Biology subjects

Alexander, R.

Publications and source records attributed to Alexander, R..

10 recordsLinked to original sources

bioRxiv2026

Loss of calcium-binding protein Cbp53E leads to delayed repolarization of photoreceptor cells in Drosophila

Calcium functions as an important second messenger in a wide variety of intracellular processes. In photoreceptor cells, calcium is involved in activation, deactivation, and adaptation in response to light stimuli. Calcium-binding protein 53E (Cbp53E, also known as calbindin-32 or cbn), a protein with 6 EF-Hand domains thought to act as a calcium buffer, was previously identified to have elevated expression levels in the eye of drosophila. While a recent study showed that transgenic flies lacking Cbp53E have aberrant axonal arborization at the neuromuscular junction, nothing is known about the role of Cbp53E in the visual system. We performed electroretinogram (ERG) recordings on Cbp53E mutant flies to test whether eye function was affected. Here, we report that Cbp53E null mutants exhibit a prolonged repolarization (or slow termination) phenotype which can be rescued by expressing Cbp53E in photoreceptor cells. The human homologs Calbindin 2, Calbindin 1, and S100G also rescue the Drosophila ERG phenotype. This supports a role for Cbp53E in regulating intracellular calcium levels of photoreceptor cells and contributing to normal sensory neuron response dynamics in vivo in Drosophila and suggests a similar function in human photoreceptor cells as well.

neuroscience↗

bioRxiv2025

Mosquito NF-κB-mediated innate immunity exerts arbovirus-specific antiviral effects at multiple stages of the viral life cycle

One third of all emerging infectious diseases are vector-borne, with the vectors ecology and physiology playing key roles in determining whether viruses can access new vertebrate host species and spread globally. Innate immunity is a known barrier to virus replication in mosquito vectors that influences arboviral vector tropism. We here generated novel CRISPR-Cas9-mediated knockouts of the NF-{kappa}B family transcription factor Rel2 in Aedes aegypti-derived Aag2 cells and tested the impact on the replication of a diverse range of arboviruses in the Flaviviridae and Togaviridae families and the class Bunyaviricetes. We found that NF-{kappa}B-mediated innate immunity has broad antiviral activity against the Ae. aegypti-borne orthoflaviviruses dengue virus (DENV), yellow fever virus (YFV) and Zika virus (ZIKV) in mosquito cells. In contrast, little impact of NF-{kappa}B-loss-of-function was observed for the alphavirus chikungunya virus (CHIKV) or phlebovirus Rift Valley fever virus (RVFV), indicating specificity in the antiviral effects of NF-{kappa}B-mediated immunity. By comparing orthoflaviviruses with different transmission routes (mosquito-borne, tick-borne, no known vector), we demonstrated that NF-{kappa}B-mediated immunity exerts its antiviral effects both early and late in the viral replication cycle, and that NF-{kappa}B-mediated immunity is not the only molecular barrier influencing the ability of orthoflaviviruses to replicate in Ae. aegypti cells. Overall, our work demonstrates the importance of mosquito NF-{kappa}B-mediated innate immunity in suppressing arbovirus replication, and shows that the barriers for arboviruses to adapt to new vector species are multifactorial and virus-specific. Our findings increase our understanding of the molecular barriers influencing arboviral emergence, and could inform the development of refractory mosquitoes incapable of transmitting human pathogens. Author SummaryMosquito-borne viruses are causing an increasing global disease burden due to urbanisation, globalisation, changing land use and the climate change-driven invasion of mosquitoes into new locations. Few vaccines and no medicines for mosquito-borne viral infections are licensed for human use. Historically, the most effective way to reduce human disease has been to kill mosquitoes using insecticides, which also harms beneficial insects and is leading to resistance. Newer technologies with lower ecological impacts are being developed, including genetically modified mosquitoes with a reduced ability to transmit viruses. Like humans, mosquitoes have an immune system that protects against viral infections, and strengthening this immune system through genetic modification has shown promise for reducing virus transmission. We here expand our understanding of the ways in which mosquito immunity could be harnessed by demonstrating that a gene called "Rel2" helps the mosquito fight mosquito-borne virus infection. Unlike previously studied mosquito immune responses, Rel2 has a very broad (but not universal) protective capacity against viruses. Our work also indicates that Rel2 works in concert with other arms of the mosquito immune system, highlighting a need for further research to fully realise the potential of genetically modifying mosquito immune responses for the prevention of human disease.

microbiology↗

bioRxiv2025

Prototaxites was an extinct lineage of multicellular terrestrial eukaryotes

Prototaxites was the first giant organism to live on the terrestrial surface, reaching sizes of 8 metres in the Early Devonian. However, its taxonomic assignment has been debated for over 165 years1-7. Tentative assignments to groups of multicellular algae or land plants1,2,8-11 have been repeatedly ruled out based on anatomy and chemistry5,7,11-16 resulting in two major alternatives: Prototaxites was either a fungus5,6,17-22 or a now entirely extinct lineage 7,16,23. Recent studies have converged on a fungal affinity5-7,17-20,22. Here we test this by contrasting the anatomy and molecular composition of Prototaxites with contemporary fungi from the 407-million-year-old Rhynie chert. We report that Prototaxites taiti was the largest organism in the Rhynie ecosystem and its anatomy was fundamentally distinct from all known extant or extinct fungi. Furthermore, our molecular composition analysis indicates that cell walls of P. taiti include aliphatic, aromatic, and phenolic components most similar to fossilisation products of lignin, but no fossilisation products characteristic of chitin or chitosan, which are diagnostic of all groups of extant and extinct fungi, including those preserved in the Rhynie chert. We therefore conclude that Prototaxites was not a fungus, and instead propose it is best assigned to a now entirely extinct terrestrial lineage.

paleontology↗

bioRxiv2025

Analyses of phylogenetics, natural selection, and protein structure of clade 2.3.4.4b H5N1 Influenza A reveal that recent viral lineages have evolved promiscuity in host range and improved replication in mammals in North America

Influenza A virus has been circulating in birds from Eurasia for more than 146 years, but human infection has been sporadic. H5N1 (clade 2.3.4.4b) has recently infected hundreds of species of wild and domestic birds and mammals in North America. Infections include 70 people with two fatalities. We have developed an analytical bioinformatics, genomics, and structural workflow to understand better how H5N1 is circulating in North America and adapting to new host species.Our time-series analysis reveals that the circulation of H5N1 (clade 2.3.4.4b) in North America follows a distinct annual pattern, with cases in the United States consistently peaking each December. Separate from this seasonal cycle, our analysis also documents an increase in the total number of cases reported since 2021. We also show that H5N1 (clade 2.3.4.4b) spreads in North America as two distinct subclades of interest for human and animal health. These viral lineages have achieved a vast host range by efficiently binding the viral surface protein Hemagglutinin to both mammalian and avian cell surface receptors. This novel promiscuity of host range is concomitant with the additional strengthening of the Polymerase basic 2 viral proteins binding for mammalian and avian immune proteins. Once bound, the immune proteins will have diminished ability to fight the virus, thus allowing for more efficient replication of H5N1 in mammalian and avian cells than seen in the recent past. Finally, structural docking analyses predict that while most current antivirals remain effective, a fatal human isolate showed significantly reduced binding to multiple drugs from different classes. In conclusion, the H5N1 virus is causing an animal pandemic through promiscuity of host rage and strengthening ability to evade the innate immune systems of both mammalian and avian cells.

genomics↗

bioRxiv2024

Delta opioid receptors engage multiple signaling cascades to differentially modulate prefrontal GABA release with input and target specificity

Opioids regulate circuits associated with motivation and reward across the brain. Of the opioid receptor types, delta opioid receptors (DORs) appear to have a unique role in regulating the activity of circuits related to reward without a liability for abuse. In neocortex, DORs are expressed primarily in interneurons, including parvalbumin- and somatostatin-expressing interneurons that inhibit somatic and dendritic compartments of excitatory pyramidal cells, respectively. But how DORs regulate transmission from these key interneuron classes is unclear. We found that DORs regulate inhibition from these interneuron classes using different G-protein signaling pathways that both converge on presynaptic calcium channels, but regulate distinct aspects of calcium channel function. This imposes different temporal filtering effects, via short-term plasticity, that depend on how calcium channels are regulated. Thus, DORs engage differential signaling cascades to regulate inhibition depending on the postsynaptic target compartment, with different effects on synaptic information transfer in somatic and dendritic domains.

neuroscience↗

bioRxiv2022

Metabolic reprogramming underlies cavefish muscular endurance despite loss of muscle mass and contractility

Physical inactivity - specifically the lack of moderate-to-vigorous activity - is a scourge to human health, promoting metabolic disease and muscle wasting. Interestingly, multiple ecological niches have relaxed investment into physical activity, providing unique evolutionary insight into adaptive physical inactivity. The Mexican cavefish Astyanax mexicanus lost moderate-to-vigorous activity following cave colonization, reaching basal swim speeds ~3-fold slower than their river-dwelling counterpart. We found that this was accompanied by a marked shift in body composition, decreasing muscle mass by 30% and increasing fat mass by 40%. This shift persisted at the single muscle fiber level via increased lipid and sugar accumulation at the expense of myofibrillar volume. Transcriptomic analysis of laboratory-reared and wild-caught cavefish indicated this shift in investment is driven by increased expression of ppar{gamma} - the master regulator of adipogenesis - with a simultaneous decrease in fast myosin heavy chain expression. Ex vivo and in vivo analysis confirmed these investment strategies come with a functional trade-off, decreasing cavefish muscle fiber shortening velocity, time to maximal force, and ultimately maximal swimming velocity. Despite this, cavefish displayed a striking degree of muscular endurance, reaching maximal swim speeds ~3.5-fold faster than their basal swim speeds. Multi-omics analysis indicated metabolic reprogramming, specifically increased phosphoglucomutase-1 abundance, phosphorylation, and activity, as contributing mechanisms enhancing cavefish glycogen utilization under metabolically strenuous conditions. Collectively, we reveal broad skeletal muscle reprogramming following cave colonization, displaying an adaptive skeletal muscle phenotype reminiscent to mammalian disuse and high-fat models while simultaneously maintaining a unique capacity for sustained muscle contraction under fatiguing conditions. SignificanceThe evolutionary consequence of decreased physical activity upon skeletal muscle physiology remains unexplored. Using the Mexican cavefish, we find loss of moderate-to-vigorous swimming following cave colonization has resulted in broad shifts in skeletal muscle investment - away from muscle mass and instead toward fat and sugar accumulation - ultimately decreasing muscle fiber twitch kinetics. Surprisingly though, cavefish possessed marked muscular endurance, reaching maximal swimming speeds rivaling their river-dwelling counterpart. Multi-omics analysis revealed carbohydrate metabolic reprogramming as a contributing component, most notably elevated abundance and phosphorylation of the glycogenolytic enzyme Phosphoglucomutase-1 - a likely adaptation to cave-specific hypoxia. These findings emphasize the impact multiple selective pressures have on skeletal muscle physiology, providing the first evolutionary insight into skeletal muscle adaptation following decreased activity.

evolutionary biology↗

bioRxiv2020

The Arabidopsis bZIP19 and bZIP23 transcription factors act as zinc-sensors to control plant zinc status

Zinc (Zn) is an essential micronutrient for plants and animals because of its structural and catalytic roles in many proteins. Zn deficiency affects ca. two billion people, mainly those living on plant-based diets that rely on crops from Zn deficient soils. Plants maintain adequate Zn levels through tightly regulated Zn homeostasis mechanisms, involving Zn uptake, distribution and storage, but it was not known how they sense Zn status. We use in vitro and in planta approaches to show that the Arabidopsis thaliana F-group bZIP transcription factors bZIP19 and bZIP23, which are the central regulators of the Zn deficiency response, act as Zn sensors by binding Zn2+ ions to a Zn sensor motif (ZSM). Deletions or modifications of this ZSM disrupts Zn binding, leading to a constitutive transcriptional Zn deficiency response, which causes a significant increase in plant and seed Zn accumulation. Since the ZSM is highly conserved in F-bZIPs across land plants, the identification of the first plant Zn-sensor will promote new strategies to improve the Zn nutritional quality of plant-derived food and feed, and contribute to tackle the global Zn deficiency health problem.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗

bioRxiv2020

Mechanics Of Flight Feathers: Effects Of Captivity?

ABSTRACTFeathers act as aerodynamic cantilevers, and to withstand the prolonged cyclical loading that occurs during flight, feathers must be stiff, lightweight and strong. We experimentally tested the differences in feather structure, primarily stiffness and size, between (a) wild and captive Barnacle Geese Branta leucopsis, and (b) primary feathers dropped during the annual flight feather moult, and those feathers freshly regrown during the moult process. We found that, despite having undergone a 5,000km round-trip migration, flight feathers dropped during moult in the wild geese were stiffer than those measured in the captive geese, both for those dropped during moult and those re-grown. We propose that this may be related to diet or stress in the captive geese.Competing Interest StatementThe authors have declared no competing interest.View Full Text

zoology↗

bioRxiv2020

Simultaneous classification of neuroactive compounds in zebrafish

Neuroactive compounds are crucial tools in drug discovery and neuroscience, but it remains difficult to discover neuroactive compounds with new mechanisms of action. To address this need, researchers have developed mid-throughput phenotype-first approaches using zebrafish. This study introduces an open, non-commercial, and extensible hardware/software platform that captures and analyzes drugmodulated phenotypic responses larval zebrafish. We provide full specifications, computer-aided design (CAD) documents, and source code. Accompanying this study, we are also publicly depositing phenotypic data on 3.9 million animals and 34,000 compounds. The data include a high-replicate benchmark set on 14 compounds, a wellcontrolled reference set of 648 known neuroactive compounds, 20 specialized reference sets, a library of 1,520 FDA-approved drugs, 3 screening libraries. This open data resource is curated, structured, tied to extensive metadata, and available under a Creative Commons CC-BY license.

systems biology↗

bioRxiv2019

Bmal1 integrates mitochondrial metabolism and macrophage activation

Metabolic pathways and inflammatory processes are under circadian regulation. While rhythmic immune cell recruitment is known to impact infection outcomes, whether the circadian clock modulates immunometabolism remains unclear. We find the molecular clock Bmal1 is induced by inflammatory stimulants, including Ifn-{gamma}/lipopolysaccharide (M1) and tumor conditioned medium, to maintain mitochondrial metabolism under these metabolically stressed conditions in mouse macrophages. Upon M1 stimulation, myeloid-specific Bmal1 knockout (M-BKO) renders macrophages unable to sustain mitochondrial function, enhancing succinate dehydrogenase (SDH)-mediated mitochondrial ROS production and Hif-1-dependent metabolic reprogramming and inflammatory damage. In tumor-associated macrophages, the aberrant Hif-1 activation and metabolic dysregulation by M-BKO contribute to an immunosuppressive tumor microenvironment. Consequently, M-BKO increases melanoma tumor burden, while administrating an SDH inhibitor dimethyl malonate suppresses tumor growth. Therefore, Bmal1 functions as a metabolic checkpoint integrating macrophage mitochondrial metabolism, redox homeostasis and effector functions. This Bmal1-Hif-1 regulatory loop may provide therapeutic opportunities for inflammatory diseases and immunotherapy.

cell biology↗