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Glossary of scientific and technical terms in bioengineering and biological engineering
Published in Megh R. Goyal, Scientific and Technical Terms in Bioengineering and Biological Engineering, 2018
Conserved sequence is an identical or highly similar sequence of nucleotides or amino acids which occurs as part, or all of a number of different genes or proteins, in either the same or different species.
Potency matters: Impacts of embryonic exposure to nAChR agonists thiamethoxam and nicotine on hatching success, growth, and neurobehavior in larval zebrafish
Published in Journal of Toxicology and Environmental Health, Part A, 2022
Shayla Victoria, Megan Hein, Elisabeth Harrahy, Tisha C King-Heiden
In-silico molecular docking models were produced in the software program, Maestro (Schrödinger, LLC, New York, NY, 2020), to evaluate interactions of TM compared to NIC in the nAChR of a vertebrate model (Homo sapiens). Human nAChR was used in the model because fish nAChR protein files are not available. However, the nAChR binding site is thought to be a conserved sequence across most vertebrates and functions as a proxy for pharmacological models (Papke et al. 2012). The three-dimensional structure of the nAChR protein (PDB ID: 6PV7; Gharpure et al. 2019) was obtained from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB; Berman et al. 2000). The chemical structures of TM and NIC were obtained from the ZINC database (Sterling and Irwin 2015). Protein and ligand preparation were conducted in Maestro using Schrödinger’s user guides (Schrödinger, LLC, New York, NY, 2020). Grid generation was performed using the binding site of crystallized NIC as reference. Glide ligand docking was conducted for both compounds. After docking was completed, state and ionization penalties, which quantify how energetically favorable the docked states are, docking and GlideScores, approximations of binding affinity and strength, and ligand interaction diagrams (LID), which display interactions between specific amino acids and ligand were generated through the program.
The Crotalaria juncea metal transporter CjNRAMP1 has a high Fe uptake activity, even in an environment with high Cd contamination
Published in International Journal of Phytoremediation, 2018
Tsugumi Nakanishi-Masuno, Nobukazu Shitan, Akifumi Sugiyama, Kojiro Takanashi, Shoko Inaba, Shuji Kaneko, Kazufumi Yazaki
Total RNA (2.5 μg) was extracted from C. juncea leaves using an RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA) and reverse-transcribed (RT) to cDNA with SuperScript III RNase H − reverse transcriptase (Invitrogen, Carlsbad, CA, USA) according to the manufacturers’ instructions. The cDNA fragments of CjNRAMP1 were amplified by polymerase chain reaction (PCR), using KOD Plus DNA polymerase (Toyobo, Osaka, Japan), a degenerate primer designed from the conserved sequence of several plant NRAMPs (forward primer 0, 5′-ACBATHACHGGNACDTAYGCBGG-3′) and a polyA reverse primer. To amplify the full-length CjNRAMP1-coding sequence, specific primers were designed from the internal sequences of the CjNRAMP1 fragments (forward primer 1, 5′-GGGGTACCATGGCTAC TGGGCAACCACAG-3′ and reverse primer 1, 5′-CCCTCGAGTCAGTCAAGGTCCACGACAG-3′), with the underlined sequences representing KpnI and XhoI sites for subsequent subcloning. Subsequently, 5′- and 3′-RACE were performed using a Gene Racer Kit (Invitrogen), according to the manufacturer’s protocol. During the process of cloning CjNRAMP1 cDNA (Accession No. AB586740), CjNRAMP2 cDNA (Accession No. AB586741) was isolated as a homologous clone.
Polyclonal antibody production against rGPC3 and their application in diagnosis of hepatocellular carcinoma
Published in Preparative Biochemistry and Biotechnology, 2018
Shenghao Wang, Muhammad Kalim, Keying Liang, Jinbiao Zhan
Glypican-3 (GPC3), a member of the glypican family, is composed of a membrane-associated protein core substituted with various heparan sulfate chains. The core protein of GPC3 is encoded by the GPC3 gene located at q26.2 of human X chromosome. It possesses 40 kDa N-terminal and 30 kDa C-terminal proteins. This protein has a conserved sequence of 14 cysteine residues, so it is easy to form disulfide within the molecule.[1] It also has two heparin sulfate chains at C-terminal near cell membrane.[2] GPC3 is overexpressed in 70% of HCC tissues but does not express in benign liver lesions, cirrhosis, hepatitis, or healthy adult tissues. So, GPC3 has been used as immunohistochemical markers for distinguishing HCC with benign liver lesions[3] because GPC3 can be cleaved from GPI anchoring site from the outer surface of the cell membrane and enter the bloodstream.[4] Clinical and laboratory studies revealed that GPC3-positive HCC patients have a lower survival rate than GPC3-negative HCC patients and showed the high potency of GPC3 in the prognosis of primary liver cancer.