Introduction:
Since the past decade, the next generation sequencing (NGS) technologies have developed the whole genome analysis field (1). The rapid development in NGS methods provide large sequencing data for each patient (3). Next generation sequencing technology enables generation of millions of DNA fragments in parallel which lead to produce a new era in medical genomics (2). These technologies have been involved in several studies including; RNA sequencing, bisulfite sequencing, DNA target, resequencing, Chromatin Immunoprecipitation sequencing, MethylCap-seq and others (3). NGS have enumerous developed platforms such as illumina/Solexa, SOLID, 454 pyrosequencing, Pacific Bio, and Ion Torrent Sequencing (5). In 2009, a study showed that NGS technologies have been applied to invistigate mRNA expression, genome sequence variations, post transcriptional and post translational (5). -----------
RNA Sequencing:
RNA-Seq is technique that allows to quantify gene expession patterns for RNA profiling dependent on NGS (4). Before RNA-Seq methodology has been used, scientists were using Microarray technique for gene expression study (4). RNA sequencing framework enables to examine the presence of all RNAs in a study sample, differentiating their sequences as well as determing their abundances simultaneously. RNA-Seq method takes place to any of many various techniques of NGS applied for gaining whole transcriptome profiles of RNA that can be explored in cell, tissue and other multicellular organisms (5). In addition, all of NGS technologies can be applied for RNA sequencing method. Each of these technologies or aggregation of them have been used as distict RNA-Seq technologies. Despite they share the same concept to produce RNA seq...
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...matics strategies exist to measure gene expression through different examination samples in the RNA-Seq method. There are several methods are emplyed for calculating differential gene such as Reads per Kilobase of Exon per Million of Mapped reads, upper-quartile and Trimmed Means of M Values. To quantify relatively significant differential gene expression, Empirical Bayesian method, Bayesian methods and Negative binominal distribution stategies can be performed (5).
However, using bioinformatics in RNA-Seq can analyze Single Nucletide Ploymorphism for example; Sequence Alignment Map is a general desgin for collecting and saving the alignmets of large nucleotide sequence which is then utilized for SNP analyses. The following steps for determing SNPs is dependent on converting SAM to Binary Variant Call Format file and then BFC file to Variant Call Format file (5).
Using PCR and Gel Electrophoresis to Determine Genotype. In certain situations, it is necessary to identify DNA retrieved from a sample. When there is a small sample in need of identification, Polymerase Chain Reactions are used to multiply the DNA. in the sample in many identical samples.
Many people feel that biology has become more advanced than physics. Biology has in fact become the new focus of the future as we tend to use it a lot in our daily lives. The study of Biotechnology is known as the branch of molecular biology that studies the use of microorganisms to perform specific industrial processes. This study shows that our lives can be transformed.
When James Watson and Francis Crick discovered the structure of DNA in 1959, they could not have known that their discovery would one day lead to the possibility of a human factory that is equipped with the capabilities to mass produce perfectly designed, immortal human beings on a laboratory assembly line. Of course, this human factory is not yet possible; genetic technology is still in its infancy, and scientists are forced to spend their days unlocking the secret of human genetics in hopes of uncovering cures for diseases, alleviating suffering, and prolonging life. In the midst of their noble work, scientists still dream of a world—a utopia—inhabited by flawless individuals who have forgotten death and never known suffering. What would become of society if such a utopia existed? How will human life be altered? Leon Kass, in Life, Liberty and the Defense of Dignity: The Challenge for Bioethics, acknowledges genetics technology’s greatness, and applauds it for its invaluable, benevolent contributions to mankind. However, Kass argues that if left to their devises and ambitions, geneticists—with the power of their technology—will steal away society’s most precious asset; genetic technology will rob society of its humanity. Genetic technology can, and will, achieve great things, but unless it is regulated and controlled, the losses will be catastrophic and the costs will far exceed the benefits.
"Polymerase Chain Reaction (PCR) Fact Sheet." National Human Genome Research Institute. 10 Dec. 2007. National Institutes of Health. .
Segal, E. A., Cimino, A. N., Gerdes, K. E., Harmon, J. K., & Wagaman, M. (2013). A
Proteogenomics is a kind of science field that includes proteomics and genomics. Proteomic consists of protein sequence information and genomic consists of genome sequence information. It is used to annotate whole genome and protein coding genes. Proteomic data provides genome analysis by showing genome annotation and using of peptides that is gained from expressed proteins and it can be used to correct coding regions.Identities of protein coding regions in terms of function and sequence is more important than nucleotide sequences because protein coding genes have more function in a cell than other nucleotide sequences. Genome annotation process includes all experimental and computational stages.These stages can be identification of a gene ,function and structure of a gene and coding region locations.To carry out these processes, ab initio gene prediction methods can be used to predict exon and splice sites. Annotation of protein coding genes is very time consuming process ,therefore gene prediction methods are used for genome annotations. Some web site programs provides these genome annotations such as NCBI and Ensembl. These tools shows sequenced genomes and gives more accurate gene annotations. However, these tools may not explain the presence of a protein. Main idea of proteogenomic methods is to identify peptides in samples by using these tools and also with the help of mass spectrometry.Mass spectrometry searches translation of genome sequences rather than protein database searching. This method also annotate protein protein interactions.MS/MS data searching against translation of genome can determine and identify peptide sequences.Thus genome data can be understood by using genomic and transcriptomic information with this proteogenomic methods and tools. Many of proteomic information can be achieved by gene prediction algorithms, cDNA sequences and comparative genomics. Large proteomic datasets can be gained by peptide mass spectrophotometry for proteogenomics because it uses proteomic data to annotate genome. If there is genome sequence data for an organism or closely related genomes are present,proteogenomic tools can be used. Gained proteogenomic data provides comparing of these data between many related species and shows homology relationships among many species proteins to make annotations with high accuracy.From these studies, proteogenomic data demonstrates frame shifts regions, gene start sites and exon and intron boundaries , alternative splicing sites and its detection , proteolytic sites that is found in proteins, prediction of genes and post translational modification sites for protein.
Genetic engineering has been around for many years and is widely used all over the planet. Many people don’t realize that genetic engineering is part of their daily lives and diet. Today, almost 70 percent of processed foods from a grocery store were genetically engineered. Genetic engineering can be in plants, foods, animals, and even humans. Although debates about genetic engineering still exist, many people have accepted due to the health benefits of gene therapy. The lack of knowledge has always tricked people because they only focused on the negative perspective of genetic engineering and not the positive perspective. In this paper, I will be talking about how Genetic engineering is connected to Brave New World, how the history of genetic engineering impacts the world, how genetic engineering works, how people opinions are influenced, how the side effects can be devastating, how the genetic engineering can be beneficial for the society and also how the ethical issues affect people’s perspective.
RNA Interference has been successfully applied in many fields of medicines used to treat issues such as, Parkinson’s and Lung Cancer. One study, sponsored by Alnylam Phar...
Shi, Y., & Zou, M. (2008). Progress in gene therapy research. In J. L. Lewis (ED.), Gene therapy and cancer research progress (pp. 23-130). New York, NY: Nova Science Publishers, Inc.
...ng RNAseq data and different measures of expression similarities. The pairwise comparisons of expression profiles reveal higher similarity between orthologs than between within-species paralogs and between-species paralogs. This study also validates the presence of background noise in expression data when a correlation coefficient is used as measure of expression similarity. However this study can be considered redundant and simplified as it only validates previous findings of Chen and Zhang using similar approaches on same type of data. This study and the studies of Altenhoff et al. and Chen and Zhang are not final proofs for ortholog conjecture. Gene expression data serves only as a proxy for gene function while GO annotations are incomplete and have biases and errors. Hence further studies using complete functional data is necessary to prove ortholog conjecture.
Nevertheless, functional genomics is an area of research which has been widely developed due to microarray technology; providing a wide-scale platform for the analysis of genes.
This paper addresses a currently relevant topic of detection of associations of copy number polymorphism with traits and will be of interest to readers of Genetics Research.
The discovery of genome sequencing by Fredrick Sanger and his team of researchers in the early 70’s gave rise to one of the most empirical research methods that was ever to exist. This revolutionary research technique has allowed scientists to finally encode organisms down to their most basic properties; helping massively in our understanding of pathways, reactions and functions of organisms. The technique involves analysing the DNA of an organism’s genome and therefore all the genes that compose it. The DNA from an organism is run through an electrophoresis gel and the sequence produced is taken up and interpreted by a computer program to then present the nucleotide sequence of the organism. Genome sequencing of pathogenic organisms has lead to huge advancements in the fight against infectious diseases within human and veterinary medicine; three notably virulent infectious diseases of the veterinary world are bluetongue virus, equine strangles and bovine tuberculosis (Goodhead, 2012).
Distinct characteristics are not only an end result of the DNA sequence but also of the cell’s internal system of expression orchestrated by different proteins and RNAs present at a given time. DNA encodes for many possible characteristics, but different types of RNA aided by specialized proteins sometimes with external signals express the needed genes. Control of gene expression is of vital importance for an eukaryote’s survival such as the ability of switching genes on/off in accordance with the changes in the environment (Campbell and Reece, 2008). Of a cell’s entire genome, only 15% will be expressed, and in multicellular organisms the genes active will vary according to their specialization. (Fletcher, Ivor & Winter, 2007).
The Use of Recombinant DNA Technology Recombinant DNA technology is the technology of preparing recombinant DNA in vitro by cutting up DNA molecules and splicing together fragments from more than one organism.(1) This is the process of using recombinant DNA technology to enable the rapid production of human protein from a single gene of insulin. Firstly the single gene required must be isolated. This can be done three ways: Either by working backwards from the protein- Finding the amino acid sequence for the protein needed, the order of bases can be established using known genetic code. New DNA can be made from this sequence of bases resulting in artificial gene made from complementary DNA.