Double-stranded Molecules Research Articles

The complete mitochondrial genome of Uroobovella oviformis (Kontschan & Stary, 2011) (Acari, Urodinychidae) and its phylogenetic position within the order Mesostigmata

ABSTRACT Mitochondrial genomes are highly conserved in genetic processes and serve as a useful molecular marker for phylogenetic and evolutionary analysis. In this study, the complete mitochondrial genome of Uroobovella oviformis was sequenced and annotated. The mitochondrial genome is a closed, double-stranded circular molecule of 14,306 bp length and contains the typical 37 genes. All of the protein-coding genes started with ATN and terminated with TAA except COX2, COX3, and CYTB, which stopped with single T. The whole mitochondrial genome of U. oviformis showed a heavy AT nucleotide bias (77.69%), a positive AT-Skew (0.035), and a negative GC-Skew (−0.320), as well as translocation of seven genes including CYTB and ND6. The phylogenetic tree was constructed by Bayesian inference and maximum likelihood methods using three different datasets (PCG, PCG12, and AA), which were constructed to discuss the phylogenetic status of Mesostigmata. The analysis showed that the branching relationships among the six trees were consistent and all families except the Laelapidae were recovered as monophyletic. Furthermore, U. oviformis forms a separate clade and is located at the base of Mesostigmata and has a closer relationship with Antennophorina.

From π-Conjugated Rods to Shape-Persistent Rings, Wheels, and Ladders: The Question of Rigidity.

ConspectusRigid-rod oligomers and polymers are mostly based on (hetero)aromatic rings connected with each other, either directly or via ethynylene or butadiynylene linkers, or by a combination of both structural elements. Although they are much more rigid than vinyl polymers, they exhibit considerable structural flexibility, often more than would be expected merely from their chemical structure. This disparity holds for both linear as well as for cyclic structures. The flexibility of rigid-rod polymers, which is directly observable for defined oligomers of different lengths at the solid-liquid interface by means of scanning-tunneling microscopy, also impacts their optical and electronic properties. The flexibility can be used, for example, to control whether an oligomer with two different fluorescent end-groups emits from either the one or the other. The flexibility of shape-persistent macrocycles also has an impact on the overall thermal stability of mechanically interlocked molecular architectures. However, the degree of flexibility can be reduced when rigid struts are covalently mounted into the inside of the rings, leading to the formation of so-called molecular spoked wheels. The combination of these two elements─rings and rods─stiffens both of them: the ring perimeter is prevented from collapsing and the internal rods from bending. These compounds have been further developed as platform molecules, where three spokes stiffen the ring and together form a tripod-like platform, while a fourth arm points─after adsorption to a solid substrate─above the plane of the molecule. This pillar makes it possible to decouple a functional group at the end of the arm from the surface. Rigidity enhancement by the introduction of rigid spacer elements can also be applied to the case of rigid-rod polymers and is visualized by sophisticated molecular dynamics simulations. In this case, formation of single-stranded oligomers and polymers, and a subsequent zipping reaction to form ladder-like structures, directly allows, by means of single-molecule fluorescence spectroscopy, a comparison of the single- and double-stranded molecules. In particular in the case of the polymers, which can be up to 100 nm in length, the enhancement of rigidity is quite remarkable. Overall, the covalent connection of two or more rigid molecular entities has a self-reinforcing effect: all parts of the molecule gain rigidity. Since overall synthetic yields for such complex high-molecular weight covalently bound shape-persistent structures can still be low, scanning tunneling microscopy and single-molecule fluorescence spectroscopy are the methods of choice for structural analyses. Preliminary results illustrate how these compounds can serve as versatile sources of deterministic single photons on demand, since rigidity also enhances the intramolecular flow of excitation energy, and suggest a range of applications in optoelectronic devices.

Complete characterization and comparative analysis of the mitochondrial genome of Indian tasar silkworm Antheraea mylitta (Lepidoptera: Saturniidae) and phylogenetic implications

The Indian tasar silkworm Antheraea mylitta (A. mylitta) is an economically important silkmoth and is native to tropical India. Our current research has deciphered the mitochondrial genome (mitogenome) of A. mylitta by recovering the complete genome sequence from the NCBI-SRA database and comparing it with other mitogenomes from the order Lepidoptera. The mitogenome is a double-stranded circular molecule spanning 15,354 bp with an A + T content of roughly 80.4%. It consists of a total of 37 genes, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs), along with a 337 bp long control region. The arrangement of PCGs is similar to other Lepidoptera mitogenomes, with the exception of Cox1 and Cox2, which have different initiation codons. The control region of A. mylitta contains a conserved five bp ATAGA motif as seen in other Antheraea species. Phylogenetic analysis supports previous morphological hypotheses that Bombycoidea, Noctuoidea, Geometroidea, Papilionoidea, and Torticoidea are monophyletic. The divergence time analysis of 13 protein-coding genes reported that A. mylitta diverged from the last common ancestor ∼ 23 million years ago. As per our knowledge, this is the first documented record of the entire mitogenome of A. mylitta.

Engineered Resistance to Tobamoviruses.

Tobacco mosaic virus (TMV) was the first virus to be studied in detail and, for many years, TMV and other tobamoviruses, particularly tomato mosaic virus (ToMV) and tobamoviruses infecting pepper (Capsicum spp.), were serious crop pathogens. By the end of the twentieth and for the first decade of the twenty-first century, tobamoviruses were under some degree of control due to introgression of resistance genes into commercial tomato and pepper lines. However, tobamoviruses remained important models for molecular biology, biotechnology and bio-nanotechnology. Recently, tobamoviruses have again become serious crop pathogens due to the advent of tomato brown rugose fruit virus, which overcomes tomato resistance against TMV and ToMV, and the slow but apparently inexorable worldwide spread of cucumber green mottle mosaic virus, which threatens all cucurbit crops. This review discusses a range of mainly molecular biology-based approaches for protecting crops against tobamoviruses. These include cross-protection (using mild tobamovirus strains to 'immunize' plants against severe strains), expressing viral gene products in transgenic plants to inhibit the viral infection cycle, inducing RNA silencing against tobamoviruses by expressing virus-derived RNA sequences in planta or by direct application of double-stranded RNA molecules to non-engineered plants, gene editing of host susceptibility factors, and the transfer and optimization of natural resistance genes.

Phase 2 randomized study of rintatolimod following FOLFIRINOX in patients with locally advanced pancreatic adenocarcinoma.

TPS4214 Background: The immunosuppressive microenvironment of pancreatic ductal adenocarcinoma (PDAC) is a driver of its lethality and resistance to immunotherapy. Strategies which modulate the immunosuppressive milieu have the potential to improve the anti-tumor response and improve outcomes in patients with PDAC. Rintatolimod is a synthetic double-stranded RNA molecule that activates the toll-like receptor 3 (TLR3) present on dendritic cells, B-cells, natural killer cells and pancreatic epithelial cells. TLR3 stimulation may increase cytotoxic T-cell activity in PDAC through dendritic cell maturation, antigen priming and downstream proliferation of cytotoxic T-cells. Twenty-seven patients were treated with rintatolimod in a single center Named Patient Program at Erasmus University Medical Center in Rotterdam between January 2017 and February 2019. All had locally advanced or metastatic PDAC which had not progressed on FOLFIRINOX (median 8 cycles). Maintenance rintatolimod, administered intravenously twice weekly for up to 18 weeks, was generally well tolerated. The most common toxicities were grade 1-2 myalgia (30%), chills (52%) and fatigue (30%); no toxicities ≥ grade 3 were observed. Progression-free and overall survival (from cycle 1 FOLFIRINOX) were 13 and 19 months. Methods: This is a phase 2 randomized, open-label, multicenter clinical trial. The primary objective is to assess the efficacy of rintatolimod compared to observation in subjects with locally advanced PDAC which has not progressed after FOLFIRINOX. Eligible patients have completed at least 4 months of FOLFIRINOX, have no evidence of progressive disease, have measurable disease by RECIST v1.1, Karnofsky Performance Status ≥80 and have adequate organ function. Subjects with resected PDAC or metastatic disease are not eligible. Subjects are randomized 2:1 to rintatolimod vs. observation. Rintatolimod is administered intravenously twice weekly until disease progression in the experimental arm. Cross-sectional imaging is performed every 8 weeks in both arms. The primary endpoint is progression-free survival, as assessed by the investigator. Secondary endpoints include overall survival, objective response rate, duration of response and safety, as assessed by CTCAE v5.0. Exploratory endpoints include quality of life and changes in immune cell composition and T-cell response in the peripheral blood to characterize the immunomodulatory effects of rintatolimod. The planned sample size is 90 subjects. The final analysis will be performed after 64 events (disease progression or death) have been observed. The study is powered to detect a hazard ratio of 0.47 for median PFS with 80% power and significance level of 5%. Clinical trial information: NCT05494697 .

Analysis of the pharmacokinetics and efficacy of RBD1016 – A GalNAc-siRNA targeting Hepatitis B Virus X gene using semi-mechanistic PK/PD model

Small interference RNA (siRNA) is a class of short double-stranded RNA molecules that cause mRNA degradation through an RNA interference mechanism and is a promising therapeutic modality. RBD1016 is a siRNA drug in clinical development for the treatment of chronic Hepatitis B Virus (HBV) infection, which contains a conjugated with N-acetylglucosamine moiety that can facilitate its hepatic delivery. We aimed to construct a semi-mechanistic model of RBD1016 in pre-clinical animals, to elucidate the pharmacokinetic/pharmacodynamic (PK/PD) profiles in mice and PK profiles in monkeys, which can lay the foundation for potential future translation of RBD1016 PK and PD from the pre-clinical stage to the clinic stage. The proposed semi-mechanistic PK/PD model fitted PK and PD data in HBV transgenic mice well and described plasma and liver concentrations in the monkeys well. The simulation results showed that our model has a reasonable predictive ability for Hepatitis B surface antigen (HBsAg) levels after multiple dosing in mice. Further PK and PD data for RBD1016, including clinical data, will assist in refining the model presented here. Our current effort focused on model building for RBD1016, we anticipate that the model could apply to other GalNAc-siRNA drugs.

A removable and cosmopolitan dsRNA Toti-like virus causes asymptomatic but productive infection in a model diatom strain

Diatoms contribute to 20 % of global primary productivity. Although some diatom viruses have been identified, the molecular mechanisms underlying their interactions with the host remain poorly understood. In this study, we report the discovery of an RNA molecule in the DNA extracts of the Phaeodactylum tricornutum strain Pt1, which possesses a well-annotated genome and has been used as a diatom model system since 1956. We confirmed this molecule to be a double-stranded linear RNA molecule and, through sequencing, demonstrated it to be a virus in the Totiviridae family that is prevalent among marine stramenopiles. We also detected this virus in Phaeodactylum tricornutum strain Pt3, which was collected in 1930s from a similar geographic location to Pt1, suggesting its prevalence within the region. By employing various inhibitors of the viral RNA-dependent RNA polymerase, we successfully generated a virus-free line isogenic to Pt1, establishing a model system to investigate the impact of RNA viruses on diatom physiology. The virus-free lines did not display obvious growth advantages or defects, indicating a tendency of the virus towards asymptomatic infection. Furthermore, we generated a robust antibody against the coat protein of this virus. By performing immunoprecipitation coupled with mass spectrometry, we found that translation-related proteins are enriched as potential interacting partners of the coat protein. Our results suggest that potential viral impacts in molecular research should be considered when Pt1 and Pt3 are used for studying translation-related processes. Additionally, our study unveiled a mode of asymptomatic but productive infection between viruses and marine algal hosts that differs from the commonly-reported virulent, lytic infections.

Characterization of the complete mitochondrial genome of Spirobolus grahami (Diplopoda: Spirobolidae) with phylogenetic analysis

Diplopoda is one of the most diverse and important groups of soil arthropods, but little research has been done on their phylogenetic relationship and evolution. Here, we sequenced and annotated the complete mitochondrial genomes of Spirobolus grahami. The total mitogenome of S. grahami was typical circular, double-stranded molecules, with 14,875 bp in length, including 13 protein-coding genes, 22 tRNAs, two rRNAs, and one control region. Base composition analysis suggested that the mitochondrial sequences were biased toward A and T, with A + T content of 58.68%. The mitogenomes of S. grahami exhibited negative AT and positive GC skews. Most of the 13 PCGs had ATN as the start codon, except COX1 start with CGA, and most PCGs ended with the T stop codon. The dN/dS values for most PCGs were lower than 1, suggesting that purifying selection was likely the main driver of mitochondrial PCG evolution. Phylogenetic analyses based on 13 PCGs using BI and ML methods support the classification of genus Spirobolus and Tropostreptus. Glomeridesmus spelaeus is distantly related to the other Diplopoda species.

A shorter inverted repeat length in a hairpin RNA results in a stronger silencing efficacy

RNA interference (RNAi), particularly hairpin RNA (hpRNA) constructs, is a potent genetic manipulation tool, influencing traits that are crucial for crop improvement. Typical hpRNA constructs consist of inverted repeat sequences derived from the mRNA of the target gene, separated by a non-complementary spacer. This configuration initiates the formation of a double-stranded RNA structure due to the complementary nature of sense and antisense sequences in the transcribed RNA. In this research, two hpRNA constructs, namely hp-TFL1-S and hp-TFL1-L, with distinct lengths of inverted repeats, were designed to target TFL1, a pivotal regulator of both flowering timing and inflorescence structure. hp-TFL1-L construct encompasses all the 150 nucleotide sequences of the hp-TFL1-S construct and an extra 135 nucleotides. These constructs included a chalcone synthase intron as a spacer, resulting in hairpin double-stranded RNA molecules of 150 and 285 base pair after transcription. The PCR and qRT-PCR analysis results confirmed the accurate design of both constructs and their successful suppression of TFL1 mRNA expression in transgenic Arabidopsis. Interestingly, Arabidopsis lines carrying hp-TFL1-S and hp-TFL1-L exhibited distinct phenotypic features. hp-TFL1-S induced more pronounced phenotypic changes, resulting in earlier flowering compared to the hp-TFL1-L and control group. Moreover, hp-TFL1-S had a significant impact on inflorescence architecture, distinguishing it from both hp-TFL1-L and control plants. This study provides an example where inverted repeat length alters the efficacy of silencing, and in this case, surprisingly the shorter construct appears to have a stronger silencing efficacy. This argues multiple sized hpRNAs should be tested in RNAi-based gene silencing experiments.

Abstract 960: Improved cfDNA methylation profiling through correction of misrepaired jagged-ends

Abstract Background: Profiling cfDNA methylation enables early cancer detection and classification, but challenges arise from "jagged ends" (JEs) for ~90% of cfDNA molecules, as well as for FFPE samples and partially degraded genomic DNA. Repair of these jagged ends introduces erroneous methylation signals, especially in shorter cfDNA fragments enriched for tumor derived molecules. Separately, DNA conversions during 5mC profiling hamper accurate simultaneous ctDNA genotyping of somatic mutations. To meet these needs, we developed a method preserving double-stranded cfDNA molecules without error-prone end-repair at jagged ends. This enables superior methylation profiling including hemimethylation detection, and simultaneous ctDNA SNV genotyping. Methods: We present JEEPERS (Jagged-End Error Polishing of Enzymatically misRepaired Sequences), a novel method for correcting errors in double-stranded library preparation for methylation profiling. JEEPERS detects and quantifies enzymatic repair errors at JEs, correcting them in silico. Leveraging duplex UMIs, it utilizes complementary strands and sibling reads from cfDNA families without jagged ends. The method exploits the 5' to 3' polarity of ER-associated errors and JE length profiles for correction. JEEPERS introduces anchor CpGs for precise correction of rare signals and enables accurate SNV calling at non CpG sites, addressing the challenge of differentiating true SNVs from conversion artifacts leading to C>T/G>A changes in sequencing data. Results: Analyzing 248 cfDNA samples (139 NSCLC patients, 109 healthy controls) by methylation profiling (EM-Seq) and ctDNA mutation genotyping (CAPP-Seq), JEEPERS correction efficiently addressed distortions, even at low tumor concentrations. Limiting dilution experiments demonstrated JEEPERS achieving a LOD95 of ~0.2% with 95% specificity (n=300). Despite ~50% lower molecular depth, JEEPERS-corrected cfDNA EM-Seq enabled accurate simultaneous methylation profiling and ctDNA genotyping, correlating strongly with CAPP-Seq genotypes (R=0.998, n=30). As expected, mutant ctDNA molecules were shorter than wild-type in both CAPP-Seq and EM-Seq data. cfDNA methylation patterns varied by oncogene vs. tumor suppressor status; EGFR mutants showed increased methylation (p<0.01), while TP53 mutants had lower methylation levels (p<0.05). Conclusions: Our method effectively corrects cfDNA methylation data, even at low tumor concentration, ensuring enhanced methylation signal accuracy and proficient SNV calling capabilities. This integrated approach offers a powerful means for investigating the link between SNVs and DNA methylation, significantly enhancing the accuracy of cancer detection using cfDNA, especially for early-stage tumors. This paves the way for a deeper understanding of the molecular mechanisms driving cancer initiation and progression. Citation Format: Rui Wang, Emily G. Hamilton, Diego Almanza, Angela Hui, Maximilian Diehn, Ash A. Alizadeh. Improved cfDNA methylation profiling through correction of misrepaired jagged-ends [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 960.

Improvement of economic and useful characters of wheat using RNA interference technology

Wheat is a strategic cereal crop of global importance and plays a leading role in the food supply of mankind. Despite the general trend to increase in its production, climatic changes leading to significant temperature changes, unpredictable precipitation or droughts and the appearance of new races of pathogens and pests significantly affect its yield. In order to prevent the negative impact of changes in climatic conditions on the productivity of this crop, it is necessary to develop innovative technologies for improving the resistance of wheat to environmental stresses. RNA interference (RNAi) represents a new potential tool for wheat breeding by introducing small non-coding RNA sequences with the ability to silence gene expression in a sequence-specific manner. A decrease in the expression of a certain gene determines the acquisition of a new characteristic through the elimination or accumulation of certain plant traits, which leads to biochemical or phenotypic changes that the original plants do not have. This literature review describes the progress achieved over the past decades in the application of RNAi to create wheat plants with improved economic and valuable traits. The main stages of the gene silencing mechanism mediated by short interfering RNA (siRNA) and microRNA (miRNA), features of their biogenesis, modes of action and distribution are presented. Examples of the use of various biotechnological approaches to wheat improvement using gene transformation, endogenous and exogenous double-stranded RNA molecules (dsRNA) are given. The possibility of using RNAi technology to increase the nutritional value and quality of grain, remove toxic compounds and allergens is highlighted. Considerable attention is paid to the practical results of various applications of RNAi to increase the resistance of wheat to biotic stress factors, in particular, viruses, bacteria, fungi, insect pests, and nematodes. Examples of the use of siRNA-mediated RNAi and the role of miRNA in improving wheat tolerance to abiotic stresses are summarized.

Utilization of Bacteriophage phi6 for the Production of High-Quality Double-Stranded RNA Molecules.

Double-stranded RNA (dsRNA) molecules are mediators of RNA interference (RNAi) in eukaryotic cells. RNAi is a conserved mechanism of post-transcriptional silencing of genes cognate to the sequences of the applied dsRNA. RNAi-based therapeutics for the treatment of rare hereditary diseases have recently emerged, and the first sprayable dsRNA biopesticide has been proposed for registration. The range of applications of dsRNA molecules will likely expand in the future. Therefore, cost-effective methods for the efficient large-scale production of high-quality dsRNA are in demand. Conventional approaches to dsRNA production rely on the chemical or enzymatic synthesis of single-stranded (ss)RNA molecules with a subsequent hybridization of complementary strands. However, the yield of properly annealed biologically active dsRNA molecules is low. As an alternative approach, we have developed methods based on components derived from bacteriophage phi6, a dsRNA virus encoding RNA-dependent RNA polymerase (RdRp). Phi6 RdRp can be harnessed for the enzymatic production of high-quality dsRNA molecules. The isolated RdRp efficiently synthesizes dsRNA in vitro on a heterologous ssRNA template of any length and sequence. To scale up dsRNA production, we have developed an in vivo system where phi6 polymerase complexes produce target dsRNA molecules inside Pseudomonas cells.

Biomimetic nanodecoys deliver cholesterol-modified heteroduplex oligonucleotide to target dopaminergic neurons for the treatment of Parkinson's disease

Parkinson's disease (PD) is the second most common neurodegenerative disorder characterized by the accumulation of α-synuclein (α-syn) aggregates called Lewy bodies leading to the gradual loss of dopaminergic (DA) neurons in the substantia nigra. Although α-syn expression can be attenuated by antisense oligonucleotides (ASOs) and heteroduplex oligonucleotide (HDO) by intracerebroventricular (ICV) injection, the challenge to peripheral targeted delivery of oligonucleotide safely and effectively into DA neurons remains unresolved. Here, we designed a new DNA/DNA double-stranded (complementary DNA, coDNA) molecule with cholesterol conjugation (Chol-HDO (coDNA)) based on an α-syn-ASO sequence and evaluated its silence efficiency. Further, Chol-HDO@LMNPs, Chol-HDO-loaded, cerebrovascular endothelial cell membrane with DSPE-PEG2000-levodopa modification (L-DOPA-CECm)-coated nanoparticles (NPs), were developed for the targeted treatment of PD by tail intravenous injection. CECm facilitated the blood-brain barrier (BBB) penetration of NPs, together with cholesterol escaped from reticuloendothelial system uptake, as well as L-DOPA was decarboxylated into dopamine which promoted the NPs toward the PD site for DA neuron regeneration. The behavioral tests demonstrated that the nanodecoys improved the efficacy of HDO on PD mice. These findings provide insights into the development of biomimetic nanodecoys loading HDO for precise therapy of PD. Statement of significanceThe accumulation of α-synuclein (α-syn) aggregates is a hallmark of PD. Our previous study designed a specific antisense oligonucleotide (ASO) targeting human SNCA, but the traumatic intracerebroventricular (ICV) is not conducive to clinical application. Here, we further optimize the ASO by creating a DNA/DNA double-stranded molecule with cholesterol-conjugated, named Chol-HDO (coDNA), and develop a DA-targeted biomimetic nanodecoy Chol-HDO@LMNPs by engineering cerebrovascular endothelial cells membranes (CECm) with DSPE-PEG2000 and L-DOPA. The in vivo results demonstrated that tail vein injection of Chol-HDO@LMNPs could target DA neurons in the brain and ameliorate motor deficits in a PD mouse model. This investigation provides a promising peripheral delivery platform of L-DOPA-CECm nanodecoy loaded with a new Chol-HDO (coDNA) targeting DA neurons in PD therapy.

Therapeutic siRNAs: small molecules with bigger function

In the realm of molecular medicine, therapeutic small-interfering RNA (siRNA) is a promising class of molecules with exciting new opportunities in healthcare. An essential component of RNA interference (RNAi) is siRNA. In clinical setup, siRNA may be engineered to specifically target genes linked to certain diseases, providing a focused and accurate method of modulating gene expression. Many important factors characterize the use of therapeutic siRNA. Target gene expression is selectively silenced by therapeutic siRNA through the use of the RNAi pathway. Guided by corresponding messenger RNA (mRNA) sequences, the double-stranded siRNA molecule is integrated into the RNA-induced silencing complex (RISC). This mechanism causes translational repression or mRNA cleavage, which in turn causes the relevant protein to be downregulated. Therapeutic siRNA is a promising avenue in several areas. siRNA can be used in oncology to target oncogenes or other important regulators, inhibiting cancer cell proliferation. Furthermore, by modifying the expression of genes linked to disease, siRNA may be used to treat viral infections, neurological conditions, and other rare and hereditary diseases. The selectivity of therapeutic siRNA is one of its main advantages. siRNA sequences can be engineered and customized to target specific genes linked to different diseases like cancer or genetic disorders. This focused strategy improves the accuracy of the therapeutic intervention and reduces off-target effects. In a recent article by Nissen et al., siRNA targeting LP(a) in a trial with 48 participants without cardiovascular disease and with lipoprotein(a) concentrations of 75 nmol/L or greater (or ≥30 mg/dL), was used to evaluate its tolerability and efficacy to reduce LP(a). Results showed that Lepodisiran was found to be well tolerated and resulted in dose-dependent, long-lasting reduction in serum lipoprotein(a) concentrations in phase 1 trial with elevated lipoprotein(a) levels. Therapeutic siRNA-based diagnosis is rapidly advancing, and several siRNA-based medications are now entering clinical trials. These trials aim to assess the pharmacokinetics, safety, and effectiveness of siRNA therapeutics in human subjects, offering crucial new information about their potential as a treatment option. Despite the therapeutic potential of siRNA, clinical translation of siRNA faces a challenge in its effective delivery. Naked siRNA molecules are more likely to degrade with a poor half-life and poor cellular uptake. Therefore, to increase the stability and delivery of therapeutic siRNA to target cells, a variety of delivery systems, such as lipid nanoparticles, viral vectors, and polymer-based carriers, are being investigated.
 

Our current understanding of the biological impact of endometrial cancer mtDNA genome mutations and their potential use as a biomarker.

Endometrial cancer (EC) is a devastating and common disease affecting women's health. The NCI Surveillance, Epidemiology, and End Results Program predicted that there would be >66,000 new cases in the United States and >13,000 deaths from EC in 2023, and EC is the sixth most common cancer among women worldwide. Regulation of mitochondrial metabolism plays a role in tumorigenesis. In proliferating cancer cells, mitochondria provide the necessary building blocks for biosynthesis of amino acids, lipids, nucleotides, and glucose. One mechanism causing altered mitochondrial activity is mitochondrial DNA (mtDNA) mutation. The polyploid human mtDNA genome is a circular double-stranded molecule essential to vertebrate life that harbors genes critical for oxidative phosphorylation plus mitochondrial-derived peptide genes. Cancer cells display aerobic glycolysis, known as the Warburg effect, which arises from the needs of fast-dividing cells and is characterized by increased glucose uptake and conversion of glucose to lactate. Solid tumors often contain at least one mtDNA substitution. Furthermore, it is common for cancer cells to harbor mixtures of wild-type and mutant mtDNA genotypes, known as heteroplasmy. Considering the increase in cancer cell energy demand, the presence of functionally relevant carcinogenesis-inducing or environment-adapting mtDNA mutations in cancer seems plausible. We review 279 EC tumor-specific mtDNA single nucleotide variants from 111 individuals from different studies. Many transition mutations indicative of error-prone DNA polymerase γ replication and C to U deamination events were present. We examine the spectrum of mutations and their heteroplasmy and discuss the potential biological impact of recurrent, non-synonymous, insertion, and deletion mutations. Lastly, we explore current EC treatments, exploiting cancer cell mitochondria for therapy and the prospect of using mtDNA variants as an EC biomarker.

Advances in transdermal siRNAs delivery: A review of current research progress.

Small interfering RNA (siRNAs) is a double-stranded RNA molecule which can hybridize with a specific mRNA sequence and block the translation of numerous genes to regulate endogenous genes and to defend the genome from invasive nucleic acids. The use of siRNAs has been studied as a treatment option for various skin conditions. One of the main obstacles in the dermal or transdermal delivery of this compound is low skin permeability, and application is limited by its negative charge, high polarity, susceptibility to degradation by nucleases, and difficulty in penetrating the skin barrier. Effective delivery of therapeutic biomolecules to their target is a challenging issue, which can be solved by innovations in drug delivery systems and lead to improvement of the efficiency of many new biopharmaceuticals. Designing of novel transdermal delivery systems garnered tremendous attention in both cosmeceutical and pharmaceutical research and industries, which offers a number of advantages. Developing safe and efficient siRNAs delivery vectors is essential for effective treatment of skin diseases. In recent years, significant progress has been made in the creation of delivery systems using lipids, polymers, cell-penetrating peptides, nanoparticles and other biologically active agents. In this review we will focus on the recent advancements in transdermal siRNAs delivery vectors, such as liposomes, dendrimers, cell-penetrating peptides, and spherical nucleic acid nanoparticles.

Possibilities of using mussels (Mytilus galloprovincialis) to predict rotavirus contamination in Albania.

Rotaviruses are non-enveloped viruses that each consist of 11 double-stranded RNA molecules. These viruses are able to persist in the environment, and therefore play a fundamental role in the epidemiology of gastroenteritis and severe diarrhoea in children worldwide. While mussels have been primarily used as indicators of chemical pollution, they can also be used to monitor viral contamination. The purpose of this study was to demonstrate that the Mytilus galloprovincialis mussel can also be used to detect microbial contamination, owing to its tendency to naturally concentrate viruses and other pathogens. A total of 102 Mytilus galloprovincialis mussel samples from Albania were collected over a three-year period: 37 samples off the Cape of Stillo in 2015, 39 samples from Butrinti Lake in 2019 and 26 samples from Butrinti Lake in 2021. The presence of rotavirus in the Cape of Stillo samples in 2015 was noted in 47% of samples from site 1, 33% from site 2, and 52% from site 3. In Butrinti Lake the percentage of infected individuals in 2019 was 33% from site 1, 41% from site 2, and 33% from site 3, whereas in 2021, it was 50% from site 1, 19% from site 2, and 0% from site 3. In total the percentage of infected individuals off the Cape of Stillo in 2015 was 44%, in Butrinti Lake in 2019 it was 36%, and in Butrinti Lake in 2021 it was 23 %. These results indicate the presence of rotavirus in the shellfish specimens tested, and further analysis is needed to assess the potential health risks associated with consuming these shellfish. This study also indicates that mussels can be used in marine virological surveillance programmes.

Comparative analysis of the mitochondrial genomes of the family Mactridae (Mollusca: Venerida) and their phylogenetic implications

Taxonomy and phylogenetic relationships within the family Mactridae have remained debatable because of the plasticity of morphological characteristics and the lack of accurate molecular data, thereby resulting in abundant synonyms and taxa rearrangements. Mitochondrial genomes (mitogenomes) have been widely used as powerful tools to reconstruct phylogenies of various groups of mollusks; however, they have not been used for studying the phylogeny of mactrids specifically. In the present study, mitogenomes of seven Mactridae species, namely Mactra chinensis, Mactra cygnus, Mactra quadrangularis, Mactra cumingii, Mactrinula dolabrata, Raeta pulchella, and Raeta sp., were sequenced by Illumina high-throughput sequencing, and a comparative mitochondrial genomic analysis was conducted. The newly sequenced mitogenomes were double-stranded circular molecules, with all functional genes encoded on the heavy strand. All the new mactrid mitogenomes had two rRNA genes (12S and 16S), 13 protein-coding genes (PCGs) (atp6, cox1, cox2, cox3, cytb, nad1, nad2, nad3, nad4, nad4l, nad5, nad6, and atp8), and 22 tRNAs. The mitogenomes showed considerable variation in AT content, GC skew, and AT skew. The results of the phylogenetic analysis confirmed monophyly of the family Mactridae and suggested that genera Mactrinula, Spisula, Rangia, and Mulinia should not be placed under subfamily Mactrinae. Our results supported that potential cryptic species existed in Mactra antiquata. We also proposed subfamily Kymatoxinae should belong to the family Mactridae rather than Anatinellidae and Mactra alta in China should be Mactra cygnus. Additionally, conservation in functional gene arrangement was found in genera Mactra, Raeta, and Lutraria. But gene orders in S. sachalinensis and S. solida were quite different, questioning their congeneric relationship. Our results further suggested that the taxonomy within the family Mactridae requires an integrative revision.

Packaging of DNA Integrated with Metal Nanoparticles in Solution.

The transformation of high-molecular DNA from a random swollen coil in a solution to a discrete nanosized particle with the ordered packaging of a rigid and highly charged double-stranded molecule is one of the amazing phenomena of polymer physics. DNA condensation is a well-known phenomenon in biological systems, yet its molecular mechanism is not clear. Understanding the processes occurring in vivo is necessary for the usage of DNA in the fabrication of new biologically significant nanostructures. Entropy plays a very important role in DNA condensation. DNA conjugates with metal nanoparticles are useful in various fields of nanotechnology. In particular, they can serve as a basis for creating multicomponent nanoplatforms for theranostics. DNA must be in a compact state in such constructions. In this paper, we tested the methods of DNA integration with silver, gold and palladium nanoparticles and analyzed the properties of DNA conjugates with metal nanoparticles using the methods of atomic force microscopy, spectroscopy, viscometry and dynamic light scattering. DNA size, stability and rigidity (persistence length), as well as plasmon resonance peaks in the absorption spectra of systems were studied. The methods for DNA condensation with metal nanoparticles were analyzed.

Complete mitogenomes characterization and phylogenetic analyses of Ceratophyllus anisus and Leptopsylla segnis.

Fleas are one of the most common ectoparasites in warm-blooded mammals and an important vector of zoonotic diseases with serious medical implications. We sequenced the complete mitochondrial genomes of Ceratophyllus anisus and Leptopsylla segnis for the first time using high-throughput sequencing and constructed phylogenetic relationships. We obtained double-stranded circular molecules of lengths 15,875 and 15,785 bp, respectively, consisting of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and two control regions. AT-skew was negative in both C. anisus (-0.022) and L. segnis (-0.231), while GC-skew was positive in both (0.024/0.248), which produced significant differences in codon usage and amino acid composition. Thirteen PCGs encoding 3,617 and 3,711 codons, respectively, isoleucine and phenylalanine were used most frequently. The tRNA genes all form a typical secondary structure. Construction of phylogenetic trees based on Bayesian inference (BI) and maximum likelihood (ML) methods for PCGs. The results of this study provide new information for the mitochondrial genome database of fleas and support further taxonomic studies and population genetics of fleas.