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The Precision Medicine Approach in Oncology
Published in David E. Thurston, Ilona Pysz, Chemistry and Pharmacology of Anticancer Drugs, 2021
Although full genome sequencing can provide the basic nucleotide sequence of an organism’s DNA (Figure 11.5), further analysis is required to interpret the biological or clinical meaning of the sequence. Computational methods for analyzing sequencing data are still being developed and refined within the field of Bioinformatics. As sequencing generates an immense amount of data (for example, there are approximately six billion base pairs in each human diploid genome), the output has to be stored electronically and requires a large amount of computing power and storage capacity. A number of public and private companies are still competing to develop full genome sequencing platforms that are sufficiently robust and reliable to commercialize for both research and clinical use (e.g., Illumina, GE Global Research (General Electric), Affymetrix, and IBM, although there are many others). A commonly referred to commercial target for the cost of sequencing is the “$1,000 genome”. As of 2015, the cost of obtaining a whole-genome sequence was around $1,500. More recently, in 2019, one company (Veritas Inc) claimed to be able to provide a full genome sequence for $600, and predicted that they could reduce the cost to the $100–$200 range by 2021.
ChIP-seq analysis
Published in Altuna Akalin, Computational Genomics with R, 2020
As explained in Chapter 1, gene expression is controlled by a special class of genes called transcription factors - genes which control other genes. Transcription factor genes encode proteins which can bind to the DNA, and control whether a certain part of DNA will be transcribed (expressed), or stay silent (repressed). They program the expression patterns in each cell. Transcription factors contain DNA binding domains, which are specifically folded protein sequences which recognize specific DNA motifs (a short nucleotide sequence). Such sequence binding imparts transcription factors with specificity, transcription factors do not bind everywhere on the DNA, rather they are localized to short stretches which contain the corresponding DNA motif.
Hot topics in medicine
Published in Viyaasan Mahalingasivam, Marc A Gladman, Manoj Ramachandran, Secrets of Success: Getting into Medical School, 2020
Veena Naganathar, Asil Tahir, Pairaw Kader, Omar Chehab
Developments in the field of genetics in the last century have opened many new avenues for research and introduced new directions in the treatment of medical conditions. Traditional methods of therapy revolved around drugs that mimic and manipulate physiological functions in the body, or surgical intervention. After the completion of the Human Genome Project, we now know the chromosome location and nucleotide sequence of many genes. Currently, research is being undertaken to identify the function of these genes and their involvement in diseases. The hope and longterm aim are that a disease can be cured by targeting the root of the error and ‘correcting’ these genes.
Vitamin B12 alleviates malathion-induced toxicity in zebra fish by regulating cytochrome P450 and PgP expressions
Published in Toxicology Mechanisms and Methods, 2023
Subrata Karmakar, Poulami Sen Gupta, Sonali Bhattacharya, Arnab Sarkar, Ashikur Rahaman, Deba Prasad Mandal, Shamee Bhattacharjee
Total RNA was isolated from liver and brain tissue using TRIzol reagent (Invitrogen, Carlsbad, CA) as instructed in manufacturer’s protocol. The purity of RNA samples was checked at 260 and 280 nm spectrophotometrically. Complementary DNAs (cDNA) were prepared by reverse transcription of total RNA using Super Reverse Transcriptase MuLV Kit (Biobharati cDNA synthesis kit, India). qRT- PCR were assembled in light-cycler 96 (Roche Life science). The reaction volume contained sample cDNA template (1:10 or more dilution), both forward and reverse primers and SYBR Green PCR Master Mix (Roche essential master mix). Data was calculated with Roche Lightcycler96 software. Gene-specific (Nucleotide sequences from the gene bank) primer pair (Table 1) was designed with Genescript.com software and self-complementarity was checked by Oligocal software. Relative mRNA levels were measured using the 2-ΔCT method and normalized with β-Actin endogenous reference gene.
Role of tRNA derived fragments in renal ischemia–reperfusion injury
Published in Renal Failure, 2022
Dan Li, Hao Zhang, Xueqin Wu, Qing Dai, Shiqi Tang, Yan Liu, Shikun Yang, Wei Zhang
Using Trizol reagent (Invitrogen life technologies) to isolate total RNA from renal cortex tissue samples according to the manufacturer’s instructions. Before the sequencing experiment, use agarose gel electrophoresis and NanoDrop ND-1000 to check the concentration and purity of each RNA sample. Next, Using rtStar™ tRF&tiRNA Pretreatment Kit (Cat# AS-FS-005, Arraystar) to remove the modification of total RNA. Then, the RNA was reversed to cDNA. Next, polymerase chain reaction amplification was performed. The reaction mixture of the sample was first incubated in the StepOne real-time qPCR system for at 95 °C for 10 min, then 40 PCR cycles (95 °C for 10 s;60 °C for 60 s). Table 1 lists the primer sequences used for RT–qPCR. U6 small nuclear RNA was used for normalization. The actual nucleotide sequence of the candidate tiRNAs is listed in Table 4.
Nucleic acid-based electrochemical biosensors for rapid clinical diagnosis: advances, challenges, and opportunities
Published in Critical Reviews in Clinical Laboratory Sciences, 2022
Abu Hashem, M. A. Motalib Hossain, Ab Rahman Marlinda, Mohammad Al Mamun, Suresh Sagadevan, Zohreh Shahnavaz, Khanom Simarani, Mohd Rafie Johan
As a result, a research focus is to identify specialized bioreceptors. The target should be designed and compared with nucleotide sequences of other genes or species so that the target probe can distinguish it from possible interferences. For the design of a perfect probe, relevant nucleotide sequences can be retrieved from the National Center for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov). The retrieved sequences are aligned using bioinformatics tools such as MEGA software to identify intra-species conserved and inter-species variable regions so the probe sequence that is designed matches completely with target species but has numerous mismatches with non-target species. Finally, the selected probe is checked for specificity between the closely related and distant species using the online Basic Local Alignment Search Tool (BLAST) in the NCBI database (http://blast. ncbi.nlm.nih.gov/Blast.cgi) so that the designed probe will be unique and hybridize with only target sequences. Repeated cycles are carried out until the specified sequence increases exponentially and low-affinity sequences are eliminated. Aptamers are capable of recognizing both small molecules and high-molecular-weight substances as well as complete cells. However, it is worth noting that aptamer commercialization is still in its early stages [103]. Thus, future improvements include developing novel bioreceptors and upgrading existing bioreceptors to cater to commercial needs.