Reverse-transcription Reaction Research Articles

Optimizing the method for expressing human monoclonal antibodies from a single peripheral blood cell from vaccinated donors

Human monoclonal antibodies are essential diagnostic and research tools and one of the most promising therapeutics. In the past years, single B cell technologies have evolved and over-come conventional methods' limitations, enabling the isolation of scarce B cell populations with desirable characteristics. In this study, we describe a simple and efficient method to isolate anti-gen-specific plasmablasts and memory B cells from hepatitis B virus vaccinated donors' peripheral blood and consequently amplification of immunoglobulin variable region genes. Amplified immunoglobulin variable region genes were cloned into expression vectors and transfected into a human cell line to produce human recombinant monoclonal antibodies. Major challenges in this protocol were isolation of antigen-specific B cells based on surface markers, recovering mRNA from a single cell for efficient amplification, and cloning the correct insert into a desired expression vector. The essential feature of our protocol was the separation of B cells from peripheral blood mononuclear cells before sorting. We identified antigen-specific binding B cells based on the expression of surface markers CD19, CD27, IgG, and binding to hepatitis B surface antigen. Efficient single-cell reverse transcription and polymerase chain reaction (RT-PCR) were achieved using a random primer mix and Kapa Hifi Hot Start Polymerase. Amplification efficiency differed among heavy and light chain variable regions (highest at heavy chain (68 %) and lowest at lambda light chain (22 %)). After co-transfection of HEK293T/17 with successfully cloned heavy and light chain vectors, 70 % of transfected cells produced recombinant monoclonal antibodies at a concentration ∼ 4 μg/ml and 7 % of them showed binding to HBsAg. Human monoclonal antibodies from peripheral blood have advantages over antibodies of mouse origin or phage display libraries, because of their high specificity and self-tolerance. Using the described protocol, we can generate fully human monoclonal antibodies to any other antigen for application in immunotherapy or basic research.

Extracellular vesicle-bound VEGF in oral squamous cell carcinoma and its role in resistance to Bevacizumab Therapy

BackgroundVascular endothelial growth factor (VEGF) is an important proangiogenic factor and has been considered as a key target of antiangiogenetic therapy in oral squamous cell carcinoma (OSCC). However, clinical application of bevacizumab, a specific VEGF antibody, didn’t improve the survival rate of OSCC patients. One possible explanation is that VEGF gene expresses diverse isoforms, which associate with extracellular vesicles (EVs), and EVs potentially contribute to VEGF resistance to bevacizumab. However, clear solution is lacking in addressing this issue.MethodsExpression of VEGF isoforms in OSCC cells was confirmed by reverse transcription and polymerase chain reaction (RT-PCR) and western blot. EVs isolated from OSCC cell’s conditioned medium (CM) were characterized by western blot, transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA). Flow cytometry, immunogold labeling and western blot were applied to study the VEGF on EVs. Tube formation assay and Matrigel plug angiogenesis assay were used for analyzing the angiogenesis capacity of EV-VEGF.ResultsThe most popular isoforms expressed by VEGF gene are VEGF121, VEGF165 and VEGF189. In this study, we demonstrated that all three isoforms of mRNA could be detected at varying levels in OSCC cells, while only VEGF165 and VEGF189 proteins were found. CM derived from OSCC cells, both soluble and non-soluble forms of VEGF could be detected. We further confirmed the presence of VGEF189 bound to EVs as a non-soluble form. EV-bound VEGF189 presented angiogenic activity, which could not be neutralized by bevacizumab. It was found that VEGF189 bound to EVs by heparan sulfate proteoglycans (HSPG). In addition, the angiogenic effect of EV-VEGF could be reversed by surfen, a kind of HSPG antagonist both in vitro and in vivo.ConclusionAntagonists targeting HSPG might potentially overcome the resistance of EV-VEGF to bevacizumab and serve as an alternative for anti-VEGF therapy in OSCC.

DNA methylation profile and expression of the phyllagrin gene in patients with atopic dermatitis: case-control study

Background. Atopic dermatitis (AD) is one of the most common inflammatory skin diseases, affecting up to 20.0% of children and 2.0–8.0% of adults worldwide. Patients with atopic dermatitis usually have dry skin and itching, they are at higher risk of developing asthma, as well as allergic rhinitis. Features of the clinical course of AD are associated with both interaction of genes and influence of environmental factors. Studying epigenetic mechanisms could provide understanding of the most likely mechanisms by which environmental factors influence gene expression and contribute to the development of AD. The aim of the study is to conduct a comprehensive molecular genetic analysis (assessment of the level of global DNA methylation and expression of the filaggrin gene (FLG) in patients with moderate to severe AD. Material and methods: The case-control study was conducted from January 2022, through June 2022. A total of 32 patients with AD and 6 healthy volunteers were recruited. The level of global DNA methylation in the blood of patients with AD and healthy individuals was assessed. The FLG expression was measured by polymerase chain reaction in the leukocyte fraction of blood. A three-stage cycle is used during PCR. To determine the expression level of the FLG gene, total RNA was isolated, followed by a reverse transcription, amplification, and detection reaction. Results. A hypermethylation of the genome in patients with AD is 2.3 times higher than the methylation of genome in controls (p = 0.003),it was also found that the expression level of the FLG gene (exon 3, position 7–8, and exon 1) in the leukocyte fraction of blood in patients with AD did not significantly differ from the control group (p = 0.41). Conclusion. The current study found that the epigenome of AD patients differs from healthy individuals. The study of pathogenetic mechanisms is the basis for the development of new methods of targeted therapy for this socially significant dermatosis.

A Fast and Sensitive One-Tube SARS-CoV-2 Detection Platform Based on RTX-PCR and Pyrococcus furiosus Argonaute.

Since SARS-CoV-2 is a highly transmissible virus, alternative reliable, fast, and cost-effective methods are still needed to prevent virus spread that can be applied in the laboratory and for point-of-care testing. Reverse transcription real-time fluorescence quantitative PCR (RT-qPCR) is currently the gold criteria for detecting RNA viruses, which requires reverse transcriptase to reverse transcribe viral RNA into cDNA, and fluorescence quantitative PCR detection was subsequently performed. The frequently used reverse transcriptase is thermolabile; the detection process is composed of two steps: the reverse transcription reaction at a relatively low temperature, and the qPCR performed at a relatively high temperature, moreover, the RNA to be detected needs to pretreated if they had advanced structure. Here, we develop a fast and sensitive one-tube SARS-CoV-2 detection platform based on Ultra-fast RTX-PCR and Pyrococcus furiosus Argonaute-mediated Nucleic acid Detection (PAND) technology (URPAND). URPAND was achieved ultra-fast RTX-PCR process based on a thermostable RTX (exo-) with both reverse transcriptase and DNA polymerase activity. The URPAND can be completed RT-PCR and PAND to detect nucleic acid in one tube within 30 min. This method can specifically detect SARS-CoV-2 with a low detection limit of 100 copies/mL. The diagnostic results of clinical samples with one-tube URPAND displayed 100% consistence with RT-qPCR test. Moreover, URPAND was also applied to identify SARS-CoV-2 D614G mutant due to its single-nucleotide specificity. The URPAND platform is rapid, accurate, tube closed, one-tube, easy-to-operate and free of large instruments, which provides a new strategy to the detection of SARS-CoV-2 and other RNA viruses.

First Report of Sugarcane Mosaic Virus Infecting Goose Grass in Shandong Province, China.

Sugarcane mosaic virus (SCMV genus Potyvirus, family Potyviridae) can infect maize, sugarcane, sorghum, other graminaceous crops, and some weed species (Alegria et al., 2003; Achon et al., 2007). In August 2023, the leaves of goose grass (Eleusine indica) plants surrounding maize fields in a village of Liaocheng City, Shandong Province, China showed mosaic and chlorotic symptoms (26%, 11 of 43 grasses; Figure S1). Three symptomatic goose grass samples were selected and pooled for total RNA isolation using TRIzol reagent (Tiangen, Beijing, China). A small RNA library was created using 2.0 μg of total RNA and the mirVana miRNA Isolation Kit, followed by size selection (18-28 nt), adapter ligation, purification, reverse transcription (RT), and polymerase chain reaction (PCR) enrichment. High-throughput sequencing (HTS) was then performed on a HiSeq 2500 platform (Illumina, San Diego, CA, USA). The adapter sequences were removed and the reads were assembled de novo into larger contigs using ABySS software v. 1.9.0 with a k-mer of 32. Fifty-one contigs were obtained after the reads were spliced and screened (alignment length > 30 bp; e-value ≤ 0.05). The contigs were compared with viral sequences in GenBank using local BLASTn. Thirty-four contigs (34-64 nt) had the highest identities (97.18-100%) with the SCMV genome sequence, covering approximately 12.8% of the SCMV genome (Table S1). The low coverage of small contigs mapping to the SCMV genome in the HTS results may be attributed to variations in sequencing depth and sample preparation quality, biological aspects of the virus affecting siRNA production and detection, as well as the variability in viral genome and its size (Golyaev et al., 2019; Valenzuela et al., 2022). The other 17 contigs did not align to any plant virus sequences, but aligned to plant sequences, including Phragmites australis and Panicum virgatum. Potyvirus-degenerated primers PotyF (5'-ATGGTHTGGTGYATHGARAAYGG-3') and PotyR (5'-TGCTGCKGCYTTCATYTG-3') (Marie-Jeanne et al. 2000) were used in RT-PCR to detect SCMV in symptomatic leaves, yielding a ~300 bp amplicon. Sanger sequencing and BLASTn analysis confirmed the 97.98% nucleotide identity with SCMV isolate BJ (GenBank accession No. AY042184.1). The sequence was deposited in GenBank under accession number OR777055. In addition, specific SCMV primers SCMV-F (5'- TCCGGAACTGTGGATGCA-3') and SCMV-R (5'- GTGGTGCTGCTGCACTCCC-3') (coat protein region, 939 bp) detected the virus in all 11 symptomatic goose grass leaves, with no detection in asymptomatic leaves. Inoculation tests using extracts from symptomatic goose grass on maize plants resulted in mosaic symptoms (7 of 15 plants) at 4-6 days post-inoculation (Figure S2 and 3). However, no symptoms were observed in maize plants following inoculation with leaf extracts from healthy goose grass. RT-PCR confirmed the presence of SCMV in the diseased maize plants. Sequencing analysis revealed that all amplified fragments shared 100% identity with the partial CP-encoding sequence of SCMV. Taken together these results support the presence of SCMV in symptomatic goose grass. To the best of our knowledge, this is the first report of SCMV in E. indica in China. In general, potyviruses can be easily transmitted in multiple ways including aphid vectors, grafting, and wounding. Therefore, investigating SCMV in goose grass is crucial for developing integrated strategies to prevent its transmission to economically important plants such as maize.

Rhein kills Actinobacillus pleuropneumoniae, reduces biofilm formation, and effectively treats bacterial lung infections in mice.

Background. Actinobacillus pleuropneumoniae, a member of the Pasteurellaceae family, is known for its highly infectious nature and is the primary causative agent of infectious pleuropneumonia in pigs. This disease poses a considerable threat to the global pig industry and leads to substantial economic losses due to reduced productivity, increased mortality rates, and the need for extensive veterinary care and treatment. Due to the emergence of multi-drug-resistant strains, Chinese herbal medicine is considered one of the best alternatives to antibiotics due to its unique mechanism of action and other properties. As a type of Chinese herbal medicine, Rhein has the advantages of a wide antibacterial spectrum and is less likely to develop drug resistance, which can perfectly solve the limitations of current antibacterial treatments.Methods. The killing effect of Rhein on A. pleuropneumoniae was detected by fluorescence quantification of differential expression changes of key genes, and scanning electron microscopy was used to observe the changes in A. pleuropneumoniae status after Rhein treatment. Establishing a mouse model to observe the treatment of Rhein after A. pleuropneumoniae infection.Results. Here, in this study, we found that Rhein had a good killing effect on A. pleuropneumoniae and that the MIC was 25 µg ml-1. After 3 h of action, Rhein (4×MIC) completely kills A. pleuropneumoniae and Rhein has good stability. In addition, the treatment with Rhein (1×MIC) significantly reduced the formation of bacterial biofilms. Therapeutic evaluation in a murine model showed that Rhein protects mice from A. pleuropneumoniae and relieves lung inflammation. Quantitative RT-PCR (Quantitative reverse transcription polymerase chain reaction is a molecular biology technique that combines both reverse transcription and polymerase chain reaction methods to quantitatively detect the amount of a specific RNA molecule) results showed that Rhein treatment significantly downregulated the expression of the IL-18 (Interleukin refers to a class of cytokines produced by white blood cells), TNF-α, p65 and p38 genes. Along with the downregulation of genes such as IL-18, it means that Rhein has an inhibitory effect on the expression of these genes, thereby reducing the activation of inflammatory cells and the production of inflammatory mediators. This helps reduce inflammation and protects tissue from further damage.Conclusions. This study reports the activity of Rhein against A. pleuropneumoniae and its mechanism, and reveals the ability of Rhein to treat A. pleuropneumoniae infection in mice, laying the foundation for the development of new drugs for bacterial infections.

Dynamics of Open States and Promoter Functioning in the appY_red and appY_green Genetic Constructions Based on the pPF1 Plasmid.

Although the role of dynamic factors in DNA function still remains unclear, research in this direction is a rapidly developing area of molecular biology. In this work, the genetic constructions appY_red and appY_green, based on the plasmid pPF1 and containing a fragment of Escherichia coli (E. coli) DNA with predicted promoter-like regions, are considered complex dynamic systems in which local sites of double helix unwinding, called open states, can arise and propagate. The purpose of the article is to show the existence of a connection between the dynamics of open states and the functioning of predicted promoters. We experimentally verified the functionality of the predicted promoters using a reporter vector. Using a reverse transcription reaction, transcription start sites were identified indicating the presence of two divergent promoters, one on each strand. In mathematical studies, a dynamic model was used that described open states as one-soliton solutions (kinks) of a system of nonlinear partial differential equations, and the influence of the torque Mτ on the dynamics of kinks was taken into account. Fluorescence analysis of colonies of E. coli cells transformed with plasmid constructions showed that one of the two promoters is stronger than the other and that the strength of the promoters depends on the orientation of the fragment under study in the plasmid. On the other hand, using mathematical modeling, the energy profiles of genetic constructions were calculated and the kink trajectories were constructed. In addition, by studying the effect of torsion moment in model studies, we found threshold torque values at which the behavior of kinks changes dramatically: from oscillatory to translational motion. The minimum values of torsion moment required to initiate the transcription process were also assessed. A comparative analysis of the results of experimental data and model calculations showed a good correlation between the preferred starting points and the direction of transcription, which in turn confirmed the existence of a relationship between the dynamics of open states and the functioning of promoters.

Reverse transcription of plasma-derived HIV-1 RNA generates multiple artifacts through tRNA(Lys-3)-priming.

In vitro reverse transcription of full-length HIV-1 RNA extracted from the blood plasma of people living with HIV-1 remains challenging. Here, we describe the initiation of reverse transcription of plasma-derived viral RNA in the absence of an exogenous primer. Real-time PCR and Sanger sequencing were applied to identify the source and to monitor the outcome of this reaction. Results demonstrated that during purification of viral RNA from plasma, tRNA(Lys-3) is co-extracted in a complex with the viral RNA. In the presence of a reverse transcription enzyme, this tRNA(Lys-3) can induce reverse transcription, a reaction that is not confined to transcription of the 5' end of the viral RNA. A range of cDNA products is generated, most of them indicative for the occurrence of in vitro strand transfer events that involve translocation of cDNA from the 5' end to random positions on the viral RNA. This process results in the formation of cDNAs with large internal deletions. However, near full-length cDNA and cDNA with sequence patterns resembling multiple spliced HIV-1 RNA were also detected. Despite its potential to introduce significant bias in the interpretation of results across various applications, tRNA(Lys-3)-driven reverse transcription has been overlooked thus far. A more in-depth study of this tRNA-driven in vitro reaction may provide new insight into the complex process of in vivo HIV-1 replication.IMPORTANCEThe use of silica-based extraction methods for purifying HIV-1 RNA from viral particles is a common practice, but it involves co-extraction of human tRNA(Lys-3) due to the strong interactions between these molecules. This co-extraction becomes particularly significant when the extracted RNA is used in reverse transcription reactions, as the tRNA(Lys-3) then serves as a primer. Reverse transcription from tRNA(Lys-3) is not confined to cDNA synthesis of the 5' end of the viral RNA but extends across various regions of the viral genome through in vitro strand transfer events. Co-extraction of tRNA(Lys-3) has been overlooked thus far, despite its potential to introduce bias in downstream, reverse transcription-related applications. The observed events in the tRNA(Lys-3)-induced in vitro reverse transcription resemble in vivo replication processes. Therefore, these reactions may offer a unique model to better understand the replication dynamics of HIV-1.

Evaluation of differences in expression pattern of three isoforms of the transforming growth factor beta in patients with lumbosacral stenosis

ABSTRACT The study investigates molecular changes in the lumbosacral (L/S) spine’s yellow ligamentum flavum during degenerative stenosis, focusing on the role of transforming growth factor beta 1–3 (TGF-β-1–3). Sixty patients with degenerative stenosis and sixty control participants underwent molecular analysis using real-time quantitative reverse transcription reaction technique (RTqPCR), enzyme-linked immunosorbent assay (ELISA), Western blot, and immunohistochemical analysis (IHC). At the mRNA level, study samples showed reduced expression of TGF-β-1 and TGF-β-3, while TGF-β-2 increased by only 4%. Conversely, at the protein level, the study group exhibited significantly higher concentrations of TGF-β-1, TGF-β-2, and TGF-β-3 compared to controls. On the other hand, at the protein level, a statistically significant higher concentration of TGF-β-1 was observed (2139.33 pg/mL ± 2593.72 pg/mL vs. 252.45 pg/mL ± 83.89 pg/mL; p < 0.0001), TGF-β-2 (3104.34 pg/mL ± 1192.74 pg/mL vs. 258.86 pg/mL ± 82.98 pg/mL; p < 0.0001), TGF-β-3 (512.75 pg/mL ± 107.36 pg/mL vs. 55.06 pg/mL ± 9.83 pg/mL, p < 0.0001) in yellow ligaments obtained from patients of the study group compared to control samples. The study did not establish a significant correlation between TGF-β-1–3 concentrations and pain severity. The findings suggest that molecular therapy aimed at restoring the normal expression pattern of TGF-β-1–3 could be a promising strategy for treating degenerative stenosis of the L/S spine. The study underscores the potential therapeutic significance of addressing molecular changes at the TGF-β isoforms level for better understanding and managing degenerative spinal conditions.

Разработка ПЦР-тест системы для выявления вируса картофеля Y

Potato virus Y infects potato plants and causes serious damage to agriculture by reducing the yield of this crop. Therefore, there is a need to identify this pathogen. Potato viruses contain RNA, so immunological methods or PCR combined with reverse transcription can be used. The aim of this work was to develop a PCR test system for the detection of Potato virus Y. Primers for the reverse transcription reaction and subsequent PCR were found. Annealing temperatures and size of the amplified fragment were calculated. Primers and reaction conditions on plant material were tested. PCR products of the calculated size were obtained. The determination of their nucleotide sequence confirmed the identification of the genetic material of Potato virus Y. Thus, this PCR test system can be used to detect Potato virus Y.

Impact of heterogeneous nuclear ribonucleoprotein A/B subtype overexpression on the expression of cancer stem cell markers CD133 and CD44 and cellular proliferation capacity.

The occurrence and progression of intestinal cancer are complex, multifactorial processes in which tumor stem cells are believed to play a crucial role. An in-depth understanding of their molecular mechanisms holds imperative clinical significance for improving intestinal cancer treatment. HT-29 and HCT116intestinal cancer cell lines were utilized as research models. The experimental group (group E) and control group (group C) were established by transfecting the hnRNPA1 subtype and empty vector, respectively. The expression (EP) levels of hnRNPA1 and changes in Wnt/β-catenin signaling-related markers were evaluated using techniques such as RNA extraction, reverse transcription reactions, real-time quantitative PCR (RT qPCR), and protein extraction. The EP of tumor stem cell markers CD133 and CD44 was assessed using immunohistochemistry. Additionally, cell invasion assays, scratch assays, and cell counting kit-8 (CCK-8) proliferation assays were conducted. Furthermore, a mouse tumor model was established to observe the growth of tumors in both groups. overexpression (OP) of hnRNPA1 in group E greatly increased the protein EP levels of β-catenin, Axin2, and Cyclin D1 and exhibited a higher positivity rate for CD133 and CD44. The invasive, migratory, and proliferative abilities of cells in group E were notably enhanced, and tumor growth was observably faster versus group C. OP of hnRNPA1 was closely associated with the activation of Wnt/β-catenin signaling and promoted the proliferation and invasive capacity of tumor cells. hnRNPA1 played an imperative role in intestinal cancer stem cells.

Organization for laboratory diagnosis of SARS-COV-2 in the conditions of an anti-tuberculosis institution

Introduction. In connection with the spread of a new coronavirus infection COVID-19 since 2020, measures have been taken in the city of Moscow to widely diagnose the causative agent of COVID-19. A laboratory PCR department was opened in the State Budgetary Healthcare Institution «MNPC for the fight against tuberculosis of the DZM», taking into account the available material and human resources. Purpose of the study: To generalize the experience of organizing the laboratory service of an anti-tuberculosis institution in the city of Moscow during the spread of a new coronavirus infection. Results. Human and material resources have made it possible to maintain the quality and availability of laboratory diagnostics of biological material from patients receiving treatment at the Moscow Regional Research and Practical Center for Combating Tuberculosis, DZM, during the COVID-19 pandemic. In the period 2020-2022 in total, 90,102 studies of biological material (smears) were carried out by RT-PCR in order to detect COVID-19 RNA. Starting from June 2020 to the present, the PCR department of the KDL Clinic 2 has been studying the direct detection of Covid-19 RNA in biological material using molecular genetic methods based on reverse transcription and polymerase chain reaction (RT-PCR) and the identification of specific immunoglobulin classes IgM and IgG to coronavirus antigens in blood serum (plasma) by the method of immunochemiluminescent analysis (ICLA) of both persons receiving treatment at the State Budgetary Institution of Healthcare Center for Combating Tuberculosis Moscow, and employees.

Improved Double-Stranded RNA Extraction and Hyphal Tip-Touch Techniques for the Detection of Mycoviruses

Mycoviruses infect a wide range of fungal species, and many of them have double-stranded RNA (dsRNA) genomes. Using a dsRNA technique makes it easier to detect unknown mycoviruses in fungi. Previously, a few studies reported dsRNA extraction methods from fungal tissues, but the procedures required a significant amount of starting material and time, particularly in growing fungal cultures. In this study, we report an efficient and quick dsRNA extraction method that is reproducible to extract quality dsRNA of mycoviruses from a small amount of fungal culture in a short time. Extracted dsRNA was subsequently used in Illumina sequencing and reverse transcription-polymerase chain reaction assays, followed by Sanger sequencing, to confirm the identity of the mycovirus. Additionally, a rapid and efficient technique named hyphal tip-touch (HTT) was developed to identify known mycoviruses without the need for dsRNA extraction. The HTT technique uses the edge of mycelia as a template for preparing complementary DNA in the reverse transcription reaction, which was used in the polymerase chain reaction assay followed by sequencing. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

First Report of Tomato spotted wilt virus infecting Helichrysum bracteatum in China.

Strawflower (Helichrysum bracteatum, Asteraceae) , an annual or biennial herb, is one of the most popular flowers in the world because of the colorful flowers and the long flowering period. However, the ornamental plants belonging to Asteraceae are susceptible to numerous viruses such as cucumber mosaic virus (CMV) (Cucumovirus, Bromoviridae) , potato virus Y (Potyvirus, Potyviridae), tomato mosaic virus (ToMV) (Tobamovirus, Virgaviridae), tobacco mosaic virus (TMV) (Tobamovirus, Virgaviridae), chrysanthemum virus B (CVB) (Carlavirus, Betaflexiviridae), tomato aspermy virus (TAV) (Cucumovirus, Bromoviridae), tomato spotted wilt virus (TSWV) (Orthotospovirus tomatomaculae, Tospoviridae), and impatiens necrotic spot virus (INSV) (Orthotospovirus impatiensnecromaculae, Orthotospovirus) resulting in severe yield loss (Verma et al. 2003; Raj et al. 2007; Kondo et al. 2011; Liu et al. 2014; Marys et al. 2014; Min et al. 2020; Gautam et al. 2021; Read et al. 2022; Supakitthanakorn et al. 2022). Among these viruses, the TSWV, a thrips-transmitted negative-stranded RNA virus, is well known to cause viral disease in several plant species while is less reported in Helichrysum, especially in China. In April 2021, viral attack symptoms were detected on the leaves of H. bracteatum during our routine checks in the greenhouse located at Shunyi District, Beijing, China, such as wilting, shrinking, chlorotic blotches, chlorotic ring spots. To investigate the virus infecting H. bracteatum, in total of 25 symptomatic and 5 asymptomatic leaves were sampled and tested by the effective double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) using antisera against CMV, PVY/PVX, ToMV, TMV, CVB, TAV, TSWV, INSV, separately (Agdia, USA). Only the TSWV showed positive in symptomatic samples, and asymptomatic samples were all negative, which implied TSWV infection. To further confirm the virus type of TSWV isolated from H. bracteatum samples, the genomic RNA of the virus was isolated using reverse transcription and polymerase chain reaction (RT-PCR), and then was cloned, sequenced and analyzed. Total RNA of five symptomatic leaves (ELISA-positive) were extracted using the FastPure Plant Total RNA Isolation Kit (Vazyme, China), and then were reverse transcribed by HiScript II Reverse Transcriptase (Vazyme, China). Each genome segments were amplified using Phanta Max Super-Fidelity DNA Polymerase (Vazyme, China) with TSWV-specific primers newly designed and listed in Table S1. The PCR setup was as follow: 95°C for 30 s, followed by 35 cycles at 95°C for 30 s, 55°C for 30 s, and 72°C for 1.5 min, with a final extension at 72°C for 10 min. All PCR products were cloned into the TA/Blunt-Zero vector (Vazyme, China) and sequenced (GENEWIZ, Inc.). We assembled and then analyzed the evolutionary relationship of three genomic fragments, that is, TSWV-BJFC-Hb S (2923 bp), M (4785 bp) and L (8971 bp) using the BLAST tools. The results showed high similarity with TSWV-henan isolated from pepper in China (99.6% to TSWV-S (MT799179.1), 99.8 % to TSWV-M (MT799178.1) and 99.8 % TSWV-L (MT799177.1)). These sequences have been submitted to the GenBank (OM982910, OM982911 and OM937131). Taking all of these evidences together, the viral disease observed in H. bracteatum was closely associated with TSWV. TSWV is currently widespread in China, infecting Nasturtium, Chrysanthemum and cowpea (Xiao et al. 2015; Hu et al. 2018; Yu et al. 2021). Epidemics of TSWV have also been reported in several other countries such as Korea, North Carolina, Turkey and India (Renukadevi et al. 2015; Koehler et al. 2016; Kwak et al. 2021; Erilmez, S. 2022). This is the first report of TSWV infection on H. bracteatum in China. Due to the fast spread and serious economic losses of TSWV, the rapid detection may be the essential way to prevent this viral disease among crops (Macharia et al. 2014).

Click display: a rapid and efficient in vitro protein display method for directed evolution.

We describe a novel method for in vitro protein display-click display-that does not depend on maintaining RNA integrity during biopanning and yields covalently linked protein-cDNA complexes from double-stranded input DNA within 2 h. The display is achieved in a one-pot format encompassing transcription, translationand reverse transcription reactions in series. Stable linkage between proteins and the encoding cDNA is mediated by a modified DNA linker-ML-generated via a click chemistry reaction between a puromycin-containing oligo and a cDNA synthesis primer. Biopanning of a click-displayed mock library coupled with next-generation sequencing analysis revealed>600-fold enrichment of target binders within a single round of panning. A synthetic library of Designed Ankyrin Repeat Proteins (DARPins) with ∼1012 individual members was generated using click display in a 25-μl reaction and six rounds of library panning against a model protein yielded a panel of nanomolar binders. This study establishes click display as a powerful tool for protein binder discovery/engineering and provides a convenient platform for in vitro biopanning selection even in RNase-rich environments such as on whole cells.

#4536 INFLUENCE OF REDUCTION IN THE MASS OF ACTIVE NEPRONS ON THE EXPRESSION OF MIRNA AND NFκB IN THE MYOCARDIA AND AORT OF WKY RATS

Abstract Background and Aims At present, there is no doubt about the relationship between the state of the kidneys and the cardiovascular system, which is reflected in the concept of the cardiorenal continuum. The emerging data suggest that miRNAs may be one of the links connecting the kidneys and the cardiovascular system. However, information about the role of epigenomic changes in the development of damage to the heart and blood vessels in chronic kidney disease remains not fully understood. Target. The aim of the work was to evaluate changes in the expression levels of microRNA-21, 133,203, as well as the nuclear transcription factor κB (NFκB) in the tissues of the myocardium and aorta in the development of remodeling of the heart and blood vessels with a chronic reduction in the mass of active nephrons in the experiment. Method Systolic blood pressure (BP, mm Hg), myocardial mass index (MMI, mg/g), relative expression levels of miRNA-21, -133, -203 and NFκB in myocardium and aorta were analyzed in rats Wistar-Kyoto (WKY) with 5/6 nephrectomy (Nx) and duration of experimental exposure 2 mo (n = 9). Controls were sham operated (SO) animals (n = 9). The reverse transcription reaction for ‘complementary’ DNA (cDNA) preparation was carried out under the StemLoop-technology separately for the studied miRNA. The following primers were used in PCR: microRNA-21–5'-GCCCGCTAGCTTATCAGACTGATG-3_, microRNA-133–5_-GCCCGCAGCTGGTAAAATGGAAC-3_, microRNA-203–5_-GCCGGTGAAATGTTTAGGACC-3_ and U6–5_-GCGCGTCGTGAAGCGTTC-3_, and common reverse 5_-GTGCAGGGTCCGAGGT-3. The semi-qualitative evaluation of the miRNA expression level (in relative units, RU) under the 2-(ΔΔCt) protocol at the laboratory referent (0.09) was used in calculations. NFκB expression was quantified using a StemLoop technology and RealTimePCR compared to the expression of the reference-gene GAPDH. Data were analyzed using Student's t-test and the Mann–Whitney, a P&amp;lt;0.05 was considered statistically significant. Results In rats WKY with an experimental decrease of the nephron mass in comparison to control, significantly higher levels (median [interquartile rang]) of blood pressure (145.5[135.0; 155.0] vs 117.5[110.0; 120.0] mm Hg; P&amp;lt;0.001) NFκB expression in the myocardium (1.25[0.87; 1.87] vs 0.89[0.31; 1.15] relative units; P&amp;lt;0.01) and aorta (0.87[0.57;1.63] vs 0.35[0.22; 0.87] relative units; P&amp;lt;0.05). The expression level of miRNA-21 in the myocardium increased in rats with NE (1.48[0.54; 3.73] vs 0.37[0.06; 1.62] relative units; P&amp;lt;0.01) relative to the SO group, but did not change significantly in the aorta (p&amp;gt;0.05). Relative expression levels of microRNA-133 and -203 both in the myocardium and in the aorta of WKY rats with NE were more than 10 times lower compared to those of the SO group (p&amp;lt;0.001). BMI in rats 2 months after NE increased relative to the SO group (p&amp;lt;0.05). Conclusion An experimental decrease in the number of functioning nephrons not only leads to an increase in blood pressure and myocardial mass in WKY rats, but also causes epigenomic changes in the myocardium and blood vessels, in particular, activation of signaling pathways associated with NFκB in the myocardium and aorta of rats. Possibly, it is accompanied by growth in expression of NFκB-associated proliferative, proinflammatory and profibrotic cytokines. It is possible that microRNA-21 is also involved in the formation of fibrosis and myocardial remodeling. However, specific mechanisms of miRNA involvement in the pathogenesis of heart and vascular remodeling require further study.

Features of DNA-Montmorillonite Binding Visualized by Atomic Force Microscopy.

In the present work, complexes of DNA with nano-clay montmorillonite (Mt) were investigated by means of atomic force microscopy (AFM) under various conditions. In contrast to the integral methods of analysis of the sorption of DNA on clay, AFM allowed us to study this process at the molecular level in detail. DNA molecules in the deionized water were shown to form a 2D fiber network weakly bound to both Mt and mica. The binding sites are mostly along Mt edges. The addition of Mg2+ cations led to the separation of DNA fibers into separate molecules, which bound mainly to the edge joints of the Mt particles according to our reactivity estimations. After the incubation of DNA with Mg2+, the DNA fibers were capable of wrapping around the Mt particles and were weakly bound to the Mt edge surfaces. The reversible sorption of nucleic acids onto the Mt surface allows it to be used for both RNA and DNA isolation for further reverse transcription and polymerase chain reaction (PCR). Our results show that the strongest binding sites for DNA are the edge joints of Mt particles.

The influence of selected microRNAs on the expression profile of genes and proteins related to the tumor necrosis factor-alpha signaling pathways in endometrioid endometrial cancer.

Tumor necrosis factor exerts many adverse biological effects, from cell proliferation to cell death. Accurate diagnosis and treatment are therefore difficult due to many factors influencing tumor necrosis factor-alpha (TNF-α) signaling, including microRNAs (miRNAs), especially in tumors. The aim of the study was to determine the influence of miRNAs on the expression profile of genes and proteins related to TNF-α signaling in endometrial cancer. The material consisted of 45 endometrioid endometrial cancer and 45 normal endometrium tissue samples. Gene expression was determined with microarrays and then validated for TNF-α, tumor necrosis factor receptor 1 (TNFR1) and 2 (TNFR2), caveolin 1 (CAV1), nuclear factor kappa B subunit 1 (NFKB1), and TGF-beta activated kinase 1 (MAP3K7)-binding protein 2 (TAB2) using real-time quantitative reverse transcription reaction (RT-qPCR). The protein concentration was assessed by enzyme-linked immunosorbent assay (ELISA). In addition, differentiating miRNAs were identified using miRNA microarrays and their relationships with TNF-α signaling genes were evaluated using the mirDIP tool. TNF-α, TNFR1, TNFR2, CAV1, NFKB1, and TAB2 were upregulated both on the mRNA and protein levels. The decrease in the activity of miR-1207-5p, miR-1910-3p, and miR-940 may be related to CAV1 overexpression. Similarly for miR-572 and NFKB1 as well as miR-939-5p and TNF-α. In turn, miR-3178 may partially inhibit TNFR1 activity up to grade 2 cancer. TNF-α signaling, especially the TNF-α/NF-κB axis, is disrupted in endometrial cancer and worsens with disease progression. The observed changes may be the result of miRNAs' activity in the initial stage of endometrial cancer and its gradual loss in later grades.

Evaluation of solvent releases from microfluidic devices made of cycloolefin polymer by temperature-desorption mass spectrometry

Microfluidic devices have been used in various biological experiments. The working temperature of the devices spans a wide range (approximately 23 °C–95 °C). Among thermoplastic materials, cyclo olefin polymers (COPs) are promising materials for microfluidic devices. This is because COP can overcome the well-known disadvantages of polydimethylsiloxane, a commonly used material, and have the advantage of better observability than polystyrene and polymethyl methacrylate. However, most COP-based devices are fabricated using solvents and adhesives during the bonding process. These solvents, which are known to affect biological experiments, may remain in the device and be released during the experiments. It is necessary to investigate whether solvents are actually released and, if so, how they are released. Here we introduce thermal desorption spectroscopy as a simple and quantitative method to observe solvent release from solvent-bonded and vacuum ultraviolet (VUV)-bonded products. Solvents are released from the solvent-bonded product at 31.5 °C, suggesting that it may have negative effects on various biological experiments. On the other hand, the VUV-bonded product releases solvents (cyclohexane and toluene), which are used during olefin polymerization in the synthesis process of COP, at temperatures above 84 °C. Therefore, the experiments conduct below 84 °C (e.g. in situ hybridization, reverse transcription (RT) and loop-mediated isothermal amplification) were not affected. In addition, the amount of solvent released above 84 °C is small (1/548–1/913 of the solvent-bound product), so it is expected that the extent of the effect on experiments conducted above 84 °C (RT and polymerase chain reaction) is small, if there is any. We conclude that solvent-bound devices can have undesirable effects in many biological applications, not just cell culture. We believe that evaluating solvent release from devices is important for the development of new devices in the future.

Designing of SiO2 mesoporous nanoparticles loaded with mometasone furoate for potential nasal drug delivery: Ex vivo evaluation and determination of pro-inflammatory interferon and interleukin mRNA expression.

The main objective of the current research work was to synthesize mesoporous silica nanoparticles for controlled delivery of mometasone furoate for potential nasal delivery. The optimized sol-gel method was used for the synthesis of mesoporous silica nanoparticles. Synthesized nanoparticles were processed through Zeta sizer, SEM, TEM, FTIR, TGA, DSC, XRD, and BET analysis for structural characterization. The in vitro dissolution test was performed for the inclusion compound, while the Franz diffusion experiment was performed for permeability of formulation. For the determination of expression levels of anti-inflammatory cytokines IL-4 and IL-5, RNA extraction, reverse transcription, and polymerase chain reaction (RT-PCR) were performed. The MTT assay was also performed to determine cell viability. Synthesized and functionalized mesoporous silica nanoparticles showed controlled release of drugs. FT-IR spectroscopy confirmed the presence of the corresponding functional groups of drugs within mesoporous silica nanoparticles. Zeta sizer and thermal analysis confirmed the delivery system was in nano size and thermally stable. Moreover, a highly porous system was observed during SEM and TEM evaluation, and further it was confirmed by BET analysis. Greater cellular uptake with improved permeability characteristics was also observed. As compared to the crystalline drug, a significant improvement in the dissolution rate was observed. It was concluded that stable mesoporous silica nanoparticles with significant porosity were synthesized, efficiently delivering the loaded drug without any toxic effect.