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Psychrophilic Microbiomes
Published in Ajar Nath Yadav, Ali Asghar Rastegari, Neelam Yadav, Microbiomes of Extreme Environments, 2021
The major requirement for application of data mining and statistical comparative approaches is the availability of psychrophilic protein sequences and structures. Authentic structural data for psychrophilic protein sequences can be obtained from Protein Data Bank (PDB) (Berman et al. 2000). The corresponding sequences can be accessed from either the PDB itself or from the NCBI protein database (https://www.ncbi.nlm.nih.gov/protein/), while the complete proteome and genome sequences can be downloaded from the NCBI ftp repository (ftp://ftp.ncbi.nlm.nih.gov/genomes/). Specialized databases such as, Prokaryotic Growth Temperature database (PGTdb) (Huang et al. 2004) provides the growth temperature data of extremophilic organisms. PGTdb classifies each organism in its database based on Optimal Growth Temperature (OGT), psychrophilic organisms being classified as having OGT less than 20°C. Another notable database which has found its value in protein stability and engineering studies is the ProtDataTherm (Pezeshgi Modarres et al. 2018). It consists of protein family-wise categorization of extremophilic protein sequences including psychrophiles. Full genome and metagenomic sequences of psychrophilic organisms can also be retrieved from databases such as Genomics Online Database (GOLD) (Mukherjee et al. 2018), MGRAST (Wilke et al. 2016), ENA (Leinonen et al. 2011) and IMG/M (Chen et al. 2017). The basic flow for an in silico approach for psychrophilic protein analysis is depicted in Fig. 10.1.
Assessment of Quercetin Isolated from Enicostemma Littorale Against Few Cancer Targets: An in Silico Approach
Published in A. K. Haghi, Ana Cristina Faria Ribeiro, Lionello Pogliani, Devrim Balköse, Francisco Torrens, Omari V. Mukbaniani, Applied Chemistry and Chemical Engineering, 2017
The mammalian target of rapamycin (mTOR) also known as mechanistic target of rapamycin or FK506 binding protein 12-rapamycin associated protein 1 (FRAP1) is a protein encoded by FRAP1 gene. mTOR is a serine/ threonine protein kinase that regulates cell growth, cell proliferation, cell motility, cell survival, protein synthesis, and transcription. mTOR belongs to the phosphatidylinositol 3-kinase-related kinase protein family. mTOR integrates the input from upstream pathways, including insulin, growth factors (such as IGF-1 and IGF-2), and amino acids. mTOR also senses cellular nutrient and energy levels and redox status. The mTOR pathway is dysregulated in human diseases, especially in certain cancers. Rapamycin is a bacterial product that can inhibit mTOR by associating with its intracellular receptor FKBP12. The FKBP12-rapamycin complex binds directly to the FKBP12-rapamycin binding (FRB) domain of mTOR. mTOR is the catalytic subunit of two molecular complexes.4
Protein Expression Methods
Published in Jay L. Nadeau, Introduction to Experimental Biophysics, 2017
You wish to make several milligrams of the photoswitchable fluorescent protein Dronpa. This is available commercially in a bacterial expression vector without any tags. The first step is to subclone the gene into the appropriate expression vector with a tag or tags of choice. A simple affinity tag will be fine; there is no need to use antibodies to detect this protein, because it is so fluorescent. Because this is a soluble protein related to the green fluorescent protein family, there is no reason to think that it will not express well in bacteria. So you decide to use the expression vector pEColi-Nterm-6xHN (Clontech), which has a His-tag followed by an enterokinase cleavage site for future removal of the protein (Figure 5.11). Ensure that the Dronpa gene is cut out of its parent vector with a restriction enzyme that puts it in frame with the tag. If such a site does not exist, use polymerase chain reaction (PCR) to amplify the Dronpa fragment in such a way that it can be inserted in frame.
Establishment of hairy root system of transgenic IRT1 brassica campestris L. and preliminary study of its effect on cadmium enrichment
Published in International Journal of Phytoremediation, 2023
Xiaoyu Liu, Wenxuan Li, Menghua Wang, Yushen Cao, Teng Zhang, Honggang Hu, Xiyu Cheng, Qiong Yan
Nowadays, the removal of environmental pollutants through hyperaccumulator plants and phytoremediation have been recognized as environmentally friendly and cost-effective sustainable technologies. However, hyperaccumulators often have defects such as low biomass, slow growth, strong regionality and long repair time (Feki et al.2021). In order to accelerate the application of phytoremediation technology and understand the molecular mechanism of hyperaccumulator, We hope to transform hyperaccumulators by genetic manipulation. The uptake and translocation of non-essential heavy metals in plant are always through metal transporters for essential micronutrient transport, including NRAMP, ZIP (Zrt- and Irt-related protein), heavy metal P-type ATPases, and YSL (Yellow Stripe-Like) transporters (Wang et al.2019). IRT1 is a member of the ZIP (zinc regulated transporter) protein family. Arabidopsis IRT1 was first discovered and cloned, and showed a diversity of metal ion absorption. Many researchers have proved that the IRT1 gene can alleviate metal toxicity through up-regulation under Cd stress condition according to comparative transcriptome analysis (Chen et al.2019; Yu et al.2018).
Toxicological and pharmacokinetic properties of sucralose-6-acetate and its parent sucralose: in vitro screening assays
Published in Journal of Toxicology and Environmental Health, Part B, 2023
Susan S. Schiffman, Elizabeth H. Scholl, Terrence S. Furey, H. Troy Nagle
Three additional genes, SHMT2, ATF3 and carbohydrate sulfotransferase 3 (CHST3), were also markedly expressed by sucralose-6-acetate with 81.23, 54.49, and 9.26-fold elevation relative to untreated control. SHMT2 encodes a key mitochondrial enzyme, serine hydroxymethyltransferase-2, that catalyzes the reaction of serine to glycine that is found in high concentrations in intestinal epithelial cells. SHMT2 initiates lymphoma development through epigenetic tumor suppressor silencing (Parsa et al. 2020), drives the progression of colorectal cancer (Cui et al. 2022; Liu et al. 2021), potentiates the aggressive process of oral squamous cell carcinoma (Zheng et al. 2022) and promotes tumorigenesis in rhabdomyosarcoma (Nguyen et al. 2021). ATF3 encodes a member of the mammalian activation transcription factor/cAMP responsive element-binding (CREB) protein family of transcription factors. ATF3 is a marker of oxidative stress (Ketola et al. 2012) and plays a role in modulation of metabolism, immunity, and oncogenesis (Yin et al. 2008; Ku and Cheng 2020). The carbohydrate sulfotransferase 3 (CHST3) gene encodes an enzyme (chondroitin 6-O-sulfotransferase 1 or C6ST–1) that plays a role in the formation of chondroitin 6-sulfate (MedlinePlus 2023). Chondroitin 6-sulfate is involved in development and maintenance of the skeleton as well as naïve T lymphocytes (Uchimura et al. 2002). Chondroitin 6-sulfate expression is upregulated in human glioma cells, and this upregulation is correlated with glioma malignancy (Pan et al. 2020).
In vitro chemo-protective effect of Eisenia foetida coelomic fluid against histone deacetylase inhibitor-induced oxidative toxicity in breast cancer cells
Published in International Journal of Environmental Health Research, 2022
Asuman Deveci Özkan, Janiah Alimudin, Yasemin Kilciler, Burcu Yuksel, Ozlem Aksoy, Zeynep Betts
The protein encoded by Bax belongs to the Bcl-2 protein family and functions as an apoptotic activator (Lessene et al. 2008). The Bax gene is an apoptosis inducer and overexpresses Bcl-2 in cancerous tissues. If proapoptotic proteins are present in a cell, the cell is more prone to apoptosis. If antiapoptotic proteins are abundant, they are less prone to apoptosis (Zhang et al. 2000). Bax is proapoptotic, while Bcl-2 is antiapoptotic. (Opferman and Kothari 2018; Alam et al. 2019). Therefore, the intracellular Bcl-2/Bax ratio is extremely important in determining whether the cell will go to apoptosis. If Bax is high, the cell will go to apoptosis; if Bcl-2 is high, apoptosis will be inhibited. The data we obtained determined that the mRNA level of Bax increased, and the expression levels of Bcl-2 decreased after only NaBu treatment. We can say that the expression levels of Bax and Bcl-2 genes related to apoptotic cell death remained unchanged in MCF-7 cells exposed to NaBu after pre-treatment with ECF, indicating that ECF has a chemoprotective effect in MCF-7 cells.