MOJ proteomics & bioinformatics最新文献

{"title":"Immunoinformatics, antigenicity epitopes prediction in the solute carrier family 11 of the natural resistance associated macrophage protein 1 (nramp) related with brucellosis in cattle","authors":"O. Hamad, M. S. Ekinci, Emin Özköse, I. Akyol","doi":"10.15406/MOJPB.2018.07.00238","DOIUrl":"https://doi.org/10.15406/MOJPB.2018.07.00238","url":null,"abstract":"Brucellosis is responsible for enormous economic losses as well as considerable human morbidity in endemic areas. The bacteria infects animals such as swine, cattle, goat, sheep, and dogs. Humans can become infected indirectly through contact with infected animals or by animal products consumption. Brucellosis occurs worldwide, but it is well controlled in most developed countries. The disease is rare in industrialized nations because of routine screening of domestic livestock and animal vaccination programmers.4 Clinical disease is still common in the Middle East, Asia, Africa, South and Central America. This review article aims to describe the prevalence of brucellosis in some countries these data are available around different regions of the world, and risk factors associated infections according to regression models.3,4 There are two species of bacterial pathogens that recorded cause brucellosis disease in cattle. Firstly, the (Brucella abortus) with genome size 3,264,306 base pairs divided into two unequal size chromosomes (https://www.ncbi.nlm.nih. gov/genome/?term=Brucella+ abortus). The whole genome that downloaded from Gen Bank of the National Center of Biotechnology and Information (NCBI), within accession numbers NC_007618.1 and NC_007624.1 for chromosome I and II respectively.5 Secondly, the (Brucella melitensis) and its genome size 3,294,931 base pairs also divide into two unequal size chromosomes (https://www. ncbi.nlm. Nih.gov/genome/?term=Brucella+melitensis). The NCBI accession numbers of whole‒genome chromosome I and II are NC_003317.1 and NC_003318.1 respectively.6 predicting the antigenic sites on proteins is of major importance for the production of synthetic artificial peptide vaccines and peptide probes of antibody structure. Many predictive methods, based on various assumptions about the nature of the antigenic response have been proposed and tested. This review will discuss the principles underlying the different approaches to predicting antigenic sites and will attempt to answer the question of how well they work. As a review of Kolaskar & Tongaonkar method which coined in 1990. Analysis of data from experimentally determined antigenic sites on proteins has revealed that the hydrophobic residues Cys, Z_XU, and Val if they occur on the surface of a protein, are more likely to be a part of antigenic sites. A semi‒empirical method which makes use of physiochemical properties of amino acid residues and their frequencies of occurrence in experimentally known segmental epitopes was developed to predict antigenic determinants on proteins. Application of this method to a large number of proteins has shown that our method can predict antigenic determinants with about 75% accuracy which is better than most of the known.7,8 In another hand, the welling method for antigenicity prediction in 1985 came in contrast. Prediction of antigenic regions in a protein will be helpful for a rational approach to the synthesis of peptides which m","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"119 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73362587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of interactions of nucleic acids with lipids in nuclear pore assembly, genome expression and carcinogenesis","authors":"K. Vasily","doi":"10.15406/MOJPB.2018.07.00237","DOIUrl":"https://doi.org/10.15406/MOJPB.2018.07.00237","url":null,"abstract":"In our days when the methods of molecular genetics are dominant in biology, traditional biochemistry and biophysics rank low and serve as Cinderella in molecular biology. Unfortunately, biochemists and biophysicist do not have enough time to estimate new methods (protocols) that emerged in molecular biology and genetics. The demerits of the methods are multiplied giving birth to other errors. The example of it is an approximately thirty‒year investigation of nuclear matrix, which according to recent data does not exist in the structure of nucleus! Furthermore, a lot of valuable ideas which were rejected because of the absence of appropriate biochemical methods in the past have not been recovered and don’t got a development after the appearance of the techniques which could be used to explain their correctness. One of the undeservingly forgotten ideas, which was exploited during investigation within 70s‒80s in the past century, was the conception of DNA‒membrane complexes,1 and as a particular case, DNA‒lipid interactions.","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81218115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessment of the Effects of Sand Harvesting On River Water Quality: Case Study in Iuuma River, Kivaa Ward, Machakos County","authors":"Kamau Gn Isika K Daniel, Mbugua Jk","doi":"10.15406/mojpb.2017.06.00181","DOIUrl":"https://doi.org/10.15406/mojpb.2017.06.00181","url":null,"abstract":"Water is the fundamental need of man to sustain life. Water is a universal solvent and picks up impurities easily and thus changes its taste, color and odour. Some contaminants are easily identified by assessing the taste, odour and turbidity of the water: pure water remains tasteless, colorless and odorless. However, most water parameters cannot be easily detected by mere observation and require chemical testing.","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"34 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80387892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The autocuidado and the security in patients with standing diabetic risk","authors":"E. Sardiñas, leana M García Rial, A. Herrera, Pedro A Pinillo Viera","doi":"10.15406/MOJPB.2018.07.00236","DOIUrl":"https://doi.org/10.15406/MOJPB.2018.07.00236","url":null,"abstract":"Diabetic foot is a chronic complication of Diabetes Mellitus, which affects the life of these patients. One of the most common complications of Diabetes Mellitus (DM) is diabetic foot ulcer (UPD), a significant source of morbidity and mortality in diabetic patients. Hence, it is suggested that between 10‒15% of diabetic patients develop an UPD at some point in their lives and of those between 10‒15% ends in an amputation. The most feared complication of diabetes mellitus is the amputation of a member, with the psychological and social burden that comes with it,1,2 It is currently estimated that more than 25% of the hospital admissions of diabetics in the US, Great Britain, Spain and Mexico are related to problems in their feet.3 In Cuba, at the National Institute of Angiology and Vascular Surgery, where there is a specialized service in diabetic angiopathy, 20% of patients who enter is diabetic foot between 8% and 13% where you can establish a causal relationship statistically.4,5 There is a criterion that approximately 15% of all patients with diabetes mellitus develop an ulcer in the foot or leg during the course of their disease, in the Province of Matanzas 13% of patients admitted is per diabetic foot, in the Municipality of Colón there is a prevalence of patients with diabetic foot ulcers of 8%, that’s why the importance of education since people with diabetes can prevent diabetic foot with a personal, individual and collective education. Self‒care is the key to maintaining health one of the great theories of nursing, Dorothea Elizabeth Orem, described Nursing in 1958 as a service. He then established his theory of self‒ care deficit as a general model and addressed self‒care as a human need. He highlighted the particular attention to be paid by nurses to the satisfaction of the need for self‒care of people, to prolong their life and health or to recover from injuries and illnesses.6,7 The educational support system that we apply in this study is based on the Dorothea Orem self‒care model, taking into account the risk factors of diabetic foot and the need to integrate self‒care as a model in the patient’s daily behavior to contribute to the reduction of complications and amputations in lower limbs,8‒10 taking into account the following objectives: Show the effectiveness of an educational intervention as the basis of the model for the comprehensive care of the diabetic, determine the epidemiological and sociodemographic clinical aspects related to diabetes mellitus, Identify the self‒care knowledge that these patients have with diabetological education and foot care.","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"73 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75235006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RANDOMSEQ: Python command‒line random sequence generator","authors":"Maurice HT Ling","doi":"10.15406/mojpb.2018.07.00235","DOIUrl":"https://doi.org/10.15406/mojpb.2018.07.00235","url":null,"abstract":"Randomization is a crucial aspect of any statistical tests as experimental control or to generate null hypotheses.1‒3 As such, at the core of many simulation experiments, such as Monte Carlo simulations, is a random number or sequence generator. For example, Monte Carlo simulations were used to study mutagenesis and probability of obtaining single cells from serial dilutions.4,5 Random nucleotide and amino acid sequences had been used in many studies; thus, demonstrating the importance of random sequence generators in sequence analyses. For example, 500 thousand randomly generated DNA sequences of 50 nucleotides each were used to examine the relationship between DNA sequences and gene expressions,6 random peptide sequences had been used to study randomly arising secondary structures,7 and natural peptides had been shown to have more long‒ disordered regions than randomly generated peptide sequences.8 Several random sequence generators had been developed over the years. Many random nucleotide or amino acid generators provided minimal options; such as, fixed length and fixed GC content (http:// www.faculty.ucr.edu/~mmaduro/random.htm), random selection from a given sequence (http://www.dave‒reed.com/Nifty/randSeq. html), and random peptide generation with defined amino acid composition to output into FASTA format (https://web.expasy.org/ randseq/). MacStAn aims to generate random nucleotide sequences for a pre‒defined GC content and dinucleotide composition, allowing for maximal base repetitions and user‒defined constant regions. Being a desktop application developed for classic Mac OS, MacStAn can be considered obsolete. RANDNA is a Windows desktop application developed in Borland Delphi for the generation of fixed length random nucleotide or amino acid sequences from a given frequency. Random ORF is a web tool to generate a random nucleotide sequence with a single open reading frame. NullSeq is a command‒line random sequence generator implemented in Python, which is able to generate random nucleotide or amino acid sequences from a given frequency or source sequence. Being a command‒line tool that writes the results into a FASTA file, NullSeq can be easily incorporated into analysis pipelines/tools.9‒12","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82972495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational annotation of protein function","authors":"H. Nadeem","doi":"10.15406/mojpb.2018.07.00233","DOIUrl":"https://doi.org/10.15406/mojpb.2018.07.00233","url":null,"abstract":"The term biological function of a protein is a little bit ambiguous. The exact meaning of this term varies and depends upon the context in which it is used. The term protein function is a broader term 3 and has more than one aspect. There are several computer-based tools which can be used for in silico prediction of protein function just out of protein sequence. While using a protein function prediction tool, it is important to consider which functional aspect is to be predicted.4","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76970145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Towards better internet bandwidth subscription in plateau state university","authors":"D. K. Aristarkus","doi":"10.15406/MOJPB.2018.07.00232","DOIUrl":"https://doi.org/10.15406/MOJPB.2018.07.00232","url":null,"abstract":"The abundance of Internet bandwidth of a Local Area Network (LAN), in Gigabit/sec, with minimal latency (less than 1ms) and also, if the packets drop rate was minimized, makes the throughput to be relatively high. When a number of users become far higher than the available bandwidth, latency, delay in traffic delivery becomes unavoidable. In this case the applications are fast with the performance regarded as good,1 with low latency. It is important to investigate if there has been better bandwidth subscribed for and also if the ISPs have been better ones. Internet service problems2 could be emanating from the quality of Internet bandwidth and also the trust-worthiness of the ISPs. Studying the effect of quality bandwidth and reliable ISPs, which has impact on the performance of the network3 is necessary in this study.","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74325243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extraction of gluten from food material","authors":"S. Bathula, B. Ravishankar, Pujar Basayya Gullaya","doi":"10.15406/mojpb.2018.07.00234","DOIUrl":"https://doi.org/10.15406/mojpb.2018.07.00234","url":null,"abstract":"Primarily, “gluten” (from Latin for “glue”) has been defined as “the rubber-like proteinaceous mass that remains, when wheat dough is washed with water or salt solution to remove soluble constituents and starch granules”. The procedure of wheat gluten preparation was first described by Beccari in 1745 and is nowadays widely used for the industrial isolation of “vital gluten”, a byproduct of wheat starch production. Gluten is a protein fraction from wheat, maida, barley, oats or their crossbred varieties and derivatives thereof, to which some people are intolerant and that is insoluble in water and 0.5 M NaCl. These proteins that naturally occur in a prohibited grain and that may cause adverse health effects in persons in celiac disease. Some food processing procedures increase gluten’s solubility, but do not necessarily diminish the protein fraction’s harmful effect.1‒5","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78457877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A computational approach of antibiotics as novel drug target for Japanese encephalitis virus NS helicase/nucleoside triphosphatase","authors":"M. Nath, B. Deb","doi":"10.15406/mojpb.2018.07.00231","DOIUrl":"https://doi.org/10.15406/mojpb.2018.07.00231","url":null,"abstract":"Japanese encephalitis (JE) is an arthropod-borne viral disease of global public health importance. The disease is prevalent in Southeast Asia and the Pacific.1 However, scientific evidence suggests that JE will soon become a global pathogen and cause of worldwide pandemics.2 JE causes the central nervous system (CNS) disease with irreversible neurological damage in humans.3 Annually 13,600 to 24,400 deaths due to acute JE infection are recorded. JE survivors with an annual report of 14,300 to 24,400 cases develop long-term neuropsychological sequelae.4 JE is caused by Japanese encephalitis virus (JEV) which belongs to genus Flavivirus under family Flaviviridae. JEV is transmitted to humans through the bite of infected Culex species mosquitoes.5 However, there is no effective antiviral therapy and only a few highly effective vaccines are licensed for human use. The search for antiviral products becomes very important. Virtual screening has repeatedly proven to be useful to meet the special challenges of antiviral drug discovery.","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86538231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of various parameters on bioenergy generation in microbial fuel cell","authors":"An, Parkash","doi":"10.15406/MOJPB.2018.07.00229","DOIUrl":"https://doi.org/10.15406/MOJPB.2018.07.00229","url":null,"abstract":"Microbial Fuel Cells (MFCs) are a sustainable energy technology with minimal carbon footprint, which is promising for wastewater remediation and generation of useful amounts of electricity.1 Microbial Fuel Cells (MFCs) are bio-electrochemical devices whose constituent electro-active bacteria harvest electrons and protons by oxidizing organic matter. Electrons travel through the anode to the cathode electrode via an external load, and cat ions diffuse through a cat ion exchange membrane that separates the anode with the cathode. Atmospheric oxygen in the cathode reacts with the incoming electrons and protons to produce water2 Miniaturization of MFCs has been reported in the literature as a more efficient way of generating electricity3 and can be utilized for powering small devices.4 Microbial fuel cells (MFCs) can convert organic matter into electricity. In contrast to conventional fuel cells, MFCs have particular advantages such as high energy-conversion efficiency and mild reaction conditions (e.g., ambient temperature, normal pressure, and neutral pH). Moreover, MFCs can convert numerous kinds of organic matters into electricity. These organic compounds include simple carbohydrates, such as glucose,5 acetate and butyrate,6 and complex organic compounds such as those in swine wastewaters,7 domestic wastewater,8 and manure sludge waste generated a maximum electrical current of roughly 60 lA and several hundred of millivolts by connecting graphite foil electrodes in an aerated aerobic zone to those in an anaerobic sludge zone. The feasibility of directly converting sewage sludge into electricity via an MFC was in part demonstrated.","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77326930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}