenotype ; DNA/genetics* ; Molecular Biology ; Forensic Genetics/methods*

PURPOSE: The disease entity mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) is characterized by an early onset of stroke-like episodes. MELAS is the most dominant subtype of mitochondrial disease. Molecular genetic testing is important in the diagnosis of MELAS. The mitochondrial DNA (mtDNA) 3243A>G mutation is found in 80% of MELAS patients. Nevertheless, molecular analysis alone may be insufficient to diagnose MELAS because of mtDNA heteroplasmy. This study aimed to evaluate whether muscle biopsy is useful in MELAS patients as an initial diagnostic evaluation method. MATERIALS AND METHODS: The medical records of patients who were diagnosed with MELAS at the Department of Pediatrics of Gangnam Severance Hospital between January 2006 and January 2017 were reviewed. The study population included 12 patients. They were divided into two subgroups according to whether the results of muscle pathology were in accordance with mitochondrial diseases. Clinical variables, diagnostic evaluations, and clinical outcomes were compared between the two groups. RESULTS: Of the 12 patients, seven were muscle pathology-positive for mitochondrial disease. No statistically significant difference in clinical data was observed between the groups that were muscle pathology-positive and muscle pathology-negative for mtDNA 3243A>G mutation. Additionally, the patients with weakness as the initial symptom were all muscle pathology-positive. CONCLUSION: The usefulness of muscle biopsy appears to be limited to an initial confirmative diagnostic evaluation of MELAS. Muscle biopsy can provide some information in MELAS patients with weakness not confirmed by genetic testing.
Biopsy* ; Diagnosis ; DNA, Mitochondrial ; Genetic Testing ; Humans ; Medical Records ; MELAS Syndrome* ; Methods ; Mitochondrial Diseases ; Mitochondrial Encephalomyopathies* ; Molecular Biology ; Pathology ; Pediatrics

Text mining has become an important research method in biology, with its original purpose to extract biological entities, such as genes, proteins and phenotypic traits, to extend knowledge from scientific papers. However, few thorough studies on text mining and application development, for plant molecular biology data, have been performed, especially for rice, resulting in a lack of datasets available to solve named-entity recognition tasks for this species. Since there are rare benchmarks available for rice, we faced various difficulties in exploiting advanced machine learning methods for accurate analysis of the rice literature. To evaluate several approaches to automatically extract information from gene/protein entities, we built a new dataset for rice as a benchmark. This dataset is composed of a set of titles and abstracts, extracted from scientific papers focusing on the rice species, and is downloaded from PubMed. During the 5th Biomedical Linked Annotation Hackathon, a portion of the dataset was uploaded to PubAnnotation for sharing. Our ultimate goal is to offer a shared task of rice gene/protein name recognition through the BioNLP Open Shared Tasks framework using the dataset, to facilitate an open comparison and evaluation of different approaches to the task.
Benchmarking ; Biology ; Data Mining ; Dataset ; Machine Learning ; Methods ; Molecular Biology ; Natural Language Processing ; Oryza ; Plants

OBJECTIVE: To decipher the possible mechanisms of Sinomenium Acutum (SA) in treating diseases by a bioinformatics method. METHODS: SA ingredients were searched according to Chinese Pharmacopoeia, Chinese Medicine Dictionary and Traditional Chinese Medicines Database (TCMD). Active compounds and target proteins of SA were acquired through the Pubchem platform. Pathway, network and function analyses of SA were performed with ingenuity pathway analysis (IPA), a bioinformatics analysis platform. Disease, biofunction-target networks were established with Cytoscape. RESULTS: Eighteen ingredients from SA were obtained. Seven active ingredients with 31 active target proteins were acquired according to PubChem Bioassay test. By IPA analysis, 277 canonical pathways belonging to 17 function categories were collected, 23 kinds of diseases, 21 categories bio-functions were obtained. Based on P value, calculated by IPA, the top 5 significant pathway of SA targets include phosphatidylinositol 3 kinase/Akt (PI3K/Akt) signaling, prostate cancer signaling, macrophage migration inhibitory factor (MIF) regulation of innate immunity, Guanosine-binding protein coupled receptor (GPCR) signaling, and ataxia telangiectasia mutated protein (ATM) signaling. Disease and bio-function network analysis indicated that mitogen activated protein kinase 1 (MAPK1), MAPK3, p65 nuclear factor κB (RELA), nuclear factor of κB inhibitor alpha (NFκBIA), interleukin 1β(IL-1β), prostaglandin G/H synthase 2 (PTGS2) and tumor protein 53 (TP53) were the critical targets in various diseases treated by SA. CONCLUSION In the different view of target, pathway, disease and bio-function, inflammation was found to be a central theme in many chronic conditions. SA could be used not only as an anti-inflammatory agent, but also for the treatment of cancers, neurological diseases, psychological disorders and metabolic diseases.
Computational Biology ; methods ; Disease ; Humans ; Molecular Targeted Therapy ; Proteins ; metabolism ; Signal Transduction ; Sinomenium ; chemistry

In order to understand biological phenomena accurately, single molecule techniques using a physical research approach to molecular interactions have been developed, and are now widely being used to study complex biological processes. In this review, we discuss some of the single molecule methods which are composed of two major parts: single molecule spectroscopy and manipulation. In particular, we explain how these techniques work and introduce the current research which uses them. Finally, we present the oral biology research using the single molecule methods.
Biological Phenomena ; Biological Processes ; Biology ; Methods ; Molecular Biology ; Optical Tweezers ; Spectrum Analysis

The laboratory-based diagnosis of viral infection has been evolving over the years, to increase objectivity, accuracy, and sensitivity via the continuous development of various technologies. Cell culture, which is one of the methods used for the diagnosis of viral infection, is a “gold-standard” approach; however, it is time consuming and is associated with a high risk of contamination. To overcome these shortcomings, molecular biology methods, such as conventional polymerase chain reaction (cPCR), real-time PCR, and sequencing, have been used recently for virus diagnosis. Realtime PCR has higher accuracy and sensitivity compared with cPCR. Moreover, realtime PCR can quantify viral nucleic acids by confirming the amplification using the threshold cycle, which is the initial amplification point. Real-time PCR applications for the detection of various types of viruses in clinical settings should be based on the use of appropriate samples, nucleic acid extraction according to virus characteristics, and selection of diagnostic methods using sensitivity and specificity targets. In addition, the implementation of real-time PCR requires to evaluate the performance of the test protocol by measuring sensitivity, specificity, accuracy, and reproducibility. The verified real-time PCR method is an easy, fast, and accurate method for monitoring the diagnosis and treatment outcomes in a clinical setting. In this review, we summarize the characteristics of the typical diagnostic methods for viral infection, especially of the advanced real-time PCR method, to detect human pathogenic viruses.
Cell Culture Techniques ; Diagnosis* ; Humans ; Methods ; Molecular Biology ; Nucleic Acids ; Polymerase Chain Reaction ; Real-Time Polymerase Chain Reaction* ; Sensitivity and Specificity

BACKGROUND: To improve Rh-related antigen negative blood supply effectively, the Korean Red Cross (KRC) blood centers have performed Rh phenotype screening tests of C, c, E and e antigens for all donors since April, 2013. Especially for rare ‘-D-/-D-’ blood supply and donor recruitment, we have implemented Rh phenotype confirmation test for all C, c, E and e antigen negative donors. In this study, we report the test results of 7 donors with ‘-D-/-D-’ phenotype. METHODS: All three KRC Blood Laboratory Centers performed Rh phenotype screening tests using the automatic machine, PK7300 (Beckman Coulter, Japan), for all 876,920 donors from January 1, 2018 to April 30, 2018. We then performed the Rh phenotype confirmation test using the tube method manually, at room temperature, 37℃ and antihuman globulin phase. RESULTS: Among 876,920 donors, 14 were Rh antigen C, c, E, e negative as results of Rh phenotype screening test. The results of Rh phenotype confirmation test of these 14 donors showed that 7 donors were Rh antigen C, c, E, e negative. The ratio of -D-/-D- phenotype for all donors was 0.000798%. CONCLUSION: Our data suggests that -D-/-D- phenotype is one of the rare blood groups among Koreans. Although ‘-D-/-D-’ phenotype was confirmed by serologic tests, it is necessary to re-confirm it by molecular genetic techniques.
Blood Group Antigens ; Hepatitis B e Antigens ; Humans ; Mass Screening ; Methods ; Molecular Biology ; Phenotype* ; Red Cross ; Serologic Tests ; Tissue Donors*

Noonan syndrome (NS) is a genetic disorder caused by autosomal dominant inheritance and is characterized by a distinctive facial appearance, short stature, chest deformity, and congenital heart disease. In individuals with NS, germline mutations have been identified in several genes involved in the RAS/mitogen-activated protein kinase signal transduction pathway. Because of its clinical and genetic heterogeneity, the conventional diagnostic protocol with Sanger sequencing requires a multistep approach. Therefore, molecular genetic diagnosis using targeted exome sequencing (TES) is considered a less expensive and faster method, particularly for patients who do not fulfill the clinical diagnostic criteria of NS. In this case, the patient showed short stature, dysmorphic facial features suggestive of NS, feeding intolerance, cryptorchidism, and intellectual disability in early childhood. At the age of 16, the patient still showed extreme short stature with delayed puberty and characteristic facial features suggestive of NS. Although the patient had no cardiac problems or chest wall deformities, which are commonly present in NS and are major concerns for patients and clinicians, the patient showed several other characteristic clinical features of NS. Considering the possibility of a genetic disorder, including NS, a molecular genetic study with TES was performed. With TES analysis, we detected a pathogenic variant of c.458A > T in KRAS in this patient with atypical NS phenotype and provided appropriate clinical management and genetic counseling. The application of TES enables accurate molecular diagnosis of patients with nonspecific or atypical features in genetic diseases with several responsible genes, such as NS.
Congenital Abnormalities ; Cryptorchidism ; Diagnosis ; Exome* ; Genetic Counseling ; Genetic Heterogeneity ; Germ-Line Mutation ; Heart Defects, Congenital ; Humans ; Intellectual Disability ; Male ; Methods ; Molecular Biology ; Noonan Syndrome* ; Phenotype ; Protein Kinases ; Puberty, Delayed ; Signal Transduction ; Thoracic Wall ; Thorax ; Wills

BACKGROUND: Trichophyton mentagrophytes complex is a heterogeneous group. A new classification, based on molecular biology, has replaced the one based on morphology, physiology, and mating behavior. OBJECTIVE: T. mentagrophytes isolates from Korean patients were classified using the new method and compared with the classic classification. METHODS: During 2010-2011, fungal isolates were collected at the Catholic skin clinic from 562 patients infected with T. mentagrophytes; clinical characteristics were reviewed. Patients were divided into four groups based on the morphological characteristics of the isolates. Thirty-four strains of T. mentagrophytes were randomly selected from the four groups for mycological and molecular biology analyses, including analyses of morphological characteristics, ribosomal DNA (rDNA) internal transcribed spacer (ITS) sequence, and rDNA nontranscribed spacer (NTS) typing. RESULTS: Among the 562 isolates, persicolor (41.6%) was the most common strain type, followed by the powdery (38.4%), downy (11.2%), and granular (8.7%) types. The granular type differed from the other three with respect to the isolation site, patient's age, seasonal variation, and microscopic characteristics. Among the selected 34 strains, the microscopic characteristics varied for each strain. The powdery, persicolor, and downy types had ITS sequences identical to those of the anthropophilic T. interdigitale/A. vanbreuseghemii. The ITS sequence of granular type was similar to that of zoophilic T. interdigitale/A. vanbreuseghemii. The granular type had different NTS types than the other types did. CONCLUSION: The T. mentagrophytes strains isolated were classified as T. interdigitale/A. vanbreuseghemii; the majority (91.7%) was anthropophilic and 8.3% were zoophilic and granular type.
Classification* ; DNA, Ribosomal ; Humans ; Methods ; Molecular Biology ; Physiology ; Seasons ; Skin ; Trichophyton*