140,369 research outputs found
Prediction of Single-Stage Limit Language and Adult Language via Yusof-Goode Approach
No full textYusof-Goode (Y-G) rule, a new symbolization of representing rule in splicing system under framework of formal language theory to model the recombinant behaviors of DNA molecules, was introduced by Yusof in 2012. A language that contains the strings resulting from a splicing system is called splicing language. Limit language is a subset of splicing language where it is restricted to the molecules that will be present in the system after the reaction has run to completion. Adult language is a subset of limit language where it does not participate in further splicing. In this paper, the new concept of single stage splicing languages is introduced and some theorems have been formulated to stipulate the final state product of single stage limit languages of Yusof-Goode splicing system based on the characteristic of one initial string andone rule
Persistency And Permanency of Two Stages DNA Splicing Languages with Respect to One Initial String and Two Rules Via Yusof-Goode (Y-G) Approach
No full textThe notion of Yusof-Goode (Y-G) splicing system was first schemed by Yusof to study the relationship between formal language theory and molecular biology. The splicing languages that are produced by splicing system have some important characteristics called persistent and permanent. In biological perspective, the recombinant DNA molecules can be manipulated by recombination action if they have persistent property. Thus, the persistency as well as permanency of splicing languages (recombinant DNA molecules) is considered to be an interesting topic in the field of DNA recombination, particularly when the recombination process is accomplished at second stage. Conducting a wet-lab experiment to show the mentioned properties of splicing languages are time consuming and expensive. Therefore, to overcome this problem, mathematical approach is chosen to investigate the persistency and permanency of splicing languages which will be then given as theorem and corollary. Thus, an initial string (with two recognition sites) and two rules are considered for introducing the above characteristics using Y-G approach
Differentiating the Persistency and Permanency of Some Two Stages DNA Splicing Language via Yusof-Goode (Y-G) Approach
No full textPredicting the existence of restriction enzymes sequences on the recombinant DNA fragments, after accomplishing the manipulating reaction, via mathematical approach is considered as a convenient way in terms of DNA recombination. In terms of mathematics, for this characteristic of the recombinant DNA strands, which involve the recognition sites of restriction enzymes, is called persistent and permanent. Normally differentiating the persistency and permanency of two stages recombinant DNA strands using wet-lab experiment is expensive and time-consuming due to running the experiment at two stages as well as adding more restriction enzymes on the reaction. Therefore, in this research, by using Yusof-Goode (Y-G) model the difference between persistent and permanent splicing language of some two stages is investigated. Two theorems were provided, which show the persistency and non-permanency of two stages DNA splicing language
Modelling the Behaviour of Single Stage Splicing Language: A Yusof Goode Computational Approach
No full textYusof-Goode (Y-G) splicing system is a formal characterization of the generative capacity of specified enzymatic activities acting on DNA molecules with new extension symbolization of representing rule. The output of Y-G splicing system can be categorized into three types of single stage splicing language namely active persistent, transient and inert persistent language. It is both money and time consuming to conduct laboratory experiments to determine the behaviour of splicing language. Hence, research has been conducted to predict the characteristic of single stage splicing language based on limit adjacency matrix computational modelling in order to optimize time and money. The utilization of software programming has been developed through Visual Basic Software for scientists to determine the behaviour of single stage splicing language as well as the number types of resulted DNA molecules restricted to at most two strings and two rules with one cutting site. The output from the program was found to match the outcomes of wet lab experiments
Persistency and permanency of two stages splicing languages via Yusof-Goode approach: two initial strings and two rules
No full textThe notation of representing restriction enzymes in the form of double-triple in order to formulate Yusof-Goode (Y-G) splicing system was mathematically proposed by Yusof in 2012. The aim of introducing Y-G splicing system was to study the process of recombinant deoxyribonucleic acid or DNA strand in a translucent way. In real situation, when the recombination action occurs, the recombinant DNA strands which will arise often contain the patterns of the restriction enzymes. Persistency and permanency are two properties of splicing system, which show whether the recombinant DNA strands will be split by the existence of restrictions enzymes or not if the reaction goes to the second stage. In this research, the persistency and permanency of two stages splicing languages according to the number of cutting sites of initial strings as well as crossing sites and context factors of splicing rules are investigated. Therefore, a Y-G splicing system consisting of two initial strings (with two cutting sites) and two rules is used to present the above properties of two stages DNA splicing languages
Two Stages Splicing System
No full textThe study of the biological process of deoxyribonucleic acid (DNA) splicing system in a translucent approach was investigated in 2012 by Yusof under the framework of formal language theory. In this work, the concepts of splicing system in two stages as well as splicing languages are mathematically and biologically discussed. Additionally, some theorems based on recognition site factor of initial strings at the existence of two initial strings and two rules are provided via Yusof-Goode (Y-G) approach. Besides, an example is also given in showing the biological meaning of the introduced concept
Some Relations Between Two Stages DNA Splicing Languages
No full textA new symbolization of Yusof-Goode (Y-G) rule, which is associated with Y-G splicing system, was introduced by Yusof in 2012 under the framework of formal language theory. The purpose of this investigation is to present the biological process of DNA splicing in a translucent way. In this study, two stages splicing languages are introduced based on Y-G approach and some relations between stage one and stage two splicing languages are presented, given as theorems. Additionally, the existing relations between two stages splicing languages based on crossings and contexts of restriction enzymes factors with respect to two initial strings (having two cutting sites) and two rules are presented as subset
Persistency and permanency of two stages splicing languages based on DNA recombination process by using Yusof-Goode (Y-G) approach
No full textThe study of the biological process of deoxyribonucleic acid (DNA) splicing was investigated by Yusof in 2012 as a translucent approach under framework of formal languages theory. The investigation was achieved by proposing a new symbolization representing the rule in splicing system called Yusof-Goode (Y-G) rule associated with Y-G splicing system. A laboratory experiment is usually performed to show the DNA splicing process under the existence of restriction enzyme and appropriate ligase. This laboratory experiment is time consuming process and it can incur a lot of expenses. In addition, to accomplish the reaction up to two stages the generating recombining DNA molecules must have persistency concept. Thus, to overcome this problem, mathematical approach via Y-G model is applied to introduce the new concept of splicing system at two stages with respect to two initial strings and two rules. Furthermore, the existence relation between the families of stage one and stage two splicing languages are investigated. In this investigation, some sufficient conditions for persistency and permanency of two stages DNA splicing languages according to the number of cutting sites of initial strings and properties of rules are provided. The de Bruijn graph is used to predict the persistency and permanency of two stages splicing languages. A user friendly interface as an alternative of wet-lab experiment is coded using Microsoft Visual C Sharp (C#) to predict the persistency and permanency, and the relations between two stages (stage one and stage two) splicing languages
The concepts of persistent and permanent in non semi-simple DNA splicing system
No full textThe investigation on the behavior of deoxyribonucleic acid (DNA) splicing languages has been of interest of many biologists and mathematicians. Yusof-Goode (Y-G) splicing system has been introduced for the purpose of showing the transparent biological process of DNA splicing systems. In this paper, the approach of Y-G splicing system is applied in presenting the persistency and permanent characteristics of non semi-simple DNA splicing system of Type I and Type II
Effects of fatty acids on inflammatory markers studied in vivo and in vitro
No full textInflammation involves interactions amongst many different cell types as a defense mechanism of the body. Inflammation is also involved in cardiovascular disease (CVD). The role of long chain n-3 polyunsaturated fatty acids (LC n-3 PUFAs) in modulating the inflammatory response has been proposed. The aim of these studies is to investigate the effects of modest intakes of n-3 PUFAs on CVD risk factors especially inflammatory markers, including soluble adhesion molecules, in adult humans with and without CVD and to identify the effects of selected fatty acids, including eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), on inflammatory responses, especially adhesion molecule expression in cultured human endothelial cells of different origin (fetal vs. adults; vein vs. artery).In the first in vivo study, healthy middle-aged men aged 35-60 years were randomized to 1.8 g/d EPA plus 0.23 g/d DHA (n = 9) or placebo oil (2.6 g/day medium-chain saturated fatty acids; n = 11) for 8 weeks. In a second in vivo study, patients awaiting carotid endarterectomy were randomised to 0.8 g/d EPA plus 0.67 g/d DHA (Omacor; n = 47) or olive oil (n = 53) as placebo for between 7 and 102 days until surgery. Supplementation with fish oil in healthy men resulted in a 363% increase in EPA and only a 13% increase in DHA in plasma phosphatidylcholine (PC). On the other hand, Omacor supplementation resulted in significantly increased EPA and DHA in plasma PC by 161% and 70%, respectively. In healthy subjects, there was very little effect of n-3 fatty acids on the risk factors measured (lipid profiles and inflammatory markers), apart from a reduction in plasma soluble intercellular molecule-1 (sICAM-1) concentration compared with placebo (P = 0.05). The change in plasma sICAM-1 concentration was significantly inversely associated with the change in DHA in plasma PC (r = -0.675; P = 0.001). Supplementation with Omacor, however, significantly decreased total plasma cholesterol, triacylglycerol (TAG) and LDL-cholesterol concentrations (P < 0.001) by 13%, 14%, and 5% respectively. In terms of inflammatory markers, supplementation with Omacor significantly decreased sE-selectin by 23% (P = 0.006) and sVCAM-1 by 25% (P < 0.0001), and had no significant effects on other plasma inflammatory markers including sICAM-1 even though trends toward decreases in these markers were observed. This study suggests some anti-inflammatory actions of moderate dose of Omacor in carotid endarterectomy patients. Based on correlation analysis between mRNA expression of inflammatory markers in plaque and plasma concentrations, it seems that soluble inflammatory markers cannot be used to reflect the expression of these molecules at the cell surface, i.e. in the vasculature or in the plaque.In the in vitro experiments the inflammatory stimulus lipopolysaccharide (LPS) up-regulated all three adhesion molecules studied at the protein (as assessed by ELISA) and the mRNA (as assessed by reverse transcription and real-time PCR) levels. VCAM-1 was affected by fatty acids to a greater extent than ICAM-1 or E-selectin. Amongst the fatty acids, DHA has the greatest and the most consistent effects on adhesion molecule protein expression. EPA was also a potent fatty acid inhibitor of adhesion molecule expression at the mRNA level. Some effects of stearic, oleic and arachidonic acids on adhesion molecules were also seen. The effects of fatty acids on the adhesion molecule expression were fatty acid, adhesion molecule and endothelial cell specific. The inhibitory effects of fatty acids were more pronounced in vein endothelial cells than arterial endothelial cells. The precise underlying mechanism on how fatty acids affect adhesion molecule expression remains to be clarified
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