Nm-Nano: Predicting 2′-O-methylation (Nm) Sites in Nanopore RNA Sequencing Data

Nm (2′-O-methylation) is one of the most abundant modifications of mRNAs and non-coding RNAs occurring when a methyl group (–CH3) is added to the 2′ hydroxyl (–OH) of the ribose moiety. This modification can appear on any nucleotide (base) regardless of the type of nitrogenous base, because each ribose sugar has a hydroxyl group and so 2′-O-methyl ribose can occur on any base. Nm modification has a great contribution in many biological processes such as the normal functioning of tRNA, the protection of mRNA against degradation by DXO, and the biogenesis and specificity of rRNA. Recently, the single-molecule sequencing techniques for long reads of RNA sequences data offered by Oxford Nanopore technologies have enabled the direct detection of RNA modifications on the molecule that is being sequenced, but to our knowledge there was only one research attempt that applied this technology to predict the stoichiometry of Nm-modified sites in RNA sequence of yeast cells. To this end, in this paper, we extend this research direction by proposing a bio-computational framework, Nm-Nano for predicting Nm sites in Nanopore direct RNA sequencing reads of human cell lines. Nm-Nano framework integrates two supervised machine learning models for predicting Nm sites in Nanopore sequencing data, namely Xgboost and Random Forest (RF). Each model is trained with set of features that are extracted from the raw signal generated by the Oxford Nanopore MinION device, as well as the corresponding basecalled k-mer resulting from inferring the RNA sequence reads from the generated Nanopore signals. The results on two benchmark data sets generated from RNA Nanopore sequencing data of Hela and Hek293 cell lines show a great performance of Nm-Nano. In independent validation testing, Nm-Nano has been able to identify Nm sites with a high accuracy of 93% and 88% using Xgboost and RF models respectively by training each model with Hela benchmark dataset and testing it for identifying Nm sites on Hek293 benchmark dataset. Thus, Nm-Nano outperforms the Nm sites predictors existing in the literature (not relying on Nanopore technology) that were only limited to predict Nm sites on short reads of RNA sequences and unable to predict Nm sites on long RNA sequence reads. By deploying Nm-Nano to predict Nm sites in Hela cell line, it was revealed that a total of 196 genes was identified to have the most abundance of Nm modification among all other genes that have been modified by Nm in this cell line. Similarly, deploying Nm-Nano to predict Nm sites in Hek393 cell line revealed that a total of 196 genes line was identified to have the most abundance of Nm modification among all other genes that have been modified by Nm in this cell line. According to this, a significant enrichment of a wide range of functional processes like high confidences (adjusted p-val < 0.05) enriched ontologies that were more representative of Nm modification role in immune response and cellular homeostasis were revealed in Hela cell line, and "MHC class 1 protein complex", "mitotic spindle assembly", "response to glucocorticoid", and "nucleocytoplasmic transport" were revealed in Hek293 cell line. The source code of Nm-Nano can be freely accessed https://github.com/Janga-Lab/Nm-Nano.

Methylation of 2-Aryl-2-(3-indolyl)acetohydroxamic Acids and Evaluation of Cytotoxic Activity of the Products

2-Aryl-2-(3-indolyl)acetohydroxamic acids demonstrate promising antitumor activity, but quickly metabolize in vivo via glucuronidation of hydroxamic acid residue. In an attempt to improve their pharmacokinetics, methyl esters were synthesized via a newly developed protocol for chemoselective mono-methylation of hydroxamic acids. The cytotoxicity of these derivatives against the HeLa cell line was evaluated and found to be inferior compared to the parent lead compounds.

A study on ER stress-induced apoptosis pathway in cervical cancer HeLa cells treated with biosynthesized gold nanoparticles

Background The expression of apoptotic family of protein plays a major role in induction of programmed cell death. There are six major apoptotic proteins such as Caspase 12, Bcl 2, BAX, Cytochrome c, PARP3 and Mcl1. All these proteins have crucial role in the regulation of apoptosis through mitochondrial degradation, DNA damage, nuclear condensation and eventually cell death of the cancerous cells. It was observed that the apoptotic pathway has been initiated in the cancer cells from the expression of the apoptotic proteins. The results emphasized that the apoptotic cell death has been induced by the nanomaterials against cervical cancer HeLa cell line. Methods Initially, the nanomaterials were individually checked for potential anticancer activities through MTT assay. The cervical cancer HeLa cell line was treated with nanoparticles, nanoconjugates, nano-dox conjugate and chitosan–nano-dox conjugates. The cell lysates were processed for SDS–PAGE followed by Western blotting. The apoptotic expression has been studied for six major apoptotic proteins such as Caspase 12, Bcl 2, BAX, Cytochrome c, PARP3 and Mcl 1. Results In the present study, the biosynthesized gold nanoparticles, nanoconjugates, nano-dox conjugate, chitosan–nano-dox conjugate were treated against cervical cancer HeLa cell line. The results demonstrated anticancer effects of the nanocompounds implying nanoparticles induced apoptotic pathway in the cancer cells. Further apoptotic expression was studied for six major apoptotic proteins such as Caspase 12, Bcl 2, BAX, Cytochrome c, PARP3 and Mcl 1. The present study was focussed on anticancer efficiency of biosynthesized nanomaterials. Conclusions The in vitro anticancer study showed that the nanomaterials induced cell death over the treated cervical cancer cells. In the process of apoptotic cell death, the caspase cascade pathway was activated. The gene expression was checked in line with some of the genes involved in apoptosis, cell death. The expression was checked for Caspase 12, BAX, Bcl2, cyt c, PARP3 and Mcl 1. The expression of apoptotic proteins suggested that the cancer cell death was mediated through ER stress-induced pathway involving the major apoptotic proteins.

L’héritage d’Henrietta Lacks

Many developments in biology and biotechnology have relied on the HeLa cell line, originally derived in 1951 from a Black cancer patient without her knowledge. This origin became generally known at the turn of the century, and the patient’s descendants have sought and obtained some recognition and some control but little compensation. They have now retained two famous attorneys to sue a biotech firm for very extensive damages, with more legal action planned against other companies. This may have important repercussions for the biotech industry, and raises complex issues regarding ownership of biological material and compensation to patients from whom these materials have been obtained.

Total phenolic and flavonoid contents, cytotoxic, immunomodulatory and anti-inflammatory potential of whole plant of Astragalus creticus (Fabaceae)

Purpose: To determine total phenolic and flavonoid contents, as well as the cytotoxic, immunemodulatoryand anti-inflammatory potentials of the whole plant of Astragalus creticus (Fabaceae).Methods: Folin-Ciocalteu (FCR) method was used for determination of total phenolic and flavonoid contents of the methanol and dichloromethane extracts of Astragalus creticus. The cytotoxic potential of the extracts on 3T3 and HeLa cell lines were evaluated using MTT assay. Brine shrimp larvae mortality was determined by lethality bioassay, while inhibitory effects were determined on mouse fibroblast (3T3)and cervical cancer (HeLa) cell lines. In vitro immunomodulatory and in vivo anti-inflammatory effectswere assessed using reactive oxygen species (ROS) chemiluminescence and formalin-induced rat paw edema assays, respectively.Results: Dichloromethane extract had higher contents of phenolics (TPC = 324.75 ± 2.47 mg GAE/g) and flavonoids (TFC = 95.51 ± 0.82 QE/g) than the methanol extract (TPC = 79.82 ± 1.53 mg GAE/g, TFC = 56.11 ± 0.93 QE/g). The dichloromethane extract exhibited high cytotoxic andimmunomodulatory potentials, with 76.66 % mortality in brine shrimp lethality bioassay and 83.9 % inhibition (IC50 = 18.0 ± 1.1 μg/mL) in chemiluminescence assay. The extract also resulted in 22 and 13 % inhibition of viability of HeLa and 3T3 cells, respectively, while the methanol extract produced 13 % inhibition of both cell lines. The methanol extract produced very significant anti-inflammatory activity,with a maximum of 49 % inhibition of paw edema at a dose of 160 mg/kg (p < 0.01).Conclusion: These results suggest that the dichloromethane and methanol extracts of Astragalus creticus (Fabaceae) exert cytotoxic, immunomodulatory and anti-inflammatory effects. These findings provide scientific validation for the traditional medicinal use of the Astragalus genus.