Biology subjects

Barnes, A.

Publications and source records attributed to Barnes, A..

9 recordsLinked to original sources

bioRxiv2026

Sex in the City: Reproductive Behaviors of Dragonflies across an Urban Landscape

Anthropogenic cityscapes provide complex habitats that influence animal communication and movement patterns, which are generally understudied in aquatic and semi-aquatic organisms. Community science, referring to public participation in scientific research, is an important tool for recording occurrence records and behavioral observations of understudied urban species. Boise, Idaho (USA), one of the fastest-growing cities in North America, has a long-established community science program for documenting occurrences of the semi-aquatic insect order Odonata (dragonflies and damselflies), making the city an ideal study system for comparing behavioral observations from community science with observations recorded using AI driven iNaturalist. In this study, we test the accuracy of iNaturalist observations and volunteer surveys to characterize dragonfly reproductive behaviors (tandem flight and tandem perching, oviposition, and mating) in the city, and use these observations to determine which dragonflies are using the urban landscape as reproductive habitat. The total numbers of species observations by volunteers and on iNaturalist in Boise were strongly correlated, while reproductive observations showed a strong observational threshold, as reproductive behaviors were rarely identified in less-observed species. iNaturalist tended to underrepresent total occurrences of ''flyer'' species, which rarely perch, while volunteer surveys underrepresented occurrences and reproductive behaviors of a more cyclical species that did not appear to be abundant in the field season in which this study was conducted. Our findings suggest that Boise provides suitable breeding habitat for both migratory and resident dragonflies. Species distribution models of three migratory and three putatively migratory species further demonstrate that these species would be expected in southwestern Idaho regardless of the presence of a city, and have persisted through urban development. This research demonstrates the value of community science in conducting basic research on understudied urban-dwelling species, although findings must be considered alongside potential biases.

ecology↗

bioRxiv2026

Regulation of PDGF-BB Signaling in Placental Pericytes by Soluble PDGFRβ Isoforms: Implications for Fetoplacental Vascular Development

ABSTRACT/SUMMARYVascular remodeling within the developing fetus and placenta is essential for supporting the growth and function of emerging tissues and organs. Pericytes (PCs) play a central role in stabilizing and maturing microvascular networks by extending along endothelial cells (ECs) and reinforcing vessel integrity. In the placenta, as in other organs, PC-EC communication is mediated in part by platelet-derived growth factor-BB (PDGF-BB) signaling, which governs PC differentiation, proliferation, migration, and survival, ultimately enabling their recruitment and retention along capillaries. In this study, we identified progressive PC investment along feto-placental capillaries in both murine and human tissues across gestation, supported by morphological and molecular evidence. Placental PCs displayed phenotypic heterogeneity comparable to that observed in the brain and heart, suggesting conserved diversity across organ systems. In addition to characterizing PC dynamics, we examined the expression of recently identified soluble PDGF Receptor-{beta} (sPDGFR{beta}) isoforms. These variants were detected at the protein and transcript levels in mouse and human placentas, as well as in a murine trophoblast-embryonic stem cell (TESC) differentiation model that recapitulates aspects of early placental vascular development. Within this model, sPDGFR{beta} expression was independent of ADAM10 activity and exogenous growth factors during early vessel formation but was markedly upregulated during hypoxia. To assess how elevated sPDGFR{beta} might influence PDGF-BB signaling, we exposed TESCl-derived vascular networks to excess PDGF-BB with or without a sPDGFR{beta} mimetic. PDGF-BB alone reduced full-length PDGFR{beta} levels while increasing receptor phosphorylation, consistent with known ligand-induced regulatory mechanisms. Inclusion of the sPDGFR{beta} mimetic shifted these responses toward baseline, suggesting a potential modulatory or feedback role for soluble receptor variants. Together, these findings demonstrate that PCs are progressively recruited to placental capillaries and exhibit diverse phenotypes during development, and that soluble PDGFR{beta} isoforms may modulate PDGF-BB signaling in a manner sensitive to oxygen tension. Understanding these mechanisms provides insight into the regulation of placental vascular maturation and may inform strategies to improve human health by targeting disorders rooted in impaired placental development.

developmental biology↗

bioRxiv2026

Birth by Cesarean Section Remodels Neonatal Brain Barriers and Associated Immune and Metabolic Pathways in Mice

Delivery mode shapes early-life physiology through multiple pathways, including stress and hormonal signalling, neonatal oxygenation, and exposure to maternal microbes. Cesarean section (CS) bypasses several of these processes and has been associated with altered immune maturation and neurodevelopmental outcomes in humans and animal models. Given that CS is known to disrupt gut barrier integrity and that gut and brain barriers operate as a coordinated network, we investigated whether CS affects early postnatal brain barriers. Using a mouse model, we compared CS-delivered pups to vaginally born (VB) controls at postnatal days 8-9. Brain barrier permeability and structure were assessed using tracer extravasation and vascular and tight junction analyses, choroid plexus immune populations were profiled, and metabolomics was performed in cortex and plasma. The blood-brain barrier in the medial prefrontal cortex was mostly preserved. In contrast, the blood-cerebrospinal fluid barrier (BCSFB) exhibited structural alterations in vascular and epithelial tight junction compartments. These changes were accompanied by immune remodelling, including expansion of antigen-presenting border-associated macrophages and reduced parenchymal microglia density. CS delivery increased brain tracer accumulation, consistent with altered barrier function during this developmental window. Metabolomic analyses revealed lower levels of key brain metabolites, including N-acetylaspartate, a marker of neuronal metabolic state. Together, these findings demonstrate that CS delivery induces early alterations in brain barrier function, BCSFB structure, the immune landscape, and metabolic profiles in mice. This identifies delivery mode as a key perinatal variable shaping neonatal brain physiology and establishes a framework for dissecting how birth context may influence long-term neurodevelopmental trajectories. HIGHLIGHTSO_LICesarean section (CS) reveals the neonatal BCSFB as a vulnerable interface shaped by birth mode C_LIO_LICS increases brain tracer accumulation despite largely preserved BBB structural markers at the mPFC C_LIO_LICS induces region-specific vascular, epithelial, and immune remodeling in the choroid plexus C_LIO_LICesarean birth increases the proportion of antigen-presenting choroid plexus macrophages C_LIO_LICS shifts mPFC metabolic profiles, including reduced N-acetylaspartate and malate C_LI

neuroscience↗

bioRxiv2025

Sustained Antigen Stimulation to Evoke and Study Negative feedback Systems responsible for Self-Tolerance /Tumor Immune Escape and transition to the M2 macrophage

Chronic inflammation plays an obscure role in cancer initiation, with broad references implicating immune exhaustion (IEX) or free radical mediated cell damage. Chronic inflammation is, however, paradoxically synonymous with the term "immune tolerance" which in other cases presents itself as a therapeutic limitation to the efficacy of tumor immune therapies particularly those involving microbial -associated molecular patterns (MAMPs) in regimens. As "tolerance" remains to this day a "phenomenon" there is a pressing need to fully understand every biological aspect of this apparent negative feedback response, because doing so will serve to guide development of targeted immune therapies. In this work, we employ a rudimentary model, which can be adopted in which it is possible to provoke negative feedback through sustained antigen stimulation in immunocompetent cells, as we monitor, define and characterize phenotype evolution using next generation whole transcriptome sequencing + validation studies. This model can be used to study /create in vitro the "M2" phenotype, which is itself involved in aggressive tumors with synergistic rapid expansion of myeloid-derived suppressor cells (MDSCs), dysfunctional CD8+ T cytotoxic (CTL)/ and dysfunctional natural killer (NK) cells. Briefly, the data in this work, shows negative feedback dominates at 7 to 11 days, after acute being associated with phase specific (time dependent) elevated checkpoints; e.g. PDL1+/MSN, HAVCR2/TIM-3+, SPP1+, C3ar1+, CD73+, IL1RN+, LILRbs+, glycoproteins, integrins etc. Here we report on phase specific patterns and bidirectional changes aligning with immune escape, much centered around loss of host defense against viral infection and malignancy. Negative feedback is associated with rampant induction of degradative proteases, SOCS/JAK/STAT/IL-10, the CCL2/7 axis tantamount to sustained loss of MHC1/2 antigen recognition systems, Type I interferon response, NOD signaling, antiviral/antibacterial defense, p62/SQSTM also aligning with a disturbed metabolic signature. The data in this work demonstrates that the colloquial terms "tolerance and IEX" are somewhat flawed terminology, because this negative feedback is a potent, intentional and formidable immune offense to eradicate the active arm of immune defense. Abstract Truncated /Removed due to word countThe data show that "tolerance" aligns with six distinct chronological differential gene (DEG) expression patterns that circumscribe extensive immune suppression which dominate during chronic inflammation. These involve the following time dependent patterns: 1) transcripts overexpressed, e.g. checkpoint receptors; PDL1+/MSN, HAVCR2/TIM-3+, SPP1+, C3ar1+, CD73+, IL1RN+, LILRbs+, glycoproteins, etc.; 2) transcripts overexpressed only in chronic; e.g cytokine suppressor signaling (SOC3/Jak/Stat), cyto/chemokines (IL-10, CCL2, CCL7), proteases (cathepsins L, D, K, Adam 8, PIM2), and adhesives (TSPAN3, QSOX1, PDPN, ITGA5), (PLK2, ADGRE1, CALM1, PCNA, etc.); 3) transcripts downregulated in acute and chronic; e.g. a severe collective loss in MHC1/II antigen presentation capacity (CD74, H2-Q4, H2-Q6, etc.), NOD signaling, and interferon (IFN) type I signaling systems; 4) transcripts downregulated in chronic only, including OXPHOS/metabolic genes (Aldo A, C, Eno2, Gpi1, etc.), antiviral/antibacterial defense genes (Lyz1, Lyz2, Card19, Ninj1), and autophagy-related genes (p62/SQSTM1). In the category of Tolerance were: 5) transcripts induced sharply in acute, no longer responsive in chronic; IFN Type 1 antiviral response genes (OAS, BST2, ISG15, ISG20, IRF7, RSAD2/Viperin), TLR2, antibacterial defense genes (SAA3, SP140), and proinflammatory cytokines (CCL5, TNF, IL1a, and IL1b) along with the IL-1/TLR signaling axis. Last, 6) reverse tolerance, corresponded to restored baseline levels to maintain cell mitotic and thymosin homeostasis. In conclusion, these data suggest chronic inflammation precipitates negative feedback, aligning with the same checkpoint targets being sought after today in tumor immune therapies.

immunology↗

bioRxiv2024

Optimized Enrichment of Murine Blood-Brain Barrier Vessels with a Critical Focus on Network Hierarchy in Post-Collection Analysis

Cerebrovascular networks contain a unique region of interconnected capillaries known as the blood-brain barrier (BBB). Positioned between upstream arteries and downstream veins, these microvessels have unique structural features, such as the absence of vascular smooth muscle cells (vSMCs) and a relatively thin basement membrane, to facilitate highly efficient yet selective exchange between the circulation and the brain interstitium. This vital role in neurological health and function has garnered significant attention from the scientific community and inspired methodology for enriching BBB capillaries. Extensive characterization of the isolates from such protocols is essential for framing the results of follow-on experiments and analyses, providing the most accurate interpretation and assignment of BBB properties. Seeking to aid in these efforts, here we visually screened output samples using fluorescent labels and found considerable reduction of non-vascular cells following density gradient centrifugation (DGC) and subsequent filtration. Comparatively, this protocol enriched brain capillaries, though larger diameter vessels associated with vSMCs could not be fully excluded. Protein analysis further underscored the enrichment of vascular markers following DGC, with filtration preserving BBB-associated markers and reducing - though not fully removing - arterial/venous contributions. Transcriptional profiling followed similar trends of DGC plus filtration generating isolates with less non-vascular and non- capillary material included. Considering vascular network hierarchy inspired a more comprehensive assessment of the material yielded from brain microvasculature isolation protocols. This approach is important for providing an accurate representation of the cerebrovascular segments being used for data collection and assigning BBB properties specifically to capillaries relative to other regions of the brain vasculature. HIGHLIGHTS- We optimized a protocol for the enrichment of murine capillaries using density gradient centrifugation and follow-on filtration. - We offer an approach to analyzing post-collection cerebrovascular fragments and cells with respect to vascular network hierarchy. - Assessing arterial and venous markers alongside those associated with the BBB provides a more comprehensive view of material collected. - Enhanced insight into isolate composition is critical for a more accurate view of BBB biology relative to larger diameter cerebrovasculature. MOTIVATIONThe recent surge in studies investigating the cerebrovasculature, and the blood-brain barrier (BBB) in particular, has inspired a broad range of approaches to target and observe these specialized blood vessels within murine models. To capture transcriptional and molecular changes during a specific intervention or disease model, techniques have been developed to isolate brain capillary networks and collect their cellular constituents for downstream analysis. Here, we sought to highlight the benefits and cautions of isolating and enriching microvessels from murine brain tissue. Specifically, through rigorous assessment of the output material following application of specific protocols, we presented the benefits of specific approaches to reducing the inclusion of non-vascular cells and non-capillary vessel segments, verified by analysis of vascular-related proteins and transcripts. We also emphasized the levels of larger- caliber vessels (i.e. arteries/arterioles and veins/venules) that are collected alongside cerebral capillaries with each method. Distinguishing these vascular regions with greater precision is critical for attributing specific characteristics exclusively to the BBB where metabolic, ion, and waste exchange occurs. While the addition of larger vessels to molecular / transcriptional analyses or follow-on experiments may not be substantial for a given protocol, it is essential to gauge and report their level of inclusion, as their contributions may be inadvertently assigned to the BBB. Therefore, we present this optimized brain microvessel isolation protocol and associated evaluation methods to underscore the need for increased rigor in characterizing vascular regions that are collected and analyzed within a given study. Graphical AbstractConstructed using resources from BioRender.com. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/613898v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@7b4448org.highwire.dtl.DTLVardef@bff92borg.highwire.dtl.DTLVardef@17fa8b3org.highwire.dtl.DTLVardef@1c950d_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Innate Immune Signaling in Hearts and Buccal Mucosa Cells of Patients with Arrhythmogenic Cardiomyopathy

STRUCTURED ABSTRACTO_ST_ABSObjectivesC_ST_ABSWe sought to determine if persistent innate immune signaling via NF{kappa}B occurs in cardiac myocytes in patients with arrhythmogenic cardiomyopathy and if this is associated with myocardial infiltration of pro-inflammatory cells expressing CCR2. We also determined if buccal mucosa cells from young subjects with inherited disease alleles exhibit NF{kappa}B signaling. BackgroundNF{kappa}B signaling in cardiac myocytes causes disease in a mouse model of arrhythmogenic cardiomyopathy by mobilizing CCR2-expressing macrophages which promote myocardial injury and arrhythmias. Buccal mucosa cells exhibit pathologic features similar to those seen in cardiac myocytes in patients with arrhythmogenic cardiomyopathy. MethodsWe analyzed myocardium from arrhythmogenic cardiomyopathy patients who died suddenly or required cardiac transplantation. We also analyzed buccal mucosa cells from young subjects with inherited disease alleles. The presence of immunoreactive signal for RelA/p65 in nuclei of cardiac myocytes and buccal cells was used as a reliable indicator of active NF{kappa}B signaling. We also counted myocardial CCR2-expressing cells. ResultsNF{kappa}B signaling was seen in cardiac myocytes in 34 of 36 cases of arrhythmogenic cardiomyopathy but in none of 19 age-matched controls. Cells expressing CCR2 were increased in patient hearts in numbers directly correlated with the number of cardiac myocytes showing NF{kappa}B signaling. NF{kappa}B signaling also occurred in buccal cells in young subjects with active disease. ConclusionsPatients with clinically active arrhythmogenic cardiomyopathy exhibit persistent innate immune responses in cardiac myocytes and buccal mucosa cells reflecting an inflammatory process that fails to resolve. Such individuals may benefit from anti-inflammatory therapy. CONDENSED ABSTRACTNF{kappa}B signaling in cardiac myocytes causes arrhythmias and myocardial injury in a mouse model of arrhythmogenic cardiomyopathy by mobilizing pro-inflammatory CCR2-expressing macrophages to the heart. Based on these new mechanistic insights, we analyzed hearts of arrhythmogenic cardiomyopathy patients who died suddenly or required cardiac transplantation. We observed active NF{kappa}B signaling in cardiac myocytes associated with marked infiltration of CCR2-expressing cells. We also observed NF{kappa}B signaling in buccal mucosa cells obtained from young subjects with active disease. Thus, anti-inflammatory therapy may be effective in arrhythmogenic cardiomyopathy. Screening buccal cells may be a reliable way to identify patients most likely to benefit. HIGHLIGHTS- Inflammation likely contributes to the pathogenesis of arrhythmogenic cardiomyopathy but the responsible mechanisms and the roles of specific classes of immune cells remain undefined. - NF{kappa}B signaling in cardiac myocytes is sufficient to cause disease in a mouse model of arrhythmogenic cardiomyopathy by mobilizing injurious myeloid cells expressing CCR2 to the heart. - Here, we provide evidence of persistent NF{kappa}B signaling in cardiac myocytes and increased CCR2-expressing cells in hearts of patients with arrhythmogenic cardiomyopathy. We observed a close correlation between the number of cardiac myocytes with active NF{kappa}B signaling and the number of CCR2-expressing cells in patient hearts. - We also provide evidence of active NF{kappa}B signaling in buccal mucosa cells associated with initial onset of disease and/or disease progression in young subjects with arrhythmogenic cardiomyopathy alleles.

pathology↗

bioRxiv2023

A Soluble Platelet-Derived Growth Factor Receptor-β Originates via Pre-mRNA Splicing in the Healthy Brain and is Differentially Regulated during Hypoxia and Aging

ABSTRACT/SUMMARYThe platelet-derived growth factor-BB (PDGF-BB) pathway provides critical regulation of cerebrovascular pericytes, orchestrating their investment and retention within the brain microcirculation. Dysregulated PDGF Receptor-beta (PDGFR{beta}) signaling can lead to pericyte defects that compromise blood-brain barrier (BBB) integrity and cerebral perfusion, impairing neuronal activity and viability, which fuels cognitive and memory deficits. Receptor tyrosine kinases (RTKs) like PDGF-BB and vascular endothelial growth factor-A (VEGF-A) are often modulated by soluble isoforms of cognate receptors that establish signaling activity within a physiological range. Soluble PDGFR{beta} (sPDGFR{beta}) isoforms have been reported to form by enzymatic cleavage from cerebrovascular mural cells, and pericytes in particular, largely under pathological conditions. However, pre-mRNA alternative splicing has not been widely explored as a possible mechanism for generating sPDGFR{beta} variants, and specifically during tissue homeostasis. Here, we found sPDGFR{beta} protein in the murine brain and other tissues under normal, physiological conditions. Utilizing brain samples for follow-on analysis, we identified mRNA sequences corresponding to sPDGFR{beta} isoforms, which facilitated construction of predicted protein structures and related amino acid sequences. Human cell lines yielded comparable sequences and protein model predictions. Retention of ligand binding capacity was confirmed for sPDGFR{beta} by co-immunoprecipitation. Visualizing fluorescently labeled sPDGFR{beta} transcripts revealed a spatial distribution corresponding to murine brain pericytes alongside cerebrovascular endothelium. Soluble PDGFR{beta} protein was detected throughout the brain parenchyma in distinct regions such as along the lateral ventricles, with signals also found more broadly adjacent to cerebral microvessels consistent with pericyte labeling. To better understand how sPDGFR{beta} variants might be regulated, we found elevated transcript and protein levels in the murine brain with age, and acute hypoxia increased sPDGFR{beta} variant transcripts in a cell-based model of intact vessels. Our findings indicate that soluble isoforms of PDGFR{beta} likely arise from pre-mRNA alternative splicing, in addition to enzymatic cleavage mechanisms, and these variants exist under normal physiological conditions. Follow-on studies will be needed to establish potential roles for sPDGFR{beta} in regulating PDGF-BB signaling to maintain pericyte quiescence, BBB integrity, and cerebral perfusion - critical processes underlying neuronal health and function, and in turn memory and cognition.

cell biology↗

bioRxiv2020

Disease Risk Analysis in sea turtles: A baseline study to inform conservation efforts

The impact of a range of different threats has resulted in the listing of six out of seven sea turtle species on the IUCN Red List of endangered species. Disease risk analysis (DRA) tools are designed to provide objective, repeatable and documented assessment of the disease risks for a population and measures to reduce these risks through management options. To the best of our knowledge, DRAs have not previously been published for sea turtles, although disease is reported to contribute to sea turtle population decline. Here, a comprehensive list of health hazards is provided for all seven species of sea turtles. The possible risk these hazards pose to the health of sea turtles were assessed and "One Health" aspects of interacting with sea turtles were also investigated. The risk assessment was undertaken in collaboration with more than 30 experts in the field including veterinarians, microbiologists, social scientists, epidemiologists and stakeholders, in the form of two international workshops and one local workshop. The general finding of the DRA was the distinct lack of knowledge regarding a link between the presence of pathogens and diseases manifestation in sea turtles. A higher rate of disease in immunocompromised individuals was repeatedly reported and a possible link between immunosuppression and environmental contaminants as a result of anthropogenic influences was suggested. Society based conservation initiatives and as a result the cultural and social aspect of interacting with sea turtles appeared to need more attention and research. A risk management workshop was carried out to acquire the insights of local policy makers about management options for the risks relevant to Queensland and the options were evaluated considering their feasibility and effectiveness. The sea turtle DRA presented here, is a structured guide for future risk assessments to be used in specific scenarios such as translocation and head-starting programs.

ecology↗

bioRxiv2017

fluxweb: a package to easily estimate energy fluxes in food webs

O_LIUnderstanding how changes in biodiversity will impact the stability and functioning of ecosystems is a central challenge in ecology. Food-web approaches have been advocated to link community composition with ecosystem functioning by describing the fluxes of energy among species or trophic groups. However, estimating such fluxes remains problematic because current methods become unmanageable as network complexity increases.\nC_LIO_LIWe developed a generalisation of previous indirect estimation methods assuming a steady state system [1, 2, 3]: the model estimates energy fluxes in a top-down manner assuming system equilibrium; each nodes losses (consumption and physiological) balances its consumptive gains. Jointly, we provide theoretical and practical guidelines to use the fluxweb R package (available on CRAN at https://bit.ly/2OC0uKF).\nWe also present how the framework can merge with the allometric theory of ecology [4] to calculate fluxes based on easily obtainable organism-level data (i.e. body masses and species groups -eg, plants animals), opening its use to food webs of all complexities. Physiological losses (metabolic losses or losses due to death other than from predation within the food web) may be directly measured or estimated using allometric relationships based on the metabolic theory of ecology, and losses and gains due to predation are a function of ecological efficiencies that describe the proportion of energy that is used for biomass production.\nC_LIO_LIThe primary output is a matrix of fluxes among the nodes of the food web. These fluxes can be used to describe the role of a species, a function of interest (e.g. predation; total fluxes to predators), multiple functions, or total energy flux (system throughflow or multitrophic functioning). Additionally, the package includes functions to calculate network stability based on the Jacobian matrix, providing insight into how resilient the network is to small perturbations at steady state.\nC_LIO_LIOverall, fluxweb provides a flexible set of functions that greatly increase the feasibility of implementing food-web energetic approaches to more complex systems. As such, the package facilitates novel opportunities for mechanistically linking quantitative food webs and ecosystem functioning in real and dynamic natural landscapes.\nC_LI

ecology↗