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MRMPath, a system which processes protein sequences to create theoretical masses of peptide and their peptide fragments following digestion of the protein was developed. Experimentally, these fragments are created using enzymes prior to being processed in a mass spectrometer. In MRMPath, these fragments are created theoretically. MRMPath can process protein sequences from three different sources:...
Biological signal and image processing (BSIP) constitutes a major field of interest in both educational aspects and research environments in biomedical engineering. In fact, the physiological knowledge improvement in a wide variety of innovative research as well as the implementation in many clinical procedures extensively makes use of these concepts in more or less sophisticated medical applications...
Cervical cancer is multi-factorial disease comprising both genetic and environmental components. Human papillomavirus is considered to be a major etiological factor for the development of cervical cancer. HPV type 16 is the most prevalent HPV accounting for more than 70% of cervical cancer cases in India, followed by HPV type 18 and other high-risk types. However, an infection with HPV is essential...
To construct recombinant clone of glutathione S-transferase (GSTs) of Schistosoma japonicum (Sj) and express recombinant SjGSTs protein with his-tag that could be purified by single-step Ni2+-NTA affinity chromatography, one pair of primers was designed according to the sequence of GSTs gene. The DNA fragment of PGEX-KG GSTs gene was amplified by PCR with template PGEX-KG. Then it was cloned into...
Nucleotides and amino acids are basic building units of RNA, DNA and protein. Although intensive studies on understanding how the change of these building blocks affect the phenotypes of these biopolymers are ever increasing, many popular alignment formats are generated by pairwise comparision tools such as the Basic Local Alignment Search Tool (BLAST). These alignments are user friendly to researchers...
The amy gene from schwaniomyces occidentalis which encodes a secretory alpha amylase isolated by primers that designed from sequences derived from Gene bank. The isolated gene is then cloned into a p426gpd vector. After cloning, the recombinant vector was transformed into E.Coli DH5x strain and recombinant vector was sent for sequencing by T7, T3 and a mid primer. After sequencing, the sequence of...
This paper is a report on the migration of the molecular docking application, “Autodock” to NVIDIA CUDA. Autodock is a Drug Discovery Tool that uses a Genetic Algorithm to find the optimal docking position of a ligand to a protein. Speedup of Autodock greatly benefits the drug discovery process. In this paper, we show how significant speed up of Autodock can be achieved using NVIDIA CUDA. This paper...
Selecting informative genes from microarray gene expression data is the most important task while performing data analysis on the large amount of data. Mining genes having regulatory relations within thousands of genes is essential. To fit this need, a number of methods were proposed from various points of view. However, most existing methods solely focus on gene expression values themselves without...
β-ketoacyl-ACP synthetase II (KAS II) which catalyzes the elongation of 16:0-ACP to 18:0-ACP, determines the ratio of palmitic acid (16:0) to stearic acid (18:0). Using Rapid Amplification of cDNA Ends (RACE) and a peanut cDNA library we had previously constructed, we isolated a 1867bp cDNA of the KAS II gene containing a 1212bp complete open reading fragment (ORF). Sequence analysis revealed that...
Kosteletzkya virginica is a halophyte species which could be used for production of industrial raw material such as biodiesel and for developing ecologically sound saline agriculture as well as for tideland soil improving. Using Rapid Amplification of cDNA Ends (RACE) method, a 1610 bp cDNA of stearoyl-ACP desaturase (SAD) gene containing a 1188 bp complete open reading fragment (ORF) was firstly...
The DPV UL46 gene( GenBank accession No. EU195108) isolated by our laboratory was amplified by PCR and cloned into pMD18-T vector. The recombinant plasmid pMD18-T-UL46 was identified by PCR, restriction enzymes (BamHI+XhoI), sequencing and nucleic acid dot-hybridization. Then the gene was analyzed by bioinformatics tools. The results showed that a 2220bp complete open reading frame of 739 amino acids...
The genetic bi-stable switch (toggle switch) consists of two genes which repress one another through their synthesised proteins. In the stochastic bi-stable case, the toggle switch exhibits noise induced flips. Using simulation based techniques, we identified three methods for reducing the random flipping probability, namely: (i) increasing the system size, (ii) increasing the synthesis rate, and...
The protein synthesised from the C/EBPβ gene interacts specifically with a C/EBP-recognition sequence and acts as a transcriptional activator. It plays a key role in lipometabolism and therefore is considered as a candidate gene for goose fat liver forming. In order to get the sequence, four pairs specificity primers were designed for amplification of C/EBPβ gene in Landes geese. The fragments of...
Abstract-An open reading frame (ORF) containing 675 nucleotides was got by sequencing the DEV gene libraries constructed by our laboratory. The ORF was identified as DEV UL45 gene by aligning with gene bank database using the software of BlastN and ORF Finder. Specific primers were designed and PCR products containing this ORF were cloned into the vector of PMD18-T. Dot blot confirmed the UL45 gene...
Gene regulatory networks are highly complex dynamical systems of biomolecular components - genes, mRNA, proteins. These components interact with each other and through those interactions determine gene expression levels, i.e., determine the rate of gene transcription to mRNA and, consequently, the rate of mRNA translation to proteins. In this paper, a particle filter with MCMC move step is employed...
Embryonic stem cells (ESCs) hold promise either as an in vitro model recapitulating early embryonic development or as a renewable source of therapeutically useful cells. However, 2D culture system, which is still generally utilized in ESCs differentiation strategies, has greatly impeded our learning more information about ESCs proliferation/differentiation in situ. Here, a high aspect ratio vessel...
In this paper we study the asymptotic stability of neutral functional differential equation (NFDE) model of genetic regulatory networks (GRNs) with time-varying delays. It is assumed that time varying delays belong to the predefined intervals. SUM regulatory logic was used for the modeling of the effects from other genes. We consider not only time delayed concentration of messenger ribonucleic acid...
The cell functions and development are regulated by complex networks of genes, proteins and other components by means of their mutual interactions. These networks are called gene regulatory networks (GRNs). GRNs are used to reveal the fundamental gene regulatory mechanisms, to determine the reasons for many diseases and interactions between drugs and their targets. The introduction of experimental...
Causal structure discovery is an important problem in protein sequences and gene-gene interaction in gene expression data, which will reveal the elementary structure of the protein sequence and the gene-gene interaction by the expression level of genes within the cell. In this paper, we investigate the feature--based causal structure learning methods for protein sequence and gene expression data respectively...
Embryonic stem (ES) cells are exposed to fluid-mechanical forces, such as cyclic strain and shear stress, during the process of embryonic development, but much remains to be elucidated concerning the role of fluid-mechanical forces in ES cell differentiation. Here we show that cyclic strain induces vascular smooth muscle cell (VSMC) differentiation in murine ES cells. Flk-1- positive (Flk -1+) ES...
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