Mehran Khorshid

Environmental RNA (eRNA) has been increasingly used to move beyond ‘who is there’ toward ‘who is active’ and ‘what is happening’ in ecosystems. Yet, most workflows have been optimised for laboratory sequencing, and decision‐grade field use has remained sporadic. In this article, field‐ready eRNA panels are defined as curated sets of transcripts paired with process controls and a transparent scoring rule, and a build–test pathway is described from marker discovery to deployment. Candidate markers are prioritised with field constraints in mind (abundance, specificity, persistence, and confounding seasonality), and RNA class choice (mRNA, rRNA, small, and other non‐coding RNAs) is treated as a design lever for robustness. Pre‐analytics are discussed as panel engineering, with emphasis placed on capture, rapid stabilisation, and inhibitor management to preserve multi‐marker relationships. Field readout options are then compared, including isothermal amplification, CRISPR‐assisted detection, portable qPCR, and portable nanopore sequencing for on‐site verification and panel refresh. Finally, minimum controls and staged validation levels are proposed to support defensible ecological claims. Deliberate attention is directed toward shared terminology and testable standards so that discussion within and between ecology, diagnostics, and conservation practice is stimulated and priorities for future investigations are sharpened.

Ornamental fish keeping has been positioned at a busy One Health interface, where global trade, retail handling, and home aquaria create repeated opportunities for microbial exchange under uneven biosecurity and intermittent antimicrobial pressures. In this review, dual eRNA biosurveillance is proposed as a practical way to move beyond agent lists by pairing environmental pathogen signals with host-state transcripts that reflect stress, barrier disruption, and immune activation. Pathogen eRNA recovered from tank or shipment water, biofilms, and filter media is considered alongside fish-derived eRNA markers to distinguish incidental detection from biologically meaningful risk, and to prioritize confirmatory testing. Evidence is synthesized for zoonotic hazards linked to ornamental systems and for exposure routes relevant to routine husbandry, including tank cleaning, splash/aerosol contact, and skin injuries from spines or abrasions; implications of antimicrobial resistance are treated as a risk amplifier where supported. Sampling points across breeder–export–transport–wholesale–retail–home pathways are mapped, and test-to-action options are aligned with signal patterns, including quarantine, hygiene and disinfection, customer risk communication, and referral to veterinary or clinical services. Minimum operational standards and reporting elements are outlined to support field validation and comparable datasets.

Environmental RNA (eRNA) has been increasingly used to move beyond “who is there” toward “who is active” and “what is happening” in ecosystems. Yet, most workflows have been optimized for laboratory sequencing, and decision-grade field use has remained sporadic. In this article, field-ready eRNA panels are defined as curated sets of transcripts paired with process controls and a transparent scoring rule, and a build–test pathway is described from marker discovery to deployment. Candidate markers are prioritized with field constraints in mind (abundance, specificity, persistence, and confounding seasonality), and RNA class choice (mRNA, rRNA, small and other non-coding RNAs) is treated as a design lever for robustness. Pre-analytics are discussed as panel engineering, with emphasis placed on capture, rapid stabilization, and inhibitor management to preserve multi-marker relationships. Field readout options are then compared, including isothermal amplification, CRISPR-assisted detection, portable qPCR, and portable nanopore sequencing for on-site verification and panel refresh. Finally, minimum controls and staged validation levels are proposed to support defensible ecological claims. Deliberate attention is directed toward shared terminology and testable standards so that discussion within and between ecology, diagnostics, and conservation practice is stimulated and priorities for future investigations are sharpened.

The fields of RNA aptamers and epitranscriptomics have each emerged as powerful dimensions of RNA biology, yet their conceptual and mechanistic overlap remains largely unexplored. RNA aptamers as in vitro-selected single-stranded RNA oligonucleotides selected through in vitro evolution (Systematic Evolution of Ligands by Exponential Enrichment [SELEX]) and related methods are well known for their ability to fold into precise three-dimensional structures and bind specific targets with high affinity. These aptamers have been widely used in diagnostics, therapeutics, and molecular sensing. In parallel, the dynamic landscape of epitranscriptomic modifications, such as N⁶-methyladenosine (m⁶A), pseudouridine (Ψ), and 5-methylcytosine (m⁵C), has been recognized as a critical regulator of RNA structure, stability, and function. In this perspective article, we chart unexplored territories at the interface of these two mechanisms, focusing on how RNA modifications may influence aptamer folding or binding, and how aptamers could, in turn, be harnessed to detect or modulate the epitranscriptomic state. We also highlight opportunities for cross-disciplinary integration in synthetic biology, post-transcriptional regulation, and RNA-based therapeutics. While the direct regulatory connections between these domains remain to be fully elucidated, we propose their potential convergence as a fertile ground for innovation. The primary aim of this article is to stimulate discussion within and between these research communities and to attract attention toward a promising frontier for future investigations.

The fields of RNA aptamers and epitranscriptomics have each emerged as powerful dimensions of RNA biology, yet their conceptual and mechanistic overlap remains largely unexplored. RNA aptamers as artificial single-stranded oligonucleotides selected through in vitro evolution (SELEX and related methods) are well known for their ability to fold into precise three-dimensional structures and bind specific targets with high affinity. These aptamers have been widely used in diagnostics, therapeutics, and molecular sensing. In parallel, the dynamic landscape of epitranscriptomic modifications, such as N⁶-methyladenosine (m⁶A), pseudouridine, and 5-methylcytosine, has been recognized as a critical regulator of RNA structure, stability, and function. In this perspective article, we chart unexplored territories at the interface of these two mechanisms, focusing on how RNA modifications may influence aptamer folding or binding, and how aptamers could, in turn, be harnessed to detect or modulate the epitranscriptomic state. We also highlight opportunities for cross-disciplinary integration in synthetic biology, post-transcriptional regulation, and RNA-based therapeutics. While the direct regulatory connections between these domains remain to be fully elucidated, we propose their potential convergence as a fertile ground for innovation. The primary aim of this article is to stimulate discussion within and between these research communities and to attract attention toward a promising frontier for future investigations.

RNA-based/associated biosensors represent a rapidly expanding area of research, providing highly sensitive tools for detecting and monitoring RNA in diverse biological contexts. These sensors offer the ability to track RNA localization, modifications, and interactions in real-time, making them particularly well-suited for developmental biology research. Despite their demonstrated utility in fields such as diagnostics, synthetic biology and environmental science, the application of RNA biosensors in developmental biology has only begun to emerge within the past decade. This gap is notable given the potential of these tools to address key questions about spatiotemporal RNA regulation and cellular signaling during development. This perspective review presents a selection of RNA biosensors, including fluorescent RNA aptamers, CRISPR-Cas-based systems, riboswitches, and catalytic RNA sensors, which have gained attraction in other scientific disciplines. These tools can be used not only to study intrinsic RNA biology, such as RNA expression, splicing, and localization, but also to detect the effects of extrinsic physical and chemical factors, including pH, temperature, redox state, and mechanical stress, on RNA behavior during developmental processes. These examples illustrate how RNA biosensors could be adapted to study developmental mechanisms in model organisms, enabling investigations into RNA dynamics and their role in shaping developmental processes. By revisiting these underutilized tools, this review highlights their relevance for advancing the understanding of molecular mechanisms in developmental biology studies.

This article reports on a bioanalytical sensor device that hosts three different transducer principles: impedance spectroscopy, quartz-crystal microbalance with dissipation monitoring, and the thermal-current-based heat-transfer method. These principles utilize a single chip, allowing one to perform either microbalance and heat transfer measurements in parallel or heat transfer and impedance measurements. When taking specific precautions, the three measurement modalities can even be used truly simultaneously. The probed parameters are distinctly different, so that one may speak about multiparametric or "orthogonal" sensing without crosstalk between the sensing circuits. Hence, this sensor allows one to identify which of these label-free sensing principles performs best for a given bioanalytical application in terms of a high signal amplitude and signal-to-noise ratio. As a proof-of-concept, the three-parameter sensor was validated by studying the spontaneous, collective detachment of eukaryotic cells in the presence of a temperature gradient between the QCM chip and the supernatant liquid. In addition to heat transfer, detachment can also be monitored by the impedance- and QCM-related signals. These features allow for the distinguishing between different yeast strains that differ in their flocculation genes, and the sensor device enables proliferation monitoring of yeast colonies over time.

In this work, we present a compact, bifunctional chip-based sensor setup that measures the temperature and electrical conductivity of water samples, including specimens from rivers and channels, aquaculture, and the Atlantic Ocean. For conductivity measurements, we utilize the impedance amplitude recorded via interdigitated electrode structures at a single triggering frequency. The results are well in line with data obtained using a calibrated reference instrument. The new setup holds for conductivity values spanning almost two orders of magnitude (river versus ocean water) without the need for equivalent circuit modelling. Temperature measurements were performed in four-point geometry with an on-chip platinum RTD (resistance temperature detector) in the temperature range between 2 °C and 40 °C, showing no hysteresis effects between warming and cooling cycles. Although the meander was not shielded against the liquid, the temperature calibration provided equivalent results to low conductive Milli-Q and highly conductive ocean water. The sensor is therefore suitable for inline and online monitoring purposes in recirculating aquaculture systems.

While exhaled breath condensate EBC is not yet used in routine clinical diagnostics and disease monitoring, recent publications indicate that exhaled air and EBC contain a wide range of molecular biomarkers that are characteristic of various medical conditions. This includes evidently lung disorders such as asthma, COPD, and cystic fibrosis, but also diabetes and several types of cancer go along with specific biomarkers exhaled from the airways. In addition, EBC samples can be collected in a non‐invasive way and, due to their small volume, they can be easily stored frozen between collection and analysis. Several home‐made EBC‐collection systems for research purposes are documented in literature while there are also a few systems from commercial suppliers that are not yet certified as medical products. In this work, a novel collection device is presented in which the EBC is condensed and frozen inside stainless steel tubes, tightly surrounded by an aluminum cylinder that is precooled in a kitchen freezer. The device is low cost, easy to use by patients at home or in a clinic, and its collection efficiency of up to 500 µL min⁻¹ of respiration is on the high side.