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We present an electrical model for the high frequency impedance spectroscopy (HFIS) response of nanoelectrodes to CCMV capsids and full virus biomolecules. The virus electrical and geometrical parameters are extracted from available atomistic descriptions. Simulations of the response at a realistic HFIS CMOS platform suggest that the frequency of optimum sensitivity is within reach of existing designs...
Soft computing technologies are the most efficient technology in the field of Bioinformatics now a days. So many researchers are very keen interested in this topic to find out many unknown facts applying soft computing techniques in the field of DNA RNA alignment, Protein Structure Prediction, Gene mapping etc. Artificial neural network is one of the good techniques for the protein structure prediction...
Prediction of Protein-RNA binding sites is one of the most challenging and intriguing problems in the field of computational biology. Here, we proposed an effectively machine learning algorithm termed PredRBR (Prediction of RNA Binding Residues), using Gradient Tree Boosting algorithm and mRMR-IFS feature selection method in combination with sequence features, structure characteristics and two categories...
Continuous increase in bottlenecks with silicon-based conventional computers inspired researchers around the world to search for a non-conventional computing alternative that led to the development of DNA Computing, Quantum Computing etc. Each computing technologies came with their own advantages and disadvantages. Biology has inspired the computing through the pathway of DNA Computing. Since its...
Information belonging to 3D structures of the proteins, which are the most fundamental macromolecules of life, plays a key role in bioinformatics studies. Protein fold recognition is considered as an important stage to determine 3D structures of the proteins. In this study, subsequence profile map (SPMap) is firstly used in protein fold recognition. The features extracted from each fold class are...
Living organisms are composed of macromolecules like DNA, RNA, proteins, and carbohydrates that dictate various processes. This chapter provides a glimpse of biological macromolecules and their interplay resulting in biological process or pathways.
The information that codes for all proteins in a cell is found on specific segments within the DNA. When a cell requires the function of a particular protein, it must initiate the steps involved in the synthesis of this protein. The overall process is termed gene expression. Transcription is the process whereby the cell makes a copy of the genetic information required to build that particular protein...
The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells. The code maps a tri-nucleotide sequence, called codons, into corresponding amino acids. Since there are 20 amino acids and 64 possible tri-nucleotide sequences, more than one among these 64 triplets can code for a single amino...
The progress of biological data acquisition technologies permit access to more massive, diverse, reliable, and less expensive data. The advent of these new technologies should provide to biologists, answers more accurate and more comprehensive. However, even if there are several work that revolve around regrouping and providing biological data for the biologists, there are still some issues to be...
Gene regulation in eukaryotes is a very complicated and myriad procedure. It is a diverse action which include finding the protein coding regions, locating transcription factor binding sites, promoter identification and determination of cis and trans regulatory elements. Transcription factor binding prediction is very costly using experimental techniques. So computational methods can be used for prediction...
A novel Or83b was cloned from antennae of Heliothis viriplaca (Lepidoptera: Noctuoidea) by using RT-PCR and RACE methods, which was named HvirOr83b (GenBank accession no. JQ394904). The cloning and sequencing results showed that the full-length of open reading frame in HvirOr83b was 1422 bp, encoding 473 amino acid residues with seven transmembrane domains, which shared typical feature of Or83b with...
Amomum villosum Lour. (officinal name Fructus Amomi) is one of the most well-known and authentic herbs in South China. Monoterpenes in its volatile oil are the main medicinal compounds. The condensation of pyruvate with D-glyceraldhyde-3-phosphate to form 1-deoxy-D-xylulose-5-phosphate (DXP) catalyzed by DXP synthase (DXS, EC: 2.2.1.7) and the conversion of DXP to 2-C-methyl-D-erythritol-4-phosphate...
Porcine transmissble gastroenteritis (TGE) is a highly contagious enteric disease of swine caused by transmissible gastroenteritis virus (TGEV). The disease is especislly severe in piglets under two weeks of age, characterized by vomiting, diarrhea and nearly 100% mortality. In this study, the complete genome sequence is available from SC-Y strain isolated in Sichuan province. Sixteen overlapping...
Soil salinity has become the most significant a biotic stress, resulting in inhibition of plant growth and even death. To search a novel molecular mechanism involved in salt stress, the translation initiation factors (eIFs) including eIF1, eIF1A, eIF4, and so on, have been found to have potentials to response salt stress. Increased expression has been found particularly in eIF1 and eIF1A, which both...
Salmonella pullorum was induced using liquid lysogeny broth medium at 4°C into viable but non-culturable (VBNC) state. The activated VBNC genes were screened by mRNA differential display. VBNC bacteria transformed to the spherical-rods or spherical shape and aggregated. Sequence analysis showed two VBNC differential fragments respectively belonged to partial sequences of ATP-dependent RNA unwindase...
The main target of this paper is to propose an algorithm to implement data hiding in DNA sequences to increase the confidentiality and complexity by using software point of view in cloud computing environments. By utilizing some interesting features of DNA sequences, the implementation of a data hiding is applied in cloud. The algorithm which has been proposed here is based on binary coding and complementary...
In nature, living organisms can be viewed as the product of their genotype-phenotype mapping (GP-map). This paper presents a GP-map loosely based on the biological phenomena of transcription and translation, to create a multi-layered GP-map which increases the level of phenotypic variability. The aim of the paper is to examine through the use of a fixed non-trivial GP-map, the impact of increased...
The cDNA of DREB transcription factor named OjDREB1 was obtained from Lilyturf (Ophiopogon japonicus) under the drought stress of 12h by RT-PCR method. Sequence analysis showed that cDNA of OjDREB1 is 1779 bp long, the open reading frame is 1062bp.The predicted protein has 353 amino acids with an estimated molecular mass of 38.69 kDa and an isoelectric point of 6.46. The deduced primary structure...
This study was aimed to isolate ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) from lilyturf (Ophiopogon japonicus). A pair of primers used in amplifying chloroplast fragment from lilyturf was designed according to the corresponding sequences in tobacco, spinach chloroplast genomes. The fragment containing rbcL gene was cloned from lilyturf chloroplast genome. Sequencing analysis...
Class prediction of a protein facilitates to enhance the process of drug discovery. In drug discovery, it is very problematic to find out the complementary protein for each protein individually. But if the class of the protein will be known for which the drug is to be discovered then it will become very smooth to find the complementary protein sequence which can be attached to the active site of the...
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