Event Files are Common, But Semantic Event Metadata Remain Uneven in OpenNeuro BIDS Datasets

Abstract: Open neuroscience repositories support reuse by making datasets accessible, but event level reuse also depends on whether task and stimulus annotations can be interpreted by software. I audited public latest OpenNeuro BIDS snapshots using public GraphQL metadata, recursive file trees, small events.json sidecars, and bounded events.tsv header ranges. Raw neural data were left untouched. Among 1,713 public latest snapshots, 1,483 had task metadata or observed event TSV files and formed the primary event relevant denominator. Event TSV files were present in 1,175/1,483 snapshots (79.2%; Wilson 95% CI 77.1%-81.2%). Candidate event JSON sidecars were present in 604/1,483 snapshots (40.7%), but an inheritance aware path and entity check found applicable JSON sidecars for 590/1,483 (39.8%), descriptive applicable sidecars for 550/1,483 (37.1%), and experiment specific applicable sidecars for 491/1,483 (33.1%). Across the full recursive file tree, 162,034/301,681 event TSV files (53.7%) had an applicable event JSON sidecar, and 147,412/301,681 (48.9%) had an applicable experiment specific sidecar. HED was detected in event JSON for 45/1,483 snapshots (3.0%) and in sampled TSV headers for 2/1,483 (0.13%). EEG had higher sidecar coverage and HED detection than fMRI, but 21.2% of EEG candidate JSON files were bookkeeping only. These results identify a repository visible metadata gap: event timing is common, but software interpretable event meaning remains uneven.

Metadata
Humans
Software
Semantics
Databases, Factual
Neurosciences
Animals


Generative AI as a transformational logic for cognitive neuroscience

Abstract: Cognitive neuroscience faces a paradox: neural data are abundant, yet conceptual synthesis has stalled because dominant contrast-based approaches show where activity differs but not how cognitive operations relate or transform. Here, we propose a generative-transformational logic grounded in AI and neural geometry, treating cognition as lawful mappings among neural states. Generative models can learn latent transformations linking states across tasks, contexts, and individuals. Because transformation success is testable, this framework enables counterfactual simulation and connects data-driven modeling with theory-driven inference. It moves cognitive neuroscience from mapping correlates toward algorithmic explanations of how the brain generates and reorganizes cognition over time.

Cognitive Neuroscience
Humans
Generative Artificial Intelligence
Cognition
Brain


Transparent fish takes center stage in $1 billion neuroscience initiative

Abstract: The once-obscure Danionella fish will be the focus of an ambitious new Howard Hughes Medical Institute project.


Image space opens up for visual neuroscience

Abstract: How a visual stimulus is perceived depends on the context provided by other stimuli in the scene. Fu et al.1 combine imaging, modeling, and innovative closed-loop stimulus generation to identify the brain computations that underlie contextual effects in primary visual cortex (V1) neurons.

Animals
Visual Cortex
Humans
Photic Stimulation
Visual Perception
Neurons
Primary Visual Cortex
Neurosciences
Visual Pathways


Machine yearning: LLMs do not capture formal linguistic structure and obscure neuroscientific inquiry

Abstract: Futrell and Mahowald argue that neural networks have learned non-trivial aspects of language. We argue that these systems have not in fact demonstrated "mastery" of syntax, marshalling recent evidence, and that they further obscure explanatory insights with respect to topics in the cognitive neuroscience of language.

Humans
Linguistics
Language
Large Language Models
Neurosciences
Neural Networks, Computer


The functional neurobiology of dispositions towards negative emotions

Abstract: People differ in their tendency to experience negative emotions. This variability is largely captured by broad psychological constructs like neuroticism, whose facets include anxiety, depression, and stress vulnerability, among others. The amygdala and salience network have been assumed to underlie such dispositions, despite inconsistent evidence. We preregistered a comprehensive test of these and other competing hypotheses-accompanied by theory-agnostic machine learning prediction-using neural responses in the two most common emotional neuroimaging tasks (scenes and faces; N = 338/424). Evidence including Bayes factors indicated that neuroticism is not associated with any region, network, affective signature, or machine learning pattern, including the amygdala. Still, a brain-wide machine learning pattern robustly predicted the neuroticism facet stress vulnerability (r = .21), replicated in an independent dataset (r = .19). Predictive performance most strongly depended on somatomotor and visual networks, rather than salience network regions, relating stress vulnerability to cortical perception-action systems. Together with a multiverse analysis spanning 14 trait constructs and 1,176 models, our findings demonstrate the highly selective predictability of emotional dispositions from brain responses to common affective tasks. Therein, they highlight the importance of construct and task selection, while challenging the role of the most commonly used neural markers, including responses of the amygdala and salience network.

Sicorello M
Gianaros PJ
Wright AGC
Petre B
Kraynak TE
Manuck SB
Schmahl C
Wager TD

Humans
Emotions
Amygdala
Female
Neuroticism
Bayes Theorem
Magnetic Resonance Imaging
Brain
Male
Machine Learning
Neurobiology
Adult
Brain Mapping
Young Adult
Stress, Psychological


The Inspiring Journeys of Women in Science

Abstract: Since 2017, the European Journal of Neuroscience has featured interviews with 27 female neuroscientists to showcase and celebrate their excellent scientific contributions and to hear their personal stories and advice for younger neuroscientists. Although these women represent different fields in neuroscience, countries, and levels of seniority, their stories share some remarkable commonalities, which we briefly discuss in this editorial. Highlighted topics include: the circuitous route of some of the careers; the importance of having good mentors and belonging to networks; the role of "good fortune" versus abilities and skills; the upsides and downsides of an academic career; some of the aspects in which women's academic careers may differ from those of men; and the advice the interviewees would like to pass on to the next generations. Although it is clear from these personal accounts that some aspects of women's careers in neuroscience have improved over the past decade, other elements seem stagnant. The European Journal of Neuroscience remains committed to equity and will continue to feature the stories of women in neuroscience to inspire future generations.

Humans
Female
Neurosciences
Academia
Mentors
Women
Career Choice
Research Personnel


New Discoveries in the Field of Neuropharmacology

Abstract: Neuropharmacology has emerged in recent years as a field of active research, driven by the need to address increasing challenges posed by clinical conditions such as neurodegenerative disorders, which affect more and more elderly people worldwide as the average life expectancy extends progressively [...].

Humans
Neuropharmacology
Neurodegenerative Diseases
Animals


Context dependency in cancer neuroscience

Abstract: Neural signaling shapes tumor progression, but it is not intrinsically tumor-promoting or tumor-restrictive. We argue that neural directionality is context-dependent and governed by tumor kinetics, tissue architecture, neural state, receptor and target-cell topology, immune-host biology, and treatment history. We propose a mechanistically interpretable and clinically actionable reporting framework for precision neuromodulatory oncology.

Humans
Neoplasms
Animals
Signal Transduction
Neurosciences


Optical voltage imaging: ready to spark systems neuroscience

Abstract: Many open questions about neural circuit and systems function could be answered if spikes and synaptic potentials could be accurately measured from many neurons simultaneously in a given network with cell-type specificity, cellular resolution, and at the millisecond time scale. Voltage imaging with genetically encoded voltage indicators (GEVIs) has advanced to the point that this is now possible for small networks or sparsely labeled neurons, and emerging optical methods promise to soon enable imaging from larger, dense cell populations. This review describes recent discoveries made using GEVIs to understand local and propagating cortical activity, network oscillations, and cortical and hippocampal microcircuit dynamics, and outlines several promising future applications in systems neuroscience.

Gomez LC
Rodriguez L
Garderes PM
Feldman DE

Animals
Neurosciences
Humans
Neurons
Voltage-Sensitive Dye Imaging
Nerve Net
Optical Imaging


Speech Neurophysiology in Realistic Contexts: Big Hype or Big Leap?

Abstract: Understanding the neural basis of speech communication is essential for uncovering how sounds are translated into meaning, how that changes with development, ageing and speech-related deficits, as well as contributing to brain-computer interfaces research. While traditional neurophysiological studies have relied on simplified, controlled paradigms, recent advances have shifted the field towards more ecologically valid approaches. Here, we describe the evolving landscape of experimental designs in speech neurophysiology, from discrete to continuous stimuli and from socially isolated listening to dynamic, multiagent communication. Realistic paradigms in that space challenge conventional methods, offering richer insights into neural encoding, functional brain mapping and neural entrainment. At the same time, they introduce significant analytical and technical complexities, particularly when incorporating social interaction. By synthesising findings across studies, we highlight how these ecologically valid speech paradigms have been contributing to refining theories of language processing and open new avenues for research. In doing so, this review critically evaluates of whether the move towards realism in speech neurophysiology represents a technological trend or a transformative leap in understanding the neural underpinnings of speech communication.

Humans
Speech
Speech Perception
Brain
Brain Mapping
Neurophysiology


Pathophysiology and neurobiology of insomnia

Abstract: Chronic insomnia, as defined by the DSM-5 and ICSD-3, is characterized by difficulties falling asleep, maintaining sleep, or waking up too early, occurring at least three times a week for more than three months, with daytime consequences. Long considered a secondary symptom, it is now recognized as a distinct condition resulting from a persistent disruption of sleep-wake regulation. Genetic and epigenetic studies show substantial heritability, suggesting a strong biological influence. More than 500 loci have been identified, linking insomnia to both metabolic and psychiatric traits. Gene-environment interactions, particularly through DNA methylation, may explain how stress can durably alter sleep system reactivity and promote chronicity. Brain imaging research highlights hyperactivation of key regions such as the anterior cingulate cortex, thalamus, insula, and precuneus, which are involved in arousal, vigilance, and emotional regulation. Electroencephalography confirms increased cortical activity, particularly in the beta and alpha bands, reflecting a persistent state of wakefulness during sleep. Explanatory models describe a set of mechanisms in which conditioning, stress reactivity, and co-activation of sleep and wake networks maintain the disorder. Insomnia thus appears as a hybrid state between wakefulness and sleep. These advances underline the complexity of insomnia and the need for integrated therapeutic approaches combining cognitive, behavioral, and physiological interventions to restore normal sleep regulation.

Sleep Initiation and Maintenance Disorders


Trauma in Attachment: Understanding the First Relationship Through Neurobiology and Psychodynamics

Abstract: Much has been elucidated about the neurobiological effects of early childhood trauma and its transgenerational transmission, although its integration into psychodynamic therapy has been challenging. Here we focus on a common area of interest to both areas-emotion and cognition rooted in past trauma experiences and how these experiences produce maladaptive behaviors transmitted to the next generation through parenting behaviors. We explore two mammalian research paradigms of early-life trauma explicitly within attachment, and transmission of transgenerational pathology through the caregiver to the offspring. We suggest that understanding the neurobiology through this mammalian nonhuman research can provide, in part, an understanding for the complex psychodynamic thought processes seen in adulthood, particularly as the mother begins to raise her own child. Specifically, while cognition and complex conscious and unconscious thoughts are characteristic of the human condition following early-life trauma, the mother-infant attachment system is a phylogenetically preserved system with some basic characteristics seen across species. We outline how embracing both the cognition and preserved trauma neural programing within attachment may provide some insight into cases, especially for the parent-child social interactions well documented to program the brain. Using mother-infant attachment, we suggest there is an area of convergence between clinical psychodynamic focus and basic research in brain function and mechanisms. Focusing on this convergence may provide a unique viewpoint to psychodynamics to supplement diagnosis and treatment.

Humans
Object Attachment
Mother-Child Relations
Animals
Neurobiology
Female
Brain
Adverse Childhood Experiences


Why do psychology students believe in neuromyths? A study of personality, contextual and cognitive predictors

Abstract: Neuromyths-misconceptions arising from misinterpretations of neuroscientific findings-are widely endorsed by educators and students, including those in psychology. Their persistence has been linked to contextual, cognitive, and personality-related factors, but evidence is mixed, especially among psychology students. This study examined predictors of neuromyth endorsement in Argentine psychology undergraduates. To identify contextual (neuroscience training, interest), personality (Need for Cognition; NFC), and cognitive (Cognitive Reflection Test; CRT) predictors of neuromyth beliefs. A convenience sample of 320 psychology students (82.5% women; M_age = 27.39 years) completed online measures assessing neuromyth endorsement, general brain knowledge, NFC, CRT, and self-reported neuroscience training and interest. Spearman correlations and hierarchical regressions were conducted to examine associations and predictive effects. Participants endorsed 41.22% of neuromyths on average, with learning styles (76.25%) and sensory-rich environments benefits (74.37%) being the most accepted. CRT scores negatively predicted neuromyth endorsement (β = -.175, p < .001), whereas the NFC "enjoyment of thinking" factor positively predicted endorsement (β = 0.145, p = .024). Age also showed a positive effect (β = 0.175, p = .002). Neuroscience interest, courses taken, and general brain knowledge did not predict neuromyth acceptance, although they were positively associated with neuroscience knowledge. Analytical thinking emerged as the strongest protective factor against neuromyths, while enjoyment of thinking unexpectedly predicted higher endorsement, possibly reflecting exposure to low-quality sources of information and/or Dunning-Kruger effects. Factual neuroscience knowledge and training did not decrease neuromyth endorsement, underscoring the importance of fostering critical thinking skills within psychology education.

Adult
Female
Humans
Male
Young Adult
Cognition
Cognitive Reflection
Neurosciences
Personality
Psychology
Students
Thinking


Convergence and innovative applications of cutting-edge biomedical technologies in brain organoid research

Abstract: Brain organoids, as three-dimensional cellular models that recapitulate human brain development and function in vitro, have emerged as a pivotal platform for neuroscience research. However, it still faces many technical challenges in aspects such as the structural and physiological relevance, functional regulation and system analysis, and urgently needs the deep integration of multi-disciplinary technologies to drive paradigm-shifting innovations. Here, we systematically summarize the main technological frameworks that support brain organoid research, including bioengineering and organoid construction technologies, biofabrication and microenvironmental modulation strategies, high-precision detection and multimodal analytical methodologies, as well as intelligent algorithms and data analysis platforms. The cross-integration of multiple technologies not only provides solutions to the existing limitations in brain organoid research, but also opens up cross-technological innovation application scenarios. We further discuss key bottlenecks in technology convergence and propose the development direction of future research. This review aims to provide a comprehensive technical roadmap for brain organoid research, promoting its in-depth application and paradigm innovation in cross-disciplinary fields including neuroscience, precision medicine, and brain-inspired computing.

Humans
Organoids
Brain
Animals
Biomedical Technology
Neurosciences
Biomedical Research
Bioengineering


Brain Cancer: Molecular Alterations and Emerging Trends in Neuropharmacology

Abstract: Central nervous system (CNS) tumors represent a heterogeneous group of neoplasms associated with significant morbidity and mortality despite their relatively low incidence. Advances in the fifth edition of the World Health Organization (WHO) classification have emphasized the integration of histopathological, immunohistochemical, and molecular features, fundamentally transforming diagnostic and prognostic frameworks in neuro-oncology. This manuscript aims to provide an overview of CNS tumor biology, focusing on key diagnostic markers, genetic and epigenetic alterations, and emerging therapeutic strategies. It further describes recent advances in multi-omics approaches and artificial intelligence, which enable deeper characterization of tumor heterogeneity and support the development of precision medicine strategies. Finally, current and emerging therapeutic modalities, including combination therapies, targeted treatments, and novel molecular targets, are examined with emphasis on overcoming resistance mechanisms and improving clinical outcomes. Overall, the integration of molecular biology, advanced diagnostics, and innovative therapeutic approaches represents a critical step toward personalized management of CNS tumors and improved patient survival.

International journal of molecular sciences

Leskova B
D'Agostino I
Mattova S
Urbanska N
Blicharova A
Simko P
Toplu A
Karaman M
Kiskova-Simkova T

Humans
Brain Neoplasms
Epigenesis, Genetic
Neuropharmacology
Biomarkers, Tumor
Precision Medicine
Animals
Artificial Intelligence
Molecular Targeted Therapy
Multiomics
Antineoplastic Agents


Perspectives from the 2024 School on Neuropharmacology Research and Drug Development in Harare, Zimbabwe: insights from participants

Abstract: Sub-Saharan Africa is experiencing a rising burden of neurological and mental disorders. The International Brain Research Organization (IBRO)-funded 2nd School on Neuropharmacology Research and Drug Development (NRDD) was held in Harare, Zimbabwe, 2024. The meeting aimed to (1) provide a theoretical foundation in neuropharmacology; (2) develop skills in experimental design, pharmacokinetics, and drug evaluation; (3) foster interdisciplinary collaboration and networking; and (4) promote cultural and scientific exchange. Thirteen participants from eight African countries attended the 1-week program. This Meeting Review evaluates the extent to which the meeting achieved its goals, drawing on structured reflections from all participants, and describes the scientific, networking, cultural, and logistical dimensions of the experience. The school successfully equipped participants with foundational knowledge in neuropharmacology and drug development. Future editions would benefit from extended hands-on sessions and structured post-program follow-up.

Senanu J
Wanyu BY
Burns J
Archibong VB
Chinheya RM
Ombel Musa NS
Zengeni S
Haj-Khlifa A
Adeniji KO
Kolo RM
Caroline M
Sakhri FZ
Chipofya E

Zimbabwe
Humans
Neuropharmacology
Drug Development


[Neuropathological Autopsies in Japan: Current Scenario and Challenges]

Abstract: Research using brain tissue obtained through autopsies is essential for the development of treatments for several neurological disorders and for elucidating their pathophysiologies. However, owing to a decline in the number of autopsies, opportunities to examine central nervous system tissues are diminishing. It is therefore necessary to collaborate with brain banks and establish a system to ensure the proper storage, research utilization, and diagnostic analysis of nervous system tissues obtained through autopsies.

Brain and nerve = Shinkei kenkyu no shinpo

Autopsy Humans Japan Brain Neuropathology


The Simons Collaboration on Ecological Neuroscience: Studying how the brain interacts with the world

Abstract: The Simons Collaboration on Ecological Neuroscience (SCENE) seeks to uncover general principles of brain function through an ecological perspective: studying perception, cognition, and action in the context of the affordances available to different agents. Here, we introduce SCENE's goals, hypotheses, and approaches outlining a collaborative vision for the next decade.

Angelaki DE
Batista A
Fitzgerald T
Kominsky JF
Lengyel M
Mathis A
Mathis MW
Moss CF
Niell CM
Noel JP
Pitkow X
Rothkopf CA
Savin C
Stachenfeld K
Suthana N
Tolias A
Ulanovsky N
Wolpert DM
Wong A
Zimmermann J

Brain Neurosciences Humans Animals Cognition


How to Foster Challenging Interdisciplinary Collaborations: Can Philosophy Support Neuroscientists?

Abstract: New conceptual and technological developments bring neuroscientists closer to other disciplines and other fields in neuroscience with different traditions. Although some neuroscientists may underrate the potential benefits of successful interdisciplinary collaborations, others may be unaware of the typical difficulties of such collaborations or are not trained in skills that render them fruitful. Here, we argue that interdisciplinary interactions have long been part of neuroscience, although they are often challenging, because neuroscientists may be confronted with concepts, assumptions, and interpretative horizons that differ from their own. This can lead to misunderstandings and little mutual appreciation. Using the historical development of brain imaging techniques, we distinguish between different types of interdisciplinary interactions and illustrate some of their benefits. In addition, we present various challenges for collaborations at the interface between traditional laboratory-type approaches and those of clinical or computational neuroscience or of ecological field approaches. To address these challenges, we invite neuroscientists to consider philosophers as collaboration partners with complementary expertise, which includes special consideration of language use, underlying assumptions and proficiency in conceptual analysis. This expertise can be used by neuroscientists to increase their understanding and address some difficulties in interdisciplinary interactions more effectively. The benefits of these interactions can be expected to outweigh challenges in the dialogue with philosophers. Importantly, neuroscientists can choose between reading philosophical literature, participating in joint events with philosophers, and integrating philosophers into neuroscience projects. This may allow neuroscientists to explore unforeseen possibilities to improve or initiate collaborations with scientists from other fields and disciplines.

Kunze M
Brun C
Badaut J
Darnaudéry M
Gross F
Peltier L
Pradeu T
Sarto-Jackson I
Konsman JP

Neurosciences
Humans
Interdisciplinary Communication
Cooperative Behavior
Philosophy
Interdisciplinary Research


Effects of standard prenatal education with and without pain neuroscience education on functionality appreciation and body surveillance in pregnant women with lumbopelvic pain: a secondary analysis of a randomized controlled trial

Abstract: Pregnancy involves profound physical and psychological changes that may increase the risk of lumbopelvic pain and affect body image. Body surveillance and functionality appreciation are key constructs in this context, yet little is known about interventions targeting them in pregnant women experiencing pregnancy-related pain. This study examined whether standard prenatal education alone or combined with pain neuroscience education could improve functionality appreciation and reduce body surveillance in women with pregnancy-related lumbopelvic pain. A total of 211 third-trimester pregnant women with pregnancy-related lumbopelvic pain were randomly assigned to standard prenatal education or a combined program with pain neuroscience education. Both programs included twelve online lessons delivered over four weeks. Functionality appreciation and body surveillance were measured at baseline and post-intervention using validated questionnaires. Linear mixed models were used for analysis under an intention-to-treat approach. Functionality appreciation improved significantly over time in both groups (p = .018), but no between-group differences were observed (Cohen's d = 0.056). Body surveillance scores remained unchanged in both groups (Cohen's d = 0.00). Adherence was higher in the SPE group (88%) compared to SPE+PNE (77.5%, p = .011). Brief online educational programs, especially standard prenatal education, can enhance functionality appreciation during pregnancy, shifting focus from appearance to bodily capacities.

García-Lucas C
Zamora Á
Amer-Cuenca JJ
Arguisuelas MD
Pardo J
Baños RM
Lisón JF
Biviá-Roig G

Humans
Female
Pregnancy
Adult
Prenatal Education
Surveys and Questionnaires
Neurosciences
Low Back Pain
Pregnant People
Body Image
Pelvic Pain
Patient Education as Topic

Journal Article
Randomized Controlled Trial


Danilo Bzdok

Abstract: In this interview with Neuron, Danilo Bzdok argues that artificial intelligence and big data herald a paradigm shift in neuroscience. Leveraging large language models, researchers can overcome traditional, intuition-driven taxonomies, bridge disciplinary silos, and reconcile today's fragmented knowledge into a unified vision of brain function.

Humans
Neurosciences
Artificial Intelligence
Animals
Brain
History, 20th Century
History, 21st Century
Big Data


Special Issue: Breakthroughs in Stroke Rehabilitation: Bridging Engineering, Neuroscience, and Motor Control

Abstract: Stroke remains one of the leading causes of death and long-term disability worldwide, often resulting in persistent motor impairments that limit independence and quality of life. This special issue highlights recent advances in stroke assessment and rehabilitation driven by the convergence of engineering, neuroscience, and motor control. The contributions are organized around four themes: (1) the importance of rigorous theoretical and methodological foundations to improve reproducibility and clinical translation; (2) the role of neuroplasticity, neuromodulation, and cognition in enhancing recovery; (3) emerging insights into neurophysiological and motor control mechanisms across cortical and spinal levels; and (4) innovations in assessment tools and rehabilitation technologies, including accessible, low-cost, and real-world solutions. Collectively, these studies demonstrate how interdisciplinary approaches are advancing both the science and practice of stroke rehabilitation, with an emphasis on clinically feasible strategies that can improve functional recovery and outcomes for individuals living with stroke.

Krishnan C
Sulzer J
Patten C
Ranganathan R

Humans
Stroke Rehabilitation
Neurosciences
Stroke
Recovery of Function
Animals
Neuronal Plasticity


MRI Goes Mobile: Assessing the Reliability and Repeatability of a Mobile vs. Stationary 1.5 T MRI for Functional Neuroscience Studies

Abstract: Mobile MRI scanners could transform neuroimaging by expanding accessibility to diverse populations and enabling data collection in remote settings. This study serves as a short-term feasibility and system commissioning report, investigating the reliability and repeatability of two mobile 1.5 T MRI scanners compared to a stationary 1.5 T reference. To evaluate the technical impact of scanner relocation and mobile housing, a comprehensive protocol was implemented: five healthy subjects underwent 10 scans each (N = 50 total sessions) across three 1.5 T systems (one stationary; two mobile). The protocol employed a test-retest design with participant repositioning on each measurement day. Stability was assessed through longitudinal fBIRN phantom scans and human imaging of magnetic field homogeneity (ΔB0), RF flip-angle mapping (B1 +), structural MP-RAGE, and functional EPI-BOLD. Initial commissioning results demonstrated that short-term relocation and mobile operation did not compromise hardware performance. Phantom QA showed stable tSNR and minimal signal drift. In human subjects, magnetic field stability (ΔB0) and B1 + distributions were equivalent across systems, with Bland-Altman plots confirming no systematic bias following transit. Structural MP-RAGE voxel-intensity distributions and tissue volumes were highly consistent, with ICCs between 0.99 and 1 for estimated WM and GM volumes. This technical validation study demonstrates the short-term feasibility of utilizing mobile 1.5 T platforms for high-quality neuroimaging. The results confirm that current mobile shielding and stabilization technologies effectively mitigate the environmental challenges of transit, establishing a reliable baseline for future longitudinal research in remote or underserved settings.

Aigner CS
Forlim CG
Santoro D
Bodammer NC
Brühl R
Sudimac S
Schmalen K
Schröder S
Mohammadi S
Kühn S

Humans
Magnetic Resonance Imaging
Reproducibility of Results
Phantoms, Imaging
Adult
Male
Brain
Female
Neurosciences


Harnessing theoretical neuroscience to understand decision-making across aging

Abstract: Understanding how decision-making changes across the lifespan is a central challenge for neuroscience, yet research on cognitive aging remains largely disconnected from the theoretical and computational advances shaping modern systems neuroscience. Over recent decades, theoretical frameworks have transformed how we study cognition in young, healthy brains. In contrast, aging research has relied on single-metric behavioral measures, cross-sectional comparisons, and descriptive neural analyses, limiting our ability to explain fundamental differences in individual aging trajectories. This gap represents a missed opportunity: aging offers a powerful platform for testing theories of neural computation, stability, and flexibility under changing biological constraints. We argue that closer integration between aging research and contemporary theoretical neuroscience will move the field from descriptive towards mechanistic insights. Here, we outline how recent advances in behavioral quantification, latent-state modeling, dynamical systems, encoding models, representational geometry, and recurrent neural networks offer a rich theoretical toolkit for studying decision-making across the lifespan.

Humans
Decision Making
Aging
Animals
Neurosciences
Brain
Models, Neurological


Designing Globally Inclusive and Ethically Deliberate Neurofutures

Abstract: Unlike any other organ, the brain's role in identity, agency, and experience makes it biologically and culturally unique. The transformative potential of global neuroscience demands robust, integrated ethical engagement across the research life cycle. Neuroscientists and neuroengineers need to be equipped with a neuroethics familiarity that transcends the compliance training of older generations. Neuroethics must be an integral part of their work. This paper advocates for a proactive "neuroethics-by-design" (NxbD) approach. NxbD offers a reflective lens as well as an operational methodology that can iteratively shape hypotheses, experiments, technological architectures, and translation of the work to wider society. While NxbD is conceived as a toolkit for researchers, the responsibility of considering and addressing these issues is not theirs alone. NxbD is most effectively conceptualized as a shared responsibility that is evaluated and enacted by multiple communities. Such an approach is an investment in our collective future in which we can all contribute.

The Journal of neuroscience : the official journal of the Society for Neuroscience


Modelling the Neurobiology of ADHD Using Human iPSC Systems: A Multimodal Platform for Mechanistic Discovery

Abstract: Attention deficit hyperactivity disorder (ADHD) is a common and highly heterogeneous neurodevelopmental condition with complex biological underpinnings. Despite substantial progress in identifying genetic and neurobiological correlates, the cellular mechanisms linking genetic variation to functional brain alterations remain poorly understood. Human induced pluripotent stem cell (iPSC) technology provides a powerful platform to investigate these mechanisms by enabling the generation of patient-specific neural cell types and the direct interrogation of molecular, cellular, and network-level phenotypes. In this review, we summarise the current understanding of the neurobiological mechanisms underlying ADHD, including dopaminergic dysregulation, delayed neurodevelopmental maturation, and excitatory/inhibitory imbalance. We then discuss how iPSC-based models, combined with genome engineering and advanced functional assays, can be used to dissect gene-specific effects, study neural circuit development, and establish scalable platforms for therapeutic discovery. Finally, we outline key methodological considerations for designing robust iPSC-based models of ADHD. Together, these approaches provide new opportunities to bridge genetic risk with cellular function and accelerate the development of mechanistically informed therapeutic strategies.

Attention Deficit Disorder with Hyperactivity


Conscious and nonconscious thought: Insights from the neuroscience of decision-making

Abstract: Conscious thought is often treated as a special class of neural processing, distinct from the nonconscious computations that guide most behavior. Here I offer a different perspective, grounded in the neuroscience of decision-making. I argue that conscious thought arises not from a unique mechanism but from a distinctive use of neural representations already engaged in nonconscious thought. Nonconscious thoughts are structured as interrogations that yield provisional intentions-decision-like commitments that guide action or inquiry without entering awareness. Using examples from perceptual decision-making and neurophysiology, I suggest that such thoughts depend on persistent neural representations that encode not only potential actions but the questions that give them meaning. These knowledge states may also preserve source-sensitive structure that supports a minimal experiential organization even when they remain nonconscious. Conscious thought, on this account, emerges when such a state is reformatted for potential report to another mind, or to oneself, recruiting theory of mind and narrative structure and placing its content in a space presumed to be shared. This proposal identifies a tractable bridge from nonconscious decision mechanisms to phenomenal consciousness, thereby placing part of the hard problem within empirical reach.

Proceedings of the National Academy of Sciences of the United States of America

Decision Making
Consciousness
Humans
Neurosciences
Thinking


Neuromuscular exercise combined with pain neuroscience education for knee osteoarthritis management in older women: protocol for a randomized controlled trial

Abstract: Knee osteoarthritis is a prevalent chronic condition in older adults, particularly postmenopausal women, affecting physical, psychological, social, and economic aspects of life. Existing neuromuscular exercise programs for knee osteoarthritis are often incomplete, focusing on isolated components such as strength or balance, without simultaneously targeting all key elements, including core stability, balance, and lower-limb strength. Additionally, these programs rarely address psychosocial factors or integrate pain neuroscience principles. Evidence suggests that combining a comprehensive neuromuscular exercise program with Pain Neuroscience Education (PNE) may offer superior benefits in reducing pain, improving function, and decreasing fear of movement compared with conventional exercise alone. This study aims to develop and present a novel integrated protocol and to evaluate its effectiveness compared with usual care in older women with knee osteoarthritis. This double-blind randomized controlled trial will enroll 60 women aged 60 years and older with knee osteoarthritis, randomly assigned to either an intervention group or a usual-care control group (30 per group). Outcome assessors and the statistician will be blinded to group allocation. The intervention group will receive an 8-week supervised neuromuscular exercise program combined with PNE, while the control group will receive usual care, defined as continuation of any ongoing medical management without any structured exercise or PNE added. The primary outcome is knee pain intensity, measured using the Visual Analog Scale. Secondary outcomes include functional disability, assessed using the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) and the Knee Injury and Osteoarthritis Outcome Score (KOOS); physical performance, evaluated via the Timed Up and Go and Sit-to-Stand tests; balance assessed through plantar pressure analysis and the Berg Balance Scale; fear of falling; and pain-related psychological factors including catastrophizing, self-efficacy, and kinesiophobia. Knee proprioception, lower-limb muscle strength, and muscle activity will also be assessed. This protocol describes a novel, integrated approach that simultaneously targets the physical and psychosocial dimensions of knee osteoarthritis in older women. If the findings demonstrate effectiveness, this low-risk, non-pharmacological intervention has the potential to inform clinical rehabilitation guidelines and offer a scalable, accessible treatment option for this growing population. Study is registered in the Iranian Registry of Clinical Trials (IRCT20190224042827N7), registration date: 17 November 2025.

Journal of orthopaedic surgery and research

Humans
Osteoarthritis, Knee
Female
Exercise Therapy
Randomized Controlled Trials as Topic
Aged
Double-Blind Method
Patient Education as Topic
Middle Aged
Pain Management
Neurosciences
Kinesiophobia
Combined Modality Therapy
Pain Measurement


From eye to AI: Studying rodent social behavior in the era of machine learning

Abstract: The study of rodent social behavior has shifted in recent years from relying on direct human observation to more nuanced approaches that integrate computational methods from artificial intelligence (AI) and machine learning. While conventional methods introduce bias and can fail to capture the complexity of rodent social interactions, modern approaches bridging computer vision, ethology, and neuroscience provide more multifaceted insights into behavior, which are particularly relevant to social neuroscience. Despite these benefits, integrating AI into social behavior research also poses several challenges. Here, we discuss the main steps involved and the tools available for analyzing rodent social behavior, examining their advantages and limitations. Additionally, we suggest practical solutions to address common hurdles, aiming to guide young investigators in adopting these methods and to stimulate further discussion among researchers regarding the evolving requirements of these tools in scientific applications.

Animals
Social Behavior
Machine Learning
Behavior, Animal
Rodentia
Artificial Intelligence
Soft Computing
Humans
Neurosciences


Zebrafish behavioral phenotyping: Current assays, automated platforms, and the emerging need for AI in neuroscience, drug discovery and toxicology

Abstract: Over the past two decades, zebrafish have become an increasingly prominent model organism for basic research, drug discovery, and toxicology. Its advantages combine low cost, high throughput amenability, high gene homology to humans, genetic flexibility and widespread use in academia. This animal model combines the ease of use of smaller animals (such as C. elegans and D. melanogaster) with the complexity of its vertebrate/mammalian counterparts, adding access to comprehensive phenotypic and behavioral studies without compromising high throughput and low cost. Similar to rodent models, a growing number of assays have recently been developed for zebrafish. This repertoire is rapidly growing and recent advancements in high-throughput techniques, computer-driven simulations, and automated tracking technologies/devices are starting to open new doors of research while simplifying the analysis of previously difficult-to-detect phenotypes. In parallel, the integration of artificial intelligence (AI) holds great promise for more effectively detecting and characterizing even the most subtle behavioral changes. Despite this rapid progress, the field would benefit from greater standardization of nomenclature, assays, and data formats. Here, we reviewed the literature associated with comprehensive zebrafish behavioral assays, with a particular focus on their applications in drug discovery and toxicology. We compiled the automated devices developed or adapted for these assays. We further discussed the advantages and limitations of these technologies and outlined potential future directions and needs in the field.

Animals
Zebrafish
Drug Discovery
Phenotype
Artificial Intelligence
Behavior, Animal
Neurosciences
Humans
Toxicology
Models, Animal


The Frankfurt 'whisper exam' - a case-based collaborative summative examination to assess clinical decision-making skills in hygiene, microbiology and virology- feasibility and evaluation

Abstract: Collaborative assessment formats have gained increasing attention in medical education due to their potential to foster clinical reasoning, teamwork, and to reduce examination-related stress. However, evidence for their feasibility and acceptance within summative undergraduate medical curricula remains limited. This study aimed to evaluate the feasibility and student perceptions of a case-based, collaborative summative examination ("whisper exam") in undergraduate medical education. Specifically, we explored students' perceptions of stress, preparation effort, teamwork, and the alignment between self-assessement and actual examination performance. A single-center, descriptive feasibility study was conducted with third-year medical students (n = 350) following a laboratory course in hygiene, microbiology, and virology. Students completed a digital, case-based examination using key-feature questions in pairs. Examination performance was recorded at the team level. Student perceptions were collected via a post-exam voluntary questionnaire and analyzed descriptively. The overall pass rate was 93.1% (326/350 students). Survey responses were obtained from 190 students (54.3%). Most respondents reported lower perceived stress compared to individual examinations and described teamwork as constructive and enjoyable. Preparation effort was reported to be comparable to that required for individual examinations. Self-assessment of performance broadly aligned with examination outcomes, although a tendency toward underestimation was observed. The whisper exam was feasible to implement within a summative undergraduate curriculum and positively perceived by the majority of participating students. Findings suggest that collaborative, case-based examinations may complement existing assessment formats. Further research using comparative and multi-institutional designs is required to evaluate educational impact and validity.

Vorbeck L
Ruesseler M
Steinmetzer J
Kohmer N
Kempf VAJ
Brandt C

Humans
Feasibility Studies
Education, Medical, Undergraduate
Educational Measurement
Students, Medical
Clinical Competence
Clinical Decision-Making
Virology
Microbiology
Male
Female
Curriculum
Surveys and Questionnaires


Strengthening India's pandemic preparedness with the four zonal institutes of virology: stakeholder consultations for outbreak response and collaborative research priorities

Abstract: The Pradhan Mantri Ayushman Bharat Health Infrastructure Mission (PM-ABHIM) scheme, supported by the World Bank, is establishing four zonal National Institutes of Virology (NIVs) in India. It is essential to identify the zonal disease and research priorities so as to focus research at zonal levels. This study reports a zonal viral disease prioritisation exercise to support outbreak response and collaborative research. It describes zonal-prioritised viral diseases, assesses concordance and differences in zonal priority lists and, and identifies cross‑cutting research themes and preparedness gaps using an multicriteria decision analysis (MCDA)‑based consensus process. We conducted a cross-sectional, multi-stakeholder consultative study across four geographical zones of India in March 2024. The zonal-level consultative workshops employed a systematic consensus-building approach using the modified One Health Zoonotic Disease Prioritisation (OHZDP) tool, adapted for emerging viral diseases and applied via MCDA. We identified zonal-level stakeholders, listed 40 viral diseases and categorised them into three groups: common occurrence (Group A), limited occurrence (Group B), and rare occurrences with a chance of emergence, evolution or importation (Group C). The stakeholders from state health departments, medical colleges, research institutes and the Virus Research and Diagnostic Laboratory (VRDL) network ranked the viral diseases and research themes in each zone. Spearman rank correlation was used to assess concordance of priority rankings between zones. A total of 186 participants (42-48 per zone) contributed to the four zonal workshops including collaborators from VRDL laboratories (26%), public health stakeholders from Integrated Disease Surveillance programme(IDSP) (28%), invited experts (21%), organisers (19%) and Indian Council of Medical Research (ICMR) representatives (6%). The key outcomes included the zone-specific lists of priority viral diseases in Groups A, B and C. There were zonal variations in viral disease prioritisation, reflecting local epidemiological patterns. Spearman rank correlation analysis showed moderate positive correlation between the Central and East zones (rho = 0.697, P = 0.031), whereas other pairwise comparisons were not statistically significant, which indicated both shared and distinct priority patterns within the zones. The top five priority viral diseases across zones included dengue, influenza, measles, Japanese encephalitis and hepatitis A. The research themes and subthemes were then decided for collaborative research. These multistakeholder consultations provided a novel, replicable template for prioritising viral diseases to develop strategies for mitigating the impact of future outbreaks through collaborative research. These zonal priorities may guide similar exercises at national, regional and global levels in future.

Pise K
Tandale B
Kumar N
Barde P
Munivenkatappa A
Mathapati B
Jadhav A
Rawat P
Basavaraj S
Gaikwad S
Deoshatwar A
Pattassery SA
Kutteyil S
Pulinchani A

India
Humans
Pandemic Preparedness
Cross-Sectional Studies
Virus Diseases
Disease Outbreaks
Virology
Research
Academies and Institutes
Stakeholder Participation
Animals


AI-Driven Approaches for the Detection, Classification, and Surveillance of Viral Pathogens: Current Advances, Challenges, and Future Directions

Abstract: Artificial intelligence (AI) has rapidly emerged as a transformative tool in virology, offering new opportunities for the detection, classification, and surveillance of viral pathogens. Recent advances in machine learning, deep neural networks, and multimodal data analysis now enable the identification of viral signatures from genomic sequences, medical images, environmental samples, and social-media-derived epidemiological signals. This review provides a comprehensive overview of state-of-the-art AI methodologies applied to viral pathogen research, with a particular focus on image-based diagnostics, automated quality assessment of virology-related digital content, and predictive modelling for outbreak monitoring. We discuss how convolutional and transformer-based architectures are being used to classify infected tissues, detect viral particles, and support laboratory workflows. Furthermore, we highlight the emerging role of AI in evaluating the reliability of user-generated images and short videos related to infectious diseases, an area increasingly relevant in the age of misinformation. Challenges such as dataset bias, limited annotated virological images, ethical concerns, and the need for standardized quality-assessment pipelines are critically examined. Finally, we outline future research directions, including hybrid AI-biological models, AI-supported viral surveillance in healthcare environments, and the integration of explainable AI to enhance clinical trust.

Artificial Intelligence
Humans
Virus Diseases
Viruses
Virology
Machine Learning


Intestinal Organoids as Models to Study Viruses: Current Application and Future Perspective

Abstract: Intestinal organoids have emerged as a transformative model system in virology, bridging the gap between conventional cell lines and animal models by recapitulating the complex cellular diversity, three-dimensional architecture, and key functions of the human intestinal epithelium. This review highlights how this technology has enabled groundbreaking studies of enteric viruses, including the successful cultivation of previously uncultivable human norovirus, and has provided critical insights into the infection mechanisms of rotavirus, enterovirus A71, and Severe Acute Respiratory Syndrome Coronavirus 2. We discuss how emerging technologies, such as co-culture systems for host-microbiome interactions, vascularization techniques, and CRISPR/Cas9 gene editing, are being integrated with organoids to create more physiologically relevant microphysiological systems. Despite challenges related to immune component integration and model standardization, intestinal organoids offer a promising platform for elucidating virus-host interactions, advancing antiviral drug screening, and promoting personalized infectious disease research.

Journal of microbiology and biotechnology

Ruting W
Jiale L
Hongxi W
Zhenjin H
Ruohan Z
Yuanbo S
Rongxin Z
Hongzhen T
Feng J

Organoids
Humans
Animals
Intestines
Viruses
Virology
Intestinal Mucosa
Host Microbial Interactions
Models, Biological
Microphysiological Systems
Host-Pathogen Interactions
Coculture Techniques


Report from the 9th Italian Society for Virology (SIV-ISV) 2025 Annual Meeting

Abstract: The 9th National Congress of the Italian Society for Virology (SIV-ISV), entitled "One Virology-One Health", took place in Turin at the Centro Congressi Lingotto from 22 to 24 June 2025. The meeting highlighted recent multidisciplinary and translational developments in virology, with a strong focus on the integration of the One Health perspective. Major themes included viral emergence and surveillance, genomic sequencing and bioinformatics, virus-host interactions, viral immunology and vaccines, structural and physical virology, environmental and food virology, zoonoses and animal infections, diagnostics and antiviral therapy, virus-based biotechnology and plant virology. The Congress aimed to: (i) bring together clinicians, basic researchers, veterinarians, environmental microbiologists, bioinformaticians, public-health professionals and industry to share methodologies and best practices; (ii) provide an interactive scientific environment promoting discussion and collaboration between senior investigators and trainees through plenaries, joint society sessions, invited talks, oral communications selected from abstracts, poster sessions, and mentoring panels; and (iii) identify priorities and inspire new research directions at the interface of human, animal and environmental health. More than 400 participants from national and international institutions attended the meeting, featuring distinguished plenary speakers, joint sessions with global networks, and numerous presentations of original unpublished data. This report summarizes the meeting's scientific highlights, cross-disciplinary discussions, and proposed actions to strengthen One Health surveillance, computational infrastructures, and translational applications of viral biology.

De Filippis A
Donalisio M
Luganini A
Caccuri F
Esposito F
Grandi N
Zannella C
Rubino L
Tramontano E
Vaccari G
Galdiero M
Caruso A

Humans
Virology
Animals
One Health
Italy
Societies, Scientific
Virus Diseases
Zoonoses
Viruses


Scanning the horizon: deep mutational scanning approaches in virology

Abstract: Studying the effects of mutations is central to virology. Deep mutational scanning (DMS) is a technique that couples high-throughput mutagenesis with deep sequencing to measure the effects of mutations in pooled assays. When adapted to viruses, DMS accelerates comprehensive measurement of mutational effects across viral genomes, mapping evolutionary constraints on viral proteins. Recently, DMS has been applied to a wider variety of problems in virology and viral evolution, quantifying the effects of mutation across host species, tissue environments, and immunological pressures. Since DMS was first applied to virology, synthetic biology has transformed the engineering of mutational libraries, opening new questions to exploration. With the technology now matured, DMS is poised to transform our understanding of viral evolution in new, exciting ways. This review will synthesize recent technological and conceptual advances in DMS methods being applied to virology, the insights it is yielding, and the opportunities for future studies.

High-Throughput Nucleotide Sequencing
Virology
Viruses
Mutation
Genome, Viral
Evolution, Molecular
DNA Mutational Analysis
Mutagenesis


Special Issue: Microscopy Methods for Virus Research

Abstract: Significant advances in microscopy methods for biomedical applications have been made in the past two decades, and these methods are now being actively pursued for virus research [...].

Microscopy Virology Viruses Humans Animals


Virologist accused of starting COVID-19 fights funding ban

Abstract: United States seeks to debar Ralph Baric for misleading NIAID on old coronavirus studies, which he disputes.

National Institute of Allergy and Infectious Diseases (U.S.)


Basic Virology

Abstract: Current generations are living through a historical event in virology: the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. If you asked people when the last major pandemic was, many would probably say the Spanish flu of 1918-1920. Pandemics happen more frequently than most people think (Sampath et al., Cureus 13:e18136-18144, 2021). There have been at least five recorded pandemics between the Spanish flu and the recent SARS-CoV-2 pandemic. While the SARS-CoV-2 pandemic has brought with it indescribable sorrow and pain, it has also increased people's awareness of the impact viruses can have on life on Earth. Terms such as hygiene, modes of infection, community spread, quarantine, vaccines, etc. have become part of our daily conversations. As this book's first chapter provided a basic review of proteomic technologies for virologists, this chapter provides a basic review of virology for proteomic scientists. While virologist may find this chapter unsatisfying, hopefully proteomic scientists will learn enough to be able to understand how proteomic technology can be used to further detail the structure, function, and life cycle of viruses. This chapter will provide both generic and specific examples of viral structures, how they infect cells, and their effects on both the infected cell and the entire organism.

Advances in experimental medicine and biology

Humans
SARS-CoV-2
Virology
Proteomics
COVID-19
Genome, Viral
Viral Proteins
Animals


Virus taxonomy and the ICTV - 21 FAQs for the perplexed virologist

Abstract: Just over 125 years has passed since the 'filterable' agents of tobacco mosaic disease and foot-and-mouth disease were first described as infectious, replicating entities smaller than bacteria. Today, viruses are formally classified into more than 16,000 species ranked into genera, families and higher taxa. The development of an official virus taxonomy has been overseen by an International Committee, first constituted in 1966 and renamed as the International Committee on Taxonomy of Viruses (ICTV) in 1975. Despite the engagement of the ICTV in virus taxonomy over the last 60 years, many aspects of virus classification and nomenclature may seem odd or sometimes incomprehensible to virologists more familiar with the taxonomy of cellular organisms. Who runs the ICTV? What are virus species demarcation criteria? Why have all virus species names become binomial? How can a sequence in a metagenomic dataset be assigned to a virus species? This article attempts to answer several such questions and outlines how a large, inclusive and global community of virologists has developed new and responsive policies for virus taxonomy in a decade when the pace of virus discovery has dramatically accelerated.

Viruses
Virology
Terminology as Topic
Classification
Genome, Viral


A two-component RUBY reporter system to assess plant virus infection

Abstract: The use of plant virus vectors to express reporter genes has significantly enhanced the study of virus biology. In this communication we expand the list of virus vectored reporter systems to include the RUBY visible reporter. RUBY utilizes a three-enzyme system to produce betalain from the amino acid tyrosine, a natural pigment responsible for the bright red coloration in beets. To adapt this system for virus expression one of the three enzymes, L-DOPA 4,5-dioxygenase (DODA), was engineered into tobacco mosaic virus (TMV) and turnip mosaic virus (TuMV) vectors. The two remaining enzymes required for betalain production, P450 oxygenase CYP76AD1 and glucosyltransferase (GT), were transformed for expression in the host plant Nicotiana benthamiana. Inoculation of TMV and TuMV vectors expressing DODA onto transgenic CYP76AD1-GT plants resulted in the production of visible red tissues that corresponded with virus infection. The development of this system provides a non-invasive and robust means to directly visualize virus infection without the need for destructive sampling, special lighting equipment or enzymatic substrates.

Genes, Reporter
Nicotiana
Plant Diseases
Genetic Vectors
Tobacco Mosaic Virus
Plants, Genetically Modified
Potyvirus
Glucosyltransferases
Plant Viruses
Virology


Protein Language Models in Virology: A Review of Advances and Applications

Abstract: Protein language models (PLMs) enable functional analysis of divergent viral sequences without homology alignment. This review covers PLM architectures from sequence encoders through structure-aware architectures to generative models and assesses their application to orphan protein structure resolution, virosphere-wide functional classification, host factor identification, and therapeutic antibody optimization. Finally, the limitations of the current model in terms of interpretability and insufficient data representation are discussed while exploring future trends toward multimodal integration and the "dry-wet" experimental loop to accelerate the adoption of artificial intelligence in precision virology.

Methods in molecular biology (Clifton, N.J.)

Humans
Virology
Viruses
Generative Artificial Intelligence
Viral Proteins
Large Language Models
Models, Molecular


RNA Large Language Models in Virology

Abstract: The viral gene sequence is regarded as a kind of special text, which constitutes a core innovation in the application of large language models to virus research. This idea breaks free from the shackles of the traditional analysis framework and opens up a new way of computing to understand the evolution of the virus. Using this method, researchers can quickly and accurately locate the key mutation sites of the virus. This helps to detect emerging variant strains in time and assess their potential impact on transmissibility and pathogenicity. Especially importantly, this technology can also reconstruct the evolutionary path of the virus and realize real-time tracking of the mutation process. This provides a powerful tool for a systematic understanding of the adaptive evolution of the virus. These profound insights based on the big language model can be used as a theoretical basis for the development of targeted vaccines and drugs. Although the relevant computing technology is in the development stage, it has shown great potential to promote the transformation of virological research to a predictable direction.

Large Language Models
Virology
Mutation
Evolution, Molecular
Genome, Viral
Viruses
RNA, Viral
Humans


HIV envelope pseudotyped virus- an indispensable tool in HIV research

Abstract: HIV env-pseudotyped viruses have become invaluable tools in HIV research. These recombinant viral particles are generated by co-transfecting HEK293T cells with an envelope cassette containing a heterologous HIV envelope glycoprotein and an envelope-deficient backbone that lacks one or more essential genes, to facilitate only single round infection. The non-infective, replication-deficient nature of env-pseudotyped viruses allows them to be safely handled in a BSL-2 facility. Because of their ability to express heterogeneously derived HIV envelopes, they serve as versatile tools for investigating co-receptor usage and tropism, screening of novel anti-HIV agents, studying neutralizing antibody responses, identifying novel broadly neutralizing antibodies (bNAbs), and for understanding the infectivity and mechanistic potential of different HIV strains. This review summarizes the current methods of generating HIV env-pseudotyped viruses using diverse packaging systems, and their varied applications, sources and limitations.

env Gene Products, Human Immunodeficiency Virus


25th Annual Meeting of the Rocky Mountain Virology Association

Abstract: Located on the traditional and ancestral homelands of the Arapaho, Cheyenne, and Ute Nations, Colorado State University's Mountain Campus hosted the 25th Annual Rocky Mountain Virology Association meeting. The three-day event, held from 26 September to 28 September 2025, welcomed 152 participants focused on the following topics: viruses, prions, immunology, transmission, structural biology, and vector biology. This year's Randall Jay Cohrs Keynote Presentation summarized ongoing research on viral glycoproteins in relation to viral entry and assembly. Understanding the role of viral glycoproteins is essential in vaccine and antiviral development for enveloped RNA viruses. Alongside rigorous scientific discourse and networking, attendees made the most of their time by hiking amidst beautiful fall colors, wildlife, and young aspens starting the forest anew. On behalf of the Rocky Mountain Virology Association, this report summarizes select presentations from the 25th annual meeting.

Byrne-Haber TJ
Pham KN
Joob A
Pinto SM
Ratnayake OC
Thompson R
Rovnak J
Perera R

Animals
Humans
Virology
Prions
Viruses
Virus Diseases
Virus Internalization
Glycoproteins


PEG-8000 precipitation as a rapid method for enrichment and purification of feline calicivirus

Abstract: Feline calicivirus (FCV) is widely used as a surrogate model to study calicivirus biology, including human noroviruses, for which robust cell culture systems are limited. The availability of concentrated and purified viral preparations is essential for structural, biochemical, and infectivity studies. Here, we describe and validate a polyethylene glycol (PEG-8000) precipitation method for the enrichment and purification of FCV from infected cell culture supernatants. PEG-8000 precipitation resulted in a more than 2-log increase in viral titers while markedly reducing contaminating cellular proteins. Purified viral particles retained infectivity and exhibited typical cytopathic effects, viral protein expression, and subcellular localization patterns during infection. Transmission electron microscopy confirmed the presence of non-enveloped viral particles with preserved morphology. Notably, both PEG-8000-purified and non-purified FCV preparations remained stable upon storage at -80 °C, maintaining infectivity after freezing. Compared with conventional ultracentrifugation-based approaches, this method is rapid, cost-effective, and does not require specialized equipment. Overall, PEG-8000 precipitation provides a reliable and straightforward strategy for FCV enrichment and purification and may be readily adapted for other members of the family Caliciviridae.

Gómez de la Madrid J
Sosa-Mondragon SI
Salazar-Villatoro L
Gutiérrez-Escolano AL

Polyethylene Glycols
Calicivirus, Feline
Animals
Cats
Chemical Precipitation
Cell Line
Virology
Microscopy, Electron, Transmission


Applications of Pseudoviruses Bearing Glycoproteins of SARS-CoV-2 and Influenza Virus

Abstract: This review discusses pseudoviruses, which are chimeric viral particles constructed by replacing the envelope glycoproteins of viruses such as human immunodeficiency virus (HIV) or vesicular stomatitis virus (VSV) with those of target viruses, and their advantages in the study of highly pathogenic respiratory viruses. These systems serve as valuable tools for elucidating viral entry mechanisms, screening antiviral drugs, quantitatively assessing virus-neutralizing antibodies, and evaluating vaccine efficacy, while reducing the safety risks associated with live viruses. Despite limitations such as applicability primarily to enveloped viruses, ongoing technological advances continue to improve pseudovirus systems, increasing their utility in vaccine development, antiviral research, and rapid response to emerging infectious diseases.

Ota M
Sano K
Yoshihara K
Watanabe S
Hasegawa H
Miyakawa K

Virology
Viral Envelope
Glycoproteins
Orthomyxoviridae
SARS-CoV-2
Vaccine Development


Identification of MA-104 cells as a novel continuous cell line for the direct primary isolation of lumpy skin disease virus

Abstract: Lumpy skin disease (LSD) poses a significant threat to cattle populations in India and worldwide, owing to its rapid spread, high morbidity rate, and continuous emergence of new variants. Reliable in vitro systems for LSD virus (LSDV) isolation are essential for diagnostic applications, virological studies, and vaccine development. Primary ruminant cells are commonly used for initial virus isolation; however, they suffer from limited availability and poor reproducibility. In this study, we systematically evaluated the susceptibility of five cell lines, Vero, MA-104, MDBK, BHK-21, and goat testis (GT) cells for the direct isolation and propagation of LSDV. Viral replication and infectivity were assessed using cytopathic effect (CPE) monitoring, conventional multi-target PCR, 50% tissue culture infectious dose (TCID₅₀) assay, and an indirect immunoperoxidase test (IPT) for antigen detection. Direct virus isolation from clinical scab material was successful only in MA-104 and GT cells. In contrast, Vero, MDBK, and BHK-21 cells did not support primary isolation but readily propagated LSDV after prior adaptation to GT cells. Subsequent one-step growth kinetics, performed at multiplicities of infection (MOI) of 0.1 and 0.01, further elucidated the distinct cell line-dependent replication patterns. Vero cells yielded the highest titers (106.33 TCID50/mL), whereas MA-104 cells supported sustained replication with peak titers of 105.5 TCID50/mL, demonstrating their strong capacity for propagation, comparable to other permissive continuous cell lines (MDBK and BHK-21 cells), which required prior viral adaptation. Unlike primary GT cells, MA-104 is a novel, permissive continuous cell line offering benefits such as reproducibility, ready availability, and reduced ethical concerns, making it a robust alternative for primary cell isolation. This study provides practical insights into the selection of appropriate cell lines and determination of optimal harvesting time points for efficient LSDV isolation and propagation, as well as downstream applications, such as pathogenesis studies and vaccine development.

Todkari AM
Kumar AP
Kelwan AP
Sahoo B
Gurav A
Mondal B
Kumar A

Animals
Lumpy skin disease virus
Cell Line
Virus Cultivation
Lumpy Skin Disease
Cattle
Virus Replication
Goats
Chlorocebus aethiops
Cytopathogenic Effect, Viral
Virology
India


Integrating metagenomics and metatranscriptomics into Orthoflavivirus diagnosis: a transformative approach for clinical virology

Abstract: Diagnostic inaccuracies are a major yet often overlooked threat to global health, leading to delayed treatment, preventable harm and systemic gaps in disease control. Among the most affected domains are Orthoflavivirus infections, which pose ongoing diagnostic challenges due to antigenic cross-reactivity, overlapping clinical symptoms and the narrow temporal sensitivity of standard tools such as serology and reverse transcription polymerase chain reaction. These constraints have led to widespread misdiagnoses and underreporting, ultimately hampering both effective clinical management and public health response. Recent advances in metagenomic and metatranscriptomic sequencing offer a transformative solution by enabling unbiased, simultaneous pathogen detection and real-time profiling of viral and host transcriptomics. In this review, we assess the diagnostic performance and translational value of these approaches in resolving Orthoflavivirus infections, with case examples from clinical settings in countries like the USA, UK, China and Germany which have already implemented these approaches into routine diagnosis in some settings. We examine key methodological considerations, including optimal sample timing, sample types and processing, sequencing strategy selection and the diagnostic performance of various platforms. We highlight the growing use of metatranscriptomics for detecting active infections, profiling viral and host responses, identifying coinfections and supporting real-time surveillance. We also discuss the key challenges such as technical expertise, lack of standardization, cost, turnaround time and regulatory approval that currently limit global implementation. Finally, we highlight emerging international efforts to integrate sequencing-based diagnostics into routine hospital workflows. Together, these innovations mark a critical shift toward precision diagnostics for Orthoflavivirus infections, with broad implications for clinical settings.

Metagenomics
Humans
RNA Viruses
Virology
Gene Expression Profiling
RNA Virus Infections
Transcriptome


How new approach methods are reshaping virology research

Abstract: Animal models are a cornerstone of basic and translational virology research, widely used to study viral pathogenesis and evaluate vaccines and therapeutics. However, growing ethical and scientific concerns, alongside recent National Institutes of Health (NIH) and Food and Drug Administration (FDA) initiatives, are accelerating a shift toward non-animal, human-relevant alternatives. Advanced cell- and tissue-based systems now offer powerful platforms to model human disease. This Gem outlines emerging tools and highlights their promise for virology research in a rapidly evolving regulatory and technological landscape.

Humans
Animals
Virology
Translational Research, Biomedical
Disease Models, Animal
United States
Virus Diseases


Animal organoids as transformative platforms for viral infections and zoonotic cross-species viral research

Abstract: Organoids have revolutionized human biomedical research since their development in 2010. However, as nearly 75% of human infectious diseases originate in animals, animal-derived organoids are essential to complement human models, yet their development in veterinary contexts remains scarce. Organoids replicate native tissue architecture, enabling species-specific and comparative studies of viral infection and host response. Thus, animal organoids represent a powerful field in organoid technology, advancing cross-species virology research and strengthening strategies for zoonotic disease preparedness.

García-Rodríguez I
García-Dorival I
Alonso C
Cuesta-Geijo MÁ

Animals
Organoids
Humans
Virus Diseases
Zoonoses
Viral Zoonoses
Biomedical Research
Host-Pathogen Interactions
Virology


[A brief history and significance of the Czechoslovak army's Antiviral Serum Bank]

Abstract: The Virology Department of the Czechoslovak army, established in response to the need for a specific approach to biological threats, was initially subordinated to the Military Institute of Hygiene and Epidemiology (founded in 1957), and later to the Central Military Medical Institute. Within this department, a systematic Virus Strain Bank was established that contained highly contagious viruses and bacteria used for diagnostic purposes and to develop defensive methods against biological threats. The preserved strains included viruses causing hemorrhagic fevers, encephalitis, yellow fever, and Rocky Mountain spotted fever, as well as the variola minor virus. The Virus Strain Bank enabled testing of the capabilities to detect and identify dangerous agents, as well as the development of specific and neutralizing antibodies against them. It was therefore essential for defensive and diagnostic purposes in the context of protection against the use of biological weapons. Keywords: virus strains; viral infection diagnosis, biological threat.

Klinicka mikrobiologie a infekcni lekarstvi

Holub M
Mankovecký L
Kubátová H
Pavliš O
Pajer P

Humans
History, 20th Century
Virus Diseases
Czechoslovakia
Military Medicine
Virology

Journal Article
Historical Article
English Abstract


Bridging virology, public health, and food safety: a comprehensive review of hepatitis A virus

Abstract: Hepatitis A virus (HAV) remains a significant global public health concern, particularly as a foodborne pathogen. Despite advances in vaccination and sanitation, HAV continues to cause outbreaks, especially in regions with uneven immunization coverage or inadequate hygiene infrastructure. This review comprehensively examines HAV from virological, clinical, and epidemiological perspectives, highlighting its pathogenesis, transmission routes, genomic diversity, and foodborne risks. We discuss the evolving global epidemiology of HAV, emphasizing the shift from high to low endemicity in vaccinated populations and the emergence of susceptible cohorts in moderately developed regions. The review underscores the challenges in foodborne HAV detection, including the limitations of current methods and the promise of emerging technologies like reverse transcription digital polymerase chain reaction (RT-dPCR) for enhanced sensitivity. Additionally, we summarize emerging antiviral approaches in food safety control, including plant-derived bioactive compounds and edible coatings, for controlling HAV transmission through the food chain. Finally, we present an overview of WHO-recommended vaccination strategies based on endemicity levels-targeted immunization for high-risk groups in low-endemic areas, universal childhood vaccination in moderate-endemic regions, and reliance on naturally acquired immunity in high-endemic zones. Our synthesis aims to bridge gaps between virology, clinical medicine, and food safety, offering insights for interdisciplinary collaboration in HAV prevention and control.

Humans
Hepatitis A
Hepatitis A virus
Public Health
Food Safety
Foodborne Diseases
Virology
Animals


High-resolution imaging techniques to interrogate virus-host interactions

Abstract: Viruses are obligate parasites that rely extensively on host cellular machinery to complete their life cycles. Therefore, examining the fundamental nature behind how viruses interact with their hosts can teach us more about the pathogenesis of these microbes while also contributing to our overall understanding of essential cell biological processes. In a 2021 mSphere of Influence article, the use of live-cell imaging to uncover a unique mechanism of viral assembly was discussed. In this Full Circle review, we highlight the high-resolution imaging techniques currently revolutionizing virology research and discuss how they can be utilized to advance our ability to identify and interrogate novel virus-host interactions.

Host-Pathogen Interactions
Host Microbial Interactions
Viruses
Humans
Virology
Animals
Virus Assembly
Microscopy
Virus Physiological Phenomena


Optimization of a GFP-PAC co-expression cassette-based purification system for efficient construction and rapid screening of recombinant HSV-1

Abstract: Oncolytic viruses (OVs) constitute a promising class of cancer therapeutics engineered to selectively replicate in and lyse malignant cells while sparing normal tissues. Among these, recombinant Herpes Simplex Virus type 1 (HSV-1), generated through targeted deletion of immediate-early (IE) genes, has emerged as a leading candidate, with several vectors currently advancing to phase III clinical trials. Genetic alterations are typically introduced into the HSV-1 genome via homologous recombination using shuttle vectors; however, isolation of recombinant viruses from parental populations by plaque purification remains labor-intensive and technically demanding. This limitation primarily results from the low efficiency of homologous recombination and the frequent persistence of parental virus, which often exhibits a replicative advantage over recombinant variants. In this study, a novel purification protocol incorporating a GFP-PAC co-expression cassette was developed and optimized to enable simultaneous puromycin selection and fluorescence-based identification of recombinant viral constructs. This dual-selection approach significantly accelerates and simplifies the isolation of recombinant HSV-1, enhancing both efficiency and purity. The optimized protocol provides a robust, scalable strategy for generating recombinant HSV-1 with broad applicability in vaccine development, gene therapy, and fundamental virology research.

Herpesvirus 1, Human
Green Fluorescent Proteins
Animals
Recombination, Genetic
Genetic Vectors
Virology
Humans
Staining and Labeling
Genes, Reporter
Cell Line


Versatile HIV Rev-dependent reporter cell system for stringent and sensitive quantification of viral reservoirs, neutralizing antibodies, and restriction factors

Abstract: Detecting and measuring HIV reservoirs, neutralizing antibodies, and restriction factors are important for HIV cure research and the development of new therapeutics and vaccines. Here we describe the development and validation of several HIV Rev-dependent indicator cell lines for these purposes. These reporter cells derive from different T-lymphoblast cell lines, including Molt4-CCR5, SupT1-CCR5, CEM-SS, A3R5, and from the adherent TZM cell platform based on HeLa clone JC53. These cells express CD4, CXCR4, and various levels of CCR5. We compared these cell lines for responsiveness to both X4 and R5-tropic viruses, and confirmed that reporter expression in these cells is not affected by stimulation from mitogens but is responsive to HIV Tat and Rev, reducing non-specific reporter induction from the leaky LTR promoter. To validate the sensitivity of the Rev-dependent reporter cell systems, we conducted a viral dilution assay with three primary HIV-1 clade C swarms from an adult in Malawi. We also validated the systems for quantifying antibody neutralization and screening restriction factors; these systems are also sensitive for viral outgrowth assays for quantifying viral reservoirs in clinical and basic research settings. Given that the systems can measure HIV accurately in complex environments with mitogens or other substances, they can be used for versatile applications, such as quantifying latent reservoirs, testing inhibitory compounds, conducting neutralizing antibody assays, and identifying new restriction factors.

Spear M
Choi J
Hetrick B
Lee J
Lê-Bury G
Vo TT
Han Y
Liang H
Guo J
Yu D
Iyer S
Mwandumba HC
Russell DG
Wu Y
Gludish DW

rev Gene Products, Human Immunodeficiency Virus


Using Porcine Gastric Mucin Coated Magnetic Beads to Concentrate and Purify Infectious Human Noroviruses for Infectivity Assays with Human Intestinal Enteroids and Zebrafish

Abstract: Human noroviruses (hNoVs) are the leading cause of foodborne gastroenteritis worldwide, yet progress in infectivity-based studies has been hindered by the lack of robust virus purification methods that preserve infectivity. Here, we evaluated porcine gastric mucin (PGM)-coated magnetic beads as a sample preparation tool for concentrating and purifying infectious hNoVs from complex clinical and food matrices for use in two emerging infectivity models, human intestinal enteroids (HIEs) and zebrafish embryos/larvae. Using 18 hNoV strains across multiple genotypes, we observed variable recovery efficiencies (0.03–40%) from stool suspensions, with PGM beads often enhancing viral binding to HIEs but sometimes reducing replication (ten hNoV strains replicated without beads but only seven demonstrated replication with addition of beads), likely due to partial blocking of cell entry. In oyster homogenates spiked with hNoV GII.4[P16], bead aggregation and toxicity issues were mitigated by sample dilution, use of zebrafish larvae instead of embryos, and incorporation of an additional purification step, enabling detection at 105 to 106 genome copies per reaction. No significant cytotoxicity was detected in HIEs or zebrafish larvae under optimized conditions. Our findings indicate that PGM bead-based purification can be a valuable optional step for infectivity assays when working with samples containing strong inhibitors. This protocol provides a practical bridge between environmental/food hNoV detection and infectivity assessment in advanced model systems.

Animals
Zebrafish
Humans
Gastric Mucins
Norovirus
Swine
Caliciviridae Infections
Feces
Intestines
Virology
Gastroenteritis
Ostreidae


Gain-of-function virology as dual-use research of concern: Variations of securitization in the United States

Abstract: Ever since the advent of recombinant DNA technology in the early 1970s concerns have been expressed about the misuse potential of this and subsequent biotechnology breakthroughs. This article focuses on the securitization of gain-of-function (GOF) virology research in the United States, utilizing an updated theoretical framework that distinguishes between "riskification" and "threatification." The paper examines three distinct cases, two historical, one ongoing. It argues that early attempts to govern GOF research primarily employed a riskification approach, characterized by self-governance by the scientific community. However, the controversy over the origins of the COVID-19 pandemic led to a shift toward threatification, bringing in high-level political actors like the U.S. President and Congress, resulting in the adoption of more restrictive, legally-enforced oversight measures. The article concludes that the application of this theoretical distinction provides a better understanding of how the governance of dual-use research has evolved in the United States.

Politics and the life sciences : the journal of the Association for Politics and the Life Sciences

United States
Virology
Humans
COVID-19
Politics
SARS-CoV-2


Cell line bias in virus research: implications for viral propagation and biological interpretation

Abstract: Cell lines are essential tools in virology for propagating viruses for characterization studies. However, reliance on a few historically popular lines-such as Vero, BHK-21, and MDCK-can introduce bias and obscure important aspects of viral biology, such as entry mechanisms and replication dynamics. A review of over 6,000 publications revealed that a small number of cell lines are used disproportionately, often due to historical precedence and general permissiveness for viral infection. Gene expression analysis showed that while these lines are enriched for pro-viral process genes, many underutilized cell lines from diverse tissue types also exhibit similar profiles. This review calls for a more strategic, molecularly informed approach to cell line selection, including the development of molecular databases for non-human cell lines, identification of virologically relevant traits, and broader use of biologically diverse panels. Such a data-driven strategy is especially vital for studying emerging and zoonotic viruses, where accurate modeling of host-virus interactions is important. Expanding and refining cell line use will improve reproducibility and yield more accurate insights into viral pathogenesis.

Frontiers in cellular and infection microbiology

Animals
Humans
Cell Line
Virology
Viruses
Virus Replication
Virus Cultivation
Host-Pathogen Interactions


David Baltimore: Scientist, leader, and mentor

Abstract: Fifty years ago, at the remarkably young age of 37, David Baltimore received the Nobel Prize (with Howard Temin and Renato Dulbecco) for "discoveries concerning the interaction between tumor viruses and the genetic material of the cell." David was a prolific scientist whose work spanned many topics, but he was first and foremost a virologist. His recent passing invites us to reflect on a remarkable intellectual trajectory that began with seminal discoveries in virology, broadened to encompass major advances in cancer biology and immunology, and culminated in a legacy-sustained by the many scientists he trained-that will continue to shape modern biomedicine for years to come.

Virology
Humans
Male
History, 20th Century
History, 21st Century
Mentors
Nobel Prize
Oncogenic Viruses
Host-Pathogen Interactions
Neoplasms


Artificial Intelligence as a Catalyst for Advancements in Medical Virology

Abstract: Artificial intelligence (AI), including machine learning (ML) and deep learning (DL), has become a crucial element in medical virology, transforming the research and treatment of viral illnesses. AI is transforming viral research and clinical practice by improving genomic analysis, diagnostic accuracy, treatment innovation, and epidemiological modeling. AI's contributions are significant and extensive, encompassing the analysis of intricate viral genomes, the expedited development of antiviral treatments, and the forecasting of disease evolution. Notwithstanding obstacles like data privacy, algorithmic bias, and ethical dilemmas, the amalgamation of AI with advanced technologies, including quantum computing and protein language models, is poised to herald a new epoch of virological advancement. This letter emphasizes the necessity for interdisciplinary collaboration to use AI's transformational capabilities while maintaining stringent ethical monitoring in combating viral infections.

Humans
Artificial Intelligence
Deep Learning
Machine Learning
Virology
Virus Diseases


Meeting report: The 3(rd) international conference of the World Society for Virology (WSV 2025) - The Virosphere of Our Cellular World

Abstract: The 3rd International Conference of the World Society for Virology (WSV 2025) was held in May 6-8, 2025, in Kuala Lumpur, Malaysia. WSV2025 adopted the integrative theme "The Virosphere of Our Cellular World." This theme denotes the universal and intricate relationships between viruses and their cellular hosts across all domains of life. The conference attracted 291 participants from 27 countries, featuring a scientific program of 83 talks and numerous poster presentations spanning human, animal, plant, insect, and bacterial viruses at basic, clinical and applied levels. This report summarizes the program highlights, key scientific discussions, and significant outcomes of the conference, confirming the WSV's role as a unifying platform for the global virology community since its founding in 2017.

Söderlund-Venermo M
Johari NAB
Muhamad A
Yusoff K
Abdelwahab SF
Moore MD
Wilson WC
Venter M
Malik YS
Saxena SK
Abdelwhab EM
Winter S
Fielding BC
Vakharia VN
Varma A
Kuhn RJ
Abdel-Moneim AS

Animals
Humans
Societies, Scientific
Virology
Virus Diseases
Viruses


First Brazilian Symposium on Viruses of Microorganisms (BrVoM 2025)

Abstract: In recent decades, there has been an increased interest in viruses of microorganisms (VoM) and international efforts to gather researchers interested in them. Here, we describe the 1st Brazilian Symposium on Viruses of Microorganisms (BrVoM), held on 1 August 2025 at the Federal University of Minas Gerais (UFMG, Belo Horizonte, Brazil) with institutional support from the Federal University of Alfenas (UNIFAL) and the Brazilian Society for Virology (SBV). The symposium greatly surpassed expectations, gathering nearly 300 attendees from all Brazilian geographical regions. The scientific program included keynote and thematic lectures covering bacteriophages, fungal viruses, giant viruses, and microbial resources regulation. The event was remarkable for its collaborative spirit and inclusion of early career attendees. The success of this first edition highlights the vitality of the Brazilian community working on microbial viruses and sets the stage for future editions.

Abrahão JS
Coelho LFL
Witt ASA
Alves AKDNN
Guimarães ACDS
Silva BSR
Neiva BN
Oliveira BF
Dias J
Carvalho JVRP
Lopes LP
Rodrigues MFDR
Barcelos MG
Arias NEC
Zerbini P
Santos VLD
Leal-Dutra CA
de Farias ST
Rodrigues RAL
Cortines JR
Thiemann OH
Boratto P
Freitas MHA
Almeida GMF

Brazil
Viruses
Virology
Bacteriophages
Humans
Fungal Viruses
Giant Viruses


[Contribution of yeast to synthetic virology]

Abstract: The yeast Saccharomyces cerevisiae has long been an essential model in molecular biology. Its exceptional recombination capacity and efficiency in propagating large DNA fragments surpass those of organisms such as Escherichia coli or Bacillus subtilis. These properties make S. cerevisiae the preferred choice for cloning and manipulating bacterial and viral genomes. Among the available methods, transformation-associated recombination (TAR) cloning has established itself as a reliable and effective approach for isolating and manipulating large DNA molecules. To date, numerous viral genomes have been successfully cloned in yeast. The ability to modify these cloned genomes and reconstitute infectious viral particles highlights the role of S. cerevisiae as a powerful bioengineering platform. Its versatility addresses various biomedical needs, including virus research, vaccine production, and gene therapy. Combining efficiency, reliability, and flexibility, S. cerevisiae stands out as an invaluable tool for advancing biomedical applications and tackling modern biological challenges.

Saccharomyces cerevisiae
Synthetic Biology
Cloning, Molecular
Genome, Viral
Recombination, Genetic
Transformation, Genetic
Virology


[Contribution de la levure à la virologie synthétique]

Abstract: The yeast Saccharomyces cerevisiae has long been an essential model in molecular biology. Its exceptional recombination capacity and efficiency in propagating large DNA fragments surpass those of organisms such as Escherichia coli or Bacillus subtilis. These properties make S. cerevisiae the preferred choice for cloning and manipulating bacterial and viral genomes. Among the available methods, transformation-associated recombination (TAR) cloning has established itself as a reliable and effective approach for isolating and manipulating large DNA molecules. To date, numerous viral genomes have been successfully cloned in yeast. The ability to modify these cloned genomes and reconstitute infectious viral particles highlights the role of S. cerevisiae as a powerful bioengineering platform. Its versatility addresses various biomedical needs, including virus research, vaccine production, and gene therapy. Combining efficiency, reliability, and flexibility, S. cerevisiae stands out as an invaluable tool for advancing biomedical applications and tackling modern biological challenges.


Leveraging Classical Virology and High Throughput Sequencing for Viral Discovery Using a Historical Viral Collection

Abstract: Northern Australia has long been a hotbed of arboviral discovery, and collections of viral isolates from Northern Australia represent an invaluable resource for both our knowledge of viral diversity and for disease preparedness and treatment. While discovery of novel viruses via classical virology methods is on the decline, next generation sequencing offers the possibility to speed up viral discovery, albeit at the expense of the collection of valuable life history data. By sequencing unknown isolates from historical viral collections, we may leverage both the rich data collected through classical virology and the power of identification using contemporary sequencing technologies. In the present study, we sequenced 76 historical viral isolates held at the Berrimah Veterinary Laboratory in Darwin, northern Australia, for which serological typing had yielded ambiguous results. We determined that 43 of these isolates belong to the genera Hapavirus, Orbivirus, and Orthobunyavirus. Several of these isolates are putatively novel genotypes or potential taxa, which has significant potential implications for human and animal health. This study demonstrates the utility of historical collections for viral discovery and characterisation and how considerable past efforts to isolate and characterise viruses can be enhanced using next generation sequencing approaches.

Sistrom M
Neave M
Joseph A
Newberry K
Andrews H
Shilton C
Bhardwaj V
Weir R

High-Throughput Nucleotide Sequencing
Animals
Phylogeny
Australia
Genome, Viral
Viruses
Virology
Orbivirus
Genotype
Orthobunyavirus
Humans


The Biology of Nucleus-Forming Jumbo Phages

Abstract: Nucleus-forming jumbo bacteriophages display a surprisingly intricate replication cycle inside of bacterial host cells, challenging the long-standing paradigm of prokaryotic simplicity. The phage nucleus encloses phage DNA in a protein shell, strictly uncouples transcription from translation, and facilitates selective protein import and messenger RNA (mRNA) export, serving the same major functions as the eukaryotic nucleus. Infection of host cells by these phages begins with the formation of a transcriptionally active membrane-bound early phage infection vesicle, demonstrating that these phages are capable of constructing subcellular compartments composed of lipids and proteins. Here, we review the current body of literature revealing the complexities of nucleus-forming phages and the history of the major discoveries. Studies of these phages are revealing new insights into basic principles of subcellular organization, viral speciation, and intracellular viral competition.

Bacteriophages
Viral Replicase Complex Proteins
Virology
Viral Genome Packaging
Virus Internalization

Journal Article
Review
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural


Application of Super-Resolution Microscopy in Virology Research: Principles, Technological Advances, and Analysis of the Viral Life Cycle

Abstract: Super-resolution microscopy (SRM) has exerted a pivotal influence on virology by surpassing the diffraction limits of conventional optical microscopy, enabling unprecedented visualization of viral structures and dynamics. Techniques such as stimulated emission depletion, photoactivated localization microscopy, stochastic optical reconstruction microscopy, and structured illumination microscopy facilitate nanoscale imaging of viruses, providing critical insights into the viral life cycle and virus-host interactions. We examine the principles and advancements in SRM techniques and their applications in virology. We discuss the development and selection of fluorescent probes, highlighting specific labeling methods. Key applications of SRM are illustrated through case studies of viruses such as influenza, HIV, and SARS-CoV-2, demonstrating the technology's impact on understanding viral mechanisms. We also explore future developments in SRM, including enhanced spatial and temporal resolution, and integration with technologies such as single-molecule imaging and fluorescence resonance energy transfer, positioning SRM as a pivotal tool for advancing viral research and therapeutic development.

Humans
Viruses
Microscopy
Virology
SARS-CoV-2
Microscopy, Fluorescence
Fluorescent Dyes


Systems virology as a cornerstone for pandemic responsiveness: A G2P-Japan perspective

Abstract: Pandemic preparedness is critical as we face potential threats of infectious diseases. Systems virology and collaborative/responsive science are key infrastructures that facilitated scientific advances during the SARS-CoV-2 pandemic. As discussed here, G2P-Japan and other consortia are examples of systems virology-based research collaborations that can guide future responses.

Humans COVID-19 SARS-CoV-2 Pandemics Japan Virology