Embedded Files
innovations and developed biotechnologies
innovations and developed biotechnologies
[1] A Novel Method for gene-specific enhancement of protein translation by targeting 5'UTRs of selected tumor suppressors. Link
[2] Self-transfecting 3’-aminoallyl-containing oligonucleotides (aa-dGoligos) that can penetrate cell membranes without requiring any transfection agents. Link
[3] A new generation of small nucleic acid-based potential therapeutics (~19 nucleotides), termed eRNA, which, in contrast to siRNA or miRNA selectively enhances protein synthesis of specific mRNA variants. These therapeutics are particularly effective for transcripts of genes where protein synthesis efficiency is inherently low or requires enhancement (e.g., tumor suppressors). The invention provides a technical and industrial solution for the selective enhancement of protein synthesis in genes such as TP53, BAX, CDKN2A, CDK4, RB1, NOD2, CHEK2, INBS1, and other genes involved in anti-cancer, anti-viral, or anti-aging pathways where increased protein synthesis efficiency is desired. link
[4] A novel application of vectors containing the CMV promoter (including a non-canonical PPRE element) capable of enhancing self-transcription of a downstream gene (e.g. luciferase) in the presence of PPAR ligands, providing a groundbreaking method for studying these ligands. This application was first introduced in the study by Koronowicz et al., 2020. link
[5] A new approach to monitor the effects of drugs on the movement of cellular microvilli and the velocity of axonal trafficking including RNA-containing neuronal granules. The method utilizes time-lapse video microscopy combined with reflected light microscopy (RLM) under 450 nm blue light. It was used to study the molecular mechanisms of paclitaxel-induced neuropathic pain (PIPN) and utilizes time-lapse video microscopy combined with reflected light microscopy (RLM) under 450 nm blue light (paper in preparation, alongside the published GEO dataset GSE249643) link
[6] An Improved Ocular Impression Cytology Method: Quantitative ocular cell transfer from nitrocellulose to microscope slides using a novel CPP polymer. link
[7] Simplified ex-vivo drug evaluation in ocular surface cells: Culture on cellulose filters of cells obtained by impression cytology. link
[8] A New Screening Jellyfish Model with a simple neuronal system for transient neuromuscular inhibition to assess the anesthetic potential of new drugs. Receptors related to anesthesia (e.g., GRIN1, GRIA1, GABRA1, CHRNA1, OPRM1) are evolutionarily conserved between jellyfish and humans (up to 50% homology), making them suitable for a cost-effective and rapid screening model (methodology paper in preparation).link
[9] New SNaPshot -based genetic diagnostics for rapid (15 minutes on a DNA sequencer) and cost-effective mutation screening in genes associated with various diseases, including: CHRNA3, CHRNA5, GSTP1, GSTM1, and ELA2 (predisposing to lung cancer); RET (thyroid cancer); BRCA1, BRCA2 and NBS1, CHEK2 (breast cancer); LDLR, APOE, and APOB (cardiovascular diseases). These diagnostic methods were successfully implemented in BioTe21 link developed diagnostic tests by disease link
[10] Optimized technology for rapid identification of mitochondrial DNA SNPs (mtDNAtest-SNP module). The carefully selected set of SNPs targets the most hypervariable regions, HVI and HVII. This technology is particularly useful in forensic sciences and genealogical research for constructing family trees. link
[11] SNP-based technology for rapid genetic identification of plant species and microorganisms using rRNA genotyping, providing a precise and efficient method for species differentiation and classification. link
[12] Improvement of a ubiquitin-based protein purification method (for biotech), including the genetically engineered UPB4 protease construct for the efficient purification of N-terminal ubiquitin-tagged insulin (detailed in my engineer’s dissertation, 2004). See Patent no. PL239062B1.
[13] Software for genetic analysis: 1) SNPtester: Automated calculator for analyzing sequencing results, automatically listing SNPs and generating comprehensive conclusions and expertise reports. 2) STRtester: Tool for the automatic analysis of STR (Short Tandem Repeat) variables, with built-in functionality for generating final reports. 3) dGenhancer: A program designed to calculate 5’UTR properties, enabling the design of oligonucleotides triggering gene-specific enhancement of protein translation. link
Selected innovations
Selected innovations
Master A, Wójcicka A, Giżewska K, Popławski P, Williams GR, Nauman A. A Novel Method for Gene-Specific Enhancement of Protein Translation by Targeting 5’UTRs of Selected Tumor Suppressors. PLoS ONE. 2016 May 12; 11(5): e0155359.
The upper panel shows known possible ways to regulate gene expression, including dGoligos (dG1, dG4), also known as eRNA, described for the first time in this paper. The middle and lower panels show an mRNA 5' UTR (blue line) with functional cis-acting elements known to inhibit protein translation (green), which can be enhanced by using synthetic trans-acting factors—dGoligos (dG1, dG4)—designed to target a.1 and 1.3 elements and minimize Gibbs energy-dependent secondary structure formation. For more details see the paper.
The middle panel shows the dGenhancer signal of a THRB 5' UTR mRNA variant, showing three peaks of potential translation inhibitory elements (the best target sites for dGoligos to enhance the translation). The lower panel shows dGoligo (dG) -mediated gene expression changes under in vitro conditions. Effects of each oligonucleotides dG1-dG10 , on in vitro transcription of luciferase reporter constructs (panels a, c) and translation efficiency (b, d), using plasmids containing weakly folded 5'UTR (a, b) or strongly folded 5'UTR in pKS plasmid (c, d). For more details see the paper. See also Translational control in cancer
Master Adam, Wojcicka Anna, Nauman Alicja. The 5’UTR-dependent enhancement of protein translation efficiency triggered by self-transfecting 3’-aminoallyl-containing oligonucleotides (aa-dGoligos) targeting a pool of strongly folded transcript variants of the THRB suppressor gene. Molecular Therapy, Volume 22, Supplement 1, S38. May 2014 (Nature Publishing Group). The 17th Annual Meeting of the American Society of Gene & Cell Therapy, May 21-24, 2014 Washington, DC, USA. Abstract link, and full poster link-1 (academia), link-2 (figshare), link-3
Upper panel shows construction of self transfecting aa-dGoligos. → A. Terminal deoxynucleotidyl transferase –mediated labeling of dGoligos with aminoanllyldUTPs (aa-dGs). B. Coupling of aa-dGs with a positively charged (+) dye (here: Cy5). C. Putative mechanism of binding of positively charged Cy5-aa-dGs to negatively charged Caki-2 cell surface (lower picture).
The upper panel shows effects of 2’-O-methyl RNA-based dGoligos on luciferase transcription levels (left panel) and translation efficiency (right panel) after 6h reaction from pGLA vector (pGL3-based plasmid expressed in eucaryotic cells) are shown normalized to control reaction (dG-). Caki-2 cells were suplemented with ’-O-methyl RNA-based dGoligos or their aminoallyl derivatives (aa-dGs). Results from three independent experiments performed in triplicates (9 repeats of every reaction) were shown as mean % mRNA or luciferase activity ± SD. The Lower panel shows Caki-2 cells with nuclei (marked with red), after transfection with fluorescently labeled, positively-charged 3’-aminoallyl -containing scrambled control (right picture) or dG6 (left picture). The circular structure reflects the first step of nephrogenesis (renal tubule formation) in cells treated with dG6. For more details see the poster. See also Translational control in cancer
Master A, Huang W, Huang L, Li W, Saglam S, Honkanen R, Rigas B. Simplified ex-vivo drug evaluation in ocular surface cells: Culture on cellulose filters of cells obtained by impression cytology. Exp Eye Res. 2021 Dec;213:108827.
Top panel - conjunctiva cells, staining: E&H + IHC of conjunct., S100A8 -brown, Goblet cells - bright pink. Lower panel - Immunofluorescence (IF) staining, ATF4-red + Dapi. For more details see the paper.
Master A, Huang W, Huang L, Honkanen R, Rigas B. An Improved Ocular Impression Cytology Method: Quantitative Cell Transfer to Microscope Slides Using a Novel Polymer. Curr Eye Res. 2022 Jan;47(1):41-50.
For fig. details see the paper.
Top-panel: Proposed chemical interactions underlying the improved IC method. Middle panel: Hematoxylin and eosin-stained human conjunctival cells. Comparison of the quality of pictures taken directly from the IC membrane and from the glass after transfer. Lower panel: Application of the IC transfer method to human oral cavity cells. For more details see the paper.
Koronowicz AA, Master A, Banks P, Piasna-Słupecka E, Domagała D, Drozdowska M, Leszczyńska T. PPAR Receptors Expressed from Vectors Containing CMV Promoter Can Enhance Self-Transcription in the Presence of Fatty Acids from CLA-Enriched Egg Yolks-A Novel Method for Studies of PPAR Ligands. Nutr Cancer. 2020;72(5):892-902.
Non-canonical PPRE element was identified (in silico) in CMV promoter by Adam Master. The promoter was confirmed experimentally and used to test new PPAR ligands by Koronowcz et al. 2020.
Previous method for PPAR ligand studies required double transfection with 2 different vectors, as described by Koronowicz et.al. 2017
sOFTWARE
sOFTWARE
dGenhancer v1 Description
Applications: Identification of cis-acting elements—potential target sites (see maxima peaks below) for dGoligos/eRNA (synthetic trans-acting factors)—designed to enhance protein translation of selected mRNA variants.
SNPtester v1 for automated identification of mutations in tested samples vs reference sequence. The program automatically generates final expertise.
Applications: mtDNA sequence annotations, genealogy, forensic sciences, screening for genetic mutations.
STRtester v1 for automated identification and annotation of STR (Short Tandem Repeats) alleles in tested samples. The program automatically generates final expertise (PDF).
Applications: Forensic sciences, paternity testing, genealogy (Y-STRs, X-STRs), cancer microsatellite instability, MSH, loss of heterozygosity, LOH
Big transcriptome databases—with the functionality of rapid gene expression search across different gene species, cell lines, animal models, and various experiments and conditions.
pRODUCTS
pRODUCTS
Copyright © 2024 Adam Master - All Rights Reserved.
Page updated
Google Sites
Report abuse