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Naturally Occurring Polymers—Animals
Published in Charles E. Carraher, Carraher's Polymer Chemistry, 2017
It appears that another way to gain complexity is the division of genes into different segments and by using them in different combinations, increasing the possible complexity. These protein coding sequences are known as exons and the DNA in between them as introns. The initial transcript of a gene is processed by a spliceosome that strips out the introns and joins the exons together into different groupings governed by other active agents in the overall process. This ability to make different proteins from the same gene is called alternative splicing. Alternative splicing is more common with the higher species. Related to this is the ability of our immune system to cut and paste together varying genetic segments that allow the immune system to be effective against unwanted invaders.
DNA Structure, Sequencing, Synthesis, and Modification: Making Biology Molecular
Published in Richard J. Sundberg, The Chemical Century, 2017
Humans have 46 chromosomes. There are 22 pairs with one coming from each parent and the XX or XY sex chromosomes. The genes that code for the various proteins are found within these chromosomes. The regions of the genes that code for protein are called exons. Although the sequence of DNA is 99.9% the same for all individuals, there is variation in the remaining 0.1%. One type of variation is called an allele, which is a small variation in a gene that can lead to a characteristic change in structure and function of protein, called a phenotype. Other variations are polymorphisms that have no recognizable effect, either because there is no change in peptide sequence, or because there is no change in protein function. Most of the variations are in introns that do not contain genes. This part of DNA contains short tandem repeats (STR), which are 3, 4, or 5-base sequences that are repeated a number of times. Related individual have very similar sequences in these regions, but that are different from those of unrelated individuals. DNA profiling depends on comparing cleavage patterns from samples of DNA.
A Survey of QSAR Studies
Published in Tanmoy Chakraborty, Lalita Ledwani, Research Methodology in Chemical Sciences, 2017
Seema Dhail, Tanmoy Chakrborty, Lalita Ledwani
DNA acts as the genetic material in each living organism. It consists of billions of nucleotides containing numerous genes, which can express several different types of proteins. DNA consists of exons and introns. Exons are the protein-coding regions, and introns are the noncoding regions. DNA undergoes transcription process and gives rise to mRNA; further, it undergoes translation process that ultimately gives rise to specific proteins. Splice junction sites are also present, and they act as boundaries where splicing occurs. Chanin et al. (2009) developed a computational approach for the recognition of DNA splice junction sites. They transformed the DNA sequences to sequences of binary numbers by converting each nucleotide’s adenine (A), tyrosine (T), guanine (G), and cytosine (C) as 0001, 0010, 0100, and 1000, respectively. Each entry of the data set describes information surrounding the splice junction site, mainly, 15 nucleotides upstream and 32 nucleotides downstream. Approximately 1424 human DNA sequences data set is made by them that is divided into two portions: i) a training set of 1000 sequences and ii) a testing set of 424 sequences. Various types of predictive models were developed using three different types of learning algorithm, which consists of i) self-organizing map, ii) back propagation neural network, and iii) support vector machine.
Nickel induces changes in expression of genes encoding 1-aminocyclopropane-1-carboxylic acid deaminase and glutathione reductase in Picea glauca
Published in Chemistry and Ecology, 2021
Meagan Boyd, Kabwe K. Nkongolo
Two genes that had been associated with nickel resistance in higher plants (GR and ACCD) were targeted to determine the effect of Ni. (Table 1) [16]. Primers flanking these gene sequences were designed based on the P. glauca genome, using the BLAST program to span the exon-exon border of the gene, when possible. The OligoAnalyzer 3.1 program by IDT (https://www.idtdna.com/calc/analyzer) was used to check primer sequences for potential hairpins, self and hetero-dimers. Four housekeeping genes were also designed including alpha tubulin, cyclophilin, E74 Like ETS Transcription Factor 1 (ELF1), and 18S RNA. Alpha tubulin provided the most consistent and reproducible results therefore, it was selected as the housekeeping reference gene for the RT-qPCR experiments.
DNA methylation modifications induced by hexavalent chromium
Published in Journal of Environmental Science and Health, Part C, 2019
Xinnian Guo, Lingfang Feng, Bernardo Lemos, Jianlin Lou
DNA methylation is catalyzed by DNA methyl transferases (DNMTs), which is the process of covalent addition of a methyl group to the carbon-5 position of cytosine (C) to form the fifth base, 5-methylcytosine (5mC), in cytosine–guanine (CpG) dinucleotide.21 The regions of the genome that are rich of CpG sequence are called CpG islands, the length of which has to exceed 200 bp, the CG content in which has to be more than 50%.22 CpGs are most often located in the promoter region of the gene 5 prime and the first exon. CpG sites outside the CpG islands are usually methylated, while those inside the CpG islands are non-methylated. Abnormal methylation of CpG sites can cause diseases, such as genetic diseases and cancers.23–25 The evidence from previous studies showed that DNA hypermethylation of specific gene and genome hypomethylation were both related to carcinogenesis.26–32
A feasible direction algorithm for nonlinear second-order cone programs
Published in Optimization Methods and Software, 2019
Alfredo Canelas, Miguel Carrasco, Julio López
Next, we describe four benchmark datasets that will be used to solve numerically problem (27), these data were scaled to the interval More information on these datasets can be found in the UCI Repository [3]. Wisconsin Breast Cancer (WBC): It contains m=569 tissue samples ( diagnosed as malignant and as benign tumors) described by n=30 continuous features.Pima Indians Diabetes (DIA): It contains m=768 samples ( tested as positive and tested as negative), with n=8 features.German Credit (GC): It presents m=1000 granted loans, good and bad payers in terms of repayment, with n=24 attributes.Splice (SPL): It contains 1000 randomly selected instances (from the complete set of 3190 splice junctions), with labeled as intro-exon and as exon-intron, described by n=60 categorical variables (the gene sequence).