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SARS-CoV-2 and COVID-19
Published in Patricia G. Melloy, Viruses and Society, 2023
Scientists around the world had heard that a virus was spreading in China by early January but had no sequence information, which was critical. The SARS-CoV-2 sequence was released to the world on January 11, 2020, thanks to the Chinese researcher, Zhang Yongzhen, and his colleagues (Cyranoski et al. 2020). One can think of a virus’s sequence as like its birth certificate and passport all rolled into one. Some have described the mutations that a virus accumulates regularly over time as being like the “stamps in a passport” (Christakis 2020). A scientist can look at a viral sequence and compare it to others, determining its last common ancestor with other related viruses, what animal it may have spilled over from, and how long it potentially has been circulating in an area. Geographic data combined with the sequence information can help one track the path of the virus and where it might be headed. As mentioned in the last chapter, this type of sequence analysis is based on the “molecular clock” idea of viral evolution (Holmes 2003; Ho 2008). Other critical scientific articles were published in late January/early February 2020, in which a novel coronavirus was described as the cause of the Wuhan epidemic of respiratory illness. Sequence analysis indicated the virus was 88%–96% identical to a virus isolated from bats, and almost 80% identical to the original SARS-CoV. These researchers also identified the ACE2 receptor as the binding site for the novel coronavirus (Zhou et al. 2020; Lu et al. 2020).
An Analysis of Protein Interaction and Its Methods, Metabolite Pathway and Drug Discovery
Published in Ayodeji Olalekan Salau, Shruti Jain, Meenakshi Sood, Computational Intelligence and Data Sciences, 2022
We can simply say that the hybrid inheritance of two protein interactions in yeast is to be tested and analysed for protein fusion [47]. The aim of Y2H method is to reconsider the interacting protein transcription factor binding. From the hybrid inherited protein A, a transcription factor of the binding DNA field is compounded from the activation domain of the protein B. Suppose in the case of these proteins have interacted, then the reporter gene spot of the activation domain in a suitable location to activate transcription [48]. In computational biology, sequence analysis is the most primitive operation. This operation performs the similarity of the biological sequences, variation of the medical analysis and genome mapping processes [49].
Endotoxemia in Primate Models
Published in Helmut Brade, Steven M. Opal, Stefanie N. Vogel, David C. Morrison, Endotoxin in Health and Disease, 2020
Heinz Redl, Günther Schlag, Soheyl Bahrami
There is now a consensus that endotoxin stimulation of human cells such as monocytes occurs via a reaction cascade, which involves lipopolysaccharide (LPS) binding to serum proteins and CD14. In particular, lipopolysaccharide-binding protein (LBP) interacts with the lipid A component of LPS and facilitates its deliv ery to membrane-bound (or soluble) CD14. The components of this LPS-binding cascade have also been studied in primates. LBP has been both isolated as well as measured from baboon (18,19). LBP was found to increase after both trauma and sepsis in an acute phase reaction with increases in plasma levels similar to C-reactive protein. Baboon LBP was isolated from septic animals with procedures previously described (20), and it was found that it has chromatographic and electro phoretic properties similar to those of its human equivalent. Its similarity is further supported by data from N-terminal sequence analysis.
Danggui Niantong granules ameliorate rheumatoid arthritis by regulating intestinal flora and promoting mitochondrial apoptosis
Published in Pharmaceutical Biology, 2022
Qi-Jin Lu, Jia-Yu Li, Hong-Xin Lin, Yi-Si Cai, Chang-Shun Liu, Li-Ping Fu, Gang Liu, Li-Xia Yuan
Faeces samples were collected randomly from three rats in each group after the last dose and frozen at −80 °C. Intestinal microbial genomic DNA extraction was performed on faecal samples according to the DNA extraction kit instructions. The integrity and purity of genomic DNA were monitored by 1% agarose gel electrophoresis, whereas NanoDropOne was used to assess the concentration and purity of DNA. PCR amplification of the V3V4 region of genomic DNA and product electrophoresis detection were performed. The Gene Tools Analysis Software (Version 4.03.05.0, SynGene) was used to compare the concentration of PCR products, calculate the required volume of each sample and mix the PCR products of each group. An E.Z.N.A.Gel Extraction kit was used to recover PCR products in TE buffer. The NEBNext Ultra DNALibrary Prep kit for Illumina was used with the high-throughput sequencing platform Illumina Hiseq to construct the sequencing library (Guangdong MagiGene Technology Co., Ltd). Sequence analysis and species annotations were performed by bioinformation analysis. OTU cluster analysis to obtain community composition and structure at different levels in each group, analysis of α and β diversity between samples and Pearson correlations between microbiota and mitochondrial apoptosis were calculated using R software based on the OTUs.
Feasibility of oral microbiome profiles associated with oral squamous cell carcinoma
Published in Journal of Oral Microbiology, 2022
Kengo Hashimoto, Dai Shimizu, Sei Ueda, Satoru Miyabe, Ichiro Oh-Iwa, Toru Nagao, Kazuo Shimozato, Shuji Nomoto
Sequence analysis was performed using the Illumina MiSeq sequencer (Illumina Inc., San Diego, CA, USA). Quality filtering was performed by the FASTX toolkit. Sequences that passed quality filtering were merged using the paired-end merge script FLASH. The merged sequences were filtered by fragment length, and only 246–260 bases were used for further analysis. Sequences that passed all filtering were checked for chimeric sequence detection using the USEARCH Uchime algorithm. The non-chimeric sequences were clustered into operational taxonomic units (OTU) using Quantitative Insights into Microbial Ecology (QIIME) with a 97% threshold against reference sequences of the Human Oral Microbiome Database (HOMD, 16S rRNA RefSeq version 15.1). The relative abundances of each oral microbiome were constructed, and group significance of abundances among the saliva samples of the three groups (OSCC, OLK, Post) was tested using Kruskal-Wallis.
A Variant of IL1B Is Associated with the Risk and Blood Lipid Levels of Myocardial Infarction in Eastern Chinese Individuals
Published in Immunological Investigations, 2022
Quanhua Pan, Ding Hui, Chuangxian Hu
Peripheral blood samples (2 mL) were collected and genomic DNA was obtained by use of the TIANamp Blood DNA kit (Tiangen Biotech, Beijing, China). Potential variants (rs1143634 C/T polymorphism) in the IL1B gene were selected from the dbSNP database (https://www.internationalgenome.org/category/dbsnp). PCR-RFLP method was used for the IL1B rs1143634 C/T polymorphism genotyping. The PCR was conducted in a 50 μL reaction volume with 100 ng of genomic DNA, 0.2 mmol/L dNTPs (Invitrogen, USA), 1 U of Taq polymerase, 0.4 mmol/L of each primer, and 2 mmol/L MgCl2 in 10 × PCR buffer (Promega, USA). The PCR products were sequenced by using an ABI 3500 Genetic Analyzer. The sequence data were investigated using the Applied Biosystems sequence analysis software version 5.4. The genotyping accuracy of the IL1B rs1143634 C/T polymorphism was ensured by blind testing, using 5% of the selected samples.