Background: HCV Alternate Reading Frame Protein (ARFP) is a frameshift product of HCV-core encoding. Here, we characterized specific anti-ARFP antibodies in Liver Transplant Candidate (LTC) and chronic HCV-infected patients. Methods: The ARFP gene was cloned and the recombinant protein was purified using Nickel chromatography and confirmed by western blotting. ELISA was developed using recombinant

Urolithiasis, which is the presence of stones in the urinary tract, has long been linked with a higher risk of causing chronic kidney diseases and associated illnesses, such as diabetes-affecting 12% of the world population. This clinical condition arises due to the supersaturation of urine and alterations in the expression of cellular and urinary proteins. The renal stone mineral composition has been

Background: Amidases are ubiquitous enzymes and biological functions of these enzymes vary widely. They are considered to be synergistically involved in the synthesis of a wide variety of carboxylic acids, hydroxamic acids and hydrazides, which find applications in commodity chemicals synthesis, pharmaceuticals agrochemicals and wastewater treatments. Methods: They hydrolyse a wide variety of amides

Introduction: Human Herpesvirus 8 (HHV-8) causes classical, endemic (African), and Acquired Immunodeficiency Syndrome (AIDS)-related Kaposi’s Sarcoma (KS), Body Cavity-Based Primary Effusion Lymphomas (BCBL), HHV-8-associated peritoneal Primary Effusion Lymphoma (PEL), and Multicentric Castleman’s Disease (MCD). HHV8 genome encodes several structural and non-structural proteins, among which vIL6 is

Background: The role of Apolipoprotein-E (APO-E) in lipid metabolism and cholesterol transport is a key component of lipid metabolism which plays a role in diseases like hypercholesterolemia, diabetes, and cardiovascular disease. The aim of this study was to determine the genotypes, allelic frequencies, gene expression and methylation related to apolipoprotein E polymorphism in Coronary Artery Disease

Background: Arginine deiminase of Mycoplasma hominis, an arginine catabolizing enzyme, is currently in clinical trial for the treatment of arginine auxotrophic cancers. However, some drawbacks such as instability and antigenicity have limited its application as a protein drug. Arginine Deiminase (ADI) belongs to the guanidino-group modifying enzyme superfamily. Despite differences in the primary amino

Background: Cell-Penetrating Peptides (CPPs), a family of short peptides, are broadly used as the carrier in the delivery of drugs and different therapeutic agents. Thanks to the existence of valuable databases, computational screening of the experimentally validated CPPs can help the researchers to select more effective CPPs for the intercellular delivery of therapeutic proteins. Arginine deiminase

Background: The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp

Background: The firefly luciferase enzyme is widely used in protein engineering and diverse areas of biotechnology, but the main problem with this enzyme is low-temperature stability. Previous reports indicated that surface areas of thermostable proteins are rich in arginine, which increased their thermal stability. In this study, this aspect of thermophilic proteins evaluated by mutations of surface

Background: Oral Squamous Cell Carcinoma (OSCC) is a major sub-type of oral cancer that shares 90% proportion of oral cavity cancers. It is declared as the sixth most frequent cancer among all cancer types throughout the world. Higher morbidity in Asian countries is reported due to frequent use of Smokeless Tobacco (SLT) products besides exposure to other risk factors. Hyperactivation of epidermal

Background: Hyperuricemia and gout are the conditions, which is a response of accumulation of uric acid in the blood and urine. Uric acid is the product of purine metabolic pathway in humans. Uricase is a therapeutic enzyme that can enzymatically reduces the concentration of uric acid in serum and urine into more a soluble allantoin. Uricases are widely available in several sources like bacteria, fungi

Background: Staphylococcus aureus (S. aureus), an important pathogen, causes a wide range of infections in human starting from food poisoning to septicemia. It affects the host cells with various exotoxins, known as virulence factors, which are synthesized in growth phase-dependent manner of the bacteria. S. aureus has been reported to become resistant to antibiotics rapidly. Among two common clinical

Background: The Cytochromes P450 (CYPs) have an essential role in the oxidation of endogenous and exogenous molecules. The CYPs are identified in all domains of life, but the CYP152A1 from Bacillus subtilis is specially considered for clinical and industrial applications. The molecular cloning of a new type of CYP from Bacillus subtilis was reported, previously. Here, we describe the hidden layer of

Background: Cervical cancer arises from the cervix and it is the 3rd most diagnosed malignancy and a foremost cause of cancer-related death in females. On the other hand, the expressions of EGFR and p53 are two important proteins observed in various studies on cervical cancer. Objective: The study aims to evaluate the beneficial effect of radiotherapy based on the regulation of p53 and EGFR gene in

Background: Familial Mediterranean Fever (FMF) is a prototypical hereditary autoinflammatory disease affecting principally Mediterranean populations and characterized by recurrent frequent fever and inflammation. The disease is essentially caused by inherited mutations in the MEFV gene which encodes pyrin protein. The reported mutations are mostly located on the B30.2 domain in the C-terminal end of

Among eukaryotic organisms a vast majority of Box H/ACA ribonucleoproteins (RNPs) are responsible for the post-transcriptional introduction of pseudouridine (Psi) into ribosomal RNAs (rRNA) and spliceosomal small nuclear RNAs (snRNA), thus influencing protein translation and pre-mRNA splicing, respectively. Additionally, a few distinct Box H/ACA RNPs are involved in the processing of rRNA, and the

Background: The subcellular localization of a protein is closely related with its functions and interactions. More and more evidences show that proteins may simultaneously exist at, or move between, two or more different subcellular localizations. Therefore, predicting protein subcellular localization is an important but challenging problem. Observation: Most of the existing methods for predicting

Background: The understanding of protein function is essential to the study of biological processes. However, the prediction of protein function has been a difficult task for bioinformatics to overcome. This has resulted in many scholars focusing on the development of computational methods to address this problem. Objective: In this review, we introduce the recently developed computational methods

Background: Finding the pathogenic gene is very important for understanding the pathogenesis of the disease, locating effective drug targets and improving the clinical level of medical treatment. However, the existing methods for finding the pathogenic genes still have limitations, for instance the computational complexity is high, and the combination of multiple genes and pathways has not been considered

Background: Tumor classification is important for accurate diagnosis and personalized treatment and has recently received great attention. Analysis of gene expression profile has shown relevant biological significance and thus has become a research hotspot and a new challenge for bio-data mining. In the research methods, some algorithms can identify few genes but with great time complexity, some algorithms

Background: Epistasis makes complex diseases difficult to understand, especially when heterogeneity also exists. Heterogeneity of complex diseases makes the distribution of case population more confused. However, the traditional methods proposed to detect epistasis often ignore heterogeneity, resulting in low power of association studies. Methods: In this study, we firstly use rank information in the

Background: Identification of Enzyme Commission (EC) number of enzymes is quite important for understanding the metabolic processes that produce enough energy to sustain life. Previous studies mainly focused on predicting six main functional classes or sub-functional classes, i.e., the first two digits of the EC number. Objective: In this study, a binary classifier was proposed to identify the full

Background: Prediction of protein subcellular location is a meaningful task which attracts much attention in recent years. Particularly, the number of new protein sequences yielded by the highthroughput sequencing technology in the post genomic era has increased explosively. Objective: Protein subcellular localization prediction based solely on sequence data remains to be a challenging problem of computational

Background: Breast cancer is one of the most common malignancies, and a threat to female health all over the world. However, the molecular mechanism of breast cancer has not been fully discovered yet. Objective: It is crucial to identify breast cancer-related genes, which could provide new biomarker for breast cancer diagnosis as well as potential treatment targets. Methods: Here we used the minimum

Background: Mathematical models play a central role in facilitating researchers to better understand and comprehensively analyze various processes in biochemical systems. Their usage is beneficial in metabolic engineering as they help predict and improve desired products. However, one of the primary challenges in model building is parameter estimation. It is the process to find nearoptimal values of

Background: In eukaryotic cells, apoptosis signaling pathways are controlled mainly by aspartic acid cysteine proteases (caspases). However, certain unicellular microorganisms, such as Giardia duodenalis, lack these proteins. Thus, other cysteine proteases may play an important role in the parasite apoptosis signaling pathway. Objective: To understand the effect of cathepsin B-like inhibition on the

Background: Plasminogen is a blood plasma glycoprotein of molecular weight about 92,000 Daltons. Physiologically, it incorporates into blood clots and after its activation by plasminogen activators to plasmin can perform a fibrinolytic function. Microplasmin is truncate polypeptide chain derivate of plasmin may be increase the fibrinolytic activity. Objective: To study the amino acid sequence of two

Background: Bioethanol derived from lignocellulosic biomass can supplement the ethanol supplies in a sustainable manner. However, the bioethanol production process is still not cost effective and researchers are looking for novel strategies like simultaneous saccharification fermentation to cut down the production cost. Thermotolerant yeast Saccharomyces cerevisiae JRC6 is reported to improve the fermentation

Background: DAB389IL-2 (Denileukin diftitox) as an immunotoxin is a targeted pharmaceutical protein and is the first immunotoxin approved by FDA. It is used for the treatment of various kinds of cancer such as CTCL lymphoma, melanoma, and Leukemia but among all of these, treatment of CTCL has special importance. DAB389IL-2 consists of two distinct parts; the catalytic domain of Diphtheria Toxin (DT)

Background: Mass spectrometry is a tool used in analytical chemistry to identify components in a chemical compound and it is of tremendous importance in the field of biology for high throughput analysis of biomolecules, among which protein is of great interest. Objective: Advancement in proteomics based on mass spectrometry has led the way to quantify multiple protein complexes, and proteins interactions

Background: Cerebrospinal fluid (CSF) contains pro-growth factors that can affect proliferation, migration and differentiation of Mesenchymal Stem Cells (MSCs). Objective: This study aimed to isolate MSC like cells from CSF of patients with meningioma and psudotumorcerebri (PTC) and identify differentially expressed proteins in these cells. Methods: Five patients with newly diagnosed intracranial meningioma

Background: Yaks inhabit high-altitude are well-adapted to the hypoxic environments. Though, the mechanisms involved in regulatory myocardial protein expression at high-altitude were not completely understood. Objective: To revel the molecular mechanism of hypoxic adaptation in yak, here we have applied comparative myocardial proteomics in between yak and cattle by isobaric Tag for Relative and Absolute

Background: CIGB-300 is a pro-apoptotic peptide that abrogates CK2-mediated phosphorylation, and can elicit synergistic interaction in vitro and in vivo when combined with certain anticancer drugs. Objective: The combination of CIGB-300 with cisplatin is studied through data mining and expressionbased proteomics to reveal the molecular basis of this interaction. Cisplatin resistance-associated proteins

Background: The molecular mechanisms or valuable biomarkers for early diagnosis of colorectal cancer (CRC) are not fully elucidated yet. Objective: To understand the proteomic changes at the global level in the carcinogenesis of CRC, differentially expressed proteins between normal intestinal epithelial cells CCD841 and colorectal cancer cells HCT116 were identified. Method: The isobaric tags for relative

Neuroproteomics, as a sub-discipline of proteomics, has enlightened the pathway for the study of different complicated diseases and brain disorders. Since four decades, various analytical and quantitative techniques have been used to cure problems related to brain and memory. Brain has a complex structure with various cells and cell types, the expressing proteins and suppressing factors too. Drug addiction

Background: Intestinal flora dynamically affects the host's systemic immune system. Liver is one of the organs that may be affected by intestinal microbiota. Materials and Methods: In this study, we aimed to identify proteome level differences between liver tissue from mice cleared intestinal flora and control using tandem mass spectrometry (LC-MS/MS) and label free quantification. Additionally, protein-protein

Objective: To verify whether the botulinum toxin heavy chain HCS has specific neuronal targeting function and to confirm whether TAT-EGFP-LC has hydrolyzable SNAP-25 and has transmembrane biological activity. Methods: We constructed the pET-28a-TAT-EGFP-HCS/LC plasmid. After the plasmid is expressed and purified, we co-cultured it with nerve cells or tumors. In addition, we used Western-Blot to identify