Scholarly Works, Biological Sciences

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Skin bacterial community differences among three species of co-occurring Ranid frogs
Gajewski, Zachary; Johnson, Leah R.; Medina, Daniel; Crainer, William W.; Nagy, Christopher M.; Belden, Lisa K. (PeerJ, 2023-07-14)
Skin microbial communities are an essential part of host health and can play a role in mitigating disease. Host and environmental factors can shape and alter these microbial communities and, therefore, we need to understand to what extent these factors influence microbial communities and how this can impact disease dynamics. Microbial communities have been studied in amphibian systems due to skin microbial communities providing some resistance to the amphibian chytrid fungus, Batrachochytrium dendrobatidis. However, we are only starting to understand how host and environmental factors shape these communities for amphibians. In this study, we examined whether amphibian skin bacterial communities differ among host species, host infection status, host developmental stage, and host habitat. We collected skin swabs from tadpoles and adults of three Ranid frog species (Lithobates spp.) at the Mianus River Gorge Preserve in Bedford, New York, USA, and used 16S rRNA gene amplicon sequencing to determine bacterial community composition. Our analysis suggests amphibian skin bacterial communities change across host developmental stages, as has been documented previously. Additionally, we found that skin bacterial communities differed among Ranid species, with skin communities on the host species captured in streams or bogs differing from the communities of the species captured on land. Thus, habitat use of different species may drive differences in host-associated microbial communities for closely-related host species.
Scaffold-free 3D-Cell Culture Model System for the Study of Metastatic Cell Behavior in the Brain TME
Sarkar, Pratistha; Ahuja, Shreya; Lazar, Iuliana M. (Cold Spring Harbor Laboratory, 2025-11-03)
Cancer is a complex disease involving dynamic interactions between cancer, stromal, and infiltrating immune cells, as well as between these cells and the extracellular matrix components of the tumor microenvironment. Brain metastases arise primarily from solid tumors and often result in fatal outcomes. An in-depth understanding of the complex intercellular interactions that evolve in the brain microenvironment is essential to enabling early cancer diagnostics and improving patient outcomes. The protected tumor microenvironment of the brain hinders, however, direct access, impeding the execution of mechanistic studies and limiting the ability to derive meaningful insights. Several in vitro 2D and 3D model systems have been developed to circumvent this problem, none, however, without limitations. The 2D models fail to recapitulate the 3D architecture of the in-vivo environment lacking therefore physiological relevance, while the 3D models present challenges related to the lack of control over cell positioning, lack of vascularization, contamination from non-human scaffolds, batch-to-batch reproducibility, and high production costs. To overcome some of these limitations, we developed an in vitro scaffold-free 3D tumor model system to simulate the in vivo brain metastatic niche. The model was constructed from human brain endothelial cells (HBEC-5i) and two different cancer cell lines derived from breast (MDA-MB-231/triple negative and SK-BR-3/HER2+) and aggressive ovarian (SK-OV-3) cancers. The development of the model relies on a newly identified affinity between the endothelial and cancer cells that enables them to self-assemble in 3D networked constructs, a feature facilitated by the high collagen production by endothelial cells and the secretion of key chemokines by both endothelial and cancer cells. The model mimics the attachment of metastasized cancer cells to the brain microvasculature, enabling the study of temporal changes in endothelial morphology and molecular signaling processes that sustain cancer cell migration, survival, proliferation, and angiogenic processes. Moreover, the model exhibits long-term stability, reproducibility, and effectiveness in evaluating anti-cancer agents. Altogether, the scaffold-free, simple 3D in vitro model systems provides a low cost, physiologically relevant tool for studying the dynamic molecular crosstalk between cancer and brain endothelial cells, and for investigating the fundamental biological processes that unfold in the tumor microenvironment.
Polygenicity in a box: Copy number variants, neural circuit development, and neurodevelopmental disorders
LaMantia, Anthony-Samuel (Elsevier, 2024-12)
Clinically defined neurodevelopmental disorders (cd-NDDs), including Autistic Spectrum Disorder (ASD) and Schizophrenia (Scz), are primarily polygenic: Multiple risk genes distributed across the genome, in potentially infinite combinations, account for variable pathology. Polygenicity raises a fundamental question: Can “core” cd-NDD pathogenic mechanisms be identified given this genomic complexity? With the right models and analytic targets, a distinct class of polygenic mutations—Copy Number Variants (CNVs): contiguous gene deletions or duplications associated with cd-NDD risk—provide a singular opportunity to define cd-NDD pathology. CNVs orthologous to those that confer cd-NDD risk have been engineered in animals as well as human stem cells. Using these tools, one can determine how altered function of multiple genes cause serial stumbles over cell biological steps typically taken to build optimal “polygenic” neural circuits. Thus, cd-NDD pathology may be a consequence of polygenic deviations—stumbles—that exceed limits of adaptive variation for key developmental steps.
Mortality Event in Rainbow Snakes Linked to Snake Fungal Disease, United States
Conley, Dane A.; Blanvillain, Gaelle; Miller, Jaimie L.; Langwig, Kate E.; Kleopfer, John D.; Lorch, Jeffrey M.; Hoyt, Joseph R. (Centers for Disease Control and Prevention, 2025-11)
We report mortality in rainbow snakes in Virginia and North Carolina, USA, linked to snake fungal disease caused by Ophidiomyces ophidiicola. During 2013–2023, we observed 46 dead rainbow snakes with lesions indicative of snake fungal disease, noted elevated disease severity compared with other species, and recorded fewer live snakes over time.
Modelling trait heterogeneity and inferring causal links in the macroevolution of growth habit in eudicot angiosperms
Neupane, Suman; Zanne, Amy E.; Lens, Frederic; Uyeda, Josef C. (Wiley, 2026-01)
Phylogenetic comparative methods (PCMs) help researchers understand and predict trait evolutionary relationships. While improvements to PCMs have focused on increasing model complexity, understanding processes remains difficult due to persistent challenges in grounding complex models in biological reality and synthesizing findings across multiple analyses. We examined the evolution of growth habit in eudicots (75% of all angiosperms) and tested how variables such as vessel diameter, leaf phenology, and minimum temperature influence macroevolutionary inference. We used a series of PCMs to synthesize our understanding of trait interrelationships, explored plausible causal relationships using phylogenetic path analysis, and employed phylogenetic cross-validation to assess predictive performance among taxa. We found that discrete coding of growth form was linked to other measured and unmeasured traits, and that these interrelationships can help overcome limitations arising from incomplete data and simplistic coding of complex traits. Analysis of growth form using phylogenetic path analysis helps reconcile competing views of trait interrelationships from previous studies. Furthermore, including identified covariates improves prediction of growth habit and other traits. Our study shows that incorporating causal structure improves macroevolutionary inference, identifies when analyses that omit key causal traits become unreliable, and underscores the importance of integrating phylogenetic models with natural-history knowledge.
Spatial and temporal variability of microplastic abundance in estuarine intertidal sediments: Implications for sampling frequency
Leads, Rachel R.; Weinstein, John E.; Kell, Sarah E.; Overcash, Johnathan M.; Ertel, Bonnie M.; Gray, Austin D. (Elsevier, 2023-02-10)
Microplastics (<5 mm) are well documented across shorelines worldwide; however, high variability in microplastic abundance is often observed within and among field studies. The majority of microplastic surveys to date consist of single sampling events that do not consider spatiotemporal variability as a potential confounding factor in the interpretation of their results. Therefore, these surveys may not accurately capture or reflect levels of microplastic contamination in the environment. Here, we provide the first investigation of small-scale spatial and temporal variability of microplastic abundance, distribution, and composition in the intertidal zone of an urbanized US estuary to better understand the short-term, daily spatiotemporal variability of microplastics in dynamic coastal environments. Intertidal sediment was collected from both the low and high intertidal zones of a sandy estuarine beach located in South Carolina, southeastern US every 1 to 2 days at low tide over 17 days (12 sampling events; total n = 72). Study-wide, microplastic abundance ranged from 44 to 912 microplastics/m² and consisted primarily of polyethylene, nylon, polyester, and tire (or tyre) wear particles. High temporal variability was observed, with microplastic abundance differing significantly among sampling events (p = 0.00025), as well as among some consecutive tidal cycles occurring within 12 h of each other (p = 0.007). By contrast, low spatial variability was observed throughout the study with no significant differences in microplastic abundance detected between the low and high intertidal zones (p = 0.76). Of the environmental factors investigated, wind direction on the day of sampling had the greatest effect on temporal microplastic variability. Our results demonstrate that there can be significant temporal variability of microplastic abundance in estuarine intertidal sediments and are important for informing the methods and interpretation of future microplastic surveys in dynamic coastal environments worldwide.
Comparing in-home and bottled drinking water quality: regulated and emerging contaminants in rural Central Appalachia
Albi, Kate; Krometis, Leigh-Anne H.; Ling, Erin; Cohen, Alasdair; Xia, Kang; Gray, Austin D.; Dudzinski, Emerald; Ellis, Kimberly P. (IWA Publishing, 2025-09)
An increasing number of Americans rely on bottled water for household use, citing perceptions of poor in-home water quality and/or distrust of public water utilities. We analyzed in-home (n = 23), roadside spring (n = 4), and bottled drinking water (n = 36) in Central Appalachia. All samples were analyzed for regulated (bacteria, inorganic ions) and emerging (PFAS, microplastics) contaminants. Study survey results indicated the majority (83%) of participants viewed their in-home water quality as satisfactory or poor due to negative organoleptic perceptions. Coliform bacteria and sodium levels exceeding recommended levels were detected in 52% of home water samples, though detections varied by source, i.e., high sodium was more often observed in municipal water, while bacteria were more often observed in private system water. Bottled water samples did not exceed any regulations, though median microplastic concentrations were statistically higher (p = 0.001, Wilcoxon rank-sum test) than those recovered from in-home samples. PFAS compounds were detected in some in-home and bottled water samples at very low levels. While in general bottled water appears to be a safe drinking water source in these areas, the associated costs in time and money for lower-income households are considerable, and were estimated by participants as $68–400/month.
Toxicological impacts of microplastic fibers: A review assessing risk to human and aquatic health
O'Connor, Amber; Irhin, Kathleen; Sabo-Attwood, Tara; Gray, Austin D. (Academic Press-Elsevier, 2025-11)
Microplastics (particles less than 5 mm in size) are emerging contaminants that are widely distributed in the environment. Among the various morphologies, microplastic fibers (MPFs) are one of the most prevalent in environmental matrices and at multiple levels of biological organization. Most existing literature on the toxicological implications of microplastics on organisms utilizes morphologies that are not commonly recovered from the field (i.e. spheres or beads), therefore limiting our understanding of true toxicological concerns. Thus, this scoping review aimed to summarize and critically discuss the available data on the toxicological impact of MPFs, providing recommendations for future assessments based on the current knowledge gaps in the literature. The novelty of our review lies in identifying similarities across studies to better understand how laboratory approaches can inform toxicological outcomes. Our review found that most of the literature meeting our search criteria focused on work specific to aquatic and mammalian systems, with the latter yielding very few studies. Through the analysis, multiple knowledge gaps in MPF research emerged, such as MPF toxicity can be an artifact of the fiber dimensions (i.e. length or aspect ratio), and that subsequent leaching of additives from fibers may contribute to toxicity. Additionally, we found that there are varying responses to MPFs versus natural fibers, and a limited understanding of the organismal response to MPFs in the presence of other co-contaminants.
Isolation and characterization of four novel Vibrio parahaemolyticus bacteriophages from oysters
Aldaroub, Joud; Walsky, Chrissy M.; Elwell, Rylee E.; Aylward, Frank O.; Stevens, Ann M.; Burke, Alison Kernell (2025-12-29)
Vibrio parahaemolyticus (VP) is a bacterial pathogen found in brackish and marine water that infects many marine organisms, such as oysters and shrimp. Consumption of raw or undercooked seafood contaminated with V. parahaemolyticus is a primary cause of seafood-borne gastroenteritis in humans. Due to increasing ocean temperatures, V. parahaemolyticus contamination of oyster beds in the United States has spread up the east and west coasts to the northern-most states. Promising new research is exploring the isolation of bacteriophages against V. parahaemolyticus with a long-term goal to possibly decontaminate oyster beds, thereby expanding the harvest season and allowing for safer consumption of seafood. In this study, storebought oysters harvested from the Chesapeake Bay in Virginia were used to isolate four bacteriophages with activity against a specific V. parahaemolyticus strain. A standard double agar overlay plaque assay was used to identify phage activity. After phage isolation, the genomes were sequenced, and transmission electron microscopy (TEM) was performed to visualize the virions. The genomes and TEM images revealed four distinct phages. Three of the phages are distinct isolates that exhibit podovirus-like morphology with short tails and genome sizes of approximately 43 kbp. One phage has siphovirus-like morphology and is a mid-sized tailed phage with a genome size of 80 kbp. Although spot tests performed with the oyster homogenates on up to 10 different V. parahaemolyticus strains recovered activity across a wide range of hosts, plaque assays with the isolated phages showed limited host range. Future work will be necessary to determine the viability of using the bacteriophages for elimination of V. parahaemolyticus in harvested oysters, treatment of aquaculture seed and spat, and/or the environment.
12/15-lipoxygenases mediate toll-like receptor 4-dependent nociplastic pain hypersensitivity in female mice
Miliano, Cristina; Chen, Irene; Brown, Brieann; Murdaugh, Laura B.; Dong, Yuyang; Eddinger, Kelly A.; Geng, Shuo; Li, Liwu; Yaksh, Tony L.; Burton, Michael D.; Buczynski, Matthew W.; Gregus, Ann M. (Lippincott Williams & Wilkins, 2025-12)
Chronic nociplastic pain syndromes are characterized by sensitization of peripheral and central nervous systems and exhibit increased incidence in women. However, nonsteroidal anti-inflammatory drugs are ineffective in mitigating nociplastic pain, and current prescription treatments, such as opioids, anticonvulsants, and antidepressants, provide limited therapeutic benefit for these indications. In the current work, we extended previous studies in rats of central Toll-like receptor 4-dependent pain hypersensitivity to male and female C57BL/6N mice, uncovering an unexpected hyperalgesic phenotype in female mice following intrathecal (IT) lipopolysaccharide (LPS). In contrast to previous reports in female C57BL/6J mice, female C57BL/6N mice displayed tactile and cold allodynia, grip force deficits, and a modest increase in locomotor activity in response to IT LPS. Congruent with our previous observations in male rats, LPS released spinal 12/15-lipoxygenase (12/15-LOX) metabolites (12/15-LMs) in female C57BL/6N mice. Likewise, 12/15-LOX enzymes are basally expressed in multiple tissues and cell types relevant to nociceptive transmission. Systemic inhibition of 12/15-LOX in female C57BL/6N mice with selective inhibitors ML355 (targeting 12-LOX-p) or ML351 (targeting 15-LOX-1) completely reversed allodynia and grip force deficits. 12/15-LMs also produce tactile allodynia when administered spinally (IT) or peripherally (paw intraplantar) at a subthreshold dose in a hyperalgesic priming model, similar to others' observations with a subthreshold dose of the cyclooxygenase metabolite prostaglandin E2. Collectively, these data suggest that 12/15-LOX enzymes contribute to peripheral and central pain hypersensitivity in rodents, with potential translatability as druggable targets across sexes and species using multiple reflexive and functional outcome measures.
Insights into the structure and initial host attachment of the flagellotropic bacteriophage 7-7-1
Noteborn, W. E. M.; Ouyang, R.; Hoeksma, T.; Sidi Mabrouk, A.; Esteves, Nathaniel C.; Pelt, D. M.; Scharf, Birgit E.; Briegel, A. (Springer, 2025-12)
Understanding the structural and functional mechanisms of bacteriophage 7-7-1, the flagellotropic phage infecting Agrobacterium sp. H13-3, offers promising insights into phage-host interactions. Using single particle analysis (SPA) cryo-electron microscopy (cryo-EM), we determined the capsid, neck region, tail, and baseplate complex structures. Combined with cryo-electron tomography (cryo-ET) and machine learning methodologies, our findings indicate that phage 7-7-1 uses capsid fibers to establish initial contact with the host flagellum, followed by subsequent attachment to cell surface receptors. The study also demonstrated that capsid fibers are flexible and can interact with other phages and host flagella, suggesting a cooperative infection strategy. These results provide crucial structural insights and may open avenues for developing phage-based therapeutics against resistant bacterial pathogens.
Extracellular Perinexal Separation Is a Principal Determinant of Cardiac Conduction
Adams, William P.; Raisch, Tristan B.; Zhao, Yajun; Davalos, Rafael V.; Barrett, Sarah; King, D. Ryan; Bain, Chandra B.; Colucci-Chang, Katrina; Blair, Grace A.; Hanlon, Alexandra L.; Lozano, Alicia; Veeraraghavan, Rengasayee; Wan, Xiaoping; Deschenes, Isabelle; Smyth, James W.; Hoeker, Gregory S.; Gourdie, Robert G.; Poelzing, Steven (Lippincott Williams & Wilkins, 2023-09-29)
BACKGROUND: Cardiac conduction is understood to occur through gap junctions. Recent evidence supports ephaptic coupling as another mechanism of electrical communication in the heart. Conduction via gap junctions predicts a direct relationship between conduction velocity (CV) and bulk extracellular resistance. By contrast, ephaptic theory is premised on the existence of a biphasic relationship between CV and the volume of specialized extracellular clefts within intercalated discs such as the perinexus. Our objective was to determine the relationship between ventricular CV and structural changes to micro- and nanoscale extracellular spaces. METHODS: Conduction and Cx43 (connexin43) protein expression were quantified from optically mapped guinea pig whole-heart preparations perfused with the osmotic agents albumin, mannitol, dextran 70 kDa, or dextran 2 MDa. Peak sodium current was quantified in isolated guinea pig ventricular myocytes. Extracellular resistance was quantified by impedance spectroscopy. Intercellular communication was assessed in a heterologous expression system with fluorescence recovery after photobleaching. Perinexal width was quantified from transmission electron micrographs. RESULTS: CV primarily in the transverse direction of propagation was significantly reduced by mannitol and increased by albumin and both dextrans. The combination of albumin and dextran 70 kDa decreased CV relative to albumin alone. Extracellular resistance was reduced by mannitol, unchanged by albumin, and increased by both dextrans. Cx43 expression and conductance and peak sodium currents were not significantly altered by the osmotic agents. In response to osmotic agents, perinexal width, in order of narrowest to widest, was albumin with dextran 70 kDa; albumin or dextran 2 MDa; dextran 70 kDa or no osmotic agent, and mannitol. When compared in the same order, CV was biphasically related to perinexal width. CONCLUSIONS: Cardiac conduction does not correlate with extracellular resistance but is biphasically related to perinexal separation, providing evidence that the relationship between CV and extracellular volume is determined by ephaptic mechanisms under conditions of normal gap junctional coupling.
Ion Clusters Reveal the Sources, Impacts, and Drivers of Freshwater Salinization
Marin, Diver E.; Grant, Stanley B.; Bhide, Shantanu V.; Rippy, Megan A.; Gomez-Velez, Jesus D.; Brent, Robert N.; Kaushal, Sujay S.; Post, Harold; Shelton, Sydney; Misra, Shalini; Hotchkiss, Erin R.; Monofy, Ahmed; Alvi, Dongmei; Schmitz, Bradley; Curtis, Shannon; Davis, Christina C.; Vikesland, Peter J.; Husic, Admin (American Chemical Society, 2025-06-16)
Population growth, land use change, climate change, and natural resource extraction are driving the salinization of freshwater resources worldwide. Reversing these trends will require data-centric approaches that identify salt sources, environmental drivers, and ecosystem responses. In this study, we applied principal component analysis and hierarchical clustering to identify ion covariance patterns, or “ion clusters,” in Broad Run, an urban stream in the Mid-Atlantic United States. These clusters correspond to distinct hydrologic regimes and reveal specific salinization risks: (1) phosphorus pollution mobilized during summer storms (Cluster 1); (2) elevated concentrations of sulfate and bicarbonate during baseflow (Cluster 2), likely reflecting groundwater discharge; and (3) elevated specific conductance and sodium, chloride, and potassium ion concentrations during snowmelt and rain-on-snow events (Cluster 3), driven by deicer and anti-icer wash-off. These ion fingerprints offer a transferable framework for diagnosing salt sources, assessing ecological risk, and identifying management targets. Our findings underscore the need for next-generation stormwater infrastructure and smart growth policies to protect aquatic life in rapidly urbanizing watersheds.
Ulk1(S555) inhibition alters nutrient stress response by prioritizing amino acid metabolism
Willoughby, Orion S.; Nichenko, Anna S.; Brisendine, Matthew H.; Amiri, Niloufar; Henry, Shelby N.; Braxton, Daniel S.; Brown, John R.; Kraft, Braeden J.; Jenkins, Kalyn S.; Addington, Adele K.; Zaitsev, Alexey V.; Burrows, Steven T.; McMillan, Ryan P.; Zhang, Haiyan; Tye, Spencer A.; Najt, Charles P.; Craige, Siobhan E.; Rhoads, Timothy W.; Warren, Junco S.; Drake, Joshua C. (Elsevier, 2025-11-24)
Metabolic flexibility, the capacity to adapt fuel utilization in response to nutrient availability, is essential for maintaining energy homeostasis and preventing metabolic disease. Here, we investigate the role of Ulk1 phosphorylation at serine 555 (S555), a site regulated by AMPK, in coordinating metabolic switching following short-term caloric restriction and fasting. Using Ulk1(S555A) global knock-in mice, we show loss of S555 phosphorylation impairs glucose oxidation in skeletal muscle and liver during short-term CR, despite improved glucose tolerance. Metabolomic, transcriptomic, and mitochondrial respiration analyses suggest a compensatory reliance on autophagy-derived amino acids in Ulk1(S555A) mice. These findings suggest Ulk1(S555) phosphorylation as a critical regulatory event linking nutrient stress to substrate switching. This work highlights an underappreciated role of Ulk1 in maintaining metabolic flexibility, with implications for metabolic dysfunction.
Long-Term Alterations of Glucocorticoid Receptor Expression and CD4+ T Cells in Adolescent Rhesus Macaques Following Early-Life Adversity
Sanchez, Mar M.; Panagiotakopoulos, Leonidas; Hayes, Timothy; Howell, Brittany R.; Ethun, Kelly; Easley, Kirk A.; Silvestri, Guido; Carnathan, Diane G.; McCandless, Jackson; Meyer, Jerrold; Neigh, Gretchen N. (MDPI, 2025-12-05)
Child maltreatment (MALT) is a devastating form of early-life adversity (ELA) and a primary risk for mental and physical illness. It is difficult to disentangle postnatal caregiving effects from heritable factors. Here we investigated the long-term effects of maternal care using a cross-fostering design to control for biological/heritable factors on immune function and inflammation during adolescence in a translational and naturalistic macaque model of MALT. We studied the impact of MALT on the immunophenotype of peripheral blood mononuclear cells (PBMCs) and assessed glucocorticoid receptor expression and function during adolescence. MALT was associated with elevated expression of NR3C1, the gene that encodes for the glucocorticoid receptor, in PBMCs. Glucocorticoid receptor function was not altered by MALT when examined for response to dexamethasone (DEX). In addition, MALT led to a reduction in the percentage of naïve CD4⁺ T cells and an increase in the percentage of central memory (Tcm) CD4⁺ T cells. These results suggest that MALT-exposed adolescents show residual effects of MALT on CD4⁺ T cells and increased expression of NR3C1 without demonstration of increased function of the glucocorticoid receptor. Taken together, these results suggest that ELA has enduring implications for cellular glucocorticoid receptor biology and CD4⁺ T cells.
Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses from the Plant Viruses Subcommittee, 2025
Rubino, L.; Abrahamian, P.; An, W.; Aranda, M. A.; Ascencio-Ibañez, J. T.; Bejerman, N.; Blouin, A. G.; Candresse, T.; Canto, T.; Cao, M.; Carr, J. P.; Cho, W. K.; Constable, F.; Dasgupta, I.; Debat, H.; Dietzgen, R. G.; Digiaro, M.; Donaire, L.; Elbeaino, T.; Fargette, D.; Filardo, F.; Fischer, M. G.; Fontdevila, N.; Fox, A.; Freitas-Astua, J.; Fuchs, M.; Geering, A. D. W.; Ghafari, M.; Hafrén, A.; Hammond, J.; Hammond, R.; Hasiów-Jaroszewska, B.; Hebrard, E.; Hernández, C.; Hily, J. M.; Hosseini, A.; Hull, R.; Inoue-Nagata, A. K.; Jordan, R.; Kondo, H.; Kreuze, J. F.; Krupovic, M.; Kubota, K.; Kuhn, J. H.; Leisner, S.; Lett, J. M.; Li, C.; Li, F.; Li, J. M.; López-Lambertini, P. M.; Lopez-Moya, J. J.; Maclot, F.; Mäkinen, K.; Martin, D.; Massart, S.; Allen Miller, W.; Mohammadi, M.; Mollov, D.; Muller, E.; Nagata, T.; Navas-Castillo, J.; Neriya, Y.; Ochoa-Corona, F. M.; Ohshima, K.; Pallás, V.; Pappu, H.; Petrzik, K.; Pooggin, M.; Prigigallo, M. I.; Ramos-González, P. L.; Ribeiro, S.; Richert-Pöggeler, K. R.; Roumagnac, P.; Roy, A.; Sabanadzovic, S.; Šafářová, D.; Saldarelli, P.; Sanfaçon, H.; Sarmiento, C.; Sasaya, T.; Scheets, K.; Schravesande, W. E. W.; Seal, S.; Shimomoto, Y.; Sõmera, M.; Stavolone, L.; Stewart, L. R.; Teycheney, P. Y.; Thomas, J. E.; Thompson, J. R.; Tiberini, A.; Tomitaka, Y.; Tzanetakis, I.; Umber, M.; Urbino, C.; van den Burg, H. A.; Van der Vlugt, R. A. A.; Varsani, A.; Verhage, A.; Villamor, D. (Microbiology Society, 2025-01-01)
In March 2025, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote, newly proposed taxa were added to those under the mandate of the Plant Viruses Subcommittee. In brief, 1 new order, 3 new families, 6 new genera, 2 new subgenera and 206 new species were created. Some taxa were reorganized. Genus Cytorhabdovirus in the family Rhabdoviridae was abolished and its taxa were redistributed into three new genera Alphacytorhabdovirus, Betacytorhabdovirus and Gammacytorhabdovirus. Genus Waikavirus in the family Secoviridae was reorganized into two subgenera (Actinidivirus and Ritunrivirus). One family and four previously unaffiliated genera were moved to the newly established order Tombendovirales. Twelve species not assigned to a genus were abolished. To comply with the ICTV mandate of a binomial format for virus species, eight species were renamed. Demarcation criteria in the absence of biological information were defined in the genus Ilarvirus (family Bromoviridae). This article presents the updated taxonomy put forth by the Plant Viruses Subcommittee and ratified by the ICTV.
Hydrologic and geochemical drivers of aluminum, barium, and copper in two drinking water reservoirs in Southwestern Virginia, USA
Bauer, Carly E.; Wood, Cecelia E.; Lofton, Mary E.; Breef-Pilz, Adrienne; Carey, Cayelan C.; Schreiber, Madeline E. (IWA Publishing, 2025-11-24)
The water quality of drinking water reservoirs is critical for human and ecosystem health. In this study, we examined the drivers of three metals, aluminum (Al), barium (Ba), and copper (Cu), across two drinking water reservoirs in southwestern Virginia, USA, over 4 years. One reservoir has a hypolimnetic oxygenation system; the other does not. We used time series modeling and multivariate analysis of water column chemistry, suspended sediment, inflow, and precipitation data to assess the relative roles of hydrologic and geochemical drivers of metal behaviors in the two reservoirs. Results suggest that Al concentrations were primarily influenced by high-flow events, consistent with the mobilization of clays from physical weathering. In contrast, Ba showed stronger sensitivity to geochemical drivers, specifically redox conditions. Drivers of Cu behavior were obscured by low Cu concentrations. For all metals, patterns varied among years. Our findings highlight the importance of long-term monitoring and integrated approaches to evaluate the drivers of metal dynamics in reservoir ecosystems and inform strategies for maintaining safe drinking water supplies.
Parasite escape mechanisms drive morphological diversification in avian lice
Kolencik, Stanislav; Stanley, Edward L.; Punnath, Aswaj; Grant, Avery R.; Dona, Jorge; Johnson, Kevin P.; Allen, Julie M. (Royal Society, 2024-03-27)
Organisms that have repeatedly evolved similar morphologies owing to the same selective pressures provide excellent cases in which to examine specific morphological changes and their relevance to the ecology and evolution of taxa. Hosts of permanent parasites act as an independent evolutionary experiment, as parasites on these hosts are thought to be undergoing similar selective pressures. Parasitic feather lice have repeatedly diversified into convergent ecomorphs in different microhabitats on their avian hosts. We quantified specific morphological characters to determine (i) which traits are associated with each ecomorph, (ii) the quantitative differences between these ecomorphs, and (iii) if there is evidence of displacement among co-occurring lice as might be expected under louse-louse competition on the host. We used nano-computed tomography scan data of 89 specimens, belonging to four repeatedly evolved ecomorphs, to examine their mandibular muscle volume, limb length and three-dimensional head shape data. Here, we find evidence that lice repeatedly evolve similar morphologies as a mechanism to escape host defences, but also diverge into different ecomorphs related to the way they escape these defences. Lice that co-occur with other genera on a host exhibit greater morphological divergence, indicating a potential role of competition in evolutionary divergence.
Neurogenomic landscape associated with status-dependent cooperative behaviour
Bolton, Peri; Ryder, T. Brandt; Dakin, Roslyn; Houtz, Jennifer; Moore, Ignacio T.; Balakrishnan, Christopher; Horton, Brent (Wiley, 2025-08-01)
The neurogenomic mechanisms mediating male-male reproductive cooperative behaviours remain unknown. We leveraged extensive transcriptomic and behavioural data on a neotropical bird species (Pipra filicauda) that performs cooperative courtship displays to understand these mechanisms. In this species, the cooperative display is modulated by testosterone, which promotes cooperation in non-territorial birds, but suppresses cooperation in territory holders. We sought to understand the neurogenomic underpinnings of three related traits: social status, cooperative display behaviour and testosterone phenotype. To do this, we profiled gene expression in 10 brain nuclei spanning the social decision-making network (SDMN), and two key endocrine tissues that regulate social behaviour. We associated gene expression with each bird's behavioural and endocrine profile derived from 3 years of repeated measures taken from free-living birds in the Ecuadorian Amazon. We found distinct landscapes of constitutive gene expression were associated with social status, testosterone phenotype and cooperation, reflecting the modular organization and engagement of neuroendocrine tissues. Sex-steroid and neuropeptide signalling appeared to be important in mediating status-specific relationships between testosterone and cooperation, suggesting shared regulatory mechanisms with male aggressive and sexual behaviours. We also identified differentially regulated genes involved in cellular activity and synaptic potentiation, suggesting multiple mechanisms underpin these genomic states. Finally, we identified SDMN-wide gene expression differences between territorial and floater males that could form the basis of 'status-specific' neurophysiological phenotypes, potentially mediated by testosterone and growth hormone. Overall, our findings provide new, systems-level insights into the mechanisms of cooperative behaviour and suggest that differences in neurogenomic state are the basis for individual differences in social behaviour.
Propagation of monocyte exhaustion memory and underlying mechanisms
Wang, Jing; Caldwell, Blake A.; Wu, Yajun; Razani, Babak; Li, Liwu (2025-12-05)
Monocyte exhaustion is a dysfunctional state characterized by prolonged pathogenic inflammation and immune suppression, commonly observed in chronic infections and sepsis. However, the mechanisms underlying the generation and propagation of exhausted monocytes remain poorly understood. In this study, we investigate the impacts of exhausted monocytes on neighboring naïve monocytes, endothelial cells, and T cell function. Using an in vitro co-culture system, we demonstrate that exhausted monocytes induced by prolonged LPS stimulation propagate the exhaustion phenotype to neighboring naïve monocytes. Meanwhile these exhausted monocytes can promote endothelial apoptosis, upregulate adhesion molecules ICAM-1 and VCAM-1, and enhance monocyte transmigration, contributing to endothelial dysfunction. Pharmacological inhibition of CD38, a key marker of monocyte exhaustion, significantly mitigates these effects, highlighting its critical role in monocyte-driven endothelial alterations. Furthermore, we show that exhausted monocytes suppress T cell proliferation and activation, a process reversed by CD38 inhibition. We also identify mTOR signaling as a key regulator of monocyte exhaustion and its propagation, with mTOR inhibition partially restoring monocyte functionality by downregulating exhaustion markers and STAT1/STAT3/S6K signaling. Collectively, our findings highlight the CD38-mTOR axis as a central driver of monocyte exhaustion and its pathological consequences, offering potential therapeutic targets for reversing immune dysfunction in inflammatory diseases. Graphical Abstract The inhibition of CD38 can alleviate monocyte exhaustion through suppressing the sustained mTORC1-STAT1 activation. Upon LPS stimulation, TLR4 signaling is activated through the TRAM-TRIF adaptor complex, leading to the phosphorylation of Src. This activation promotes mTORC1 signaling, characterized by the recruitment of Raptor and the activation of S6K. mTORC1 activation subsequently drives STAT1/3 signaling, which further induces CD38 expression and forms a sustained positive feedback loop. Elevated CD38 levels contribute to monocyte exhaustion by depleting NAD⁺, a key metabolic cofactor. NAD⁺ depletion negatively impacts mTORC2 signaling, leading to impaired Akt phosphorylation, resulting in diminished expression of PGC1α/β, CREB and CD86, both of which are associated with exhausted monocyte immune suppression. The CD38 inhibitor 78c disrupts this exhaustion pathway, offering a potential therapeutic strategy to mitigate monocyte dysfunction during monocyte exhaustion.

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