Mfold web server for nucleic acid folding and hybridization prediction

Computational identification and experimental validation of novel Saccharum officinarum microRNAs along with their targets through RT-PCR approach

Various metabolic and cell signaling processes impact the functions of sugarcane plant cells. MicroRNAs (miRNAs) play critical regulatory roles in enhancing yield and providing protection against various stressors. This study seeks to identify and partially characterize several novel miRNAs in sugarcane using in silico tools, while also offering a preliminary assessment of their functions. This was accomplished by predicting novel conserved miRNAs in sugarcane plants using a variety of genomics-based techniques like BLASTn, MFOLD, psRNA Target, sequence logo, Weblogo, primer-3, etc. and annotated using miRBase and NCBI. For validation, RT-PCR method was used along with agarose gel. After the preparation of fourteen randomly chosen primers, they were validated by RT-PCR. Accordingly, they contain fifty specific targeted proteins with substantial targets in the structural, transcriptional protein, etc. Furthermore, the sof-miR5025a directs the heat repeat protein while the voltage-dependent anion is governed by sof-miR8005a. Similarly, the sof-miR7768b and sof-miR6249b monitor the pathogenesis-related protein and zinc finger, C2H2 type protein, which assist as transcription factors. Thus, the novel sugarcane miRNAs target a wide range of important genes help regulate the environment for sugarcane to generate a higher-quality crop.

Programming anti-ribozymes to sense trigger RNAs for modulating gene expression in mammalian cells

Synthetic RNA-based switches provide distinctive merits in modulating gene expression. Simple and flexible RNA-based switches are crucial for advancing the field of gene regulation, paving the way for innovative tools that can sense and manipulate cellular processes. In this research, we have developed programmable ribozymes that are capable of suppressing gene expression in response to specific, endogenously expressed trigger RNAs. We engineer ribozymes by introducing upstream antisense sequences (anti-ribozymes) to inhibit the self-cleaving activity of the hammerhead ribozyme and open the expression of the target gene. The trigger RNA is designed to recognize and bind to complementary sequences within the anti-ribozymes, thereby inhibiting their ability to direct protein synthesis. The anti-ribozyme performance is optimized by regulating the essential sequence modules that play a crucial role in determining the specificity and efficiency of the anti-ribozyme's interaction with its trigger RNA. By applying this switch mechanism to various ribozyme designs, we have shown that it is possible to achieve control over gene expression across a wide range of trigger RNAs. By exploiting these programmable anti-ribozymes, we aim to create a powerful tool for controlling gene expression in mammalian cells, which could have important implications for basic research, disease diagnosis, and therapeutic interventions.

An electrochemical quinine detection approach based on small molecule promoted split aptamer click ligation reaction

Quinine is a natural antimalarial drug that also serves as a food additive; however, excessive consumption can result in harmful side effects. Here, we propose a simple and cost-effective electrochemical strategy for quinine detection based on the small molecule-templated split aptamer click ligation (SMT-SpA-CLR), where the integrity of the aptamer is restored through the template-promoted proximity effect. We first investigate the effects of two splitting sites on the affinity of quinine aptamer and find that the loop of the stem with more Watson-Crick base pairs is more suitable for splitting, which can maintain the affinity to a great extent. The affinity of the Split 1 design (Kd = 48 μM) is slightly reduced compared to the affinity of the parent aptamer. The stable quinine recognition and its sensitive detection are achieved by integrating the SMT-SpA-CLR with an electrochemical signal output. The linear response range for quinine detection is from 0.05 μM to 10 μM with a low detection limit of 25 nM (at S/N = 3). This strategy provides a novel ideal for the design of small molecule-templated split aptamer reaction and can potentially be expanded for detecting other small molecules and proteins.

Novel strategy for screening aptamers of Staphylococcus aureus enterotoxin A based on active fragments and fusion design

BACKGROUND

Staphylococcus aureus enterotoxin A (SEA) is the major toxin responsible for food poisoning caused by Staphylococcus aureus infection. Aptamers are an ideal solution for visual detection of SEA. However, screening for aptamers is generally expensive and time-consuming. Therefore, a new method for efficient screening of high-affinity SEA aptamers needs to be established and supplemented with smartphone image recognition to enable visual and rapid detection of SEA.

RESULTS

A new aptamer for sensitive detection of SEA was screened using active fragments and fusion design. The novel high-affinity aptamer (BX1) was derived by intercepting active nucleotide fragments of several aptamers and fusing them; it was verified to have high affinity, with a Kd value of 4.16 ± 0.22 nM. Molecular dynamic simulation illustrated that BX1 formed a stable complex conformation with SEA, which maintained its stability for 200 ns. This novel aptamer can be used for visual inspection of SEA. A smartphone-assisted aptasensor was designed to sensitively detect SEA in milk with a wide linear range (1-250 ng/mL), low detection limit (0.42 ng/mL), and satisfactory spiked recovery.

SIGNIFICANCE

A new method for screening SEA aptamers based on active fragments and fusion design was developed, which can rapidly screen high-affinity aptamers in a short duration and at a low expenditure. In addition, a new strategy for the rapid detection of SEA using a smartphone-assisted colorimetric aptamer sensor was successfully applied. This research method may provide a reference for the highly sensitive detection of other biotoxins.

The influence of downstream structured elements within mRNA on the dynamics of intersubunit rotation in ribosomes

Proper codon/anticodon pairing within the ribosome necessitates linearity of the transcript. Any structures formed within a messenger RNA (mRNA) must be unwound before the respective codon is interpreted. Linearity, however, is not always the norm; some intricate structures within mRNA are able to exert unique ribosome/mRNA interactions to regulate translation. Intrinsic kinetic and thermal stability in many of these structures are efficient in slowing translation causing pausing of the ribosome. Altered translation kinetics arising from atypical interactions have been shown to affect intersubunit rotation. Here, we employ single-molecule Förster resonance energy transfer (smFRET) to observe changes in intersubunit rotation of the ribosome as it approaches downstream structured nucleic acid. The emergence of the hyperrotated state is critically dependent on the distance between downstream structure and the ribosome, suggesting interactions with the helicase center are allosterically coupled to intersubunit rotation. Further, molecular dynamics (MD) simulations were performed to determine ribosomal protein/mRNA interactions that may play a pivotal role in helicase activity and ultimately unwinding of downstream structure.

Adaptive SELEX Strategies Against HCV Core Protein Lead to the Same Aptamer

Herein, we demonstrate the accuracy of aptamer selection among different SELEX procedures, in different labs, using different variations of the same target and slightly different aptamer initial libraries. In our lab, we have selected DNA aptamers against HCV core protein by applying two consecutive selection approaches (in which two different variations of the target were used): using lysates of E. coli M15 bacteria expressing full-length HCV core protein (genotype 1a) as well as mature HCV core recombinant protein (genotype 1b). Three aptamers were finally identified: AptHCV14F, AptHCV4.2F and AptHCV7.2R, from which AptHCV14F resulted to be identical (within the variable region) to the previously reported (in this journal) aptamer AptD-1312. Functionality of these aptamers were deeply investigated by SPR and ELONA, resulting as high affinity binders of HCV core protein suitable for the development of new generation tools for hepatitis c virus detection and screening.

Role of the SAF-A/HNRNPU SAP domain in X chromosome inactivation, nuclear dynamics, transcription, splicing, and cell proliferation

SAF-A/HNRNPU is conserved throughout vertebrates and has emerged as an important factor regulating a multitude of nuclear functions, including lncRNA localization, gene expression, and splicing. Here we show the SAF-A protein is highly dynamic and interacts with nascent transcripts as part of this dynamic movement. This finding revises current models of SAF-A: rather than being part of a static nuclear scaffold/matrix structure that acts as a stable tether between RNA and chromatin, SAF-A executes nuclear functions as a dynamic protein, suggesting contacts between SAF-A, RNA, and chromatin are more high turnover interactions than previously appreciated. SAF-A has several functional domains, including an N-terminal SAP domain that binds directly to DNA and RNA. Phosphorylation of SAP domain serines S14 and S26 are important for SAF-A localization and function during mitosis, however whether these serines are involved in interphase functions of SAF-A is not known. In this study we tested for the role of the SAP domain, and SAP domain serines S14 and S26 in X chromosome inactivation, protein dynamics, gene expression, splicing, and cell proliferation. Here we show that the SAP domain, and SAP domain serines S14 and S26 are required to maintain XIST RNA localization and XIST-dependent histone modifications on the inactive X chromosome, to execute normal protein dynamics, and to maintain normal cell proliferation. In addition, we present evidence that a Xi localization signal resides in the SAP domain, enabling SAF-A to engage with the Xi compartment in a manner distinct from other nuclear territories. We found that the SAP domain is not required to maintain gene expression and plays only a minor role in mRNA splicing. We propose a model whereby dynamic phosphorylation of SAF-A serines S14 and S26 mediates rapid turnover of SAF-A interactions with nuclear structures during interphase. Our data suggest that different nuclear compartments may have distinct requirements for the SAF-A SAP domain to execute nuclear functions, a level of control that was not previously known.

PCR-based SNP genotyping: A comprehensive comparison of methods for affordable and accurate detection of class IV mutations

Single nucleotide polymorphisms (SNPs) influence gene function and impact health and disease. Identifying and genotyping SNPs is crucial in various areas of research and applications. This study compared five PCR-based methods for detecting a challenging T-to-A SNP, rs9939609: ARMS-PCR, PIRA-PCR, TaqMan qPCR, CADMA with HRM, and HRM, using snapback primers. Sanger sequencing served as the gold standard. Five assays were designed and compared for genotyping rs9939609. Performance was evaluated based on affordability, ease of use, robustness, and sensitivity. Melting curve analysis was used for the CADMA and snapback primer HRM assays. All methods successfully genotyped the rs9939609 variant. ARMS-PCR was the simplest and most cost-effective method but was potentially less sensitive. PIRA-PCR offered increased sensitivity but required specific restriction enzymes, increasing cost and complexity. TaqMan qPCR was fast and sensitive but expensive due to probe requirements. The combination of CADMA with HRM balanced affordability and speed with good sensitivity and applicability to standard qPCR platforms. The snapback primer HRM offered high sensitivity but required longer assay times and careful optimization. CADMA emerged as the most balanced method, combining affordability with sensitivity and comparable to that of Sanger sequencing and TaqMan qPCR. Its effectiveness for challenging mutations and compatibility with standard qPCR platforms make it a practical choice for various laboratories. Each method offers trade-offs in cost, sensitivity, and complexity, catering to specific research and diagnostic needs. Future advancements may further refine these techniques for broader application.

Impact of a single 8-oxoguanine lesion on Watson-Crick and Hoogsteen base pair hybridization in telomeric DNA quantified using single-molecule force spectroscopy

8-Oxoguanine (8-oxoG) is a common DNA oxidative lesion prevalent in telomeric regions. However, the impact of 8-oxoG modification on the Watson-Crick base pairing energy remains controversial, potentially due to the formation of partially folded intermediates. Here, we used single-molecule magnetic tweezers to characterize the mechanical stability and equilibrium folding/unfolding transitions of human telomeric hairpins containing a single 8-oxoG lesion at different positions. Our results reveal that fully folded hairpins with a centrally located 8-oxoG exhibit similar hybridization energy (ΔΔG ∼ 1 kBT) and folding/unfolding rates to the wild type. This provides valuable data for refining the energy contribution of 8-oxoG-C base pair. In contrast, a single 8-oxoG lesion near the unzipping termini (5'-end or 3'-end) significantly enhances end fraying and hinders the complete folding of the hairpin under force. A 5'-end 8-oxoG lesion increased the unfolding rates by a 130-fold compared to the wild type at 10.1 pN. These findings provide insights into the unzipping dynamics of DNA duplexes containing 8-oxoG lesions at replication and transcription forks. Furthermore, we observed that an 8-oxoG at 5'-end of telomeric G-quadruplexes (G4s) significantly decreases folding rates and folding free energy (from 5.9 kBT to 2.3 kBT), shedding light on the dynamics of G4s under oxidative stress.

Quantum Mechanical Tunnelling Probes with Redox Cycling for Ultra-Sensitive Detection of Biomolecules

Quantum mechanical tunnelling sensors (QMTs) have emerged as a promising technology for next-generation single-molecule detection. Furthermore, QMT sensors can be combined with redox species resulting in repeated oxidation and reduction (redox cycling).. We developed robust QMT probes with electrode gap distances below 2 nm. Using the generator-collector (GC) mode, we verified that redox cycling of the ferrocyanide/ferricyanide (Fe(CN)6 3-/4-) couple occurs both in the tunnelling regime and on the electrode surface. Our findings indicated that the current enhancement is affected by both the gap distance and surface modifications of the probes. These QMT probes exhibited remarkable sensitivity, capable of detecting Fe(CN)6 3-/4- concentrations down to sub-picomolar levels. Utilising this ability to modulate redox reactions, we adapted the QMT probes to serve as electrochemical sensors for detecting viral proteins. By modifying the electrode surfaces, our functionalised QMT probes achieved sub-pM detection limits with high selectivity in biofluids such as nasopharyngeal secretions. These findings highlight the potential of QMT probes to develop into a new class of electrochemical tunnelling sensors, offering significant advancements in biomedical diagnostics.

Resolution of complex mixtures of duplex and antiparallel triplex DNA structures by capillary electrophoresis and multivariate analysis

Triplex DNA structures, which are formed by the addition of an extra strand to a target B-DNA duplex, have attracted increasing interest due to their analytical and therapeutic applications. These structures are classified into parallel and antiparallel, depending on the orientation of the Triplex-Forming Oligonucleotide (TFO) relative to the B-DNA duplex. Whereas the formation of parallel triplexes is easily detected by monitoring spectral changes in the UV region, the formation of antiparallel triplexes produces small or even no spectral variations, which makes their detection difficult and uncertain. In this study, we propose the use of capillary electrophoresis with ultraviolet absorption spectrophotometric (CE-UV) detection combined with the multivariate curve resolution-alternating least squares (MCR-ALS) chemometric method to analyse mixtures of DNA sequences capable of forming mixtures of B-DNA duplex and triplex antiparallel structures. Rapid and reproducible CE-UV analysis in hydroxypropylcellulose (HPC)-coated capillaries are done in a pH 7.4 buffer containing Mg(II) for the stabilization of the intermolecular species. Spectra measured from 220 to 300 nm along the CE-UV analysis of individual DNA strands and of their mixtures at different ratios are merged into an augmented data matrix. This is later analyzed with MCR-ALS to deconvolute characteristic pure spectra and electropherograms for each one of the CE-UV analysis considered. This procedure has allowed the resolution and detection of DNA species present in mixtures of DNA strands capable of forming duplexes, as well as antiparallel triplex structures.

Split-and-pool synthesis to generate scalable combinatorial oligonucleotide libraries on magnetic nanoparticles

The generation of combinatorial oligonucleotide libraries is desirable for applications such as DNA aptamers, data storage, DNA origami, or synthetic genomes, but conventional libraries present challenges in detection and analysis. Synthesis of unique oligonucleotide sequences on magnetic nanoparticles would enhance the ability to manipulate, recover, and detect them. Here, we present a protocol for generating a scalable combinatorial oligonucleotide library on magnetic nanoparticles using split-and-pool synthesis. We then describe the process for preparing the library for conventional and next-generation sequencing (NGS) DNA sequencing. For complete details on the use and execution of this protocol, please refer to Nguyen et al.1.

A bacterial regulatory uORF senses multiple classes of ribosome-targeting antibiotics

Expression of many bacterial genes is regulated by cis- and trans-acting elements in their 5' upstream regions (URs). Cis-acting regulatory elements in URs include upstream ORFs (uORFs), short ORFs that sense translation stress that manifests as ribosomes stalling at specific codons within the uORF. Here, we show that the transcript encoding the Escherichia coli TopAI-YjhQ toxin-antitoxin system is regulated by a uORF that we name 'toiL'. We propose that in the absence of translation stress, a secondary structure in the UR represses translation of the topAI transcript by occluding the ribosome-binding site. Translation repression of topAI leads to premature Rho-dependent transcription termination within the topAI ORF. At least five different classes of ribosome-targeting antibiotics relieve repression of topAI. Our data suggest that these antibiotics function by stalling ribosomes at different positions within toiL, thereby altering the RNA secondary structure around the topAI ribosome-binding site. Thus, toiL is a multipurpose uORF that can respond to a wide variety of translation stresses.

An Efficient Luminol-H2O2 Electrochemiluminescence System with Porous Bimetallic Organic Gels as Signal Booster and Elaborate Heterosequence Aptamer as Recognition Component for Ultrasensitive Biosensing

Herein, an efficient luminol-H2O2 electrochemiluminescence (ECL) system with bimetallic organic gels as an ECL signal booster and an innovative heterosequence aptamer recognition as a target conversion strategy is used to construct a sensitive and specific ECL aptasensor for the detection of β2-microglobulin (B2M), a key biomarker for end-stage renal disease (ESRD). Impressively, the porous Fe@Cu bimetallic organic gels (Fe@Cu MOGs) act as coreaction accelerators and confinement-enhanced reactors of the luminol-H2O2 ECL system, amplifying the ECL signal by 21-fold compared to the traditional luminol-H2O2 ECL system, which greatly enhanced the sensitivity of the biosensor. Compared to the homosequence aptamer approach with competitive binding of aptamers to a single site, the heterosequence aptamer approach with synergistic binding to multiple sites could greatly improve the specificity of aptasensor, which is validated by experiments and molecular docking simulations. Therefore, the developed aptasensor exhibits a remarkable dynamic range of 10 fg/mL-1 μg/mL with an ultralow detection limit of 0.9 fg/mL, which is superior to previously reported works. Additionally, the aptasensor demonstrated consistent performance with conventional clinical immunoturbidimetric assays for high B2M concentration detection in 14 clinical samples, as well as exhibiting superior sensitivity for trace B2M levels that are undetectable by immunoturbidimetry. This strategy offers a sensitive and accurate platform for biomarker recognition, with promising applications in trace clinical biomarker detection, disease diagnosis, and therapeutic monitoring, as well as in advancing scientific research on early pathological changes and biomarker discovery.

Inhibition of PolyGA Dipeptide Repeat Protein Aggregation by Nucleic Acid Aptamers in C9 Amyotrophic Lateral Sclerosis-Frontotemporal Dementia Models

Hexanucleotide (GGGGCC) repeat expansion in non-coding region of C9ORF72 is the main genetic cause of amyotrophic lateral sclerosis-frontotemporal dementia (ALS-FTD). Gain of toxic function, via RNA or proteins, or loss of function via haploinsufficiency, are probable mechanisms of disease progression. Expanded GGGGCC repeat codes for dipeptide repeat (DPR) proteins which form inclusions in the brain. Among all the dipeptides, aggregates formed by polyGA sequence are the most toxic. In this work, inhibition of aggregation of polyGA DPRs using aptamers has been explored as a therapeutic strategy to delay disease progression. Target-specific, high-affinity RNA aptamers were selected against monomeric (GA)30. Selected aptamers showed significant inhibition of aggregation of (GA)30 in vitro. Inhibitory RNA sequences were seen to form typical secondary structures which was missing in a non-inhibitory sequence. Some of the RNA aptamers showed increased solubilisation of DPRs formed by (GA)30 and (GA)60 in a neuronal cell model of ALS-FTD. Decreased aggregation was accompanied by lower oxidative stress and improved cell survival. Importantly, expression level of one of the markers of autophagy was significantly enhanced in the presence of aptamers, explaining lower aggregation observed in these cells. Thus, aptamers may be developed as potential therapeutic agents in C9 ALS-FTD.

Prevalence of Group II Introns in Phage Genomes

Although bacteriophage genomes are under strong selective pressure for high coding density, they are still frequently invaded by mobile genetic elements (MGEs). Group II introns are MGEs that reduce host burden by autocatalytically splicing out of RNA before translation. While widely known in bacterial, archaeal, and eukaryotic organellar genomes, group II introns have been considered absent in phage. Identifying group II introns in genome sequences has previously been challenging because of their lack of primary sequence similarity. Advances in RNA structure-based homology searches using covariance models has provided the ability to identify the conserved secondary structures of group II introns. Here, we discover that group II introns are widely prevalent in phages from diverse phylogenetic backgrounds, from endosymbiont phage to jumbophage.

Designer circRNAGFP reduces GFP-abundance in Arabidopsis protoplasts in a sequence-specific manner, independent of RNAi pathways

KEY MESSAGE

We demonstrate non-immunogenic circRNA as a tool for targeted gene regulation in plants, where it acts in an isoform- and sequence-specific manner, enabling future agronomic applications. Circular RNAs (circRNAs) are single-stranded RNA molecules characterized by their covalently closed structure and are emerging as key regulators of cellular processes in mammals, including gene expression, protein function and immune responses. Recent evidence suggests that circRNAs also play significant roles in plants, influencing development, nutrition, biotic stress resistance, and abiotic stress tolerance. However, the potential of circRNAs to modulate target protein abundance in plants remains largely unexplored. In this study, we investigated the potential of designer circRNAs to modulate target protein abundance in plants using Arabidopsis protoplasts as a model system. We show that PEG-mediated transfection with a 50-nt circRNAGFP containing a 30-nt GFP-antisense sequence results in a dose- and sequence-dependent reduction of GFP reporter target protein abundance. Notably, a single-stranded open isoform of circRNAGFP had little effect on protein abundance, indicating the importance of the closed circular structure. Additionally, circRNAGFP also reduced GFP abundance in Arabidopsis mutants defective in RNA interference (RNAi), suggesting that circRNA activity is independent of the RNAi pathway. We also show that circRNA, unlike dsRNA, does not induce pattern-triggered immunity (PTI) in plants. Findings of this proof-of-principle study together are crucial first steps in understanding the potential of circRNAs as versatile tools for modulating gene expression and offer exciting prospects for their application in agronomy, particularly for enhancing crop traits through metabolic pathway manipulation.

Gated Nanosensor for Sulphate-Reducing Bacteria Detection

Desulfovibrio vulgaris is an anaerobic microorganism belonging to the group of sulphate-reducing bacteria (SRB). SRB form biofilms on metal surfaces in water supply networks, producing a microbiologically influenced corrosion (MIC). This process produces the deterioration of metal surfaces, leading to high economic costs and different environmental safety and health problems related to its chemical treatment. For that reason, rapid and accurate detection methods of SRB are needed. In this work, a new detection system for Desulfovibrio has been developed using gated nanoporous materials. The probe is based on hybrid nanoporous alumina films encapsulating a fluorescent molecule (rhodamine B), whose release is controlled by an oligonucleotide gate. Upon exposure to Desulfovibrio's genomic material, a movement of the oligonucleotide gatekeeper happens, resulting in the selective delivery of the entrapped rhodamine B. The developed material shows high selectivity and sensitivity for detecting Desulfovibrio DNA in aqueous buffer and biological media. The implementation of this technology for the detection of Desulfovibrio as a tool for monitoring water supply networks is innovative and allows real-time in situ monitoring, making it possible to detect the growth of Desulfovibrio inside of pipes at an early stage and perform timely interventions to reverse it.

pTripleTREP - A vector for tightly controlled expression and purification of virulence factors in Staphylococcus aureus

BACKGROUND

Recombinant proteins facilitate and contribute to detailed studies of the virulence mechanisms and pathophysiology of the major human pathogen Staphylococcus aureus. Of particular interest are secreted virulence factors. However, due to their potential toxicity and specific post-translational processing, virulence factors are difficult targets for heterologous protein production. Purified proteins with native conformation and adequate purity can therefore often only be achieved by elaborate multi-step purification workflows. While homologous expression in S. aureus theoretically offers a promising alternative in this regard, its application remains limited due to the lack of systems that ensure both tightly controlled expression and subsequent efficient purification.

RESULTS

To bridge this gap, we present pTripleTREP as a versatile expression vector for S. aureus, which enables the homologous expression and purification of staphylococcal virulence factors. It features a strong SigA-dependent staphylococcal promoter overlapped by three tetracycline responsive elements (TRE), which ensures tight repression under control conditions and high expression levels upon induction of the target gene. This allowed very precise controlled production of the exemplary targets, serine protease-like protein A (SplA) and B (SplB). A simple single-step protein purification workflow using a Twin-Strep-tag and Strep-Tactin®XT coated magnetic beads yielded endotoxin-free Spl samples with purities above 99%. Thereby, the homologous production host facilitates native secretion and maturation without the need to engineer the target gene sequence. Proper signal peptide cleavage and the corresponding enzymatic activity of the generated protein products were confirmed for SplA and B.

CONCLUSION

The expression vector pTripleTREP adds an important element to the staphylococcal molecular toolbox, facilitating the tightly controlled homologous expression and rapid native purification of secreted staphylococcal virulence factors. The optimised architecture and genetic features of the vector additionally provide a solid background for further applications such as plasmid-based complementation or interaction studies. Thus, pTripleTREP will support research on the role of staphylococcal virulence factors, paving the way for future therapeutic strategies to combat this pathogen.

A novel anti-PD-L1 DNA aptamer, Apta35 enhances non-small cell lung cancer cell cytotoxicity and apoptosis through lung cancer-activated T lymphocytes

The prevalence of Programmed death ligand 1 (PD-L1) expression in the population of NSCLC patients and blocking the PD1/PD-L1 pathway by inhibiting the PD-1 receptor on immune cells or the PD-L1 ligand on tumour and/or immune cells can inhibit tumour growth. EFBALite algorithm that enables efficient and cost-effective selection of aptamers, expediting the process. Here, we present the development, computational validation, and in vitro analysis of NSCLC of DNA aptamers targeting PD-L1. The Gibbs free energy of two anti-PD-L1 aptamers, Apta35 and Apta90 with -3.06 and - 2.4 kcal/mol respectively. The docking score for Apta35 was -272.3 and 1171.765 for HDOCK and ZDOCK respectively. Further, the Apta35 was taken for the in vitro studies as it was more stable and incubated with NCI-H460. Initially, we confirmed the binding of the TAMRA-labelled Apta35 to the NCI-H460 cell surface through microscopic imaging and further confirmed through FACS analysis. Further experimental results showed that the Apta35 treated along with the act-T cells group reduced the percentage of viability (28 ± 3.5), increased toxicity, and reduced count of NCI-H460 cells when compared with the cells treated only with the act-T cells concerning the treatment to 50 nM concentration. In summary, targeting PD-L1 with a specific aptamer provides an innovative strategy for targeting NSCLC. Apta35 aptamer showed no significant toxicity in the BALB/c nude mice while it was injected every 2 days for a total of 12 days of treatment.

Large-scale prediction shows that the dominant structure of the HIV-1 domain closed by the U5-AUG duplex contains the alternative SDa hairpin, and the domain variant without SD is rare

Using several models of the HIV-1 5' leader, it was shown that the domain containing the structural elements that regulate the processes of dimerization and genome packaging, as well as the initiation of reverse transcription, is closed by the U5-AUG duplex. However, there is no consensus in the literature on the structure of the upper part of this domain. Currently, the model proposed by Keane et al. in 2015 is dominant, although the question of whether it is general structure or specific to the experimental HIV-1 genome NL4-3 of subtype B remains open. To clarify this issue, we conducted large-scale in silico studies on the secondary structure of the domain closed by the U5-AUG duplex in 2754 HIV-1 genomes of different subtypes. Our investigation showed that the proportion of HIV-1 genomes in which the structure of the domain under study is similar to that in Keane et al. model is low. It forms mainly in HIV-1 genomes of subtype B with the frequency of 3.8 % in the optimal foldings or foldings with the energy increment of the lowest change in free energy (ΔΔG)<1.0 kcal/mol. In particular, certain base changes in common SD hairpin or base changes stabilizing Psi hairpin contribute to the formation of this domain variant. The dominant structure of the domain closed by the U5-AUG duplex is similar to that in Wilkinson et al. model (2008) but with the alternative SD hairpin. We found also new variants of this domain, which occur in foldings with ΔΔG<1.0 kcal/mol and may co-exist with dominant structure. However, it is possible that the variants of the domain closed by the U5-AUG duplex similar to Wilkinson et al. or Keane et al. models are formed only in the early stages of HIV-1 replication, while in the late stage (in the presence of nucleocapsid protein) the domain adopts structure similar to that in Sakuragi et al. (2012) model and the initiation of the reverse transcription occurs just in this structure. Extreme conservation of GACGC-GCGUC duplex, proposed in Sakuragi et al. model, supports this assumption.

Molecular mechanisms driving the unusual pigmentation shift during eggplant fruit development

Fruit pigmentation is a major signal that attracts frugivores to enable seed dispersal. In most fleshy fruit, green chlorophyll typically accumulates early in development and is replaced by a range of pigments during ripening. In species such as grape and strawberry, chlorophyll is replaced by red anthocyanins produced by the flavonoid biosynthetic pathway. Eggplant (Solanum melongena) is unique, as its fruit accumulates anthocyanins beginning from fruit set, and these are later replaced by the yellow flavonoid-pathway intermediate naringenin chalcone. To decipher the genetic regulation of this extraordinary pigmentation shift, we integrated mRNA and microRNA (miRNA) profiling data obtained from developing eggplant fruit. We discovered that SQUAMOSA PROMOTER BINDING-LIKE (i.e., SPL6a, SPL10, and SPL15), MYB1, and MYB2 transcription factors (TFs) regulate anthocyanin biosynthesis in early fruit development, whereas the MYB12 TF controls later accumulation of naringenin chalcone. We further show that miRNA157 and miRNA858 negatively regulate the expression of SPLs and MYB12, respectively. Taken together, our findings suggest that opposing and complementary expression of miRNAs and TFs controls the pigmentation switch in eggplant fruit skin. Intriguingly, despite the distinctive pigmentation pattern in eggplant, fruit development in other species makes use of homologous regulatory factors to control the temporal and spatial production of different pigment classes.

Viscous dissipation in the rupture of cell-cell contacts

Cell-cell adhesions mediated by adherens junctions, structures connecting cells to each other and to the cortical cytoskeleton, are essential for epithelial physical and biological integrity. Nonetheless, how such structures resist mechanical stimuli that prompt cell-cell rupture is still not fully understood. Here we challenge the conventional views on cell-cell adhesion stability, highlighting the importance of viscous dissipation at the cellular level. Using microdevices to measure the rupture energy of cell-cell junctions and synthetic cadherins to discriminate cadherin binding energy from downstream cytoskeletal regulation, we demonstrate that the balance between cortical tension and cell shape recovery time determines a transition from ductile to brittle fracture in cell-cell contact. These findings suggest that junction toughness, defined as the junction disruption energy, is a more accurate measure of junctional stability, challenging the current emphasis on bond energy and tension. Overall, our results highlight the role and the regulation of energy dissipation through the cytoskeleton during junction deformation for epithelial integrity.

Integrated Taxonomic Approaches to Gastrointestinal and Urinary Capillariid Nematodes from Wild and Domestic Mammals

Fine nematodes of the family Capillariidae parasitize various organs and tissues in fish, amphibians, reptiles, avians, and mammals. Currently classified into more than 20 genera, these nematodes are primarily distinguished based on the caudal structures of male worms. Morphological and molecular analyses were conducted on 15 mammal-parasitic species belonging to the genera Aonchotheca (A. putorii, A. suzukii n. sp., A. suis n. comb. (syn. Capillaria suis), A. riukiuensis, and A. bilobata), Pearsonema (P. neoplica n. sp., P. feliscati, P. iharai n. sp., and P. toriii n. sp.), Liniscus (L. himizu), Calodium (C. hepaticum), Echinocoleus (E. yokoyamae n. sp.), and Eucoleus (E. kaneshiroi n. sp., E. aerophilus, and Eucoleus sp.), using specimens from various wild and domestic animals in Japan and brown rats in Indonesia. As demonstrated in this study, nearly complete SSU rDNA sequencing is a powerful tool for differentiating closely related species and clarifying the phylogenetic relationships among morphologically similar capillariid worms. Additionally, most capillariid worms detected in dogs and cats are suspected to be shared with their respective wildlife reservoir mammals. Therefore, molecular characterization, combined with the microscopic observation of these parasites in wildlife mammals, provides a robust framework for accurate species identification, reliable classification, and epidemiological assessment.

JAX-RNAfold: scalable differentiable folding

SUMMARY

Differentiable folding is an emerging paradigm for RNA design in which a probabilistic sequence representation is optimized via gradient descent. However, given the significant memory overhead of differentiating the expected partition function over all RNA sequences, the existing proof-of-concept algorithm only scales to ≤50 nucleotides. We present JAX-RNAfold, an open-source software package for our drastically improved differentiable folding algorithm that scales to 1,250 nucleotides on a single GPU. Our software permits the natural inclusion of differentiable folding as a module in larger deep learning pipelines, as well as complex RNA design procedures such as mRNA design with flexible objective functions.

AVAILABILITY AND IMPLEMENTATION

JAX-RNAfold is hosted on GitHub (https://github.com/rkruegs123/jax-rnafold) and can be installed locally as a Python package. All source code is also archived on Zenodo (https://doi.org/10.5281/zenodo.15003072).

Harnessing Synthetic Riboswitches for Tunable Gene Regulation in Mammalian Cells

RNA switches regulated by specific inducer molecules have become a powerful synthetic biology tool for precise gene regulation in mammalian systems. The engineered RNA switches can be integrated with natural RNA-mediated gene regulatory functions as a modular and customizable approach to probe and control cellular behavior. RNA switches have been used to advance synthetic biology applications, including gene therapy, bio-production, and cellular reprogramming. This review explores recent progress in the design and functional implementation of synthetic riboswitches in mammalian cells based on diverse RNA regulation mechanisms by highlighting recent studies and emerging technologies. We also discuss challenges such as off-target effects, system stability, and ligand delivery in complex biological environments. In conclusion, this review emphasizes the potential of synthetic riboswitches as a platform for customizable gene regulation in diverse biomedical applications.

Leaf miRNAs of Withania somnifera Negatively Regulate the Aging-Associated Genes in C. elegans

Aging is a physiological process that culminates in cellular senescence, a phenomenon that has significant implications for health and longevity. Plant-based therapeutics, particularly the root of Withania somnifera, have been reported to delay the onset and progression of aging and its associated disorders, including Alzheimer's disease, Parkinson's disease, and other neurodegenerative disorders. However, the role of leaf-derived microRNAs (miRNAs) from W. somnifera in the molecular regulation of genes involved in aging remains poorly understood. Caenorhabditis elegans serves as an indispensable model organism for studying aging-associated gene regulation due to its short lifespan, conserved human orthologs, and ease of laboratory cultivation. In this study, we explored the regulatory interactions between miRNAs derived from the leaf tissues of W. somnifera and aging-associated genes, utilizing C. elegans as a model organism. We employed bioinformatics to identify miRNAs that interact with aging-associated genes in C. elegans and found that three specific miRNAs in the leaf tissue of W. somnifera interacted with these genes. To assess the physiological effects of these miRNAs on C. elegans, we conducted biochemical assays, including lifespan, chemotaxis, and stress resistance assays. Additionally, we investigated the differential gene expression of the interacting genes in the presence and absence of W. somnifera leaf miRNA treatment using real-time PCR. The results indicated that the expression levels of the age-1 and sel-12 genes were significantly downregulated, while the apl-1 gene was upregulated following treatment with leaf miRNAs in C. elegans. These findings suggest that miRNAs derived from W. somnifera leaves may play a crucial role in regulating aging-associated gene expression. This is the first study, to our knowledge, that identifies the miRNAs of W. somnifera leaf involved in aging-associated gene regulation, thereby paving the way for future research into the therapeutic potential of plant-derived miRNAs in combating age-related disorders.

Artificial intelligence-driven circRNA vaccine development: multimodal collaborative optimization and a new paradigm for biomedical applications

Circular RNA (circRNA) vaccines have emerged as a groundbreaking innovation in infectious disease prevention and cancer immunotherapy, offering superior stability and reduced immunogenicity compared to conventional linear messenger RNA (mRNA) vaccines. While linear mRNA vaccines are prone to degradation and can trigger strong innate immune responses, covalently closed circRNA vaccines leverage their unique circular structure to enhance molecular stability and minimize innate immune activation, positioning them as a next-generation platform for vaccine development. Artificial intelligence (AI) is revolutionizing circRNA vaccine design and optimization. Deep learning models, such as convolutional neural networks (CNNs) and Transformers, integrate multi-omics data to refine antigen prediction, RNA secondary structure modeling, and lipid nanoparticle delivery system formulation, surpassing traditional bioinformatics approaches in both accuracy and efficiency. While AI-driven bioinformatics enhances antigen screening and delivery system modeling, generative AI accelerates literature synthesis and experimental planning-though the risk of fabricated references and limited biological interpretability hinders its reliability. Despite these advancements, challenges such as the "black-box" nature of AI algorithms, unreliable literature retrieval, and insufficient integration of biological mechanisms underscore the necessity for a hybrid "AI-traditional-experimental" paradigm. This approach integrates explainable AI frameworks, multi-omics validation, and ethical oversight to ensure clinical translatability. Future research should prioritize mechanism-driven AI models, real-time experimental feedback, and rigorous ethical standards to fully unlock the potential of circRNA vaccines in precision oncology and global health.

Screening and Identification of Novel DNA Aptamer for Targeted Delivery to Injured Podocytes in Glomerular Diseases

Selective drug delivery to podocytes remains a challenge. Aptamers, nucleic acids that bind specific cells, offer a potential solution, though podocyte-targeting aptamers have not yet been developed. Podocytes stimulated with adriamycin, puromycin aminonucleoside, and high glucose are used to screen an single-stranded DNA (ssDNA) library (10¹⁵ sequences). High-throughput sequencing identifies nucleotide sequences, and the aptamer's affinity, stability, cytotoxicity, uptake, biodistribution (especially to podocyte), target protein and ability to deliver siRNA are evaluated. After 11-14 rounds of selection, high-affinity pools are identified. Sequencing reveals 23,848 unique sequences, narrowed down to 12 candidates. Aptamer S7 is specifically bound to podocytes, and its truncated version, RLS-2, demonstrates superior affinity (50-70 nM) and improved stability with phosphorothioate modifications. RLS-2 exhibits no significant cytotoxicity, is internalized by podocytes, and localized to lysosomes. In adriamycin-induced and diabetic nephropathy mice, RLS-2 preferentially accumulates within glomeruli. Its specificity to podocyte is verified by colocalization examination and quantitated via flowcytometry. EPB41L5 is identified as a target protein. Aptamer-siRNA chimeras based on RLS-2 successfully downregulate gene expression without the need for transfection reagents in vitro. These findings underscore the potential of RLS-2 as a promising agent for the development of podocyte-targeted drug delivery systems.

Novel endornaviruses infecting Phytophthora cactorum that attenuate vegetative growth, promote sporangia formation and confer hypervirulence to the host oomycete

Two novel endornaviruses were found in Phytophthora cactorum isolated from black lesions on Boehmeria nivea var. nipononivea plants in a Japanese forest. These two endornaviruses were named Phytophthora cactorum alphaendornavirus 4 (PcAEV4) and Phytophthora cactorum alphaendornavirus 5 (PcAEV5) and have site-specific nick structures in their positive RNA strands, which are hallmarks of alphaendornaviruses. Ribavirin and cycloheximide treatment of the protoplasts effectively cured the host oomycete (strain Kara1) of the viruses. The resultant virus-free strain (Kara1-C) displayed abundant mycelial growth with less zoosporangia formation as compared to the Kara1 strain. Remarkably, the Kara1-C strain exhibited a reduced ability to form black lesions on B. nivea leaves, suggesting that the presence of PcAEV4 and PcAEV5 in the Kara1 strain led to enhanced virulence in host plants. Under osmotic pressure and cell wall synthesis inhibition, the Kara1 strain exhibited less growth inhibition compared with the Kara1-C strain. In contrast, the Kara1 strain showed more growth inhibition in the presence of membrane-permeable surfactant compared with the Kara1-C strain, indicating that the two endornaviruses can alter the susceptibility of the host oomycete to abiotic stresses. Co-localization and cell fractionation analyses showed that PcAEV4 and PcAEV5 localized to intracellular membranes, particularly the endoplasmic reticulum membrane fraction. Furthermore, infection with these two endornaviruses was found to affect the host's response to exogenous sterols, which enhanced vegetative growth and zoosporangia formation, as well as virulence of the host oomycete. These results provide insights into the effects of endornavirus infection in Phytophthora spp. and also highlight the usefulness of protoplast-based methods in advancing Phytophthora virus studies.

The use of aptamers as therapeutic inhibitors and biosensors of TNF-alpha

Tumor necrosis factor-alpha (TNF-α) is a pivotal cytokine in the pathogenesis of numerous inflammatory and autoimmune diseases. Precise and sensitive detection of TNF-α is essential for both clinical applications and research endeavors. In the realm of cytokine detection, particularly TNF-α, the development of highly sensitive and specific biosensors has become a focal point. The biosensing landscape encompasses a variety of biorecognition elements, each with its unique set of characteristics. TNF inhibitors come with a significant price tag and, notably, do not yield positive responses in all patients. Despite the availability of numerous FDA-approved biologic agents (e.g., infliximab, adalimumab, certolizumab pegol, etc.) and monoclonal antibodies (e.g., adalimumab) targeting TNF-α, aptamers tailored for blocking TNF-α activities have yet to receive approval. Aptamers have rapidly gained recognition as readily available, versatile, and highly effective molecular tools for both therapeutic and diagnostic purposes in the context of TNF-alpha. In this manuscript, we explore the potential of short single-stranded DNA or RNA sequences known as aptamers as biorecognition elements in biosensors designed for the detection of TNF-α. We delve into the progress made in the development of aptamer-based TNF-α inhibitors and shed light on successful studies in this burgeoning field.

Structural analysis of the ribosome assembly factor Nep1, an N1-specific pseudouridine methyltransferase, reveals mechanistic insights

Nucleolar essential protein 1 (Nep1; also known as ribosomal RNA small subunit methyltransferase Nep1) is a crucial factor in forming small ribosomal subunits in eukaryotes and archaea. Nep1 possesses an S-adenosyl-L-methionine (SAM)-dependent SpoU-TrmD (SPOUT) ribosomal RNA (rRNA) methyltransferase (MTase) fold and catalyzes pseudouridine (Ψ) methylation at specific sites of the small subunit (SSU) rRNA. Mutations in Nep1 proteins result in a severe developmental disorder in humans and reduced growth in yeast, suggesting its role in ribosome biogenesis. In this study, the crystal structures of Nep1 from the archaebacterium Pyrococcus horikoshii (PhNep1), both in its apo and holo (adenosine or 5-methylthioadenosine bound) forms have been reported. The structural analysis of PhNep1 revealed an α/β fold featuring a deep trefoil knot akin to the SPOUT domain, with two novel extensions-a globular loop and a β-α-β extension. Moreover, the cofactor-binding site of PhNep1 exhibits a preformed pocket, topologically similar to that of other SPOUT-class MTases. Further, structural analysis of PhNep1 revealed that it forms a homodimer coordinated by inter-subunit hydrogen bonds and hydrophobic interactions. Moreover, the results of this study indicate that PhNep1 can specifically methylate consensus RNAs, having a pseudouridine (ψ) located at position 926 of helix 35 (h35) of 16S rRNA in P. horikoshii. The stability of the Nep1-RNA complex seems to be primarily assisted by the conserved arginine residues located at the dimeric interface.

The design and engineering of synthetic genomes

Synthetic genomics seeks to design and construct entire genomes to mechanistically dissect fundamental questions of genome function and to engineer organisms for diverse applications, including bioproduction of high-value chemicals and biologics, advanced cell therapies, and stress-tolerant crops. Recent progress has been fuelled by advancements in DNA synthesis, assembly, delivery and editing. Computational innovations, such as the use of artificial intelligence to provide prediction of function, also provide increasing capabilities to guide synthetic genome design and construction. However, translating synthetic genome-scale projects from idea to implementation remains highly complex. Here, we aim to streamline this implementation process by comprehensively reviewing the strategies for design, construction, delivery, debugging and tailoring of synthetic genomes as well as their potential applications.

Improved recombinant protein expression using the 5'-untranslated region in Chinese hamster ovary cells

Chinese hamster ovary (CHO) cells are major expression platforms for the transient production of recombinant therapeutic proteins (RTPs). Most improvement strategies have focused on promoting transcriptional expression in CHO cells. However, methods for promoting the yield of RTPs through translational regulation remain unclear. In this study, we investigated characteristics of the 5'-untranslated region (UTR) that influence recombinant protein expression in CHO cells and identified sequences that have positive effects on protein expression using ribosome sequencing. Some elements and characteristics of 5'-UTR differentially affected the translation of the main open reading frame and increased recombinant protein expression by 1.5-fold in CHO cells. The findings may help relieve the bottleneck of the yield of RTPs on translation enhancement.

Genetic protection from type 1 diabetes resulting from accelerated insulin mRNA decay

Insulin gene (INS) variation and beta-cell stress are associated with the risk of development of type 1 diabetes (T1D) and autoimmunity against insulin. The unfolded protein response alleviating endoplasmic reticulum (ER) stress involves activation of inositol-requiring enzyme 1α (IRE1α) that impedes translation by mRNA decay. We discover that the IRE1α digestion motif is present in insulin mRNA carrying SNP rs3842752 (G>A). This SNP in the 3' untranslated region of INS associates with protection from T1D (INSP). ER stress in beta cells with INSP led to accelerated insulin mRNA decay compared with the susceptible INS variant (INSS). Human islets with INSP showed improved vitality and function and reversed diabetes more rapidly when transplanted into diabetic mice than islets carrying INSS only. Surrogate beta cells with INSP expressed less ER stress and INS-DRiP neoantigen. This explanation for genetic protection from T1D may act instead of or in concert with the previously proposed mechanism attributed to INS promoter polymorphism.

Regulating mRNA endosomal escape through lipid rafts: A review

Messenger RNA (mRNA) therapeutics, enabled by lipid nanoparticles (LNPs) delivery systems, have revolutionized modern medicine by facilitating the delivery of genetic cargo to target cells. However, the efficient release of mRNA from LNPs within the endosomal pathways into the cytosol remains a major bottleneck in this field. Revisiting the formulation and function of mRNA-LNPs, it has been found that lipid rafts formed by cholesterol and distearoylphosphatidylcholine during the self-assembly process plan an essential role in the intracellular delivery and endosomal escape of mRNA-LNPs. These lipid rafts enhance the rigidity and stability of LNPs, facilitating mRNA encapsulation and closely contributing to improved intracellular delivery efficiency. By adjusting the composition or behavior of lipid rafts within LNPs-such as substituting cholesterol or altering the lipid phase-endosomal membranes can be destabilized, facilitating the escape of mRNA into the cytoplasm. This approach provides a promising strategy for rational design of mRNA delivery system and optimization of LNPs formulation. Additionally, methods for studying the mRNA escape process are summarized, as they serve as the foundation for achieving reliable and reproducible results.

Refinement and Truncation of DNA Aptamers Based on Molecular Dynamics Simulations: Computational Protocol and Experimental Validation

Aptamers have proven useful for a wide variety of applications, such as drug delivery systems and analytical reagents for diagnosis or food safety control. Conventional aptamer selection methods typically produce sequences longer than necessary, which are optimized through a postselection trial and error process to obtain the shortest-length sequence that preserves binding affinity. Herein, we describe a general strategy to obtain the tridimensional structure of DNA aptamers using a semiautomated molecular dynamics protocol, which serves as a guide to rationally improve experimentally selected candidates. Based on this approach, we designed truncated aptamers from previously described ligands recognizing different peptides and proteins, which are 20-35% shorter than the original candidates and present similar or even improved binding affinities. Moreover, we also discriminate between energetically similar secondary structures in terms of the energetic scoring of the molecular dynamics trajectories and rationally explain the role of poly thymine spacers in the (de)stabilization of the structure. This work demonstrates how a protocol for generating the aptamers tridimensional structure can accelerate their optimization for obtaining better analytical reagents and therapeutic agents.

Phylogenetic Analyses of Bostrichiformia and Characterization of the Mitogenome of Gibbium aequinoctiale (Bostrichiformia Ptinidae)

BACKGROUND

Ptinidae, within the infraorder Bostrichiformia, are a cosmopolitan, ecologically diverse but poorly known group. The phylogeny within Bostrichiformia and the monophyly of Ptinidae and its phylogenetic placement in Bostrichiformia remain contentious.

METHODS

In this research, we determined the entire mitochondrial genome (mitogenome) of Gibbium aequinoctiale, the first representative mitogenome of the subfamily Ptininae, and reconstructed the phylogenetic relationships for Bostrichiformia based on four mitochondrial datasets using maximum likelihood (ML) and Bayesian inference (BI) methods.

RESULTS

The mitogenome of G. aequinoctiale is a circular molecule spanning 17,020 bp and harbors 37 mitochondrial genes and a presumed control region (CR). The mitogenome exhibited a marked preference for the utilization of A and T bases, which was also observed in three kinds of genes and CR. AAT was inferred as the putative candidate initiation codon for cytochrome oxidase subunits 1 (COI). The control region contains three tandem repeats (TDRs) and one poly-thymine stretch (Poly-T) in both coding strands. The phylogenetic results appeared to support the monophyly of four families, Nosodendridae, Derodontidae, Dermestidae, and Bostrichidae, and the basal position of the latter two families within Bostrichiformia. However, the family Ptinidae was not verified as monophyly because of one species diverging from the main lineage. Three families, Dermestidae, Bostrichidae, and Ptinidae, clustered as the major clade in Bostrichiformia, among which Bostrichidae and Ptinidae grouped together as sister groups.

CONCLUSIONS

The present study provides valuable mitochondrial information for Ptinidae and provides novel perspectives on the inner phylogeny within the infraorder Bostrichiformia.

C. elegans transgenerational avoidance of P. fluorescens is mediated by the Pfs1 sRNA and vab-1

In its natural habitat, Caenorhabditis elegans must distinguish friend from foe. Pseudomonas are abundant in the worm's environment and can be nutritious or pathogenic. Previously, we found that worms learn to avoid Pseudomonas aeruginosa and Pseudomonas vranovensis through a small RNA (sRNA)-mediated pathway targeting the C. elegans gene maco-1, and this behavior is inherited for four generations. Here, we show that C. elegans learns to transgenerationally avoid another pathogenic bacteria Pseudomonas fluorescens 15 (PF15). The PF15 sRNA, Pfs1, targets the VAB-1 ephrin receptor through 16 nt of perfect match, suggesting the evolution of a distinct bacterial sRNA/C. elegans gene target pair. Knockdown of both maco-1 and vab-1 induce PF15 avoidance, and vab-1 loss reduces maco-1 expression, placing both genes in the sRNA-targeted pathogenic avoidance pathway. Thus, multiple genes in this avoidance pathway can act as targets for bacterial sRNAs, expanding the possibilities for evolution of trans-kingdom regulation of C. elegans behavior.

Replicative DNA polymerase epsilon and delta holoenzymes show wide-ranging inhibition at G-quadruplexes in the human genome

G-quadruplexes (G4s) are functional elements of the human genome, some of which inhibit DNA replication. We investigated replication of G4s within highly abundant microsatellite (GGGA, GGGT) and transposable element (L1 and SVA) sequences. We found that genome-wide, numerous motifs are located preferentially on the replication leading strand and the transcribed strand templates. We directly tested replicative polymerase ϵ and δ holoenzyme inhibition at these G4s, compared to low abundant motifs. For all G4s, DNA synthesis inhibition was higher on the G-rich than C-rich strand or control sequence. No single G4 was an absolute block for either holoenzyme; however, the inhibitory potential varied over an order of magnitude. Biophysical analyses showed the motifs form varying topologies, but replicative polymerase inhibition did not correlate with a specific G4 structure. Addition of the G4 stabilizer pyridostatin severely inhibited forward polymerase synthesis specifically on the G-rich strand, enhancing G/C strand asynchrony. Our results reveal that replicative polymerase inhibition at every G4 examined is distinct, causing complementary strand synthesis to become asynchronous, which could contribute to slowed fork elongation. Altogether, we provide critical information regarding how replicative eukaryotic holoenzymes navigate synthesis through G4s naturally occurring thousands of times in functional regions of the human genome.

Morphology and Phylogenetic Positions of Two Novel Gogorevia Species (Bacillariophyta) from the Han River, South Korea

This study reports two novel species, Gogorevia contracta sp. nov. and G. recticentralis sp. nov., which were isolated from freshwater environments in South Korea. Using an integrative taxonomic approach, we conducted morphological analyses using light microscopy and scanning electron microscopy, along with molecular phylogenetic investigations using SSU rRNA and rbcL gene sequences. Phylogenetic reconstructions highlighted the distinct characteristics of both species, confirming their classification within the genus Gogorevia and elucidating their evolutionary relationships. Morphologically, G. contracta was characterized by a bow-tie-shaped central area and circular depressions in the rapheless valve, whereas G. recticentralis exhibited a rectangular-to-wedge-shaped central area with parallel striae near the center of the raphe valve. Our findings highlighted the ecological significance of Gogorevia species and suggested their potential role as bioindicators of water quality in relatively unpolluted freshwater systems. Over the past decade, our research has focused on the taxonomic and ecological study of diatoms in the Han River system and identified 136 species, including nine newly described taxa. The findings of the present study contribute to a growing understanding of Gogorevia diversity, underscore the importance of region-specific diatom indices, and support the integration of morphological and molecular methods into diatom systematics.

Roquin exhibits opposing effects on RNA stem-loop stability through its two ROQ domain binding sites

The interaction of mRNA and regulatory proteins is critical for posttranscriptional control. For proper function, these interactions, as well as the involved protein and RNA structures, are highly dynamic, and thus, mechanistic insights from structural biology are challenging to obtain. In this study, we employ a multifaceted approach combining single-molecule force spectroscopy (SMFS) with NMR spectroscopy to analyze the concerted interaction of the two RNA-binding interfaces (A-site and B-site) of the immunoregulatory protein Roquin's ROQ domain with the 3' untranslated region (UTR) of the Ox40 mRNA. This 3'UTR contains two specific hairpin structures termed constitutive and alternative decay elements (CDE, ADE), which mediate mRNA degradation through Roquin binding. Our single-molecule experiments reveal that the CDE folds cooperatively, while ADE folding involves at least three on-pathway and three off-pathway intermediates. Using an integrated microfluidics setup, we extract binding kinetics to Roquin in real time. Supported by NMR data, we find opposing effects of the two Roquin subdomains on distinct regions of the ADE: While the A-site interacts strongly with the folded apical stem-loop, we find that the B-site has a distinct destabilizing effect on the central stem of the ADE owed to single-strand RNA binding. We propose that RNA-motif nature and Roquin A- and B-sites jointly steer mRNA decay with context-encoded specificity, and we suggest plasticity of stem structures as key determinant for Roquin-RNA complex formation. The unique combination of NMR and SMFS uncovers a mechanism of a dual-function RNA-binding domain, offering a model for target RNA recognition by Roquin.

The Druggable Transcriptome Project: From Chemical Probes to Precision Medicines

RNA presents abundant opportunities as a drug target, offering significant potential for small molecule medicine development. The transcriptome, comprising both coding and noncoding RNAs, is a rich area for therapeutic innovation, yet challenges persist in targeting RNA with small molecules. RNA structure can be predicted with or without experimental data, but discrepancies with the actual biological structure can impede progress. Prioritizing RNA targets supported by genetic or evolutionary evidence enhances success. Further, small molecules must demonstrate binding to RNA in cells, not solely in vitro, to validate both the target and compound. Effective small molecule binders modulate functional sites that influence RNA biology, as binding to nonfunctional sites requires recruiting effector mechanisms, for example degradation, to achieve therapeutic outcomes. Addressing these challenges is critical to unlocking RNA's vast potential for small molecule medicines, and a strategic framework is proposed to navigate this promising field, with a focus on targeting human RNAs.

Biochemical Characterization of a Non-G4-Type RNA Aptamer That Lights Up a GFP-like Fluorogenic Ligand

The 17-3 RNA aptamer recognizes DMHBI and induces its fluorescence. We showed that the 17-3 RNA aptamer predominantly induced emission of the phenolate form of DMHBI. We also demonstrated that the active structure of the minimal form of the 17-3 aptamer possessed three stem elements and two large loop elements, which we named Karashi and its sequence-optimized variant, Jigarashi, respectively. Chemical modification experiments suggested that the two loop regions formed tertiary interactions and/or non-Watson-Crick base pairs, and no remarkable structural alterations occurred upon DMHBI binding. AlphaFold3 also predicted a tertiary structure of the ligand-free form of Jigarashi RNA, which was consistent with the results of chemical modification experiments.

Multicomponent DNA Nanomachines for Amplification-Free Viral RNA Detection

The rapid and accurate detection of viral infections is of paramount importance, given their widespread impact across diverse demographics. Common viruses such as influenza, parainfluenza, rhinovirus, and adenovirus contribute significantly to respiratory illnesses. The pathogenic nature of certain viruses, characterized by rapid mutations and high transmissibility, underscores the urgent need for dynamic detection methodologies. Quantitative reverse transcription PCR (RT-qPCR) remains the gold-standard diagnostic tool. Its reliance on costly equipment, reagents, and skilled personnel has driven explorations of alternative approaches, such as catalytic DNA nanomachines. Diagnostic platforms using catalytic DNA nanomachines offer amplification-free nucleic acid detection without the need for protein enzymes and demonstrate feasibility and cost-effectiveness for both laboratory and point-of-care diagnostics. This study focuses on the development of multicomponent DNA nanomachines with catalytic proficiency towards a fluorescent substrate, enabling the generation of a fluorescent signal upon the presence of target nucleic acids. Specifically tailored variants are designed for detecting human parainfluenza virus type 3 (HPIV) and respiratory syncytial virus (RSV). The engineered DNA nanomachine features six RNA-binding arms for recognition and unwinding of RNA secondary structures, along with a catalytic core for nucleic acid cleavage, indicating potential utility in real clinical practice with minimal requirements. This research showcases the potential of DNA nanomachines as a reliable and sensitive diagnostic tool for RNA virus identification, offering promising prospects for clinical applications in the realm of infectious disease management.

Investigating the interplay between RNA structural dynamics and RNA chemical probing experiments

Small molecule chemical probes that covalently bond atoms of flexible nucleotides are widely employed in RNA structure determination. Atomistic molecular dynamic (MD) simulations recently suggested that RNA-probe binding can be cooperative, leading to measured reactivities that differ from expected trends as probe concentrations are varied. Here, we use selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE), dimethyl sulfate (DMS) chemical probing, and nuclear magnetic resonance (NMR) spectroscopy to explore the relationship between RNA structural dynamics and chemical probe reactivity. Our NMR chemical exchange experiments revealed that SHAPE-reactive base-paired nucleotides exhibit high imino proton exchange rates. Additionally, we find that as the concentration of a probe increases, some nucleotides' modification rates shift unexpectedly. For instance, some base-paired nucleotides that are unreactive at one probe concentration become reactive at another, often corresponding with a shift in the modification rate of the complementary nucleotide. We believe this effect can be harnessed to infer pairing interactions. Lastly, our results suggest that the overmodification of an RNA can impact its conformational dynamics, leading to modulations in the structural ensembles representing the RNA's fold. Our findings suggest an intricate interplay between RNA conformational dynamics and chemical probing reactivity.

A novel plasmid-encoded transposon-derived small RNA reveals the mechanism of sRNA-regulated bacterial persistence

Small regulatory RNAs (sRNAs) in bacteria are crucial for controlling various cellular functions and provide immediate response to the environmental stresses. Antibiotic persistence is a phenomenon that a small subpopulation of bacteria survives under the exposure of a lethal concentration of antibiotics, potentially leading to the development of drug resistance in bacteria. Here, we reported a novel transposon-derived sRNA called stnpA, which can modulate fosfomycin persistence of the bacteria. The stnpA sRNA located in the transposon with its own promoter is highly conserved among the prevalent multidrug resistance (MDR) plasmids in various pathogenic bacteria and expressed in response to the fosfomycin stress. It can directly bind to the ABC transporter, YadG, whereas this protein-RNA interaction modulated the export of fosfomycin and led to the enhancement of bacterial persistence. According to our knowledge, stnpA is the first identified transposon-derived sRNA, which controlled antibiotic persistence of bacteria, and our work demonstrated that nonresistance genes on MDR plasmids such as plasmid-encoded sRNA can provide additional survival advantages to the bacterial host against the antibiotics. In addition, the stnpA sRNA can be potentially utilized as the druggable target for the development of novel therapeutic strategies to overcome bacterial persistence.

IMPORTANCE

This study unveils a groundbreaking discovery in the realm of bacterial antibiotic persistence, highlighting the pivotal role of a newly identified small RNA (sRNA) called stnpA, which is a multidrug resistance plasmid-encoded transposon-derived sRNA that interacts directly with ABC transporter YadG to modulate the efflux of fosfomycin. Our findings elucidate a novel mechanism of small RNA-regulated fosfomycin persistence in bacteria that provides the potential pathway for the emergence of drug resistance in bacteria upon antibiotic treatment. Importantly, this study provides the first example of linking sRNA regulation to antibiotic persistence, presenting stnpA sRNA as a potential therapeutic target. This study underscores the critical role of noncoding RNAs in bacterial adaptation and offers valuable insights for developing new strategies to combat antibiotic persistence.

Analysis of Processing, Post-Maturation, and By-Products of shRNA in Gene and Cell Therapy Applications

Short hairpin RNAs (shRNAs) are potent tools for gene silencing, offering therapeutic potential for gene and cell therapy applications. However, their efficacy and safety depend on precise processing by the RNA interference machinery and the generation of minimal by-products. In this protocol, we describe how to systematically analyze the processing of therapeutic small RNAs by DROSHA and DICER1 and their incorporation into functional AGO complexes. Using standard small RNA sequencing and tailored bioinformatic analysis (QuagmiR), we evaluate the different steps of shRNA maturation that influence processing efficiency and specificity. We provide guidelines for troubleshooting common design pitfalls and off-target effects in transcriptome-wide profiling to identify unintended mRNA targeting via the miRNA-like effect. We provide examples of the bioinformatic analysis that can be performed to characterize therapeutic shRNA. Finally, we provide guidelines for troubleshooting shRNA designs that result in suboptimal processing or undesired off-target effects. This protocol underscores the importance of rational shRNA design to enhance specificity and reduce biogenesis by-products that can lead to off-target effects, providing a framework for optimizing the use of small RNAs in gene and cell therapies.

A bifunctional snoRNA with separable activities in guiding rRNA 2'-O-methylation and scaffolding gametogenesis effectors

Small nucleolar RNAs are non-coding transcripts that guide chemical modifications of RNA substrates and modulate gene expression at the epigenetic and post-transcriptional levels. However, the extent of their regulatory potential and the underlying molecular mechanisms remain poorly understood. Here, we identify a conserved, previously unannotated intronic C/D-box snoRNA, termed snR107, hosted in the fission yeast long non-coding RNA mamRNA and carrying two independent cellular functions. On the one hand, snR107 guides site-specific 25S rRNA 2'-O-methylation and promotes pre-rRNA processing and 60S subunit biogenesis. On the other hand, snR107 associates with the gametogenic RNA-binding proteins Mmi1 and Mei2, mediating their reciprocal inhibition and restricting meiotic gene expression during sexual differentiation. Both functions require distinct cis-motifs within snR107, including a conserved 2'-O-methylation guiding sequence. Together, our results position snR107 as a dual regulator of rRNA modification and gametogenesis effectors, expanding our vision on the non-canonical functions exerted by snoRNAs in cell fate decisions.

Selection of DNA Aptamers That Promote Neurite Outgrowth in Human iPSC-Derived Sensory Neuron Organoid Cultures

Sensory neurons in the dorsal root ganglia transmit sensory signals from the periphery to the central nervous system. Induced pluripotent stem cell derived models of sensory neurons and dorsal root ganglia are among the most advanced available tools for the study of sensory neuron activity and development in human genetic backgrounds. However, few available reagents modify sensory neuron growth with disease or other model-relevant outcomes. Small molecules, peptides, or oligonucleotides that predictably alter sensory neuron behavior in these contexts would be valuable tools with potentially wide-ranging application. Here we describe the selection and characterization of DNA aptamers that specifically interact with human sensory neurons. Several selected aptamers increase neurite outgrowth from sensory neuron organoid cultures after single-dose treatments.