Colored Petri Net: Its application to Sucrose Biosynthesis Pathway in Plasmodium falciparum

Sucrose plays major role as macromolecule used in organisms including Plasmodium falciparum (P.f.) to generate glucose for energy production in the glycolysis pathway. A metabolic pathway is a series of chemical reactions, which goes through various intermediate compounds to transform input compounds into a product. In this work, we modelled a metabolic pathway in Plasmodium falciparum using Colored Petri Net Markup Language (CPNML). The model was used to examine the dynamic behavior of the sucrose biosynthesis pathway which shows the interactions between the metabolites and the reactions in the sucrose biosynthesis pathway of Plasmodium falciparum. We further analyzed the model for its structural and quantitative properties using Petri Net theory. Our model gives more insight to the structure of the pathway and helps to improve our understanding of the biological processes within this pathway.Keywords: Sucrose, Colored Petri Net, Plasmodium falciparu

Soft Clustering Technique on Academics Performance Evaluation

Clustering techniques are  unsupervised learning methods  of mining complex and multi-dimensional data sets such that observations in the same cluster are similar in some sense.  The  student  academic  performance  evaluation  problem  can  be  considered  as  a clustering problem where clusters are formed on the basis of students intelligence. Choosing the  right  clustering  technique  for  a  given  dataset  is  a  research  challenge.  Therefore,intelligence-based  grouping  is  essential  for  maintaining  the  homogeneity  of  the  group; otherwise it would be difficult to provide good educational recommendation to the highly diverse  student  population.  Homogenous  grouping  of  students  with  similar  result  ranking into   classes  would  further  make  student  academic  performance  analysis  detailed  and sufficient  for  recommendation.  Grouping  of  students  using  Fuzzy  C-Means  (FCM) techniques  with  the  level  of  their  degree  of  membership  into  different  clusters  allows  for overlapping of boundaries and resolve sharp boundary  problems  as opposed to crisp-based method. FCM technique will reveal the degree of membership trend in the clusters which is the focus of this work. In  this work, we implemented Soft clustering technique (Fuzzy CMeans)  in  C++  for  student  academic  performance  analysis.  This  will  proffer recommendations that will enhance student performance

Assessment of Plasmodium Falciparum RNA Pseudouridylate Synthase (Putative) as Novel Drug Target

Malaria is a major public health problem associated with high mortality, morbidity rates and undue economic burden in sub-Saharan countries. Presently, every year, 300 to 500 million people suffer clinically from malaria and 90% of them in sub-Saharan Africa. About 1.5 to 3 million people die of malaria every year and 85% of these occur in Africa. One child dies of malaria somewhere in Africa every 20 second, and there is one malarial death every 12 sec somewhere in the world. This is also a damaging economic burden for these sub-Saharan Africa countries as huge work force time and resources are expended for treatment. Plasmodium falciparum (hence forth Pf) is the most severe of all the human malaria parasites. This organism is continuing to develop resistance to all known drugs and therapeutic regime. One of the mechanisms of resistance in Pf is the modification of the drug target. Hence, it is expedient to continuously discover novel drug targets in Pf and to discover or develop new drugs against such targets. Drug-able signaling pathways have been shown to have inherent mechanism capable of deterring drug resistance. Using computational techniques, we have identified some proteins in the signaling pathways of Pf as putative targets for anti-plasmodia drug. RNA pseudouridylate synthase, which also plays a key role in RNA synthesis and ribosomal function, is one of such proteins. Initial virtual screening of this enzyme against drug and chemical databases has been performed to identify compounds that can inhibit this enzyme. This led us to compounds which inhibit nucleotide metabolism. This is a work in progress whose current state is hoped for presentation at this conference. In order to determine the identified compounds IC50, the identified compounds will be screened in vitro against the enzyme. We have currently completed the establishment of the enzyme functionally expression in E. coli and purification. Thereafter, the drugs will be screened for their anti-plasmodia activity using cultured Pf and the IC50 for each drug will be determined. In order to assess their safety, the selectivity index of compounds that showed in vitro anti-plasmodia activity will be determined using human cultured cell lines. The last stage of this study will involve screening the compounds in an in vivo mouse model of malaria. It is hoped that the result of this study will prove this enzyme as a novel target for antimalarial drug. And provide as input, critical drug targets in to our established Structure Based Drug Design (SBDD) pipelin

Colored Petri Net: Its application to Sucrose Biosynthesis Pathway in Plasmodium falciparum

Sucrose plays major role as macromolecule used in organisms including Plasmodium falciparum (P.f.) to generate glucose for energy production in the glycolysis pathway. A metabolic pathway is a series of chemical reactions, which goes through various intermediate compounds to transform input compounds into a product. In this work, we modelled a metabolic pathway in Plasmodium falciparum using Colored Petri Net Markup Language (CPNML). The model was used to examine the dynamic behavior of the sucrose biosynthesis pathway which shows the interactions between the metabolites and the reactions in the sucrose biosynthesis pathway of Plasmodium falciparum. We further analyzed the model for its structural and quantitative properties using Petri Net theory. Our model gives more insight to the structure of the pathway and helps to improve our understanding of the biological processes within this pathway.Keywords: Sucrose, Colored Petri Net, Plasmodium falciparu

Implementation of Secured Message Transmission using DES and RSA Cryptosystem

In the past, Cryptography was used in keeping military information, diplomatic correspondence secure and in protection of national security. Nowadays, the range of cryptography applications have been expanded a lot in the modern area after the development of communication means; cryptography is essentially required to ensure that data are protected against penetrations. This is used to ensure that the contents of a message are confidentially transmitted and would not be altered. In this paper, we have implemented a cryptosystem (encrypting/decryption) for text data using both Data Encryption Standard (DES) and Rivest-Shamir-Adleman (RSA) cryptosystem. The asymmetric algorithm was used for the key encryption and decryption process because it provides a means to deliver keys on a secure channel, while the data to be sent will be encrypted and decrypted using the symmetric algorithm. This system was designed to accomplish a number of security features such as authentication, confidentiality, integrity, and non-repudiation. Also the combination of the speed and strength of the symmetric algorithm with the robustness and key management capability of the asymmetric algorithm, thereby producing an enhanced encryption algorithm and we employed text data as our experimental data.Key words: Cryptography, encrypion, decryption, cryptosyste

Modeling of the Glycolysis Pathway in using Petri Nets

Malaria is one of the deadly diseases, which affects a large number of the world's population. The Plasmodium falciparum parasite during erythrocyte stages produces its energy mainly through anaerobic glycolysis, with pyruvate being converted into lactate. The glycolysis metabolism in P. falciparum is one of the important metabolic pathways of the parasite because the parasite is entirely dependent on it for energy. Also, several glycolytic enzymes have been proposed as drug targets. Petri nets (PNs) have been recognized as one of the important models for representing biological pathways. In this work, we built a qualitative PN model for the glycolysis pathway in P. falciparum and analyzed the model for its structural and quantitative properties using PN theory. From PlasmoCyc files, a total of 11 reactions were extracted; 6 of these were reversible and 5 were irreversible. These reactions were catalyzed by a total number of 13 enzymes. We extracted some of the essential reactions in the pathway using PN model, which are the possible drug targets without which the pathway cannot function. This model also helps to improve the understanding of the biological processes within this pathway

Implementation of Secured Message Transmission using DES and RSA Cryptosystem

In the past, Cryptography was used in keeping military information, diplomatic correspondence secure and in protection of national security. Nowadays, the range of cryptography applications have been expanded a lot in the modern area after the development of communication means; cryptography is essentially required to ensure that data are protected against penetrations. This is used to ensure that the contents of a message are confidentially transmitted and would not be altered. In this paper, we have implemented a cryptosystem (encrypting/decryption) for text data using both Data Encryption Standard (DES) and Rivest-Shamir-Adleman (RSA) cryptosystem. The asymmetric algorithm was used for the key encryption and decryption process because it provides a means to deliver keys on a secure channel, while the data to be sent will be encrypted and decrypted using the symmetric algorithm. This system was designed to accomplish a number of security features such as authentication, confidentiality, integrity, and non-repudiation. Also the combination of the speed and strength of the symmetric algorithm with the robustness and key management capability of the asymmetric algorithm, thereby producing an enhanced encryption algorithm and we employed text data as our experimental data.Key words: Cryptography, encrypion, decryption, cryptosyste

Cluster analysis of Plasmodium RNA-seq time-course data identifies stage-specific co-regulated biological processes and regulatory elements [version 1; referees: 1 approved, 2 approved with reservations]

In this study, we interpreted RNA-seq time-course data of three developmental stages of Plasmodium species by clustering genes based on similarities in their expression profile without prior knowledge of the gene function. Functional enrichment of clusters of upregulated genes at specific time-points reveals potential targetable biological processes with information on their timings. We identified common consensus sequences that these clusters shared as potential points of coordinated transcriptional control. Five cluster groups showed upregulated profile patterns of biological interest. This included two clusters from the Intraerythrocytic Developmental Cycle (cluster 4 = 16 genes, and cluster 9 = 32 genes), one from the sexual development stage (cluster 2 = 851 genes), and two from the gamete-fertilization stage in the mosquito host (cluster 4 = 153 genes, and cluster 9 = 258 genes). The IDC expressed the least numbers of genes with only 1448 genes showing any significant activity of the 5020 genes (~29%) in the experiment. Gene ontology (GO) enrichment analysis of these clusters revealed a total of 671 uncharacterized genes implicated in 14 biological processes and components associated with these stages, some of which are currently being investigated as drug targets in on-going research. Five putative transcription regulatory binding motifs shared by members of each cluster were also identified, one of which was also identified in a previous study by separate researchers. Our study shows stage-specific genes and biological processes that may be important in antimalarial drug research efforts. In addition, timed-coordinated control of separate processes may explain the paucity of factors in parasites

Soft Clustering Technique on Academics Performance Evaluation

Clustering techniques are  unsupervised learning methods  of mining complex and multi-dimensional data sets such that observations in the same cluster are similar in some sense.  The  student  academic  performance  evaluation  problem  can  be  considered  as  a clustering problem where clusters are formed on the basis of students intelligence. Choosing the  right  clustering  technique  for  a  given  dataset  is  a  research  challenge.  Therefore,intelligence-based  grouping  is  essential  for  maintaining  the  homogeneity  of  the  group; otherwise it would be difficult to provide good educational recommendation to the highly diverse  student  population.  Homogenous  grouping  of  students  with  similar  result  ranking into   classes  would  further  make  student  academic  performance  analysis  detailed  and sufficient  for  recommendation.  Grouping  of  students  using  Fuzzy  C-Means  (FCM) techniques  with  the  level  of  their  degree  of  membership  into  different  clusters  allows  for overlapping of boundaries and resolve sharp boundary  problems  as opposed to crisp-based method. FCM technique will reveal the degree of membership trend in the clusters which is the focus of this work. In  this work, we implemented Soft clustering technique (Fuzzy CMeans)  in  C++  for  student  academic  performance  analysis.  This  will  proffer recommendations that will enhance student performance

Simulation and analysis of pentose phosphate pathway in Plasmodium falciparum using colored petri nets model

No AbstractKeywords: Plasmodium falciparum, metabolic pathway, Colored Petri Net, Pentose phosphate pathwa