Evaluating the Effect of 3′-UTR Variants in DICER1 and DROSHA on Their Tissue-Specific Expression by miRNA Target Prediction

Untranslated gene regions (UTRs) play an important role in controlling gene expression. 3′-UTRs are primarily targeted by microRNA (miRNA) molecules that form complex gene regulatory networks. Cancer genomes are replete with non-coding mutations, many of which are connected to changes in tumor gene expression that accompany the development of cancer and are associated with resistance to therapy. Therefore, variants that occurred in 3′-UTR under cancer progression should be analysed to predict their phenotypic effect on gene expression, e.g., by evaluating their impact on miRNA target sites. Here, we analyze 3′-UTR variants in DICER1 and DROSHA genes in the context of myelodysplastic syndrome (MDS) development. The key features of this analysis include an assessment of both “canonical” and “non-canonical” types of mRNA-miRNA binding and tissue-specific profiling of miRNA interactions with wild-type and mutated genes. As a result, we obtained a list of DICER1 and DROSHA variants likely altering the miRNA sites and, therefore, potentially leading to the observed tissue-specific gene downregulation. All identified variants have low population frequency consistent with their potential association with pathology progression

High-Level Systemic Expression of Conserved Influenza Epitope in Plants on the Surface of Rod-Shaped Chimeric Particles

Recombinant viruses based on the cDNA copy of the tobacco mosaic virus (TMV) genome carrying different versions of the conserved M2e epitope from influenza virus A cloned into the coat protein (CP) gene were obtained and partially characterized by our group previously; cysteines in the human consensus M2e sequence were changed to serine residues. This work intends to show some biological properties of these viruses following plant infections. Agroinfiltration experiments on Nicotiana benthamiana confirmed the efficient systemic expression of M2e peptides, and two point amino acid substitutions in recombinant CPs significantly influenced the symptoms and development of viral infections. Joint expression of RNA interference suppressor protein p19 from tomato bushy stunt virus (TBSV) did not affect the accumulation of CP-M2e-ser recombinant protein in non-inoculated leaves. RT-PCR analysis of RNA isolated from either infected leaves or purified TMV-M2e particles proved the genetic stability of TMV‑based viral vectors. Immunoelectron microscopy of crude plant extracts demonstrated that foreign epitopes are located on the surface of chimeric virions. The rod‑shaped geometry of plant-produced M2e epitopes is different from the icosahedral or helical filamentous arrangement of M2e antigens on the carrier virus-like particles (VLP) described earlier. Thereby, we created a simple and efficient system that employs agrobacteria and plant viral vectors in order to produce a candidate broad-spectrum flu vaccine

Cajal bodies and their role in plant stress and disease responses

<p>Cajal bodies (CBs) are distinct sub-nuclear structures that are present in eukaryotic living cells and are often associated with the nucleolus. CBs play important roles in RNA metabolism and formation of RNPs involved in transcription, splicing, ribosome biogenesis, and telomere maintenance. Besides these primary roles, CBs appear to be involved in additional functions that may not be directly related to RNA metabolism and RNP biogenesis. In this review, we assess possible roles of plant CBs in RNA regulatory pathways such as nonsense-mediated mRNA decay and RNA silencing. We also summarize recent progress and discuss new non-canonical functions of plant CBs in responses to stress and disease. It is hypothesized that CBs can regulate these responses <i>via</i> their interaction with poly(ADP ribose)polymerase (PARP), which is known to play an important role in various physiological processes including responses to biotic and abiotic stresses. It is suggested that CBs and their components modify PARP activities and functions.</p

Mechanisms of indole-3-acetic and acid biossthesis and the regulatory effects of auxins on antibiotic production in a biocontrol rhizobacerium

Resumen de la comunicación oral presentada en: XXIX Congreso de la Sociedad Española de Microbiología SEM. Microorganismos: un universo en continua evolución. Burgos, España. 25-28 junio (2023)Polyethylene terephthalate (PET) is a versatile, and low-cost polyester with low reactivity properties that has become a key element in modern society. It is used in a wide variety of applications, such as bottles, packaging, and textile fibers. However, the lack of an effective recycling system has led to an alarming accumulation of PET and other plastics in landfills and oceans, posing a significant threat to the environment and human health (1). The main goal of this work is to develop an optimal biocatalyst for the efficient biodegradation of PET into its monomers (terephthalic acid (TPA) and ethylene glycol (EG)). The development of such a biocatalyst could offer a viable and environmentally friendly alternative to existing recycling processes that are either less specific or more contaminant. Our approach involved the combination of two engineering strategies. First, we used Ancestral Sequence Reconstruction (ARS) to infer the protein sequence of a hypothetical ancient hydrolase, using the modern sequence of PET hydrolase from Ideonella sakaiensis (IsPETase) as a reference (2). This strategy allowed us to generate a new set of functional enzymes that retain the spatial structure of IsPETase, yet exhibit significant amino acid sequence changes. The resulting enzymes showed increased robustness and improved stability properties (3). After a preliminary characterization, the putative ancestral enzyme with most promising features was selected as a parental template in a directed evolution campaign to improve its PET-degrading activity. This strategy required the development of a reliable High-Through Put Screening (HTPS) protocol to detect significant improvements among mutants and select the most suitable candidate for industrial applications. The combination of both strategies allowed us to identify regions that have been highly conserved across evolution, as well as regions where novel mutations could potentially enhance PET-hydrolyzing activity.This study was supported through grants from the Spanish Ministry for Science and Innovation/Agencia Estatal de Investigación 10.13039/501100011033 (PID2019-103972GA-I00 to M.A.M., grant PID2020-112612GBI00 to T.K. and PID2020-116261GB-I00 to J.A.G.), the Junta de Andalucía (grant P18-FR-1621 to T.K.) and by NIH Grant 1R35GM131760 (to I.B.Z.

TECHNOLOGY Development of Fatty Acids Obtaining From Soapstok Using Saponification

The processing of oil refining waste is essential from economic and environmental points of view. An important issue is the processing of soapstock to extract fatty acids, which are raw materials for various industries. The two-stage method of fatty acids obtaining from soapstock using saponification with sodium hydroxide solution and decomposition with sulfuric acid is investigated. The peculiarity of the work is the study of the influence of soapstock saponification conditions on the key efficiency indicators of fatty acid extraction: yield and neutralization number. A sample of soapstock was obtained as a result of alkaline neutralization of sunflower oil. Soapstock quality corresponds to DSTU 5033 (CAS 68952-95-4): mass fraction of total fat – 68.5 %, fatty acids – 62.6 %, neutral fat – 5.9 %. Rational saponification conditions were determined: duration (85 min.) and concentration of sodium hydroxide solution (45 %). After saponification, the soapstock was subjected to decomposition with sulfuric acid under the following conditions: temperature 90 °C, duration 40 min. Under the rational saponification conditions, the yield of fatty acids (91.8 %) and the neutralization number (187.1 mg KOH/g) were determined. The obtained fatty acids correspond to the first-grade fatty acids according to DSTU 4860 (CAS 61788-66-7). Acid indicators: mass fraction of moisture and volatile substances – 1.5 %, mass fraction of total fat – 98.0 %, cleavage depth – 69.2 % oleic acid. The use of the soapstock saponification stage before decomposition leads to an improvement in the quality indicators and an increase in the neutralization number of fatty acids by 4 %, yield – by 16.2 %. The results of the study make it possible to produce fatty acids from soapstock by two-stage technology with high yield and neutralization numbe

Protective action of water-soluble fullerene adducts on the example of an adduct with L-arginine

We present radioprotective, antiglycating, and photoprotective properties of a water-soluble C60 fullerene derivative with L-arginine (C60-Arg) and composite films based on collagen containing C60-Arg. The synthesis of these materials is described. The identification of the synthesised materials was carried out using modern physicochemical methods of analysis. The physicochemical properties of aqueous solutions of C60-Arg, such as, particle size distribution, zeta potentials, distribution coefficient in the octan-1-ol–water system were measured. The computer simulation of the process of C60-Arg association in aqueous and isotonic solutions was carried out using Molecular Dynamics. Composite films based on collagen containing C60-Arg demonstrate significant improvement in mechanical properties, cell adhesion, and cell proliferation when the nano-modifier is added. This shows high potential for the use of the C60-Arg adduct in biomedicine

Genome-Wide MicroRNA Analysis Implicates miR-30b/d in the Etiology of Alopecia Areata

Alopecia areata (AA) is one of the most common forms of human hair loss. Although genetic studies have implicated autoimmune processes in AA etiology, understanding of the etiopathogenesis is incomplete. Recent research has implicated microRNAs, a class of small noncoding RNAs, in diverse autoimmune diseases. To our knowledge, no study has investigated the role of microRNAs in AA. In this study, gene-based analyses were performed for microRNAs using data of the largest genome-wide association meta-analysis of AA to date. Nominally, significant P -values were obtained for 78 of the 617 investigated microRNAs. After correction for multiple testing, three of the 78 microRNAs remained significant. Of these, miR-30b/d was the most significant microRNA for the follow-up analyses, which also showed lower expression in the hair follicle of AA patients. Target gene analyses for the three microRNAs showed 42 significantly associated target genes. These included IL2RA , TNXB , and ERBB3 , which had been identified as susceptibility loci in previous genome-wide association studies. Using luciferase assay, site-specific miR-30b regulation of the AA risk genes IL2RA, STX17, and TNXB was validated. This study implicates microRNAs in the pathogenesis of AA. This finding may facilitate the development of future treatment strategie