Complement component 2 deficiency (C2D) is the most common inherited complement deficiency and is associated with severe bacterial infections and autoimmunity. We describe a 14-year-old Ashkenazi Jewish boy presenting with bullous cutaneous lupus erythematosus and lupus nephritis, whose diagnosis of C2D was prompted by a family history of fatal pneumococcal meningitis in a sibling. Genetic analysis identified homozygosity for the recurrent C2 c.841_849 + 19del variant, and complement studies confirmed absent classical pathway activity and profoundly reduced C2 levels. Population analysis of approximately 33,000 exomes from the Hadassah Medical Center database demonstrated marked enrichment of the variant among Ashkenazi Jews, with an estimated carrier frequency of ~3%, whereas the variant was rare in Mizrahi Jews and not detected among Israeli Arabs in our cohort. These findings support a founder effect in the Ashkenazi Jewish population and suggest that C2D may be substantially underdiagnosed.
Field phenotyping of a recently established NAM population for stem rust resistance, combined with high-density genotyping, enabled the identification of novel sources of stem rust resistance in Italian ryegrass. Stem rust, caused by Puccinia graminis ssp. graminicola, is a major disease affecting the outcrossing species Italian ryegrass (Lolium multiflorum Lam.) and leading to substantial reductions in seed yield. Until now, knowledge on the genetic control of stem rust resistance in Italian ryegrass has been limited to a few quantitative trait loci identified in biparental mapping populations. To discover novel resistance sources for use in breeding programs, appropriate plant populations, reliable phenotyping methods and advanced genomic tools are essential. In this study, we utilized a previously established F2 nested association mapping (NAM) population comprising 708 individuals derived from 24 founder plants, exhibiting high variation in stem rust resistance. Phenotypic evaluation was conducted under natural inoculation in three location-by-year combinations. By integrating reduced-representation sequencing of the NAM population with whole genome sequencing of the founder plants, we identified 3,199,253 SNP markers for association mapping. The high SNP marker density, together with the strong detection power of the NAM population, enabled the identification of four novel candidate genes. Two of these genes, located on chromosomes 6 and 7, encode receptor-like serine/threonine kinases that are known to play a role in stem rust resistance in other crops. Within the serine/threonine kinase gene Chr7.32208, two superior haplotypes were identified that can be directly implemented as selection criteria in breeding programs. The novel stem rust resistance candidate genes reported here provide promising targets for functional validation and the improvement of stem rust resistance in Italian ryegrass breeding.
Rare variants in SETD1A , encoding a histone H3K4 methyltransferase, are among the strongest genetic risk factors for schizophrenia. Exome sequencing (n = 3,736) revealed a population-enriched SETD1A missense variant (P596L) in the Lancaster Old Order Amish founder population, presenting a unique opportunity to elucidate variant-specific, multi-scale mechanisms. Psychiatric and cognitive phenotyping revealed nearly two-fold increased risk for bipolar disorder, accompanied by allele dose-dependent cognitive deficits in adulthood. Induced pluripotent stem cells (iPSCs) from homozygous carriers exhibited signatures of SETD1A hypofunction, including reduced proliferation and heightened susceptibility to replication stress and DNA double-strand breaks. During forebrain-directed differentiation, homozygous mutant cells displayed premature activation of neurodevelopmental transcriptional programs but impaired neural rosette formation, reduced neurite complexity, and early progenitor senescence. Multi-omic profiling revealed dysregulation of gene modules converging on replication stress pathways and neuronal regulatory networks enriched for autism and psychiatric risk genes. Pharmacologic inhibition of the H3K4 demethylase KDM5 partially rescued replication stress and neurite deficits, supporting an epigenetic mechanism and suggesting therapeutic tractability. Together, these findings link a population-enriched missense variant to disrupted chromatin regulation, genome stability, and neurodevelopmental timing, bridging human genetic risk with cellular pathophysiology.
Biological invasions offer large-scale experiments for examining rapid evolution and testing the predictability of adaptive change. Assessing the repeatability of such adaptive responses, however, requires replicated introductions that share similar demographic and environmental contexts. Single introduction events are common during biological invasion, but replicated secondary introductions from a shared source are rare. Here, we take advantage of a unique study system involving the introduced rusa deer (Cervus timorensis) to investigate whether synchronous secondary introductions from a shared bridgehead population show similar evolutionary trajectories. We utilised 5298 DArTSeq Single Nucleotide Polymorphisms (SNPs) from a bridgehead population and two secondary populations to estimate genetic diversity, characterise population structure and detect SNPs putatively under selection. We found an apparent reduction in genetic diversity across serial introductions, consistent with strong founder effects. Population genetic analyses revealed two genetic clusters, indicating strong differentiation and independent evolutionary trajectories between secondary populations. A genome-wide scan using BayPass identified outlier SNPs potentially involved in adaptive responses and some evidence of parallel selection, likely driven by common environmental pressures. We found candidate genes linked to the outlier loci that were associated with functions consistent with adaptive mechanisms. This study highlights that repeated introductions from a common source can further reduce genetic diversity and increase population differentiation, yet still produce parallel adaptive responses under similar environmental conditions.
RNA viruses are responsible for many zoonotic disease transmission events, and remain a global health challenge. To evade immune detection, RNA viruses suppress the numbers of immunostimulatory oligonucleotide motifs (INMs) present in their genomes. Although this is thought to occur in human immunodeficiency virus-1 (HIV-1), our bioinformatic analysis on well characterized clinical datasets, along with in vitro studies, demonstrate that HIV-1 is enriched for INMs within its transmitted/founder (T/F) population relative to non-transmitting variants. Importantly, our data suggests that within the host, there is an evolutionary genetic replacement of T/F viruses that otherwise exhibit high transmission fitness and low replicative fitness, with variants having low transmission fitness but high replicative fitness. These findings provide insights into HIV-1 transmission by studying within-host and between-host evolutionary dynamics, enabling us to identify a framework for HIV infection biology, with viral RNA playing a role in transmission and replication processes.
Stathmin-2 (STMN2) is a microtubule-associated protein that plays a role in the stability of microtubules in axons of the nervous system of animals. In this study, we generated a novel zebrafish STMN2 knockout (KO) model. STMN2 is represented by two genes in the zebrafish genome: stmn2a and stmn2b. Using the CRISPR/Cas9 mutagenic system, we selected founder fish lines harboring frameshift mutations in both genes and bred these together to generate a double stmn2a and stmn2b KO model. Using these models, we observed increased developmental lethality in our double stmn2a and stmn2b KO model and impaired motor function at embryonic stages of development. Examination of the neuromuscular junction (NMJ) revealed a slight increase in the number of orphaned NMJs in trunk musculature as well as a reduction in the amplitude of miniature endplate currents in our double stmn2a and stmn2b KO model. In a final series of experiments, we show impaired ventral root axon regrowth following transection in double stmn2a and stmn2b KO zebrafish. Our findings suggest that while not essential for motor function development, loss of stmn2a and stmn2b expression results in a minor motor phenotype and impairs the ability to regenerate motor axons following injury.
Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli), a bacterium resistant to most β-lactam antibiotics, is a critical clinical global health concern, posing significant health risks to humans and animals including giant pandas. The Chengdu Research Base of Giant Panda Breeding (CRBGP) has the world's largest captive population of giant pandas. This study aimed to investigate the prevalence, antibiotic resistance characteristics, and molecular epidemiology of ESBL-producing E. coli among captive giant pandas at the CRBGP. ESBL production was screened in 100 E. coli isolates from 100 individual giant pandas (different ages and sexes) using the Clinical and Laboratory Standards Institute (CLSI) double-disc combination test. ESBL isolates were subjected to antimicrobial susceptibility testing of 34 antibiotics using the Kirby-Bauer disk diffusion susceptibility test (K-B). Whole genome sequencing (WGS) was performed to characterize genotypes, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and multilocus sequence typing (MLST), and the molecular epidemiology of the isolates was further investigated using MLST and the goeBURST algorithm. Twenty-nine ESBL-producing E. coli strains were identified (29.0%, 29/100), representing a marked increase from the 8% prevalence reported during 2020-2021. All 29 isolates exhibited high resistance to β-lactam antibiotics, with 100.0% resistance to amoxicillin, ampicillin, cefazolin, cefuroxime and cefotaxime. A total of 120 different ARG subtypes and 19 ESBL gene subtypes were detected; bla CTX-M-4 was the most prevalent (100.0%), followed by bla SHV-1 (96.6%), bla CTX-M-1 and bla CTX-M-3 (93.1% each). Analysis of MGEs revealed high carriage rates of IS26 (89.7%), intI1 (89.7%), and the conjugation-associated gene traA (51.7%). MLST identified 10 sequence types (STs) and one clonal complex (CC1), with ST132 as the founder. ST595 and ST973 were the most common STs (each n = 7). The prevalence of ESBL-producing E. coli in captive giant pandas at the CRBGP has risen sharply (29.0%), with high-level multidrug resistance (MDR), a large ARG repertoire, and abundant MGEs indicative of strong horizontal gene transfer (HGT) potential. The presence of shared STs with other hosts suggests potential interspecies transmission. These findings underscore the urgent need for enhanced antimicrobial stewardship and continuous One Health surveillance to protect giant pandas and the broader ecosystem.
Metastatic microenvironments vary widely not only in their biochemical composition but also in their mechanical properties. Here, we examined how the mechanical rigidity of the metastatic niche affects metastases seeding and the local efficacy of antitumor immunosurveillance. Cancer cells stiffened in response to increasing environmental rigidity, a biophysical change that mechanically sensitized them to killing by cytotoxic lymphocytes. In immunodeficient mice, rigidity sensing by cancer cells yielded robust bone colonization, accompanied by marked stiffening of the cancer cells themselves. Conversely, in immunocompetent hosts, stiffer cancer cells were selectively eliminated, and bone metastasis was suppressed. In patients, metastatic cell stiffness was associated directly with environmental rigidity and inversely with immune infiltration. Expression of Spp1, encoding the secreted glycoprotein osteopontin, defined a subset of cancer cells that expanded in the bone, and deletion of Spp1 limited environmentally induced cancer cell stiffening, bone colonization, and immune vulnerability. Thus, environmental mechanosensing regulates both metastases seeding and antitumor immunity, providing an immunological basis for metastatic site selection.
Background: Treatment options are limited, and outcomes remain poor for patients with metastatic uveal melanoma (MUM). We conducted an investigator-initiated, prospective, single-arm, single-institution, phase II study evaluating the combination of an FAK inhibitor (defactinib) with a RAF/MEK inhibitor (avutometinib) for the treatment of MUM. Methods: From February 2021 through January 2023, 12 patients with MUM were treated with the combination of defactinib and avutometinib. Defactinib was given 200 mg twice daily, and avutometinib was given 3.2 mg twice a week. Both drugs were given for 3 weeks on and 1 week off (28-day cycle). Disease control rate was the primary endpoint of this study. Results: Median lines of prior therapies for the patients were two. After two cycles, six patients achieved stable disease while six patients developed progressive disease (disease control rate of 50%). With a median follow-up of 20.0 months, the median progression-free survival was 3.0 months and the median overall survival was 20.0 months. The combination was quite tolerable for patients, with no patients requiring dose reduction or discontinuation. Trial enrollment was stopped early by study sponsors before the anticipated accrual of 18 patients due to no patients having a significant reduction in disease. Conclusions: This is the first study reporting on the use of an FAK inhibitor combination in MUM. Further research should seek to elucidate an optimal combination treatment strategy for MUM, such as FAK and PKC inhibitors, for improved blockade of the signaling pathways downstream of GNAQ/GNA11 driver mutations.
Methicillin-resistant Staphylococcus aureus (MRSA) remains a major clinical challenge, particularly intracellular MRSA infections are difficult to treat because antimicrobial agents must combine stability, host-cell access and bacterial target engagement. Cyclotides offer highly stable cyclic scaffolds for peptide engineering, but their use as intracellular antimicrobial protein inhibitors remains largely unexplored. Here, we engineered a cyclotide-grafted derivative of the antimicrobial peptide KTR by inserting it into the MCoTI-I scaffold, generating the cyclic construct MCo-KTR2. Molecular docking and molecular dynamics suggested potential interactions between MCo-KTR2 and the resistance-associated penicillin-binding protein PBP2a. Site-directed mutagenesis and fluorescence polarization assays indicated that specific residues contribute to binding in vitro. Although MCo-KTR2 displayed lower activity than linear KTR in standard MIC assays, cyclotide grafting increased serum stability by more than 30-fold and enhanced cellular uptake, colocalising with cytosolic S. aureus during infection. These properties were associated with improved activity against intracellular bacteria without detectable cytotoxicity or haemolytic activity. Furthermore, MCo-KTR2 showed higher antibacterial activity when combined with the membrane-active compound Visomitin as well as in combination with vancomycin and gentamicin. Together, these findings identify cyclotide grafting as a strategy to improve peptide stability and intracellular delivery, and support MCo-KTR2 as a scaffold for further optimization against intracellular MRSA infections.
Large-scale perturbation atlases have transformed systems biology, yet no equivalent resource exists for the human heart, where contractile function and transcriptomic state must be measured together. Here, we establish Cardiopedia-Ligand, a comprehensive perturbation-function-transcriptome atlas generated by stimulating human cardiac organoids (hCOs) with 87 ligands targeting 98 cell-membrane receptors expressed in the human heart. We developed an automated high-throughput pipeline enabling individualized contractility measurements and single-organoid mRNA sequencing. We use this pipeline to define both recognized and previously unrecognized functional and transcriptional clusters, including inotropes, endothelin peptides, extracellular matrix regulators, and multiple inflammatory clusters. Clustering analysis, machine learning, and the "fingerprinting" of human heart failure biopsies revealed previously underappreciated similarities between ligands and an interferon-γ signaling signature driving heart failure with preserved ejection fraction (HFpEF). Together, this comprehensive Cardiopedia-Ligand dataset provides a valuable and accessible resource for interrogating cardiac biology and human disease.
Donor organs are frequently discarded because of concerns about quality or pathogen risk, challenges that could be mitigated through ex vivo gene editing or silencing during machine perfusion. Here, we discuss the development of CRISPR-based approaches for ex vivo gene silencing in human donor organs, from proof of concept in kidney biopsies to the challenges of organ-scale translation.
Concepts of how the immune system functions have evolved during the last half century. From widespread acceptance of Self-Nonself Discrimination to explain adaptive immunity, to increasing understanding of receptor-mediated activation of innate immunity through the Danger Model, understanding of the role of the immune response continues to grow with ever broader models such as the Damage Response Framework and the Discontinuity Model. The realisation that the majority of foreign antigens, such as those comprising the microbiome, are tolerated by the immune system, allows a re-appraisal of immune tolerance and how it relates to these conceptual shifts. Disease induced by both autoantigens and foreign antigens occurs most readily when the abundantly redundant immune system is defective, for genetic or other reasons, in one or more critical component. When fully competent, the primary role of the immune system is to "physiologically manage" both foreign and self-antigens by quietly engaging in activities such as waste disposal, autophagy, removal of apoptotic cell debris, tissue repair and metabolism. This is evidenced for foreign antigens by the limited incidence of clinical disease in pandemics despite widespread exposure of the population to the infectious agent: instead, many asymptomatic infected individuals harbour latent infections controlled by a healthy immune system, and are mainly at risk of developing overt disease when immune competency is impaired. In the case of autoantigens, by definition, exposure is 100% yet disease incidence is minimal and similarly requires a failure of immune competence, initiated by the same aberrant response to a coincident foreign antigen.
The ongoing threat of avian influenza over the past three decades represents a significant challenge for global health, livestock farming, and animal conservation. Notwithstanding the considerable strides made in research and the formulation of control strategies, the persistence of highly pathogenic strains gives rise to concerns pertaining to both animal and human health. This review examines the history and the role of the "One Health" concept in combating the disease, while first investigating the historical spread of avian influenza, its circulation in wild bird populations, the amplification and adaptation in domestic poultry, and its occasional spillover into humans, often facilitated by close contact in agricultural and live animal market settings. Historical patterns are key in understanding the dynamics of the virus and developing adequate countermeasures. Such surveillance methods and novel and rapid monitoring techniques now play a bigger role than ever. Meanwhile, improvements in genome sequencing have revolutionized our understanding of viral evolution allowing for more detailed monitoring of epidemics. Moreover, recent arguments in favor of vaccination of animals against avian influenza highlight its potential to reduce virus burden at source, reduce economic losses in agriculture, and reduce the risk of spillover to humans and other animal species, underlining its role in a comprehensive One Health approach. By integrating insights from recent technological and methodological innovations, this work advocates for a more coordinated, interdisciplinary approach to surveillance, monitoring, and vaccination. Addressing these gaps will be essential for improving outbreak preparedness and reducing the impact of this enduring threat.
Interest in using gene therapy to treat osteoarthritis (OA) is growing and a number of clinical trials have been initiated. This commentary identifies three intersecting areas that need to be addressed for the field to move forward expeditiously. The first relates to lowering the cost of manufacturing clinical grade viral vectors, addressing various aspects of their deployment, and overcoming immune barriers to dosing and re-dosing. The second area requires an improved understanding of the pathophysiology of OA, including its stratification by endotype and phenotype. Coupled to the development of reliable biomarkers, this will enable the creation of personalized gene therapies, facilitate patient selection, and aid the identification of additional molecular targets. Moreover, progress in the early diagnosis of OA will enable administration of gene therapeutics at a stage when they are most likely to be successful. Finally, important issues with regard to financing and regulation are discussed. Top line data from two pivotal Phase III clinical trials are expected to be released this year. The findings from these trials will exercise considerable influence on the future development of the field.
Sleep complaints are common in India, where recent meta-analytic estimates place the prevalence of insomnia among the highest reported anywhere. Over the same period, digital screen use has risen steeply, with very high daily smartphone use. Light-emitting diode (LED) screens are rich in short-wavelength ("blue") light. That part of the spectrum drives the intrinsically photosensitive retinal ganglion cells (ipRGCs) that set the circadian clock. Evening screen use can therefore blunt melatonin and push circadian timing later. Screen use is not, however, the same as the melanopic light dose actually reaching the retina. Associations between screen time and poor sleep may also reflect a later bedtime, mental and emotional arousal, notifications, and the type of content viewed. A lens would not change any of these. In this narrative review, we trace the melanopsin-ipRGC-suprachiasmatic nucleus pathway, ask how closely LED emission overlaps circadian photoreception, and weigh the evidence for spectacle-lens filtration as an adjunct to sleep hygiene, with a specific eye on India. Standard blue-light-filtering (BLF) lenses and longer-wavelength ("amber"/"orange") wavelength-selective lenses are held to the same evidentiary standard throughout. Systematic-review evidence rates the case that BLF lenses improve sleep as of low certainty, with findings that are indeterminate and heterogeneous rather than clearly negative. Trials of longer-wavelength lenses are small, clinically mixed, mostly unblinded, and at high risk of bias. Two pooled analyses of this literature reach different conclusions: an earlier one reported a small favorable effect on total sleep time, whereas a later analysis restricted to actigraphic outcomes from randomized crossover trials found no significant effect, with confidence intervals wide enough to indicate imprecision rather than a demonstrated absence of effect. What matters, recent work suggests, is a lens's measured melanopic filtering density rather than the color on its label, and this varies widely between products. Taken together, the evidence does not yet support recommending any spectacle-lens class as a treatment for disturbed sleep; the mechanistic case for lowering evening melanopic light is firmer than the clinical case for any particular lens. We set out why India is a priority setting and what an adequately powered, India-based trial would need to look like. Where filtration is used at all, it should sit alongside, not replace, established behavioral sleep hygiene and proper medical assessment.
Fluorescent voltage indicators are widely used to report relative changes in membrane potential, but mapping absolute voltages remains difficult. Here we present Voltage Measurement by Activated Photocycles (VMAP), a simple method for absolute voltage imaging based on a photophysical switch between voltage-insensitive and sensitive indicator states. VMAP requires no specialized hardware or additional labeling, and is applicable across species, sample preparations, and microscope configurations. Using VMAP, we quantified drug-induced shifts in neuronal resting potential, revealed the emergence of bioelectric patterns during multi-day recordings of human iPSC populations, and created 3D membrane-potential maps across whole live zebrafish embryos. By making absolute voltage imaging accessible from cellular to organismal scales and from milliseconds to days, VMAP opens a route to mapping bioelectrical organization in complex living systems.
Background/Objectives: This study used the neuroclasis nerve injury model to compare the long-term histomorphological, cellular, and inflammatory consequences of epineuroclasis and endoneuroclasis stretch injuries. Methods: Upon IACUC approval, 45 male Sprague-Dawley rats were allocated to 6 injury groups: an epineuroclasis and an endoneuroclasis group with follow-up at 2 weeks (n = 6 each), 6 weeks (n = 8 each), and 12 weeks (n = 8 and 9). Rats underwent left median nerve stretch to epineuroclasis or endoneuroclasis thresholds using load-deformation curve monitoring. Nerves were harvested at follow-up for qualitative histology and immunohistochemistry (H&E, NF200, S100, CD68, and Glut-1). Results: At 2 weeks, both injury levels demonstrated minimal NF200 staining, consistent with Wallerian degeneration. Epineuroclasis resulted in persistent epineurial rupture with exposed endoneurial tubes at 2, 6, and 12 weeks, indicating no structural restoration of the epineurium. At 12 weeks, axonal regrowth was observed primarily in regions with an intact epineurium and was limited in regions lacking epineurial coverage. Endoneuroclasis was associated with neuroma formation in 16/17 nerves (13/14 in-continuity) at 6 and 12 weeks, characterized by hypervascularity, aberrant fascicle formation, diffuse axonal sprouting, Schwann cell hypercellularity, and sustained macrophage infiltration. Conclusions: Epineurial integrity appears more important for axonal regeneration than previously thought. Persistent epineurial disruption was associated with limited axonal regrowth, whereas endoneurial disorganization was associated with neuroma formation despite macroscopic nerve continuity at time zero. Understanding the regenerative consequences of distinct degrees of connective tissue damage after stretch injury may help guide the development of tools that could diagnose these injuries early and potentially predict recovery after nerve injury.
Glycogen is a highly conserved macromolecule across species, and its visualization provides critical insights into both physiological processes and disease states. Existing approaches for glycogen imaging in Caenorhabditis elegans rely primarily on traditional microscopy slides, which introduce variability in image acquisition and downstream data analysis, limit throughput, and require substantial hands-on time and technical expertise. Here, we present a standardized, cost-effective, and high-throughput imaging method that enables efficient visualization and quantification of glycogen in C. elegans. Our approach utilizes a custom-designed three-dimensional pad containing two to four chambers, allowing control and experimental samples to be processed simultaneously under identical conditions. Worms are exposed to iodine crystals, ensuring uniform staining while minimizing reagent use and handling variability. Imaging is performed using a simple binocular microscope, and analysis is conducted in Fiji, making the workflow accessible to laboratories with minimal specialized equipment or training. This method also reduces technical variability, shortens turnaround time, and requires only basic reagents and expertise, making it well-suited for both research and teaching laboratories. Importantly, the platform is readily adaptable to other nematode species and scalable for large-scale genetic or pharmacological screening applications. Together, this workflow minimizes technical variability and provides a robust platform for comparative glycogen analysis in C. elegans. Key features • Standardized glycogen staining method allows less data variability. • Provides a quantitative tool to measure glycogen buildup in C. elegans. • Requires a customized pad for imaging. • Macro is available for batch processing.
Optical nanofibers provide a versatile platform for exploring strong light-matter interactions at the single-quantum level, a central goal of quantum optics. Their subwavelength diameter supports tightly confined guided modes with strong evanescent fields, enabling efficient coupling between photons and nearby atoms. By incorporating fiber Bragg gratings, nanofibers can form fully fiber-integrated high-finesse cavities, combining strong atom-photon coupling with efficient and low-loss optical input-output interfacing in the setting of cavity quantum electrodynamics (QED). In parallel, nanofiber systems naturally realize waveguide QED, where atoms interact strongly with propagating photons in a one-dimensional geometry. In this review, we introduce the underlying physical principles, summarize key experimental techniques and representative phenomena, and discuss prospects for applications in quantum information processing, quantum networks, and related quantum technologies.